JOBNAME: RNA 12#12 2006 PAGE: 1 OUTPUT: November 10 14:27:49 2006 csh/RNA/125784/reviewers-index

RNA: Reviewers for Volume 12, 2006

The editors wish to thank the following individuals whose efforts in reviewing papers for RNA in the past year are greatly appreciated.

Juan Alfonzo Donald Burke Fritz Eckstein Carol Greider Frederic Allain John Burke Martin Egli Sam Griffiths-Jones Emily Allen Samuel Butcher Sherif Abou Elela Claudio Gualerzi Sidney Altman Ronald Emeson Alexander Gultyaev Victor Ambros Gail Emilsson Samuel Gunderson Mark Caprara James Anderson Luis Enjuanes Christine Guthrie Paul Anderson Massimo Caputi Anne Ephrussi Raul Andino James Carrington Jay Evans Charles Carter Gordon Hager Mohammed Ararzguioui Eduardo Eyras Paul Hagerman Manuel Ares Richard Carthew Jamie Cate Stephen Hajduk Jean Armengaud Dan Fabris Jean Cavarelli Kathleen Hall Brandon Ason Philip Farabaugh Guillaume Chanfreau Michelle Hamm Gil Ast Jean Feagin Tien-Hsien Chang Scott Hammond Pascal Auffinger Martha Fedor Lawrence Chasin Maureen Hanson Johanna Avis Yuriy Fedorov Chang-Zheng Chen Eoghan Harrington Juli Feigon Eric Christian Michael Harris James Fickett Kristian Baker Christine Clayton Roland Hartmann Carol Fierke Alice Barkan Peter Clote Stephen Harvey Susan Baserga Witold Filipowicz Jeffery Coller Michelle Hastings Brenda Bass Andrew Fire Kathleen Collins Christopher Hayes Christoph Flamm David Bartel Richard Collins Christopher Hellen William Folk Robert Batey Elena Conti Matthias Hentze Maurille Fournier Peter Becker Howard Cooke Thomas Herdegen Joachim Frank David Bedwell Barry Cooperman John Hershey Karen Beemon Stefan Franzen Anita Corbett Klemens Hertel Michael Been Kurt Fredrick David Corey Hans Heus Xiang-Dong Fu Jean Beggs Carl Correll Tetsuro Hirose Frances Fuller-Pace Sven-Erik Behrens Gilbert Cote Ivo Hofacker Dmitry Fyodorov Rob Benne Daniel Coughlin Thomas Hohn David Bentley Benoit Cousineau Stephen Holbrook Ben Berkhout Patrick Cramer Fred Gage Martin Holcik Harris Bernstein Don Ganem Jorge Cruz-Reyes Torgeir Holen Joe Gall Marla Berry Michael Culbertson David Horowitz Philip Bevilacqua Bryan Cullen Daniel Gallie Craig Hunter Albrecht Bindereif Gloria Culver Andrea Gamarnik Barbara Birshtein Jim Curran Mariano Garcia-Blanco Michael Bittner Paul Gardner Hiroaki Imataka Glenn Bjo¨rk Fa´tima Gebauer Elisa Izaurralde Doug Black James Dahlberg Lee Gehrke Ewan Blanch Charles Daniels David Giedroc Aimee Jackson Benjamin Blencowe Beverly Davidson Richard Giege´ Richard Jackson Thomas Blumenthal Kwaku Dayie Robert Giegerich Allan Jacobson Paul Bohjanen Joe DeRisi Greg Gilmartin Se´bastien Jacquemont Linda Bonen Victoria DeRose Antonio Giraldez Luc Jaeger Eric Bouhassira Thomas Dever Gregory Goodall William James Volker Brendel Thorsten Dieckmann Jan Gorodkin Eckhard Jankowsky Gary Brewer Jonathan Dinman Jonatha Gott Michael Jantsch David Brian Carl Dobkin Susan Gottesman Artur Jarmolowski Ian Brierley Olga Dontsova Paula Grabowski Nayef Jarrous Juergen Brosius Timothy Doran Brenton Graveley Kuan Teh Jeang David Brow Jennifer Doudna Michael Gray Richard Jorgensen James Brown Francois Dragon Nicola Gray Leemor Joshua-Tor John Brown David Draper Rachel Green Arlen Johnson Karen Browning Theo Dreher Nancy Greenbaum Brian Johnston Stephen Buratowski James Deshler Arno Greenleaf Søren Jonstrup

RNA (2006), 12:2211-2212. Published by Cold Spring Harbor Laboratory Press. Copyright Ó 2006 RNA Society. 2211

PROOF_RNA_125784_REVIEWERS-INDEX JOBNAME: RNA 12#12 2006 PAGE: 2 OUTPUT: November 10 14:27:51 2006 csh/RNA/125784/reviewers-index

Reviewers index

Akira Kaji Steve Marquez Anna Marie Pyle Gisela Storz K. Kalantidis Robert Martienssen William Strauss Charles Query C. Cheng Kao Susan Martinis Scott Strobel George Kassavetis Thomas Mason Nikolaus Rajewsky Ken Stuart Gabriel Kaufmann David Mathews Venki Ramakrishnan Beatrix Suess Alexei Kazantsev John Mattick Doron Rapaport Liam Keegan Stuart Maxwell Laurie Read Clifford Tabin Jack Keene John McCarthy Robert Reenan Toshimitsu Takagi Walter Keller David McKay Philippe Re´gnier Frank Kempken Michael McManus Marc Rehmsmeier Woan-Yuh Tarn Anastasia Khvorova Mark McNally Jaanus Remme Warren Tate Jeffrey Kieft Tom Meier John Richardson John Taylor Mike Kiledjian Craig Mello Jeffrey Roberts Lisa Timmons Kostas Tokatlidis V. Narry Kim Josh Mendell Marina Rodnina David Tollervey Karla Kirkegaard William Merrick Pascale Romby Leif Kirsebom Peter Meyer Daniel Romero Davide De Pietri Tonelli Tama´s Kiss Shulamit Michaeli Michael Rosbash Mina Tsagris Herbert Tschochner Jorgen Kjems Francxois Michel John Rossi Rob Knight Ronald Micura Jean-Pierre Rousset David Turner Nikolay Kolev Allen Miller David Rowlands Kazimierz Tycowski Magda Konarska Peter Moore Anthony Russell Jan Kooter Christoph Moroni Martin Ryan Olke Uhlenbeck Alberto Kornblihtt David Morrissey Brian Rymond Elisabetta Ullu Gary Kunkel Zissimos Mourelatos Peter Unrau Sidney Kushner David Muddiman Matthew Sachs Jaunius Urbonavicius Alan Kutach Oliver Mu¨hlemann Helen Salz Berndt Mu¨ller Kevin Sanbonmatsu Saba Valadkhan Michael Mulligan John Santa Lucia Juan Valca´rcel Andrea Ladd Stephen Munroe Peter Sarnow Sandro Valentini Daniel Lafontaine Elizabeth Murchison Michael Sattler Umesh Varshney Alan Lambowitz Karin Musier-Forsyth Olav Schiemann Marc van de Vijver Paolo Landini Carl Schmid Dre van der Merwe Neocles Leontis Peter Nagy Mark Schmitt Maarten van Lohuizen Fran Lewitter Yoshikazu Nakamura Dietmar Schmucker Gabriele Varani Hong Li David Neuhaus Robert Schneider Anders Virtanen Stephen Liebhaber Andrew Newman Daniel Schoenberg Lee Lim Henrik Nielsen Rene´e Schroeder Elmar Wahle Ren-Jang Lin Knud Nierhaus Daniel Schu¨mperli Scott Walker Lasse Lindahl Edward Niles Gadi Schuster Nils Walter Patrick Linder Kazuko Nishikura Beate Schwer Peter Walter Joachim Lingner Harry Noller Bert Semler Vassie Ware Maxine Linial Carl Novina Bertrand Seraphin Jonathan Warner Peter Linsley Alexander Serganov Karen Wassarman John Lis Mary O’Connell Phillip Sharp Joseph Wedekind Qinghua Liu Marie O¨ hman Ivan Shatsky Alan Weiner Jon Lorsch Dirk Ostareck Stewart Shuman Karsten Weis Todd Lowe Antje Ostareck-Lederer Ann-Bin Shyu K. Andrew White John Lucchesi Robert Silverman James Wilhelm Reinhard Lu¨hrmann Richard Padgett Scott Silverman Miles Wilkinson Peter Lukavsky Michael Palladino Anne Simon Bryan Williams Elsebet Lund Tao Pan Larry Simpson Jeffrey Wilusz Carol Lutz Arthur Pardi Robert Singer Wolfgang Wintermeyer Jens Lykke-Andersen Roy Parker Frank Slack Jo Ann Wise Kristen Lynch Amy Pasquinelli Christopher Smith John Woolford Christopher Pearson Harold Smith Jacek Wower Stefan Maas Brenda Peculis Eric Snijder Clinton MacDonald Renee Reijo Pera Dieter Soll Shaohua Xiao Paul Macdonald Alessio Peracchi Barbara Sollner-Webb George Mackie John Perona Erik Sontheimer Anthony Yachnis Janine Maddock Jean-Pierre Perreault Tobin Sosnick Bauke Ylstra Jim Maher Tatyana Pestova Christian Spahn Li Yong Jacek Majewski Joseph Piccirilli Jiri Sponer Yi-Tao Yu Francois Major Ramesh Pillai Peter Stadler Marat Yusupov Alexander Mankin Eric Phizicky Nancy Standart James Manley Ophry Pines Alexander Stark Phillip Zamore Mano Manoharan Ronald Plasterk Gerhard Steger Mihaela Zavolan Lynne Maquat Vinayaka Prasad Cy Stein Byoung-Tak Zhang Anita Marchfelder Nick Proudfoot Joan Steitz Steven Zimmerly Christian Marck Ger Pruijn Gary Stormo Larry Zipursky

2212 RNA, Vol. 12, No. 12 JOBNAME: RNA 12#12 2006 PAGE: 1 OUTPUT: November 14 01:06:06 2006 csh/RNA/125784/author-index

RNA: Author Index for Volume 12, 2006

Aagaard, L., 256 Berman, H.M., 533 Chen, Z.-x., 256 Dreher, T.W., 1338 Abbondi, M., 1262 Bert, A.G., 1074 Cheng, S.-C., 765 Dundr, M., 1206 Adhya, S., 1505 Bill, A., 1650 Chmiel, N.H., 283 Durbin, R., 1786 Agol, V.I., 1671 Bindewald, E., 342 Cho, B., 2118 Duronio, R.J., 396, 2103 Agris, P.F., 1254 Birmingham, A., 1188 Chou, J.J., 567 Dutertre, S., 1790 Aiba, H., 248 Bla¨si, U., 674 Christian, E.L., 1463 Dybkov, O., 410 Alatortsev, V.S., 476 Bleys, A., 1633 Christiansen, J.K., 1383 Alenius, M., 1161 Bloch, D.B., 547, 707 Chrzanowska-Lightowlers, Z., Easton, L.E., 683 Alhonen, L., 1569 Bloch, K.D., 547, 707 1397 Ebersbach, T., 1383 Altman, R.B., 533 Bonano, V.I., 2073 Churcher, M.J., 375 Eckert, D.M., 807 Amarzguioui, M., 256 Bonnet, C., 1408 Cifuentes-Rojas, C., 1219 Egebjerg, J., 1350 Ambros, V., 589 Bonoli, M., 832 Clayton, C., 2171 Egecioglu, D.E., 26 An, C.-I., 710 Bonven, B., 1350 Cleary, M., 1179 Egle, R., 1431 Anderson, E.M., 988, 1188 Boon, K.-L., 198 Clerte, C., 457 Ehsani, A., 256 Anderson, J.R., 1810 Bove, J., 2035 Collins, K., 1475 Eisenberg, E., 1802 Anderson, J.T., 508 Bowers, H.A., 903 Copela, L.A., 644 Eldho, N.V., 235 Ara, T., 1794 Brandi, L., 1262 Corda, B., 192 Ellingham, M., 1970 Araki, L., 980 Branlant, C., 1583 Cornish, P.V., 1959 Engelke, D.R., 533, 1023 Arhin, G.K., 53 Brazas, R.M., 2073 Corral-Debrinski, M., 1408 Ernst, N.L., 819, 1038 Atkins, J.F., 332, 1149 Breaker, R.R., 607 Corsini, L., 410 Este´vez, A.M., 2171 Brenner, S.E., 533 Costa, M., 338 Evans, K., 1594 Baass, A., 1556 Brenner, T.J., 862 Coughlin, D.J., 1023 Babendure, J.L., 851 Brooks, B.S., 1315 Court, D.L., 1229 Fabbretti, A., 1262 Babendure, J.R., 851 Brown, J.W., 533 Cousineau, B., 1980 Faber, A.W., 263 Baev, V., 1612 Brown II, B.A., 1092 Cruz-Reyes, J., 476, 1219, 1292 Fabian, M.R., 1304, 2199 Ba¨hr, M., 1431 Brunelle, J.L., 33 Culver, G.M., 1229, 2080 Fahr, A., 1431 Baird, N.J., 598 Bubunenko, M., 1229 Cusack, S., 1817 Fairman, M.E., 903 Baird, S.D., 1755 Bunka, D.H.J., 1970 Czaplinski, K., 213 Famulok, M., 1650 Baker, B.F., 163 Buratti, E., 948 Fan, K., 1397 Baker, K.E., 1441 Burch, B.D., 396 Dai, Q., 2025 Fang, Y., 1271 Bakhmutov, D.V., 1671 Burchard, J., 1179, 1197 Dangott, L.J., 1219 Farabaugh, P.J., 1154 Balatskaya, S.V., 446 Burke, D.H., 1846, 2118 Darzacq, X., 2057 Faustino, P., 2160 Baldi, P.F., 2047 Burtle, B., 1397 Davis, J.H., 567 Fedorov, Y., 988, 1188 Baldwin, D.A., 187 Dayie, K.T., 235, 1693 Feigon, J., 40, 1475 Bao, S., 2020 Cadieux, A., 1661 de Boer, P., 263 Feinberg, J.S., 580 Barbazza, A., 674 Cagan, R., 2020 De Nova-Ocampo, M., 1219 Ferna´ndez-Miragall, O., 223 Barberan-Soler, S., 15 Caizergues-Ferrer, M., 40, 832, Decatur, W.A., 2025 Fierke, C.A., 1023 Barreau, C., 1790 1868 Dennis, P.P., 1708 Fleck, M., 1038 Barta, A., 631 Calabrese, J.M., 2092 Depicker, A., 1633 Fok, V., 872 Baserga, S.J., 1092 Capeyrou, R., 1868 Deras, M., 2014 Forster, V., 1408 Bass, B.L., 807 Carlson, J.W., 1922 Desai, P.M., 725 Fournier, M.J., 2025 Basturea, G.N., 426 Carothers, J.M., 567 Deutscher, M.P., 426 Fox-Walsh, K.L., 2047 Baumstark, T., 147 Carstens, R.P., 1129 Di Stefano, M., 1262 Francklyn, C.S., 1315 Bax, R., 2005 Casey, J.L., 1521 Dickinson, D., 1229 Frank, J., 1240 Beckham, C., 94 Cassiday, L.A., 620 Dickman, M.J., 691 Frank, R., 410 Beemon, K.L., 102 Castoldi, M., 913 Dietz, G.P.H., 1431 Freese, S., 2171 Been, M.D., 1282 Cech, T.R., 387, 1721 Ding, J.-H., 851 Frilander, M.J., 1883 Beggs, J.D., 198 Celniker, S.E., 1922 Ding, Y., 323 Fu¨tterer, J., 841 Behm-Ansmant, I., 1583 Chabanon, H., 1397 Dinman, J.D., 666 Behzadnia, N., 1738 Chakshusmathi, G., 644 Dobbs, D., 1450 Ganem, D., 733 Belaya, K., 921 Champion, E.A., 1092 Domdey, H., 435 Gao, H.Q., 717 Beliakova-Bethell, N., 94 Chan, S.-P., 765 Domingo, G.J., 1038 Garber, M.B., 1229 Bellare, P., 292 Chanfreau, G.F., 26 Dominski, Z., 396 Garcia-Blanco, M.A., 2073 Benecke, B.-J., 1494 Chang, A., 1708 Donia, M., 717 Garges, S., 1505 Benelli, D., 674 Chang, J., 1061 dos Reis, M., 933 Gautheret, D., 1794 Benes, V., 913 Chau, B.N., 1179 Dou, Y., 2047 Gehring, N.H., 1015 Bergman, N., 883 Chaudhuri, B.R., 1229 Doudna, J.A., 283 Geisinger, E., 1271 Berlanga, J.J., 1556 Chen, C.-H., 765 Dovc, P., 498 George, A.T., 147

RNA (2006), 12:2213–2216. Published by Cold Spring Harbor Laboratory Press. Copyright Ó 2006 The RNA Society. 2213

AUTHOR-INDEX JOBNAME: RNA 12#12 2006 PAGE: 2 OUTPUT: November 14 01:06:07 2006 csh/RNA/125784/author-index

Author index

Gesteland, R.F., 332 Hook, B., 1594 Kjems, J., 1747 Lowe, T.M., 15 Ghattas, B., 1794 Hopkinson, A., 1104 Kloosterman, W.P., 187 Lu, J.-Y., 883 Giddings Jr., T.H., 94 Hord, C.L.H., 2035 Knight, R., 1 Lu¨hrmann, R., 410, 903, 1418, Giedroc, D.P., 1959 Hornby, D.P., 691 Koch, J., 1747 1494, 1738 Gilliam, T., 819 Hossbach, M., 1494 Koduvayur, S., 2149 Lukavsky, P.J., 683 Gmyl, A.P., 1671 Hovhannisyan, R.H., 1129 Kolitz, S.E., 751 Lutz, C.S., 111 Godfrey, A.C., 396 Hsieh, J., 1023 Kong, J., 2160 Lynch, K.W., 925 Golovanov, A.P., 1933 Hu, Y., 959, 1206 Korepanov, A., 1229 Gong, C., 1468 Huang, C.E., 476 Korhonen, A., 1569 Ma, J., 122 Goodall, G.J., 1074 Huang, Y., 1446 Korneluk, R.G., 1755 Magnier, M., 797 Gooding, A.R., 387 Hudak, K.A., 1683 Kos`, M., 921 Maher III, L.J., 620 Goulah, C.C., 1545 Hyvo¨nen, M.T., 1569 Koslowksy, D.J., 1050 Maiva¨li, U¨ ., 790 Grainger, R.J., 198 Krainer, A.R., 1116 Major, F., 533 Granjeaud, S., 1794 Imataka, H., 1825 Krasilnikov, A.S., 598 Manche, L., 1116 Graveley, B.R., 1640 Immel, F., 1583 Kraynack, B.A., 163 Mansouri, S., 1683 Grech, A., 872 Irmer, H., 2171 Kulozik, A.E., 913, 1015 Maroney, P.A., 903 Green, R., 33 Ivanov, I.P., 332 Kumar, A., 620 Marshall, W., 1197 Gre´pin, R., 1074 Iwai, N., 1626 Kunz, J.B., 1015 Marshall, W.S., 988, 1188 Grundhoff, A., 733 Kupsco, J.M., 396, 2103 Marszalkowski, M., 1915 Gualerzi, C.O., 1262 Kurihara, T., 980 Martin, M.B., 353 Jackman, J.E., 1007 Guarraia, C., 1154 Kurihara, Y., 206 Martinez, J., 1161 Jackson, A.L., 1179, 1197 Gudima, S.O., 1061 Kutach, A.K., 292 Martı´nez-Salas, E., 223 Jackson, S.A., 2149 Gudjonsdottir-Planck, D., 2171 Kyriakopoulou, C., 1603 Martins, R., 2160 Jagannathan, I., 1229 Guilligay, D., 1817 Martinson, H.G., 1534 Jan, E., 894 Gulick, T., 547, 707 Lai, D., 1446 Marzluff, W.F., 396, 1206, 1853, Jankowsky, E., 903 Gullerova, M., 631 Laird-Offringa, I.A., 1168 2103 Janne, J., 1569 Gumbs, O.H., 1693 ¨ Lambowitz, A.M., 1271 Massenet, S., 1583 Jantsch, M.F., 1802, 1993 Gunderson, S.I., 122 Lancaster, A.M., 894 Matera, A.G., 1206 Jensen, S.T., 1612 Guo, F., 387 Lang, B.F., 1661 Mathews, D.H., 533 Jensen, T.H., 435 Guo, J., 1197 Larsson, P., 1603 Matsuda, D., 1338 Jernigan, R.L., 1450 Guschina, E., 1494 Law, J.A., 476 Mattaj, I.W., 213 Jiang, F., 1514 Guth, E., 1315 Law, M.J., 1168 Maxwell, E.S., 1092 Jiang, Y.-F., 561 Guthrie, C., 292, 862, 994 Lazzarini, A., 1262 McKay, D.B., 959 Johansson, C., 40 Leake, D., 988, 1188, 1197 McKeehan, W.L., 1129 Johnson, J.M., 1197 Haile, S., 2171 Lecoeuvre, G., 1408 Meaux, S., 1323 Johnston, B.H., 446 Hajarnavis, A., 1786 Lee, J.-H., 1450 Megraw, M., 1612 Jona, I., 607 Halbig, K., 1219, 1292 Lee, M., 607 Mehta, P., 2187 Jones, R.B., 1129 Hall, K.B., 457 Lee, R.C., 589 Meier, U.T., 2057 Jonstrup, S.P., 1747 Hall, M.P., 488 Lenasi, T., 498 Melchers, W.J.G., 1671 Jorgensen, R., 1350 Hallegger, M., 1993 Leontis, N.B., 533 Merrick, W.C., 717 Joseph, S., 580 Hamann, M.T., 717 Lerner, R.S., 775 Michel, F., 338 Jossinet, F., 533 Hammell, C.M., 589 Lescoute, A., 83 Mickleburgh, I., 1397 Harris, E., 1893 Leuschner, P.J.F., 1161 Miller, M.M., 1292 Harris, M.E., 1463 Kadaba, S., 508 Levanon, E.Y., 1802 Miller, W.A., 1893 Hartmann, R.K., 1915, 2135 Kadlec, J., 1817 Levinger, L., 1104 Mir, M.A., 272 Hartmuth, K., 1738 Kajimoto, K., 1626 Levinson, N., 925 Mitton-Fry, R.M., 872 Harusawa, S., 980 Kalantidis, K., 1612 Lewis, S.E., 533 Miyakawa, S., 1825 Harvey, S.C., 533 Kalidas, S., 1514 Li, C.-H., 2171 Mondrago´n, A., 598 Haseno¨hrl, D., 674 Kallipolitis, B.H., 1383 Li, H., 53, 63 Moore, C., 435 Hatzigeorgiou, A.G., 192, 1612 Kaltimbacher, V., 1408 Li, W., 1240 Moore, M.J., 360 Hautbergue, G.M., 1933 Kao, C.C., 303 Li, X., 248 Moraes, K.C.M., 1084, 1810 He, X., 435, 841 Kao, D.-I., 765 Li, Y., 699 Morgado, A., 2160 Heding, A., 1350 Kao, T.-C., 765 Lian, L.-Y., 1933 Morris, K.V., 256 Heikkinen, S., 1569 Kapp, L.D., 751 Liang, S., 111 Motorin, Y., 1583 Henkin, T.M., 1254 Karginov, F.V., 959 Liebhaber, S.A., 2160 Mougin, A., 1868 Henras, A.K., 26 Karpilow, J., 988, 1188, 1197 Lilley, D.M.J., 980 Mourelatos, Z., 187 Henry, Y., 832, 1868 Karzai, A.W., 2187 Lim, L., 1179, 1197 Mozdy, A.D., 1721 Hentze, M.W., 913, 1015 Kasprzak, W.K., 1521 Lin, J.-Y., 765 Muckenthaler, M.U., 913 Hernandez, A., 1219 Kastner, B., 903 Lin, P., 1168 Muh, S.J., 1129 Hertel, K.J., 2047 Kauppinen, S., 187 Lin, Y.-T., 1486 Mukherjee, D., 1810 Hesketh, J., 1397 Kazakov, S.A., 446 Lingor, P., 1431 Mullen, M.A., 2035 Heus, H.A., 1671 Kazerouninia, A., 1534 Linnstaedt, S.D., 1521 Mulligan, R.C., 797 Hilgers, V., 1835 Keina¨nen, T.A., 1569 Linsley, P.S., 1179, 1197 Musier-Forsyth, K., 1315 Hinman, R., 925 Kelley, T., 2080 Liu, F., 63 Muthukumaraswamy, K., 1810 Hirano, R., 248 Keppetipola, N., 73 Liu, L., 1603 Ho, C.K., 488 Khanna, M., 40 Liu, Q., 1514 Na, H., 2199 Hoareau-Aveilla, C., 832 Khvorova, A., 988, 1188, 1197 Liu, S., 1418 Nag, A., 1534 Hohn, T., 841 Kikkert, B.J., 1373 Liu, X., 1514 Nahvi, A., 607 Holbrook, S.R., 533 Kim, K., 63 Locker, N., 683 Nakamura, Y., 1825 Holcik, M., 1755 King, S.R., 542 Londei, P., 674 Naraba, H., 1626 Holen, T., 1620 Kirsebom, L.A., 1603 Lopez, F., 1794 Narsinh, K., 1534 Hollingworth, D., 555 Kirthi, N., 2080 Lorkovic, Z.J., 631 Na¨rva¨nen, A., 1569 Honavar, V., 1450 Kittur, N., 2057 Lorsch, J.R., 751 Nasser, T., 435

2214 RNA, Vol. 12, No. 12 JOBNAME: RNA 12#12 2006 PAGE: 3 OUTPUT: November 14 01:06:08 2006 csh/RNA/125784/author-index

Author index

Neeman, Y., 1802 Quevillon-Cheruel, S., 1868 Sharma, D., 33 Trippe, R., 1494 Nelson, A.R., 1254 Sharp, P.A., 2092 Tschudi, C., 53, 943, 2063 Nelson, P.T., 187 Rader, S.D., 2014 Sherrer, R.L., 644 Tsien, R.Y., 851 Neu-Yilik, G., 1015 Rakotondrafara, A.M., 1893 Shi, H., 943, 2063 Turcotte, M., 1755 Newman, A.J., 198, 375 Ramajo, J., 223 Shibuya, T., 360 Turner, I.A., 375 Newman, E.A., 1129 Raman, A., 1154 Shuman, S., 73, 1468, 2126 Nicchitta, C.V., 775 Ramos, A., 555 Silva, A.L., 2160 Uhlenbeck, O.C., 959 Nichols, K., 1197 Ramos, K.S., 699 Silverman, S.K., 313, 1142 Uimari, A., 1569 Nielsen, F.C., 1350 Ramos, R., 223 Simon, A.E., 147 Ullu, E., 53, 943, 2063 Nielsen, J.S., 1383 Ranjith-Kumar, C.T., 303 Singer, R.H., 2057 Umamoto, S., 63 Nilsen, T.W., 903 Rath, B.K., 1240 Smielewska, M., 1640 Unrau, P.J., 1949 Noble, C.G., 555 Raue´, H.A., 263, 2005 Smit, S., 1 Urlaub, H., 1494 Noerholm, M., 913 Rauhut, R., 1418 Smith, D., 1514 Norman, C.M., 198, 375 Ravelli, R.B., 1817 Smith, K.M.J., 1463 Vadas, M.A., 1074 Normand, C., 1868 Read, L.K., 1292, 1545 Smith, P., 1468 Valentin-Hansen, P., 1383 Nourollahzadeh, E., 1683 Reidt, U., 410 So¨derbom, F., 1603 van Hoof, A., 1323 Novick, R.P., 1271 Remme, J., 790 Søgaard-Andersen, L., 1383 Van Houdt, H., 1633 Nugent, R.L., 1023 Rentmeister, A., 1650 Sollner-Webb, B., 476 van Venrooij, W.J., 1373 Nury, D., 1397 Sonenberg, N., 1556, 1825 Reynolds, A., 988, 1188, 1197 Vermeulen, A., 988 Sontheimer, E.J., 292 Rice, A.J., 1168 Villeneuve, L.M., 256 Richards, J., 2187 Sosnick, T.R., 598 Virtanen, A., 1603 Obernosterer, G., 1161 Richards, R.J., 1475 Spadaccini, R., 410 Vornlocher, H.-P., 1418 O’Connor, C.M., 1475 Richardson, J.S., 533 Spena, S., 948 Vos, H.R., 263 O’Farrell, H.C., 725 Rife, J.P., 725 Springola, M., 1361 Vos, J.C., 263, 2005 Oguro, A., 1825 Riggs, A.R., 256 Srividya, N., 598 O’Hearn, S.F., 476 Riley, K.J.-L., 620 Stahl, G., 1154 Ohtsu, T., 1825 Rines, A.K., 292 Stammler, S.N., 1959 Wadkins, T.S., 1282 Oltean, S., 2073 Rio, D.C., 283 Stapleton, M., 1922 Wagner, E.J., 1206 Omer, A.D., 1708 Roberson, L.M., 1907 Stark, M.R., 2014 Wahl, M.C., 410 Onafuwa-Nuga, A.A., 542 Robert, F., 717 Steger, G., 1915 Wahle, T., 1650 O’Rear, J., 819 Robinson, K., 988, 1188 Steitz, J.A., 872 Wahlfors, J., 1569 Osborne, H.B., 1790 Romao, L., 2160 Stephenson, C.R.J., 925 Wahlfors, T., 1569 Ospina, J.K., 1206 Rosbash, M., 968 Sterzer, U., 435 Walter, J., 1650 Ouellet, J., 980 Rosen, A.E., 1315 Stier, G., 410 Walter, N.G., 522 Overgaard, M.T., 959 Rosenthal, J.J.C., 1907 Stockwell, B.R., 797 Wang, L.K., 2126 Rossi, J.J., 256 Stonehouse, N.J., 1970 Wang, S., 959 Roth, A., 607 Stribinskis, V., 699 Wang, X., 508 Padgett, R.A., 235, 1693 Rowlands, D.J., 1970 Striggles, J.C., 353 Wang, Y., 313, 1142 Paillard, L., 1790 Roy, S., 2057 Stroupe, M.E., 360 Warzecha, C.C., 1129 Palakodeti, D., 1640 Roy-Chaudhuri, B., 2080 Stuart, K., 819 Watanabe, Y., 206 Pan, T., 598, 2025 Roychowdhury-Saha, M., 1846 Stuart, K.D., 1038 Watkins, R.A., 1949 Panganiban, A.T., 272 Rudd, K.E., 426 Sukhodolets, M.V., 1505 Wegscheid, B., 2135 Panigrahi, A.K., 1038 Ruokolainen, A., 1883 Sullivan, C.S., 733 Weil, J.E., 102 Parker, G.S., 807 Rusinov, V., 1612 Szostak, J.W., 567 Weinberg, M.S., 256 Parker, R., 94, 1441, 1835 Ryabova, L.A., 841 Weissleder, R., 797 Patil, A., 925 Tacahasi, Y., 435 Welting, T.J.M., 1373 Patton, J.R., 1583 Sacharidou, A., 1219 Tagami, H., 248 Werner, S., 925 Patton, J.T., 133 Sadri, N., 883 Takashi, Y., 206 Wernisch, L., 933 Pelletier, J., 717 Sahel, J.-A., 1408 Taliaferro, D., 1154 West, S., 655 Pelletier, M., 1545 Saikia, M., 2025 Tange, T.Ø., 360 Westhof, E., 83, 533 Pellinen, R., 1569 Sakkas, D., 1446 Tardiff, D.F., 968 White, K.A., 1304, 2199 Pendergrass, S.A., 1853 Salavati, R., 819, 1038 Tarun Jr., S., 819 Whitfield, M.L., 1853 Pereira, F.J.C., 2160 Salm, H., 2171 Taschner, A., 1993 Whoo, G.H.C., 925 Perera, N., 1463 Sandmeyer, S., 94 Taylor, I.A., 555 Wickens, M., 1594 Perrotta, A.T., 1282 Sarnow, P., 894 Taylor, J.M., 1061 Will, C., 410 Pessa, H.K.J., 1883 Sattler, M., 410 Teixeira, D., 1835 Will, C.L., 1738 Peterlin, B.M., 498 Scaringe, S.A., 2014 Telesnitsky, A., 542 Williamson, J.R., 533 Phillips, C., 122 Schattner, P., 15 Tenchini, M.L., 948 Willkomm, D.K., 1915 Phizicky, E.M., 1007 Schauer, U.E., 177 Terribilini, M., 1450 Wills, N.M., 1149 Piccirilli, J.A., 2025 Schelter, J., 1179, 1197 Tessari, M., 1671 Wilson, S.A., 1933 Piganeau, N., 177 Scherrer Jr., F.W., 1361 Teune, J.-H., 1915 Wilson, T.J., 980 Plant, E.P., 666 Schmidt, F.J., 353 Thapar, R., 2103 Wilusz, C.J., 1084, 1810 Plante, I., 1980 Schmidt, S., 913 Tinsley, R.A., 522 Wilusz, J., 1084, 1810 Plasterk, R.H.A., 187 Schneider, R.J., 883 Tintaru, A.M., 1933 Winey, M., 94 Pleiss, J.A., 2014 Schroeder, R., 177 Tollervey, D., 921 Wipf, P., 925 Polacek, C., 1893 Schuster, J., 1603 To¨nges, L., 1431 Withers, M., 933 Pooggin, M.M., 841 Schwer, B., 2126 Toro, N., 338 Wolin, S.L., 644 Poulsen, H., 1350 Seay, D., 1594 Tortorici, M.A., 133 Woodson, S.A., 2149 Preker, P.J., 994 Seetharaman, M., 235 Townley-Tilson, W.H.D., 1853 Wu, H., 40, 1475 Proudfoot, N.J., 655 Seif, E., 1661 Tran, E.J., 1092 Wu, M.-J., 2103 Pruijn, G.J.M., 1373 Sengupta, J., 1240 Trang, P., 63 Pulicherla, N., 725 Sethupathy, P., 192 Trantirek, L., 1475 Xiao, J., 925 Pulk, A., 790 Shapiro, B.A., 133, 342, 1521 Trinh, V.B., 710 Xiao, M., 561

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Author index

Xiao, S., 1023 Yen, P.H., 1486 Zaher, H.S., 1949 Zhao, Z.-y., 980 Xu, R.-M., 1116 Yin, P., 561 Zareen, N., 1104 Zhelkovsky, A., 435 Yokobayashi, Y., 710 Zaret, K., 655 Zhelonkina, A.G., 476 Yan, C., 1450 Youngman, E.M., 33 Zhang, G., 147 Zhong, J., 1271 Yang, W.-H., 547, 707 Yu, J.H., 547 Zhang, J., 147 Zhou, T., 63 Yao, J., 1271 Yu, L.E., 1050 Zhang, Q.-S., 1116 Zhu, Y., 699 Yarus, M., 1 Zhang, X., 1092 Zimmerman, R.M., 396 Yen, L., 797 Zago, M., 1708 Zhang, Y., 561 Zoll, J., 1671

2216 RNA, Vol. 12, No. 12 JOBNAME: RNA 12#12 2006 PAGE: 1 OUTPUT: November 17 02:07:17 2006 csh/RNA//subject-index

RNA: Subject Index for Volume 12, 2006

2-difluoromethylornithine, polyamine 16S rRNA nucleotides in intersubunit bridges T4 DNA ligase for RNA 59-adenylation depletion by (Hyvo¨nen et al.), (Pulk et al.), 790–795 (Wang and Silverman), 1142–1146 1569–1580 20S editosome, KREPA4 from Trypanosoma Adenylyltransferase, T4 RNA ligase 1 29-OMe-mediated RNAi (Kraynack and brucei and (Salavati et al.), 819–829 (Wang et al.), 2126–2133 Baker), 163–175 30S ribosomal subunit Adipocyte, microRNA and 3T3-L1 29O-methylation (Saikia et al.), 2025–2032 16S rRNA nucleotides in intersubunit pre-adipocyte differentiation 29-O-methyl ribosyl modification, of siRNAs bridges (Pulk et al.), 790–795 (Kajimoto et al.), 1626–1632 (Jackson et al.), 1197–1204 assembly, role of S15 in (Bubunenko et al.), Affinity, GTP aptamer structure 29-O-methyltransferase, Trypanosoma brucei 1229–1238 (Carothers et al.), 567–578 TbMT57 protein (Arhin et al.), 53–61 GE82832 inhibition of translocation Affinity purification, of eukaryotic 48S 29-O-ribose methylation, in Archaea (Omer (Brandi et al.), 1262–1269 initiation complexes (Locker et al.), et al.), 1708–1719 S5 ram mutant protein (Kirthi et al.), 683–690 39-cap-independent translational enhancer 2080–2090 AIF1 (Haseno¨hrl et al.), 674–681 (39CITE), in TBSV (tomato bushy stunt 40LoVe, interaction with Vg1LE binding Albumin, transcriptional termination sequences virus) (Fabian and White), 1304–1313 proteins (Czaplinski and Mattaj), 213–220 in mouse gene (West et al.), 655–664 3D structure, RNA Ontology Consortium 48S complexes, affinity purification of Algorithm and (Leontis et al.), 533–540 (Locker et al.), 683–690 genetic algorithm (GA), IRES prediction 39 end formation, in yeast NMD (Baker and 50-54-nt boundary rule (Silva et al.), with (Baird et al.), 1772–1773 Parker), 1441–1445 2160–2169 predicting effective siRNAs with 39 hairpin, of U65 snoRNA (Khanna et al.), siRNArules 1.0 (Holen), 1620–1625 40–49 A A-loop:tRNA interaction in peptidyl transfer 39 processing endonuclease, tRNase Z (Brunelle et al.), 33–39 (Zareen et al.), 1104–1114 AAUAAA hexamer, direction of a-Amanatin-mediated suppression of 3T3-L1 pre-adipocyte differentiation transcriptional pausing by (Nag et al.), siRNA-induced TGS (Weinberg et al.), (Kajimoto et al.), 1626–1632 1534–1543 256–261 39 untranslated region (39 UTR) Absorbance spectroscopy, of RNase P RNA Alternative splice-site activation, in human 39-UTR-mediated translation starting at folding (Baird et al.), 599–600, 604–605 genomes (Dou et al.), 2047–2055 the 59-end (Rakotondrafara et al.), Acceptor stem microhelix (Rosen et al.), Alternative splicing 1893–1905 1315–1320 amplified sensitivity of a splicing reporter elongation factor 1a binding and Acid-base, in transition metal ion-mediated (Levinson et al.), 925–929 perinuclear localization of ribozyme catalysis (Roychowdhury-Saha distal regulation by splicing enhancer in metallothionein-1 mRNA (Mickleburgh and Burke), 1846–1851 equine b-casein intron 1 (Lenasi et al.), et al.), 1397–1406 A complexes, in vitro assembly of 498–506 intergenic polyadenylation sites (Lopez spliceosomal (Behzadnia et al.), identification of RNA-binding proteins that et al.), 1794–1800 1738–1744 regulate FGFR2 splicing through the use mitochondrial targeting of ATP6 protein Active site, fluorescence and solution NMR of sensitive and specific dual color (Kaltimbacher et al.), 1408–1417 study of 160-kDa group II intron fluorescence minigene assays (Newman ribosomal protein mRNAs in nematodes ribozyme (Gumbs et al.), 1693–1704 et al.), 1129–1139 (Hajarnavis and Durbin), 1786–1789 Adaptive Poisson-Boltzmann electrostatics, of imaging in vivo (Bonano et al.), 2073–2080 stabilization of termination codons in the Pylaiella littoralis ribosomal RNA intron P-element somatic inhibitor protein unspliced RNA of Rous sarcoma virus (Seetharaman et al.), 235–246 (Chmiel et al.), 283–290 (Weil and Beemon), 102–109 Adenosine deaminases acting on RNA spermidine/spermine N1-acetyltransferase tomato bushy stunt virus (TBSV) (Na et al.), (ADARs) (Hyvo¨nen et al.), 1569–1580 2199–2209 dimerization mediated by double-stranded Alzheimer’s disease 5.8S rRNA processing, Pop1p and RNA binding domain (Poulsen et al.), BACE1 modulation by aptamers (Xiao et al.), 1023–1036 1350–1359 (Rentmeister et al.), 1650–1659 59 cap, role in translation and mRNA decay double-stranded RNA-binding domain trans-frame proteins in (Wills and Atkins), (Meaux and Hoof), 1323–1335 (dsRBD) (Hallegger et al.), 1993–2003 1149–1152 5-fluorouridine, ribozyme self-cleavage role of a metastable RNA secondary Aminoacyl-tRNA, inhibition by pokeweed inhibition by (Yen et al.), 797–805 structure in hepatitis delta virus genotype antiviral protein (PAP) (Mansouri et al.), 59 untranslated region (59-UTR) III RNA editing (Linnstaedt et al.), 1683–1691 assessing IRES activity in (Bert et al.), 1521–1532 Aminoacyl-tRNA synthetase, effect of 1074–1082 targets in Drosophila (Stapleton et al.), La protein and tRNA modification interactions with regulatory tRNA 1922–1930 (Copela et al.), 644–652 (Nelson et al.), 1254–1260 Adenosine deamination, in fluorescent assay Antibacterial agent GE82832, as 30S 7-methylguanosine cap, role in translation for RNA editing (Roberson and inhibitor of translocation (Brandi et al.), and mRNA decay (Meaux and Hoof), Rosenthal), 1907–1911 1262–1269 1323–1335 Adenylation Anticodon recognition by tRNAHis 7SL/SRP RNA in HIV-1 (Onafuwa-Nuga stress inhibition of mRNA deadenylation in guanylyltransferase (Jackman and et al.), 542–545 yeast (Hilgers et al.), 1835–1844 Phizicky), 1007–1013

RNA (2006), 12:2217–2233. Published by Cold Spring Harbor Laboratory Press. Copyright Ó 2006 RNA Society. 2217

PROOF_RNA_125784_SUBJECT-INDEX JOBNAME: RNA 12#12 2006 PAGE: 2 OUTPUT: November 17 02:07:18 2006 csh/RNA//subject-index

Subject index

Antisense AUG-proximity effect (Silva et al.), intergenic polyadenylation sites (Lopez 29-OMe-mediated RNAi (Kraynack and 2160–2169 et al.), 1794–1801 Baker), 163–175 AU-rich element (ARE) microRNA promoter element discovery in inhibition of miRNAs that are up-regulated AUF1 interaction with eIF4G and PABP Arabidopsis (Megraw et al.), 1612–1618 during adipogenesis (Kajimoto et al.), (Lu et al.), 883–891 predicting effective siRNAs with 1626–1632 binding by RNAse PH domain (Anderson siRNArules 1.0 (Holen), 1620–1625 small interfering RNAs directing histone et al.), 1810–1814 prediction of RNA binding sites in proteins methylation and transcriptional gene CUG-BP and (Moraes et al.), 1084–1089 (Terribilini et al.), 1450–1461 silencing in human cells (Weinberg lipofection and (Barreau et al.), 1790–1793 RNA editing in mouse genome (Neeman et al.), 256–261 Autoantibodies, processing body (Bloch et al.), 1802–1808 Antizyme, Saccharomyces cerevisiae et al.), 707–709 Biological ontology, RNA Ontology (Ivanov et al.), 332–336 Autoantigen Consortium and (Leontis et al.), 533–540 Apocytochrome b, gRNA/mRNA complex processing bodies as (Bloch et al.), Bioluminescence resonance energy transfer (Yu and Koslowsky), 1050–1059 707–709 (BRET) study, of ADAR2 dimerization APP+1, role in neurodegenerative diseases RAP55 (Yang et al.), 547–554 (Poulsen et al.), 1350–1359 (Wills and Atkins), 1149–1152 Autokinase, Kin.46 ribozyme (Cho and Boltzmann ensemble, in RNA secondary Aptamers Burke), 2118–2124 structure prediction (Ding), 323–330 binding the double-stranded RNA-binding Box C/D RNA (Zhang et al.), 1092–1102 Box H/ACA snoRNA, analysis of Cbf5p domain (dsRBD) (Hallegger et al.), B 1993–2003 binding to (Normand et al.), 1868–1880 to eIF4G (Miyakawa et al.), 1825–1833 Bacillus subtilis Box H/ACA snoRNP (Normand et al.), high-affinity RNA to GTP (Carothers et al.), DEAD-box helicase YxiN (Wang et al.), 1868–1880 567–578 959–966 Brain tumors, microRNAs and (Nelson et al.), modulation of BACE1 (Rentmeister et al.), tRNA regulation of gene expression 187–190 1650–1659 (Nelson et al.), 1254–1260 Branched RNA, in lariat RNA synthesis regulation of RNAi (An et al.), 710–715 Bacteriophage l phosphatase (Keppetipola (Wang and Silverman), 313–320 to RNA-dependent RNA polymerase from and Shuman), 73–81 BRET (bioluminescence resonance energy foot and mouth disease virus (Ellingham Barley yellow dwarf virus class of transfer) study, of ADAR2 dimerization et al.), 1970–1978 cap-independent translation elements (Poulsen et al.), 1350–1359 Aquificales, RNAse P RNA (Marszalkowski (BTE) (Rakotondrafara et al.), 1893–1905 Brønsted analysis, of hepatitis delta virus et al.), 1915–1920 Base composition, patterns in rRNA (HDV) genomic ribozyme (Perrotta Arabidopsis thaliana secondary structure (Smit et al.), 1–13 et al.), 1282–1290 AtCyp59 cyclophilin from (Gullerova Base flipping, functional conformations of Brr5 (Zhelkovsky et al.), 435–443 et al.), 631–642 the L11-rRNA complex (Li et al.), BTE (barley yellow dwarf virus class of microRNA promoter element discovery in 1240–1252 cap-independent translation elements) (Megraw et al.), 1612–1618 Base rescue study, of HDV genomic ribozyme (Rakotondrafara et al.), 1893–1905 transitive RNA silencing of Arabidopsis (Perrotta et al.), 1282–1290 Bunyavirus RNA chaperone (Mir and endogenes (Bleys et al.), 1633–1638 Base triple, luteoviral mRNA pseudoknot Panganiban), 272–281 Archaea (Cornish et al.), 1959–1967 box C/D sRNP-guided nucleotide Bayesian statistical inference, in RNA C methylation (Zhang et al.), 1092–1102 secondary structure prediction (Ding), structure-function of sno-like RNAs (Omer 323–330 Caenorhabditis elegans et al.), 1708–1719 B-cell differentiation (Ma et al.), 122–131 high-affinity binding of RDE-4 homodimer Sulfolobus solfataricus translation initiation Beet western yellows virus (BWYV) (Cornish (Parker et al.), 807–816 factor 1 (Haseno¨hrl et al.), 674–681 et al.), 1959–1967 interacting endogenous and exogenous ARE. See AU-rich element (ARE) b-amyloid precursor protein, aberrant form RNAi pathways (Lee et al.), 589–596 Arginine methylation, and regulation of APP+1 in neurodegenerative diseases ribosomal mRNA sequence motif trypanosome mitochondrial gene (Wills and Atkins), 1149–1152 (Hajarnavis and Durbin), 1786–1789 expression (Goulah et al.), 1545–1554 b-casein splicing enhancer, distal effects of Cajal body Argonaute proteins (Lenasi et al.), 498–506 hNaf1 and (Hoareau-Aveilla et al.), 29-OMe-mediated RNAi (Kraynack and b-hairpin, of U65 snoRNA (Khanna et al.), 832–839 Baker), 163–175 40–49 ZFP100 (zinc finger protein) association human Ago2 expression (Shi et al.), b-secretase, BACE1 modulation by aptamers with (Wagner et al.), 1206–1217 943–946 (Rentmeister et al.), 1650–1659 cAMP receptor protein (CRP), tmRNA Artificial virus-like particles (AVPs), for Biacore analysis, of role of RNA structure tagging and (Li et al.), 248–255 transfection of siRNA into rat neurons in U1A/U1hpII binding (Law et al.), Candida ribozyme, folding of (Jiang et al.), (To¨nges et al.), 1431–1438 1168–1176 561–566 A-site, inhibition by pokeweed antiviral Binding affinity, P-element somatic inhibitor Cap protein (PAP) (Mansouri et al.), 1683–1691 protein (Chmiel et al.), 283–290 role in translation and mRNA decay AtCyp59 (Gullerova et al.), 631–642 Binding, PTB1 to RNA (Clerte and Hall), (Meaux and Hoof), 1323–1335 A-to-I RNA editing, in mouse genome 457–473 translational control by mRNA structure (Neeman et al.), 1802–1808 Biogenesis, plant microRNA processing near caps (Babendure et al.), 851–860 Atomic group ‘‘mutagenesis’’ study, of -1:73 (Kurihara et al.), 206–211 Cap 4 modification in Trypanosoma brucei base pair recognition by S. cerevisiae Bioinformatics (Arhin et al.), 53–61 HisRS (Rosen et al.), 1315–1320 alternative splice-site activation in human Cap-dependent translation, inhibition by ATP6 protein, mitochondrial targeting of genomes (Dou et al.), 2047–2055 RNA aptamers to eIF4G (Miyakawa recoded (Kaltimbacher et al.), archaeology and evolution of transfer RNA et al.), 1825–1833 1408–1417 genes in the Escherichia coli genome Cap-independent translation (Rakotondrafara AUF1, interaction with eIF4G and PABP (Withers et al.), 933–941 et al.), 1893–1905 (Lu et al.), 883–891 compositional patterns in rRNA secondary Capping ribozymes (Zaher et al.), AUG codon, dicistronic mRNA from structure (Smit et al.), 1–13 1949–1958 proximal (Matsuda and Dreher), a computational screen for mammalian CARNAC, IRES prediction with (Baird et al.), 1338–1348 H/ACA RNAs (Schattner et al.), 15–24 1774

2218 RNA, Vol. 12, No. 12 JOBNAME: RNA 12#12 2006 PAGE: 3 OUTPUT: November 17 02:07:19 2006 csh/RNA//subject-index

Subject index

Casein gene, distal effects of b-casein splicing Codon usage, in tRNA genes (Withers et al.), transfection reagents (To¨nges et al.), enhancer (Lenasi et al.), 498–506 933–941 1431–1438 Catalysis Coiled-coil domain, of Nop56/58 core D nucleobase catalysis in a ribozyme protein (Zhang et al.), 1092–1102 (Wilson et al.), 980–987 Commitment complex, blocked in vivo D5 RNA from the Pylaiella littoralis large P4 metal binding site in RNase P RNA splicing complexes (Tardiff and ribosomal RNA intron (R5-PL) (Christian et al.), 1463–1467 Rosbash), 968–978 (Seetharaman et al.), 235–246 transition metal ion-mediated ribozyme Comparative genomics, computational Database catalysis (Roychowdhury-Saha and screen for mammalian H/ACA RNAs IRESes (Baird et al.), 1764–1766 Burke), 1846–1851 (Schattner et al.), 15–24 TarBase (Sethupathy et al.), 192–195 Catalytic domain, of RNase MRP and RNase Computational analysis DAZAP1 (deleted in Azoospermia Associated P RNAs (Zhu et al.), 699–705 identification of gamma-herpesvirus Protein 1), nucleocytoplasmic shuttling Catalytic RNA, HDV genomic ribozyme microRNAs (Grundhoff et al.), of (Lin and Yen), 1486–1492 (Perrotta et al.), 1282–1290 733–749 DCL1 (Kurihara et al.), 206–211 CAT gene family, susceptibility to transitive screen for mammalian H/ACA RNAs DEAD-box protein silencing signals (Bleys et al.), (Schattner et al.), 15–24 discriminatory RNP remodeling by 1633–1638 ComRNA, IRES prediction with (Bowers et al.), 903–911 Cauliflower mosaic virus (CaMV), ribosome (Baird et al.), 1775 RNA helicases, YxiN from Bacillus shunting mechanism (Pooggin et al.), Conformational changes, involved in subtilis (Wang et al.), 959–966 841–849 initiation of minus-strand synthesis of Deadenylation, CUG-BP recruitment of Cbf5p (Normand et al.), 1868–1880 a virus-associated RNA (Zhang et al.), PARN deadenylase for (Moraes et al.), CCA-RNase P RNA interaction (Wegscheid 147–161 1084–1091 and Hartmann), 2135–2147 Copper chaperone for superoxide Debranching enzyme, in lariat RNA synthesis CD. See Circular dichroism (CD) dismutase-1 (CCS), binding to BACE1 (Wang and Silverman), 313–320 spectroscopy cytoplasmic domain (Rentmeister et al.), Decapping, and stress inhibition of mRNA Cd2 + ion-mediated ribozyme catalysis 1650–1659 deadenylation in yeast (Hilgers et al.), (Roychowdhury-Saha and Burke), Cotranscriptional processing/splicing 1835–1844 1846–1851 distal effects of b-casein splicing Decoding, functional conformations C/D-box RNA (Omer et al.), 1708–1719 enhancer (Lenasi et al.), 498–506 of the L11-rRNA complex (Li et al.), Cell cycle regulation of YRA1 expression (Preker 1240–1252 histone mRNAs and (Townley-Tilson et al.), and Guthrie), 994–1005 DED1 (Lancaster et al.), 903–911 1853–1866 transcriptional termination sequences in Degradation, of mRNA by Trypanosoma ZFP100 Zn fingers in histone pre-mRNA mouse serum albumin gene brucei 59 ! 39 exoribonuclease processing (Wagner et al.), 1206–1217 (West et al.), 655–664 (Li et al.), 2171–2184 Cellular localization, of AtCyp59 cyclophilin Coxsackie B virus, mRNA translation at the Dehydration, RNA catalysis induced by (Gullerova et al.), 635–637 endoplasmic reticulum (Lerner and (Kazakov et al.), 446–454 c-fos, CUG-BP role in mRNA decay (Moraes Nicchitta), 775–787 Deleted in Azoospermia Associated Protein 1 et al.), 1084–1090 CPF (cleavage/polyadenylation factor) of (DAZAP1), nucleocytoplasmic shuttling Chain terminators, in fluorescent assay for Saccharomyces cerevisiae (Zhelkovsky of (Lin and Yen), 1486–1492 RNA editing (Roberson and Rosenthal), et al.), 435–443 Dengue virus, 39-UTR-mediated translation 1907–1911 Cricket paralysis virus (CrPV) (Lancaster starting at the 59-end (Rakotondrafara Chaperone, bunyavirus RNA (Mir and et al.), 894–901 et al.), 1893–1905 Panganiban), 272–281 CRP (cAMP receptor protein), tmRNA Deoxyribozyme, in lariat RNA synthesis Chlorolissoclimides (Robert et al.), 717–723 tagging and (Li et al.), 248–255 (Wang and Silverman), 313–320 Chromatin immunoprecipitation (ChIP) Cryo-EM analysis, functional conformations Design, predicting effective siRNAs with analysis of the L11-rRNA complex (Li et al.), siRNArules 1.0 (Holen), 1620–1625 blocked in vivo splicing complexes 1240–1252 DexH/D proteins, RNA remodeling by (Tardiff and Rosbash), 968–977 Cryptic splice site, usage in the FGB gene (Bowers et al.), 903–911 hnRNP A1 and telomere association (Spena et al.), 948–956 Dicer (Zhang et al.), 1120–1122, 1126 Crystal structure, of stabilizing mutations in Dicer-2, R2D2 coordination in siRNA Circular dichroism (CD) spectroscopy Tetrahymena ribozyme (Guo et al.), binding (Liu et al.), 1514–1520 P-element somatic inhibitor protein 387–394 Dicer-like1 protein of Trypanosoma (Chmiel et al.), 283–290 CstF, transcriptional pausing and brucei (Shi et al.), 2063–2070 RNase P RNA folding (Baird et al.), (Nag et al.), 1534–1535, 1541–1542 high-affinity binding of RDE-4 homodimer 599–600, 604–605 C-terminal domain (Parker et al.), 807–816 Circular templates, for RNA-dependent RNA high-affinity binding of RDE-4 homodimer RNAi regulation by small molecules and polymerase (Ranjith-Kumar and Kao), (Parker et al.), 807–816 (An et al.), 710–715 303–311 RNA polymerase II interaction with tissue-specific microRNA expression Cleavage/polyadenylation factor (CPF) of cyclophilin (Gullerova et al.), (Obernosterer et al.), 1161–1166 Saccharomyces cerevisiae (Zhelkovsky 631–642 Dicistronic reporter, use in assessing IRES et al.), 435–443 CUG-BP, recruitment of PARN deadenylase activity in HIF-1a and other 59 UTRs Cloning, inverted repeats for RNAi (Bao and (Moraes et al.), 1084–1091 (Bert et al.), 1074–1082 Cagan), 2020–2024 Cyclophilin, AtCyo59 from Arabidopsis Differentiation, in microRNA and adipogenesis Clostridium thermocellum, polynucleotide thaliana interaction with RNA (Gullerova (Kajimoto et al.), 1626–1632 kinase-phosphatase from (Keppetipola et al.), 631–642 Dim1 methyltransferase (O’Farrell et al.), and Shuman), 73–81 Cytidine deamination, in fluorescent assay 725–731 Clustering, in statistical and Bayesian for RNA editing (Roberson and Dimerization, of ADAR2 mediated by approaches to RNA secondary structure Rosenthal), 1907–1911 double-stranded RNA binding domain prediction (Ding), 323–330 Cytomegalovirus, inhibition of gene (Poulsen et al.), 1350–1359 c-myc, assessing IRES activity in (Bert et al.), expression by external guide sequence Dimethyltransferases, characterization of 1074–1082 RNA (Li et al.), 63–71 KsgA/Dim1 (O’Farrell et al.), 725–731 Codon discrimination, context effect on Cytotoxicity, of stearylated octaarginine Dinuclear metal cluster, in Clostridium initiation (Raman et al.), 1154–1160 and artificial virus-like particles as thermocellum polynucleotide

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Subject index

kinase-phosphatase (Keppetipola and EIF4G freezing-induced ribozyme ligation Shuman), 73–81 AUF1 interaction with 883-891 (Lu et al.), (Kazakov et al.), 446–453 Distance constraints, in topological 883–891 KsgA/Dim1 dimethyltransferases (O’Farrell stabilization of Kin.46 ribozyme inhibitory RNA aptamer to (Miyakawa et al.), 725–731 (Cho and Burke), 2118–2124 et al.), 1825–1833 ribozyme stability (Guo et al.), 387–394 Divalent ions, role in superfast ribozyme EJC. See Exon junction complex (EJC) RNA interaction frequency (Striggles et al.), kinetics (Roychowdhury-Saha and Electrophoretic mobility-shift assays 353–358 Burke), 1846–1857 L22 binding to EBER 1 (Fok et al.), 872–880 RNase MRP and RNase P RNAs (Zhu et al.), DNA ligase, in ligation-based approach to RNA interaction of p14 and p14-Sf3b155 699–705 study RNA modifications (Saikia et al.), by (Spadaccini et al.), 416–423 small RNAs influence on (Bove et al.), 2025–2032 Elongation factor 1a, binding to perinuclear 2042 Dna-Q-H family exonuclease Snipper (Snp) mRNA localization signal (Mickleburgh tRNA evolution as a selfish process (Kupsco et al.), 2103–2116 et al.), 1397–1406 (Withers et al.), 933–941 Double-stranded RNA-binding domain Elongation, open and closed RdRp complexes Exon. See Splicing (dsRBD), aptamers binding (Hallegger (Ranjith-Kumar and Kao), 303–311 Exon junction complex (EJC) et al.), 1993–2003 Embryonic stem cells eIF4AIII regions necessary for (Shibuya Double-stranded RNA binding motif (DRBM), alternative splicing of (SSAT) spermidine/ et al.), 360–372 dimerization of ADAR2 mediated by spermine N1-acetyltransferase (Hyvo¨nen function of hUpf3a and hUpf3b in (Kunz (Poulsen et al.), 1350–1359 et al.), 1569–1580 et al.), 1015–1021 Double-stranded RNA (dsRNA) short RNAs bound by P19 in (Calabrese Exon silencing, of FGFR2 exon IIIb (Bonano high-affinity binding of RDE-4 homodimer and Sharp), 2092–2100 et al.), 2073–2078 (Parker et al.), 807–816 Endonuclease Exonuclease siRNA induction of interferon response T. brucei RNase III editosomes (Panigrahi RNAse PH domain binding to RNA (Reynolds et al.), 988–993 et al.), 1038–1048 (Anderson et al.), 1810–1814 Double-stranded RNA (dsRNA) binding tRNase Z (Zareen et al.), 1104–1114 Snipper from Drosophila melanogaster proteins, in plant microRNA processing Endoplasmic reticulum, mRNA translation (Kupsco et al.), 2103–2116 (Kurihara et al.), 206–211 compartmentalized to (Lerner and Trypanosoma brucei 59!39 Drosophila Nicchitta), 775–787 exoribonuclease (Li et al.), 2171–2184 ADAR targets (Stapleton et al.), Enzyme Exosome 1922–1930 bacterial polynucleotide kinase-phosphatase nuclear RNA surveillance (Kadaba et al.), cloning inverted repeats for RNAi (Bao (Keppetipola and Shuman), 73–81 508–519 and Cagan), 2020–2024 evolution of capping enzyme triphosphatase polyadenylation-dependent RNA Dicer-2 and R2D2 coordination binding (Gong et al.), 1468–1473 processing (Egecioglu et al.), 26–31 siRNA (Liu et al.), 1514–1520 Epstein-Barr virus translation and decay of uncapped or genetic analysis of U7 snRNA (Godfrey EBER 1, L22 binding to (Fok et al.), unadenylated mRNA (Meaux and Hoof), et al.), 396–407 872–881 1323–1335 P-element somatic inhibitor protein (PSI) identification of gamma-herpesvirus Export, RNA binding and export factors (REFs) (Chmiel et al.), 283–290 microRNAs (Grundhoff et al.), 733–749 (Golovanov et al.), 1933–1946 Snipper (Snp) exonuclease (Kupsco et al.), ERI-1, Snipper as homolog (Kupsco et al.), Expression profiling, miRNA-microarray 2103–2116 2103–2116 based on LNA technology (Castoldi Duplex length, siRNA induction of ERPIN, IRES prediction with (Baird et al.), et al.), 913–919 interferon response (Reynolds et al.), 1776–1777 External guide sequence RNA, inhibition of 988–993 Escherichia coli human cytomegalovirus gene expression Dynalign, IRES prediction with (Baird et al.), 16S rRNA nucleotides in intersubunit (Li et al.), 63–71 1774, 1775 bridges (Pulk et al.), 790–795 Eyring analysis, topological stabilization of Dyskeratosis congenita, NAP57 mutation identification of the RsmE RNA kinase ribozyme (Cho and Burke), and (Kittur et al.), 2057–2058, 2061 methyltransferase (Basturea et al.), 2118–2124 426–433 9 E RNase P RNA, tRNA 3 -CCA contact F with (Wegscheid and Hartmann), EBER 1 (Fok et al.), 872–881 2135–2147 Fetal fibroblast, alternative splicing of (SSAT) EBV. See Epstein-Barr virus role of S15 in 30S subunit assembly spermidine/spermine N1-acetyltransferase EDEN (embryonic deadenylation element) (Bubunenko et al.), 1229–1238 in (Hyvo¨nen et al.), 1569–1580 CUG-BP and (Moraes et al.), 1084–1089 S5 ram mutant protein (Kirthi et al.), FGB, cryptic splice site usage in (Spena et al.), lipofection and (Barreau et al.), 1790–1793 2080–2090 948–956 Editing. See RNA editing tRNA evolution as a selfish process Fibrinogen Bb-chain gene, cryptic splice site Editing complexes, interaction with site for (Withers et al.), 933–941 in (Spena et al.), 948–956 full-round U deletion in Trypanosoma Ty3 stimulator effect on translation Fibroblast Growth Factor Receptor-2 (FGFR2) brucei (Sacharidou et al.), 1219–1226 initiation (Raman et al.), 1154–1160 identification of RNA-binding proteins that Editosome ESE, cryptic splice site usage in the FGB regulate (Newman et al.), 1129–1139 integrity, KREPA4 from Trypanosoma gene (Spena et al.), 948–955 imaging alternative splicing of (Bonano brucei and (Salavati et al.), 819–829 Ethanol, RNA catalysis induced by (Kazakov et al.), 2073–2078 T. brucei RNase III (Panigrahi et al.), et al.), 446–454 Fluctuation analysis, RNA interaction 1038–1048 Eukaryotic initiation factors, and affinity frequency (Striggles et al.), 353–358 ED_SCAN, IRES prediction with purification of 48S complexes (Locker Fluorescence anisotropy, pyrrolo-C (Baird et al.), 1771 et al.), 683–690 fluorescent probe for RNA (Tinsley and EEF1a, binding to perinuclear mRNA Evolution Walter), 522–528 localization signal (Mickleburgh et al.), capping enzyme triphosphatase (Gong Fluorescence gel shift assay, of active site of 1397–1406 et al.), 1468–1473 160-kDa group II intron ribozyme EF-G, translocation of 29-deoxy-substituted conservation of functionally important (Gumbs et al.), 1693–1704 P-tRNA (Feinberg and Joseph), 580–587 backbone phosphate group critical for Fluorescence loss in photobleaching (FLIP) EIF4AIII, mutational analysis of (Shibuya aminoacylation of histidine tRNAs analysis, of nucleo-cytoplasmic shuttling et al.), 360–372 (Rosen et al.), 1315–1320 in yeast (Belaya et al.), 921–924

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Fluorescence microscopy, of Ty3 interaction Gel mobility shift assay, OF PTB1-RNA Ll.LtrB intron of Lactococcus lactis with P-bodies (Beliakova-Bethell et al.), binding (Clerte and Hall), 459–463, 466, (Plante and Cousineau), 1980–1991 94–100 469, 471, 473 targetron use for gene disruption in Fluorescence quenching, pyrrolo-C fluorescent Gene delivery, by gene insertion within the Staphylococcus aureus (Yao et al.), probe for RNA (Tinsley and Walter), Lactococcus lactis Ll.LtrB group II intron 1271–1280 522–528 (Plante and Cousineau), 1980–1991 GST-pulldown assay Fluorescence recovery after photobleaching Gene expression 40LoVe interaction with Vg1LE binding (FRAP) analysis, of nucleo-cytoplasmic arginine methylation regulation of proteins (Czaplinski and Mattaj), shuttling in yeast (Belaya et al.), 921–924 mitochondrial gene expression in 216–217, 220–221 Fluorescence studies Trypanosoma brucei (Goulah et al.), analysis of interactions among PSF, for RNA editing (Roberson and Rosenthal), 1545–1554 p54nrb, p68 and U1A by (Liang 1907–1911 characterization of a Paip2 homolog and Lutz), 113–114, 119 translational control by mRNA structure (Berlanga et al.), 1556–1567 GTP aptamer structure (Carothers et al.), near caps (Babendure et al.), 851–860 inhibition of cytomegalovirus by external 567–578 Fluorescent minigenes, dual color splicing guide sequence RNA (Li et al.), 63–71 GTPase reporter (Newman et al.), 1129–1139 RIP-Chip analysis of mRNAs bound to SLBP assembly of Snu114 into U5 snRNP and FMR1 (Chmiel et al.), 284, 287 (Townley-Tilson et al.), 1853–1866 (Brenner and Guthrie), 862–869 Folding RNA binding and export factors (REFs) GTPase-associated center (GAC), bunyavirus RNA chaperone (Mir and (Golovanov et al.), 1933–1946 functional conformations of L11-rRNA Panganiban), 272–281 tRNA regulation of (Nelson et al.), complex (Li et al.), 1240–1252 fragmented tRNAMet (Feinberg and Joseph), 1254–1260 Guide RNA (gRNA) 581 Gene networks, three-hybrid screen mRNA interaction (Yu and Koslowsky), kinetics, pyrrolo-C as a fluorescent probe identification of mRNAs controlled by 1050–1059 for RNA (Tinsley and Walter), 522–528 a regulatory protein and (Seay et al.), RBP16 stimulator of trypanosome RNA monovalent cations resolving ribozyme 1594–1599 editing in vitro (Miller et al.), 1292–1302 misfolding (Jiang et al.), 561–566 General acid-base catalysis GYYA hairpin loop, nuclear magnetic partitioning of native and misfolded RNA in hairpin ribozyme (Wilson et al.), resonance (NMR) structure of (Melchers populations in yeast (Jackson et al.), 980–987 et al.), 1671–1681 2149–2157 hepatitis delta virus (HDV) genomic statistical methods for (Ding), 323–330 ribozyme (Perrotta et al.), 1282–1290 H structural basis of RNA thermostability Gene regulation (Baird et al.), 598–608 inhibitors of ribozyme self-cleavage in H/ACA RNAs, computational screen for topology of three-way junctions in folded mammalian cells (Yen et al.), 797–805 mammalian (Schattner et al.), 15–24 RNAs (Lescoute and Westhof), 83–91 tRNA regulation of gene expression H/ACA RNPs, dynamics of (Kittur et al.), Foot-and-mouth disease virus (FMDV) (Nelson et al.), 1254–1260 2057–2061 aptamers to RNA-dependent RNA Gene targeting H/ACA snoRNPs polymerase from (Ellingham et al.), RNase P as a gene-targeting agent hNaf1 and (Hoareau-Aveilla et al.), 1970–1978 (Li et al.), 63–71 832–839 IRES (Ferna´ndez-Miragall et al.), 223–231 targetron use for gene disruption in structures and interaction of U65 snoRNA Footprinting assays, of Cbf5p binding to Staphylococcus aureus (Yao et al.), and Nop10 (Khanna et al.), 40–50 snoRNA (Normand et al.), 1873–1876, 1271–1280 Hairpin. See also Short hairpin RNA (shRNA) 1880 Gene therapy, RNase P as a gene-targeting FMDV IRES and (Ferna´ndez-Miragall et al.), Fragile X mental retardation protein (FMRP), agent (Li et al.), 63–71 223–232 interaction with nuclear export factor Genetic algorithm (GA), IRES prediction identification of gamma-herpesvirus NXF2 (Lai et al.), 1446–1449 with (Baird et al.), 1772–1773 microRNAs (Grundhoff et al.), 733–749 Frameshifting Genetic depletion, blocked in vivo splicing nuclear magnetic resonance (NMR) context effect on initiation codon complexes (Tardiff and Rosbash), structure of a GYYA (Melchers et al.), discrimination (Raman et al.), 968–978 1671–1681 1154–1160 Genome annotation, of intergenic role of RNA structure in U1A/U1hpII effects of heptameric slippery site polyadenylation sites (Lopez et al.), binding (Law et al.), 1168–1176 composition on (Plant and Dinman), 1794–1800 translational control by mRNA structure 666–672 Genome complexity, U1 snRNA variants near caps (Babendure et al.), 851–860 in expression of S. cerevisiae antizyme and (Kyriakopoulou et al.), 1603–1609 Hairpin ribozyme mRNA (Ivanov et al.), 332–336 Genome restoration, hepatitis delta virus nucleobase catalysis in (Wilson et al.), structure of poorly functional frameshifting (HDV) (Gudima et al.), 1061–1072 980–987 pseudoknot (Cornish et al.), 1959–1967 glmS ribozyme, characteristics of (Roth et al.), RNA catalysis induced by freezing and FRAP (fluorescence recovery after 607–618 dehydration (Kazakov et al.), 446–454 photobleaching) analysis, of Glucosamine 6-phosphate, glmS ribozyme Hammerhead ribozyme nucleo-cytoplasmic shuttling in yeast and (Roth et al.), 607–618 kinetics (Roychowdhury-Saha and Burke), (Belaya et al.), 921–924 GNRA motif, IRES activity and 1846–1851 Freezing, RNA catalysis induced by (Kazakov (Ferna´ndez-Miragall et al.), 223–232 study of translation and decay of uncapped et al.), 446–454 GPRM, IRES prediction with (Baird et al.), or unadenylated mRNA (Meaux and Functional genomics, targetron use for gene 1775 Hoof), 1323–1335 disruption in Staphylococcus aureus G-quadruplex, hrRNP A1 unwinding Haploinsufficiency, telomerase (Mozdy and (Yao et al.), 1271–1280 (Zhang et al.), 1116–1126 Cech), 1721–1736 Gram-positive bacteria, tRNA regulation HCV RNA, PTB1 binding to (Clerte and Hall), G of gene expression in (Nelson et al.), 457–473 1254–1260 Helicase GABA pre-mRNA, PTB1 binding to (Clerte Group II intron discriminatory RNP remodeling by and Hall), 457–473 alternative group II intron–exon pairings a DEAD-box protein (Bowers et al.), GA bulge, in Tetrahymena telomerase RNA (Costa et al.), 338–340 903–911 stem–loop IV domain (Richards et al.), D5 (domain 5) structure and ion binding YxiN from Bacillus subtilis (Wang et al.), 1475–1484 (Seetharaman et al.), 235–246 959–966

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Helix I temperature sensitivity of group II intron acceptor stem microhelix (Rosen et al.), splicing revealed by targetron use in 1315–1320 Identity elements, tRNA (Kapp et al.), Staphylococcus aureus (Yao et al.), topology of three-way junctions in folded 751–762 1271–1280 RNAs (Lescoute and Westhof), 83–91 IgM secretory poly(A) site (Ma et al.), Intron-exon pairings, alternative group II Heparin, RNA synthesis and (Ranjith-Kumar 122–131 (Costa et al.), 338–340 and Kao), 303–308 Imidazole, substituted ribozyme (Wilson Intronic splicing enhancer elements (ISEs), Hepatitis C virus (HCV) et al.), 980–987 dual color fluorescent splicing reporters magnesium effect on translation Imino proton exchange, in luteoviral mRNA for (Newman et al.), 1129–1139 (Lancaster et al.), 894–901 pseudoknot (Cornish et al.), 1959–1967 Inverted repeat, cloning for RNA interference RNA-dependent RNA polymerase (RdRp) Immunoprecipitation analysis, of mRNAs (Bao and Cagan), 2020–2024 (Ranjith-Kumar and Kao), 303–311 bound to SLBP (Townley-Tilson et al.), Ion pair reverse phase chromatography, Hepatitis delta virus (HDV) 1853–1866 RNA enrichment and analysis (Dickman genomic ribozyme (Perrotta et al.), In situ hybridization, for micro-RNA and Hornby), 691–695 1282–1290 expression and localization in archival IRES. See Internal ribosome entry site (IRES) restoration in vivo of defective hepatitis human brain (Nelson et al.), 187–190 Isothermal titration calorimetry analysis, of delta virus RNA genomes (Gudima In vitro selection Sf3b155-p14-U2AF-RNA interaction et al.), 1061–1072 aptamer isolation for FMDV RNA-dependent (Spadaccini et al.), 411–412, 423 role of RNA secondary structure in RNA RNA polymerase (Ellingham et al.), 1970–1978 editing (Linnstaedt et al.), 1521–1532 J Herpesvirus, identification of RNA 59-adenylation by T4 DNA ligase gamma-herpesvirus microRNAs (Wang and Silverman), 1142–1146 Jab1/MPN domain, of Prp8p (Bellare et al.), (Grundhoff et al.), 733–749 In vivo complementation studies, of RNase P 292–300 Heterokaryon assay, nucleo-cytoplasmic (Wegscheid and Hartmann), 2135–2147 Jakobids, mitochondrial RNase P RNAs in shuttling in yeast (Belaya et al.), 921–924 In vivo imaging, of alternative splicing (Seif et al.), 1661–1668 Hfq protein, small binding RNAs in Listeria (Bonano et al.), 2073–2078 Junction, topology of three-way in folded monocytogenes (Christiansen et al.), In vivo RNA-RNA interaction, detection RNAs (Lescoute and Westhof), 83–91 1383–1394 with yeast RNA-hybrid system (Piganeau et al.), 177–183 HIF-1a, assessing IRES activity in (Bert et al.), K 1074–1082 In vivo SELEX, of GCUA tetranucleotide High-throughput screening (HTS) assay, for loop in poliovirus ori L KH domains, of Drosophila P-element ribozyme self-cleavage inhibitors (Melchers et al.), 1671–1681 somatic inhibitor protein (Chmiel et al.), (Yen et al.), 797–805 Initiation 283–290 Histidyl-tRNA synthetase (HisRS), critical conformational switch involved in virus Kin.46 ribozyme (Cho and Burke), 2118–2124 59 monophosphate group for replication (Zhang et al.), 147–161 Kinetics aminoacylation of histidine tRNAs rotavirus RNA replication (Tortorici et al.), capping ribozyme (Zaher et al.), 1949–1958 (Rosen et al.), 1315–1320 133–145 fluorescence and solution NMR study of Histone Initiation coupling, dicistronic mRNA from the active site of a 160-kDa group II blockaged pre-mRNA processing by U7 proximal AUG codons (Matsuda and intron ribozyme (Gumbs et al.), snRNA mutations in Drosophila Dreher), 1338–1348 1693–1704 (Godfrey et al.), 396–407 Initiation factor role of RNA structure in U1A/U1hpII methylation, siRNA-mediated TGS inhibitory RNA aptamer to eIF4G binding (Law et al.), 1168–1176 (Weinberg et al.), 256–261 (Miyakawa et al.), 1825–1833 superfast ribozyme (Roychowdhury-Saha Histone mRNA Paip2B (Berlanga et al.), 1556–1567 and Burke), 1846–1851 RIP-Chip analysis of mRNAs bound to SLBP Initiator tRNA, identity elements of (Kapp Kissing stem–loop (Rakotondrafara et al.), (Townley-Tilson et al.), 1853–1866 et al.), 751–762 1893–1905 Snipper degradation of (Kupsco et al.), Interferon response, induction by siRNA KREPA4, from Trypanosoma brucei (Salavati 2103–2116 (Reynolds et al.), 988–993 et al.), 819–829 ZFP100 Zn fingers in histone pre-mRNA Internal initiation of translation, RNA motifs KsgA/Dim1 dimethyltransferases, processing (Wagner et al.), 1206–1217 and IRES activity (Ferna´ndez-Miragall characterization of (O’Farrell et al.), HIV-1 et al.), 223–232 725–731 7SL/SRP RNA in (Onafuwa-Nuga et al.), Internal ribosome entry site (IRES) KSHV, identification of gamma-herpesvirus 542–545 activity determined by RNA structural microRNAs (Grundhoff et al.), 733–749 siRNA-mediated TGS (Weinberg et al.), motifs (Ferna´ndez-Miragall et al.), K-turn, structure-function of archaeal sno-like 256–261 223–232 RNAs (Omer et al.), 1708–1719 hNaf1 (Hoareau-Aveilla et al.), 832–839 activity in HIF-1a and other 59 UTRs (Bert et al.), 1074–1082 hnRNP A1, stimulation of telomerase L activity (Zhang et al.), 1116–1126 affinity purification of 48S complexes hnRNP D (Locker et al.), 683–690 L11, functional conformations of complex 40LoVe (Czaplinski and Mattaj), 213–220 review (Baird et al.), 1755–1777 with rRNA (Li et al.), 1240–1252 AUF1 (Lu et al.), 883–891 translation in HCV, effect on (Lancaster L22 ribosomal protein (Fok et al.), 872–881 Homology blocks, of tRNase Z (Zareen et al.), et al.), 894–901 Lactococcus lactis LI.LtrB group II intron 1104–1114 Intersubunit bridges, 16S rRNA nucleotides gene insertion within (Plante and hTERT, prediction of RNA binding sites in (Pulk et al.), 790–795 Cousineau), 1980–1991 (Terribilini et al.), 1450–1461 Intramolecular RNA recombination, and targetron use for gene disruption in Human genomes, alternative splice-site restoration in vivo of defective hepatitis Staphylococcus aureus (Yao et al.), activation in (Dou et al.), 2047–2055 delta virus RNA genomes (Gudima 1271–1280 Human slicer Argonaute2, expression in et al.), 1061–1072 La protein (Copela et al.), 644–652 Trypanosoma brucei (Shi et al.), Intron. See also splicing Lariat RNA synthesis, two-step strategy for 943–946 Mer1p-dependent intron requirement of (Wang and Silverman), 313–320 HYL1 (Kurihara et al.), 206–211 Bud13p for splicing activation and Leaky scanning, and study of proximal AUG Hyperthermophiles, structure-function of nuclear retention (Scherrer and codons and dual initiation (Matsuda sno-like RNAs in (Omer et al.), 1708–1719 Spingola), 1361–1370 and Dreher), 1338–1348

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Subject index

Ligation Mechanistic invariant (Zaher et al.), post-transcriptional regulation of of hairpin ribozyme in cis induced by 1949–1958 miRNA expression (Obernosterer et al.), freezing and dehydration (Kazakov Melting transition, pyrrolo-C fluorescent 1161–1166 et al.), 446–454 probe for RNA and (Tinsley and Walter), promoter element discovery in Arabidopsis RNA-ligase mediated creation of synthetic 522–528 (Megraw et al.), 1612–1618 RNAs (Stark et al.), 2014–2019 Mer1p, splicing regulation and nuclear short RNAs bound by P19 in ES cells Lipofection, of RNA (Barreau et al.), retention (Scherrer and Spingola), (Calabrese and Sharp), 2092–2100 1790–1793 1361–1370 siRNA off-target silencing compared Liposome-mediated RNA transfection Metal ion (Jackson et al.), 1179–1186 (Barreau et al.), 1790–1793 capping ribozymes and (Zaher et al.), Mitochondria Listeria monocytogenes, identification of 1949–1958 arginine methylation regulation of small Hfq-binding RNAs in (Christiansen glmS ribozyme (Roth et al.), 607–618 mitochondrial gene expression in et al.), 1383–1394 P4 metal binding site in RNase P RNA, Trypanosoma brucei (Goulah et al.), Localization, in liposome-mediated RNA substrate positioning affect on affinity 1545–1554 transfection (Barreau et al.), 1790–1793 (Christian et al.), 1463–1467 RBP16 stimulator of trypanosome RNA Locked Nucleic Acid - in site hybridization, of role in superfast ribozyme kinetics editing in vitro (Miller et al.), 1292–1302 micro-RNA expression and localization (Roychowdhury-Saha and Burke), RNase P RNAs in jakobids (Seif et al.), in archival human brain (Nelson et al.), 1846–1857 1661–1668 187–190 Metallothionein-1 (MT-1) mRNA, elongation targeting of recoded ATP6 protein Locked nucleic acids (LNA), factor 1a binding and perinuclear (Kaltimbacher et al.), 1408–1417 miRNA-microarray based on (Castoldi localization (Mickleburgh et al.), MLN51, eIF4AIII binding site (Shibuya et al.), et al.), 913–919 1397–1406 360–372 Long-distance RNA interactions, in oscillating Metastable structure, in partitioning of native Modification interference, 16S rRNA kissing stem–loop interaction-mediated and misfolded RNA populations in nucleotides in intersubunit bridges and 59 scanning-dependent translation by yeast (Jackson et al.), 2149–2157 (Pulk et al.), 790–795 viral 39-cap-independent translation Methanocaldococcus jannaschii, box C/D Molecular dynamics simulations, of element (Rakotondrafara et al.), sRNP-guided nucleotide methylation in functional conformations of L11-rRNA 1893–1905 (Zhang et al.), 1092–1102 complex (Li et al.), 1240–1252 Loop–loop interaction, in RNA-hybrid Methylation Molecular misreading, and trans-frame system for the detection of RNA–RNA arginine methylation regulation of proteins in neurodegenerative diseases interactions in vivo (Piganeau et al.), mitochondrial gene expression in (Wills and Atkins), 1149–1152 177–183 Trypanosoma brucei (Goulah et al.), Monovalent cations, ribozyme misfolding Lsm11, interaction with ZFP100 (zinc finger 1545–1554 resolution (Jiang et al.), 561–566 protein) (Wagner et al.), 1206–1217 ligation-based approach to study (Saikia Mouse Luciferase reporter, study of proximal AUG et al.), 2025–2032 alternative splicing of (SSAT) spermidine/ codons and dual initiation (Matsuda and Methyltransferase, identification of the RsmE spermine N1-acetyltransferase (Hyvo¨nen Dreher), 1338–1348 RNA (Basturea et al.), 426–433 et al.), 1569–1580 Luteovirus MFOLD, IRES prediction with (Baird et al.), miRNA-microarray based on LNA 39-UTR-mediated translation starting at 1771–1772, 1773 technology (Castoldi et al.), 913–919 the 59-end (Rakotondrafara et al.), miChip (Castoldi et al.), 913–919 molecular interaction between FMRP and 1893–1905 Microarray NXF2 (Lai et al.), 1446–1449 mRNA pseudoknots (Cornish et al.), for identification of gamma-herpesvirus pseudouridine synthase 1 (mPus1p) 1959–1967 mircroRNAs (Grundhoff et al.), (Behm-Ansmant et al.), 1583–1592 733–749 RNA editing in mouse genome (Neeman M miRNA-microarray based on LNA et al.), 1802–1808 technology (Castoldi et al.), 913–919 mPus1p, modification of U2 snRNA m7G methyltransferase, from Trypanosoma RIP-Chip analysis of mRNAs bound to and tRNAs (Behm-Ansmant et al.), brucei (Hall and Ho), 488–496 SLBP (Townley-Tilson et al.), 1853–1866 1583–1592 Machine learning, in RNA structure microRNA target, database of supported mRNA. See also Pre-mRNA prediction from sequence alignments targets (Sethupathy et al.), 192–195 capping by Trypanosoma RNA m7G (Bindewald and Shapiro), 342–351 microRNAs (miRNAs) methyltransferase (Hall and Ho), Magnesium ion 3T3-L1 pre-adipocyte differentiation 488–496 binding, and Pylaiella littoralis ribosomal (Kajimoto et al.), 1626–1632 dicistronic mRNA from proximal RNA intron (Seetharaman et al.), database of supported targets (Sethupathy AUG codons (Matsuda and Dreher), 235–246 et al.), 192–195 1338–1348 effect on translation in HCV (Lancaster detection system based on padlock probes gRNA interaction (Yu and Koslowsky), et al.), 894–901 and rolling circle amplification (Jonstrup 1050–1059 P4 metal binding site in RNase P RNA, et al.), 1747–1751 inhibitors of ribozyme self-cleavage in substrate positioning affect on affinity enrichment and analysis of RNA centered mammalian cells (Yen et al.), 797–805 (Christian et al.), 1463–1467 on ion pair reverse phase methodology molecular interaction between FMRP and transition metal ion-mediated ribozyme (Dickman and Hornby), 691–695 NXF2 (Lai et al.), 1446–1449 catalysis (Roychowdhury-Saha and identification of gamma-herpesvirus RIP-Chip analysis of mRNAs bound to SLBP Burke), 1846–1851 (Grundhoff et al.), 733–749 (Townley-Tilson et al.), 1853–1866 Magoh, eIF4AIII interaction (Shibuya et al.), in archival human brain (Nelson et al.), RNA binding and export factors (REFs) 361, 366–371 187–190 (Golovanov et al.), 1933–1946 Malaria, capping enzyme triphosphatase interacting endogenous and exogenous translation and decay of uncapped or (Gong et al.), 1468–1473 RNAi pathways in Caenorhabditis unadenylated (Meaux and Hoof), Manganese ion-mediated ribozyme catalysis elegans (Lee et al.), 589–596 1323–1335 (Roychowdhury-Saha and Burke), microarray based on LNA technology translocation of 29-deoxy-substituted 1846–1851 (Castoldi et al.), 913–919 P-tRNA (Feinberg and Joseph), 580–587 Mass spectrometry, of blocked in vivo splicing planarian (Palakodeti et al.), 1640–1647 transport and molecular interaction complexes (Tardiff and Rosbash), plant microRNA processing (Kurihara between FMRP and NXF2 (Lai et al.), 968–978 et al.), 206–211 1446–1449

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Subject index

mRNA cleavage Mutual information, in RNA structure Nuclear assembly factor (NAF1), association Pcf11–RNA interactions (Hollingworth prediction from sequence alignments and localization of (Kittur et al.), et al.), 555–559 (Bindewald and Shapiro), 342–351 2057–2061 tmRNA tagging at rare codons (Li et al.), Myotonic dystrophy, CUG-BP and (Moraes Nuclear encoded ATP6 gene, mitochondrial 248–255 et al.), 1085, 1090 targeting of (Kaltimbacher et al.), mRNA decay. See also Nonsense-mediated 1408–1417 mRNA decay (NMD) Nuclear exosome, and polyadenylation- N AUF1 interaction with eIF4G and PABP dependent RNA processing (Egecioglu (Lu et al.), 883–891 Naive Bayes classifier, use by RNABindR et al.), 26–31 CUG-BP recruitment of PARN deadenylase tool (Terribilini et al.), 1450, 1451, Nuclear export factor NXF2, interaction with (Moraes et al.), 1084–1091 1453, 1456–1457, 1460 fragile X mental retardation protein hUPF1 cysteine-histidine-rich domain Natural selection, and compositional patterns (FMRP) (Lai et al.), 1446–1449 structure (Kadlec et al.), 1817–1823 in rRNA secondary structure (Smit et al.), Nuclear localization signal, and H/ACA RNP processing body autoantibodies (Bloch 1–13 proteins (Kittur et al.), 2057–2061 et al.), 707–709 Nematode, ribosomal mRNA sequence Nuclear magnetic resonance (NMR) RAP55 shuttle between P-bodies and motif in (Hajarnavis and Durbin), analysis of the Sf3b155-p14-U2AF–RNA stress granules (Yang et al.), 547–554 1786–1789 interaction (Spadaccini et al.), 410–424 RNAse PH domain of PM-Scl-75 Nervous system, and role of ADAR GTP aptamer structure (Carothers et al.), (Anderson et al.), 1810–1814 targets in Drosophila (Stapleton et al.), 567–578 role of cap and poly(A) tail in (Meaux and 1922–1930 GYYA hairpin loop (Melchers et al.), Hoof), 1323–1335 Neurodegenerative diseases, trans-frame 1671–1681 tmRNA role in (Mehta et al.), 2187–2198 proteins in (Wills and Atkins), 1149–1152 Pcf11–RNA interactions (Hollingworth mRNA degradation Neurons, reagents for transfection of siRNA et al.), 555–559 39 end formation in yeast NMD (Baker and into (To¨nges et al.), 1431–1438 Pylaiella littoralis ribosomal RNA intron Parker), 1441–1445 NMR. See Nuclear magnetic resonance (Seetharaman et al.), 235–246 lipofection and (Barreau et al.), (NMR) solution structure of REF2-1 (Golovanov 1790–1793 NMR chemical shift perturbation analysis, of et al.), 1933–1946 Trypanosoma brucei 59 ! 39 160-kDa group II intron ribozyme active structure of a poorly functional exoribonuclease (Li et al.), 2171–2184 site (Gumbs et al.), 1693–1704 frameshifting pseudoknot (Cornish et al.), mRNA localization Non-AUG initiation codons, effect of Ty3 1959–1967 40LoVe (Czaplinski and Mattaj), 213–220 stimulator on usage (Raman et al.), structures and interaction of U65 snoRNA elongation factor 1a binding and 1154–1160 and Nop10 (Khanna et al.), 40–50 perinuclear localization of Noncanonical 59 splice site (Kyriakopoulou Tetrahymena telomerase RNA stem–loop metallothionein-1 mRNA (Mickleburgh et al.), 1603–1609 IV domain (Richards et al.), 1475–1484 et al.), 1397–1406 Noncoding RNA, interacting endogenous and Nuclear retention, by Mer1p (Scherrer and to mitochondrial surface and import of exogenous RNAi pathways in Spingola), 1361–1370 ATP6 protein (Kaltimbacher et al.), Caenorhabditis elegans (Lee et al.), Nuclear RNA surveillance, in Saccharomyces 1408–1417 589–596 cerevisiae (Kadaba et al.), 508–519 Ty3 interaction with P-bodies Nonsense-mediated mRNA decay (NMD) Nuclease footprinting, of PTB1-RNA binding (Beliakova-Bethell et al.), 94–100 39 end formation in yeast (Baker and (Clerte and Hall), 464–466, 467, 472 mRNA processing Parker), 1441–1445 Nucleobase catalysis in the hairpin ribozyme 39-end processing, role of Brr5/Ysh1 alternative splicing of (SSAT) spermidine/ (Wilson et al.), 980–987 subunit in (Zhelkovsky et al.), 435–443 spermine N1-acetyltransferase (Hyvo¨nen Nucleocapsid protein, bunyavirus (Mir and disruption by U7 snRNA mutation in et al.), 1569–1580 Panganiban), 272–281 Drosophila (Godfrey et al.), 396–407 AUG-proximity effect (Silva et al.), Nucleocytoplasmic shuttling mRNA processing body 2160–2169 deleted in Azoospermia Associated Protein autoantibodies (Bloch et al.), 707–709 eIF4AIII regions necessary for (Shibuya 1 (DAZAP1) (Lin and Yen), 1486–1492 RNA-associated protein 55 (RAP55) et al.), 360–372 H/ACA RNP proteins (Kittur et al.), localization to (Yang et al.), 547–554 function of hUpf3a and hUpf3b in (Kunz 2057–2061 mRNA splicing. See Alternative splicing; et al.), 1015–1021 in yeast (Belaya et al.), 921–924 Pre-mRNA splicing; Splicing hUPF1 cysteine-histidine-rich domain Nucleotide methylation (Zhang et al.), mRNA stability structure (Kadlec et al.), 1817–1823 1092–1102 CUG-BP recruitment of PARN deadenylase Mer1p effect on (Scherrer and Spingola), NXF2, interaction with fragile X mental (Moraes et al.), 1084–1091 1361–1370 retardation protein (FMRP) (Lai et al.), three-hybrid screen identification of stabilization of RSV RNA by 39 UTR (Weil 1446–1449 mRNAs controlled by a regulatory and Beemon), 102–109 protein (Seay et al.), 1594–1599 Non snRNP-bound U1A (Ma et al.), 122–131 O Mutagenesis Nonstop mRNA Bacillus subtilis DEAD-box helicase tmRNA determinants required for (Mehta Off-target effects, toxicity of siRNA-induced (Wang et al.), 959–966 et al.), 2187–2198 (Federov et al.), 1188–1195 Pop1p (Xiao et al.), 1023–1036 tmRNA tagging at rare codons (Li et al.), Off-target silencing Prp8 protein dissection (Boon et al.), 248–255 reduction by chemical modification of 198–205 Non-Watson–Crick binding, and RNA siRNAs (Jackson et al.), 1197–1204 Trypanosoma RNA m7G methyltransferase interaction frequency (Striggles et al.), siRNA seed region-mediated (Jackson (Hall and Ho), 488–496 353–358 et al.), 1179–1186 Mutational analysis Nop10 (Khanna et al.), 40–50 Oogenesis eIF4AIII (Shibuya et al.), 360–372 Nop56/58, coiled-coil domain of (Zhang 40LoVe interaction with Vg1LE binding Pop1 RNase P subunit (Xiao et al.), et al.), 1092–1102 proteins (Czaplinski and Mattaj), 1023–1036 Northern blot analysis 213–220 T4 RNA ligase 1 (Wang et al.), identification of gamma-herpesvirus disruption by U7 snRNA mutation in 2126–2133 microRNAs (Grundhoff et al.), 733–749 Drosophila (Godfrey et al.), 396–407 Mutations, in RNase P (Wegscheid and miChip data confirmation by (Castoldi Ornithine decarboxylase antizyme (Ivanov Hartmann), 2135–2147 et al.), 915–919 et al.), 332–336

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P analysis of a 39-translational enhancer in Post-transcriptional processing, and TBSV (tomato bushy stunt virus) (Fabian gRNA and mRNA interaction (Yu and p14-Sf3b155-U2AF–RNA interaction and White), 1304–1313 Koslowsky), 1050–1059 (Spadaccini et al.), 410–424 luteoviral mRNA pseudoknot (Cornish Post-transcriptional regulation, of microRNA P19 suppresor of RNA silencing (Calabrese et al.), 1959–1967 expression (Obernosterer et al.), and Sharp), 2092–2100 microRNA processing (Kurihara et al.), 1161–1166 p53, and RNA binding in yeast three-hybrid 206–211 Prediction system (Riley et al.), 620–629 nrb Penn State Symposium in Plant Physiology IRES (internal ribosome entry sites) p54 (Liang and Lutz), 111–120 (Bove et al.), 2035–2043 (Baird et al.), 1755–1777 p65, Tetrahymena telomerase RNA stem–loop Plasmodium, capping enzyme triphosphatase RNA binding sites in proteins from IV domain (Richards et al.), 1475–1484 in (Gong et al.), 1468–1473 amino acid sequence (Terribilini et al.), Padlock probes, microRNA detection system PM-Scl-75 (Anderson et al.), 1810–1815 1450–1461 based on (Jonstrup et al.), 1747–1751 Point mutations, in RNase P (Wegscheid RNA structure prediction from sequence Paip2 homolog, characterization of (Berlanga and Hartmann), 2135–2147 alignments (Bindewald and Shapiro), et al.), 1556–1567 Poisoned primer extension assay, for RNA 342–351 Panhandle, bunyavirus (Mir and Panganiban), editing (Roberson and Rosenthal), statistical and Bayesian approaches to 272–279 1907–1911 RNA secondary structure prediction Pararetrovirus, and ribosome shunting Pokeweed antiviral protein, depurination of (Ding), 323–330 mechanism (Pooggin et al.), 841–849 ribosome (Mansouri et al.), 1683–1691 Prediction software, for IRESes (Baird et al.), PARN deadenylase, recruitment by CUG-BP Poliovirus, GCUA tetranucleotide loop in 1771–1777 (Moraes et al.), 1084–1091 oriL (Melchers et al.), 1671–1681 Premature termination codons (PTCs), and Partial nuclease T1 digestion, RNase P RNA Poly(A) binding protein (PABP) stabilization of RSV RNA by 39 UTR folding (Baird et al.), 600–601, 605 39 end formation in yeast NMD and (Weil and Beemon), 102–109 Partition function, in RNA secondary structure (Baker and Parker), 1441–1445 Pre-mRNA prediction (Ding), 323–330 AUF1 interaction with 883-891 (Lu et al.), nuclear retention by Mer1p (Scherrer and P-body 883–891 Spingola), 1361–1370 autoantibodies (Bloch et al.), 707–709 characterization of a Paip2 homolog processing disruption by U7 snRNA RNA-associated protein 55 (RAP55) (Berlanga et al.), 1556–1567 mutation in Drosophila (Godfrey et al.), localization to (Yang et al.), 547–554 Polyadenylation 396–407 Ty3 interaction with (Beliakova-Bethell changing U1A levels (Ma et al.), 122–131 SF-A complex and cleavage during et al.), 94–100 dependent RNA processing (Egecioglu polyadenylation (Liang and Lutz), Pcf11–RNA interactions (Hollingworth et al.), et al.), 26–31 111–120 555–559 intergenic polyadenylation sites (Lopez Pre-mRNA splicing P-element somatic inhibitor (PSI) (Chmiel et al.), 1794–1800 alternative splice-site activation in human et al.), 283–290 role of Brr5/Ysh1 subunit in mRNA genomes (Dou et al.), 2047–2055 Penn State Symposium in Plant Physiology processing (Zhelkovsky et al.), 435–443 amplified sensitivity of a splicing reporter (Bove et al.), 2035–2043 role of SF-A complex in (Liang and Lutz), (Levinson et al.), 925–929 Peptide bond formation, role of A-loop:tRNA 111–120 analysis of the Sf3b155-p14-U2AF–RNA interaction in (Brunelle et al.), 33–39 Trf4p-dependent (Kadaba et al.), interaction (Spadaccini et al.), 410–424 Peptidyl transferase, A-loop:tRNA interaction 508–519 assembly of Snu114 into U5 snRNP and and (Brunelle et al.), 33–39 Poly(A)-dependent termination, and AAUAAA (Brenner and Guthrie), 862–869 Persephonella marina, RNAse P RNA hexamer direction of transcriptional blocked in vivo splicing complexes (Marszalkowski et al.), 1915–1920 pausing (Nag et al.), 1534–1543 (Tardiff and Rosbash), 968–978 PFOLD, IRES prediction with (Baird et al.), 1774 Polyamine eIF4AIII regions necessary for (Shibuya pGEM-WIZ (Bao and Cagan), 2020–2024 antizyne control of biosynthesis (Ivanov et al.), 360–372 Phosphatase, component of Clostridium et al.), 332 protein–protein interactions in human thermocellum polynucleotide polyamine-regulated unproductive splicing tri-snRNPs (Liu et al.), 1418–1429 kinase-phosphatase (Keppetipola and and translation of spermidine/spermine regulation of YRA1 expression (Preker Shuman), 73–81 N1-acetyltransferase (Hyvo¨nen et al.), and Guthrie), 994–1005 Phosphate recognition, by histidyl-tRNA 1569–1580 RNA interactions of splicing factor prp8 synthetases (Rosen et al.), 1315–1320 Poly(A) signal (Turner et al.), 375–384 Phosphoesterase, Clostridium thermocellum AAUAAA hexamer direction of ubiquitin binding by the Prp8p Jab1/MPN polynucleotide kinase-phosphatase transcriptional pausing (Nag et al.), domain (Bellare et al.), 292–300 (Keppetipola and Shuman), 73–81 1534–1543 in vitro assembly of functional A complexes Phosphohydrolase, structure-function transcriptional termination sequences in (Behzadnia et al.), 1738–1744 analysis of Plasmodium triphosphatase mouse serum albumin gene (West et al.), Pre-rRNA binding, Rrp5p and (de Boer et al.), (Gong et al.), 1468–1473 655–664 263–270 pH-rate profile (Brunelle et al.), 33–39 Poly(A) tail, role in translation and mRNA Pre-rRNA processing Phylogenetics, of tRNA genes (Withers et al.), decay (Meaux and Hoof), 1323–1335 partitioning of native and misfolded RNA 933–941 Polyglutamine disease, ribosomal populations in yeast (Jackson et al.), Phylogeny, in comparative study of the effects frameshifting and (Wills and Atkins), 2149–2157 of heptameric slippery site composition 1149–1152 Slx9p and (Bax et al.), 2005–2011 on frameshifting (Plant and Dinman), Polynucleotide kinase-phosphatase (Pnkp) Prespliceosome, and stepwise snRNP 666–672 from Clostridium thermocellum recruitment (Tardiff and Rosbash), 968–978 Picornavirus, mRNA translation at (Keppetipola and Shuman), 73–81 Pre-tRNA processing endoplasmic reticulum with (Lerner and Polynucleotide ligase, T4 RNA ligase 1 (Wang 39 end processing by tRNase Z (Zareen Nicchitta), 775–787 et al.), 2126–2133 et al.), 1104–1114 Planarians, microRNAs from (Palakodeti Polypyrimidine tract binding protein (PTB), Pop1p (Xiao et al.), 1023–1036 et al.), 1640–1647 binding to RNA (Clerte and Hall), Probe, pyrrolo-C as fluorescent for RNA Plants 457–473 (Tinsley and Walter), 522–528 39 untranslated region in the tomato Positional Weight Matrices (PWM), for Processing body. See P-body bushy stunt virus genome (Na et al.), microRNA discovery in Arabidopsis Processing, polyadenylation-dependent 2199–2209 (Megraw et al.), 1612–1618 (Egecioglu et al.), 26–31

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Processivity, hnRNP A1 stimulation of Pylaiella littoralis Reverse transcriptase (Yao et al.), 1271–1280 telomerase (Zhang et al.), 1116–1126 160-kDa group II intron ribozyme Ribonuclease complexes, composition of Programmed frameshifting (Gumbs et al.), 1693–1704 (Welting et al.), 1373–1381 context effect on initiation codon ribosomal RNA intron (Seetharaman et al.), Ribonucleoprotein (RNP) discrimination (Raman et al.), 1154–1160 235–246 40LoVe complex (Czaplinski and Mattaj), effects of heptameric slippery site Pyrrolo-C (PC) (Tinsley and Walter), 213–220 composition on (Plant and Dinman), 522–528 composition of the human RNase MRP and 666–672 Pyrrolo-cytosine ribonucleoside (Tinsley and RNase P complexes (Welting et al.), Promoter Walter), 522–528 1373–1381 microRNA promoter element discovery in discriminatory remodeling by DEAD-box Arabidopsis (Megraw et al.), 1612–1618 protein (Bowers et al.), 903–911 R tomato bushy stunt virus (Na et al.), 2199 hNaf1 and (Hoareau-Aveilla et al.), Promoter targeting, siRNA-mediated TGS R2D2, and Dicer-2 coordination in siRNA 832–839 (Weinberg et al.), 256–261 binding (Liu et al.), 1514–1520 Pop1p complex (Xiao et al.), 1023–1036 PROSITE RNA binding motifs, detection by RAKE, micro-RNA expression and localization Ribonucleoprotein (RNP) dynamics, H/ACA RNABindR tool (Christian et al.), in archival human brain (Nelson et al.), (Kittur et al.), 2057–2061 1457–1458 187–190 Ribosomal frameshifting Proteasome, characterization of Paip2 Ram mutant, S5 protein (Kirthi et al.), context effect on initiation codon homolog (Berlanga et al.), 1556–1567 2080–2090 discrimination (Raman et al.), Protein domains, of Prp8 protein RAP55 (RNA-associated protein 55) (Yang 1154–1160 (Boon et al.), 198–205 et al.), 547–554 effects of heptameric slippery site Protein family identification, of RsmE RNA Rare codons, tmRNA tagging at (Li et al.), composition on (Plant and Dinman), methyltransferase (Basturea et al.), 248–255 666–672 426–433 Rat1, Trypanosoma brucei homolog (Li et al.), role in generating aberrant proteins Protein interaction sites, of Prp8 protein 2171–2184 implicated in neurodegenerative diseases (Boon et al.), 198–205 RBDs (RNA Binding Domains), of PTB1 (Wills and Atkins), 1149–1152 Protein–protein interactions (Clerte and Hall), 457–472 Ribosomal mRNA polyadenylation network within the human UF/U6.U5 RDE-4 homodimer, high-affinity binding of (Hajarnavis and Durbin), 1786–1789 tri-snRNP (Liu et al.), 1418–1429 (Parker et al.), 807–816 Ribosomal protein L22 (Fok et al.), 872–881 RNAPII and Pcf11 (Hollingworth et al.), RdRp. See RNA-dependent RNA polymerase Ribosomal protein S15 (Bubunenko et al.), 555–559 (RdRp) 1229–1238 Protein–RNA interactions. See RNA–protein Real-time PCR study, of telomerase levels in Ribosomal RNA. See rRNA interactions yeast (Mozdy and Cech), 1721–1736 Ribosome Protein synthesis REF2-1, domain and functional architecture 16S rRNA nucleotides in intersubunit characterization of a Paip2 homolog of (Golovanov et al.), 1933–1946 bridges (Pulk et al.), 790–795 (Berlanga et al.), 1556–1567 REFs (RNA binding and export factors) affinity purification of 48S complexes inhibition by chlorolissoclimides (Robert (Golovanov et al.), 1933–1946 (Locker et al.), 683–690 et al.), 717–723 Regulated unproductive splicing and comparative study of the effects of initiator tRNA identity elements (Kapp translation (RUST), of spermidine/ heptameric slippery site composition et al.), 751–762 spermine N1-acetyltransferase (Hyvo¨nen on frameshifting (Plant and Dinman), mRNA translation at the endoplasmic et al.), 1569–1580 666–672 reticulum (Lerner and Nicchitta), Repeats functional conformations of the L11-rRNA 775–787 cloning inverted repeats for RNAi (Bao complex (Li et al.), 1240–1252 Prp8 protein and Cagan), 2020–2024 GE82832 as 30S inhibitor of translocation assembly of Snu114 into U5 snRNP and RNA editing in the mouse genome and (Brandi et al.), 1262–1269 (Brenner and Guthrie), 862–869 (Neeman et al.), 1802–1808 mRNA translation at the endoplasmic dissection (Boon et al.), 198–205 triplet repeat expansions diseases, reticulum (Lerner and Nicchitta), 775–787 RNA interactions with (Turner et al.), ribosomal frameshifting and (Wills and pokeweed antiviral protein depurination of 375–384 Atkins), 1149–1152 (Mansouri et al.), 1683–1691 ubiquitin binding by variant Jab1/MPN Replication, and bunyavirus RNA chaperone role of A-loop:tRNA interaction in peptidyl domain in (Bellare et al.), 292–300 (Mir and Panganiban), 272–281 transfer (Brunelle et al.), 33–39 Prp19-associated complex (Chen et al.), Reporter, splicing role of S15 in 30S subunit assembly 765–773 amplified sensitivity of (Levinson et al.), (Bubunenko et al.) , 1229–1238 Pseudoknot 925–929 Rrp5p and yeast ribosome biogenesis in capping ribosyme (Zaher et al.), dual color fluorescent (Newman et al.), (de Boer et al.), 263–270 1949–1958 1129–1139 S5 ram mutant protein (Kirthi et al.), glmS ribozyme (Roth et al.), 607–618 Residual dipolar coupling, in Pylaiella 2080–2090 luteoviral mRNA, structure of poorly littoralis ribosomal RNA intron study shunting in Rice tungro bacilliform functional frameshifting (Cornish et al.), (Seetharaman et al.), 235–246 pararetrovirus (Pooggin et al.), 841–849 1959–1967 Retention and Splicing (RES) complex stalling and tmRNA tagging at rare codons Pseudouridine (Scherrer and Spingola), 1361–1370 (Li et al.), 248–255 activities of mouse and yeast Pus1p Retrotransposon translocation inhibition by (Behm-Ansmant et al.), 1583–1592 temperature sensitivity of group II intron chlorolissoclimides (Robert et al.), structures and interaction of U65 snoRNA splicing revealed by targetron use in 717–723 and Nop10 (Khanna et al.), 40–50 Staphylococcus aureus (Yao et al.), translocation of 29-deoxy-substituted Pseudouridine synthase, Cbf5p (Normand 1271–1280 P-tRNA (Feinberg and Joseph), 580–587 et al.), 1868–1880 Ty3 interaction with P-bodies Ribosome ambiguity (ram) mutant, S5 Pseudouridylation guides, in computational (Beliakova-Bethell et al.), 94–100 (Kirthi et al.), 2080–2090 screen for mammalian H/ACA RNAs Retrovirus Ribosome biogenesis (Schattner et al.), 15–24 RNA packaging (Onafuwa-Nuga et al.), KsgA/Dim1 dimethyltransferases PTB1 (polypyrimidine tract binding protein1), 542–545 (O’Farrell et al.), 725–731 binding to RNA (Clerte and Hall), Ty3 interaction with P-bodies Slx9p and pre-rRNA processing, 457–473 (Beliakova-Bethell et al.), 94–100 2005–2011

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Ribosome-inactivating proteins (Mansouri 40LoVe (Czaplinski and Mattaj), 213–220 T. brucei RNase III editosomes (Panigrahi et al.), 1683–1691 CUG-BP (Moraes et al.), 1084–1091 et al.), 1038–1048 Ribosome scanning study, of proximal AUG eEF1a binding to perinuclear mRNA TUTase action in U-deletion (Zhelonkina codons and dual initiation (Matsuda localization signal (Mickleburgh et al.), et al.), 476–485 and Dreher), 1338–1348 1397–1406 RNA evolution. See Evolution Riboswitch, glmS ribozyme (Roth et al.), Hfq protein in Listeria monocytogenes RNA experimental model (Nelson et al.), 607–618 (Christiansen et al.), 1383–1394 1254–1260 Ribozyme identification with dual color fluorescent RNA folding. See Folding alternative group II intron–exon pairings splicing reporters (Newman et al.), RNAfold, IRES prediction with (Baird et al.), (Costa et al.), 338–340 1129–1139 1772 capping (Zaher et al.), 1949–1958 KREPA4 from Trypanosoma brucei RNAGA, IRES prediction with (Baird et al.), chemical rescue, multiple ionizable (Salavati et al.), 819–829 1774 groups, and general acid-base catalysis nucleocytoplasmic shuttling of DAZAP1 RNA-hybrid system (Piganeau et al.), in the HDV genomic ribozyme (Perrotta (Lin and Yen), 1486–1492 177–183 et al.), 1282–1290 RBP16 stimulator of trypanosome RNA RNA interactions, of splicing factor Prp8 evolution of stability in (Guo et al.), editing in vitro (Miller et al.), 1292–1302 (Turner et al.), 375–384 387–394 Rrp5p (de Boer et al.), 263–270 RNA interference (RNAi) fluorescence and solution NMR study of Yra1p (Preker and Guthrie), 994–1005 29-OMe-mediated (Kraynack and Baker), the active site of a 160-kDa group II RNABindR computational tool (Terribilini 163–175 intron ribozyme (Gumbs et al.), et al.), 1450–1461 Dicer-2 and R2D2 coordination binding 1693–1704 RNA capping siRNA (Liu et al.), 1514–1520 glmS (Roth et al.), 607–618 Plasmodium triphosphatase, Dicer-like1 protein of Trypanosoma brucei inhibitors of self-cleavage in mammalian structure-function analysis of (Gong (Shi et al.), 2063–2070 cells (Yen et al.), 797–805 et al.), 1468–1473 high-affinity binding of RDE-4 homodimer kinetics, superfast (Roychowdhury-Saha ribozyme (Zaher et al.), 1949–1958 (Parker et al.), 807–816 and Burke), 1846–1851 RNA 59-adenylation by T4 DNA ligase human Ago2 expression (Shi et al.), mitochondrial RNase P RNAs in jakobids (Wang and Silverman), 1142–1146 943–946 (Seif et al.), 1661–1668 RNA catalysis, by Pylaiella littoralis interacting endogenous and exogenous monovalent cations resolve ribozyme ribosomal RNA intron (Seetharaman RNAi pathways in Caenorhabditis misfolding (Jiang et al.), 561–566 et al.), 235–246 elegans (Lee et al.), 589–596 nucleobase catalysis in (Wilson et al.), RNA chaperone, bunyavirus (Mir and predicting effective siRNAs with 980–987 Panganiban), 272–281 siRNArules 1.0 (Holen), 1620–1625 RNA catalysis induced by freezing and RNA-dependent RNA polymerase (RdRp) reduction of off-target silencing by dehydration (Kazakov et al.), 446–454 aptamers to FMDV (Ellingham et al.), chemical modification of siRNAs temperature sensitivity of group II intron 1970–1978 (Jackson et al.), 1197–1204 splicing revealed by targetron use in C. elegans endogenous RNAi (Lee et al.), regulation through aptamer-small molecule Staphylococcus aureus (Yao et al.), 589–596 interaction (An et al.), 710–715 1271–1280 conformational switch in virus replication siRNA-mediated TGS (Weinberg et al.), topological stabilization of Kin.46 (Zhang et al.), 147–161 256–261 ribozyme (Cho and Burke), 2118–2124 open and closed complexes (Ranjith-Kumar siRNA seed region-mediated off-target translation and decay of uncapped or and Kao), 303–311 transcript silencing (Jackson et al.), unadenylated mRNA (Meaux and Hoof), rotavirus RNA replication (Tortorici et al.), 1179–1186 1323–1335 133–145 Snipper exonuclease and (Kupsco et al.), Rice tungro bacilliform virus (RTBV) (Pooggin RNA-directed transcription, hepatitis delta 2103–2116 et al.), 841–849 virus (Gudima et al.), 1061–1072 stearylated octaarginine and artificial RIP-Chip analysis, of mRNAs bound to SLBP RNA/DNA end-healing (Keppetipola and virus-like particles for transfection of (Townley-Tilson et al.), 1853–1866 Shuman), 73–81 siRNA into primary rat neurons (To¨nges RISC complex RNA editing et al.), 1431–1438 29-OMe-mediated RNAi (Kraynack and ADAR targets in Drosophila, 1922–1930 toxicity of siRNA off-target effects (Federov Baker), 163–175 aptamers binding the double-stranded et al.), 1188–1195 processing body autoantibodies (Bloch RNA-binding domain (dsRBD) Trypanosoma brucei TbMT57 protein et al.), 707–709 (Hallegger et al.), 1993–2003 (Arhin et al.), 53–61 RNA 59-adenylation, by T4 DNA ligase editing complex interactions with site for RNA labeling (Wang and Silverman), (Wang and Silverman), 1142–1146 full-round U deletion in Trypanosoma 1142–1146 RNA aptamers. See Aptamers brucei (Sacharidou et al.), 1219–1226 RNA ligase, for creation of large, synthetic RNA-associated protein 55 (RAP55) (Yang fluorescent assay for (Roberson and RNAs (Stark et al.), 2014–2019 et al.), 547–554 Rosenthal), 1907–1911 RNA modification RNA binding gRNA and mRNA interaction (Yu and human U6 snRNA-TUTase (Trippe et al.), arginine methylation regulation of Koslowsky), 1050–1059 1494–1503 mitochondrial gene expression in KREPA4 from Trypanosoma brucei and identification of the RsmE RNA Trypanosoma brucei (Goulah et al.), (Salavati et al.), 819–829 methyltransferase (Basturea et al.), 1545–1554 in mouse genome (Neeman et al.), 426–433 Bacillus subtilis DEAD-box helicase 1802–1808 systematic approach to study (Saikia et al.), (Wang et al.), 959–966 RBP16 stimulator of trypanosome RNA 2025–2032 role of RNA structure in U1A/U1hpII editing in vitro (Miller et al.), RNA motif binding (Law et al.), 1168–1176 1292–1302 RNA Ontology Consortium (Leontis et al.), site prediction from amino acid sequence role of ADAR2 double-stranded RNA 533–540 (Terribilini et al.), 1450–1461 binding domain (Poulsen et al.), topology of three-way junctions in folded RNA binding and export factors (REFs) 1350–1359 RNAs (Lescoute and Westhof), 83–91 (Golovanov et al.), 1933–1946 role of metastable RNA secondary structure RNAMotif, IRES prediction with (Baird et al.), RNA Binding Domains (RBDs), of PTB1 in hepatitis delta virus genotype III 1776 (Clerte and Hall), 457–472 RNA editing (Linnstaedt et al.), RNA Ontology Consortium (ROC) (Leontis RNA-binding protein 1521–1532 et al.), 533–540

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Subject index

RNA polymerase RNA replication fluorescence and solution NMR study of AAUAAA hexamer direction of 39 untranslated region in the tomato the active site of a 160-kDa group II transcriptional pausing (Nag et al.), bushy stunt virus genome (Na et al.), intron ribozyme (Gumbs et al.), 1534–1543 2199–2209 1693–1704 enhancement of transcriptional cycling by conformational switch involved in virus GCUA tetranucleotide loop in poliovirus S1 (Trippe et al.), 1505–1512 replication (Zhang et al.), 147–161 oriL (Melchers et al.), 1671–1681 RNA polymerase II (RNAPII) rotavirus (Tortorici et al.), 133–145 gRNA and mRNA interaction (Yu and AtCyp50 cyclophilin interaction with RNA–RNA interactions Koslowsky), 1050–1059 (Gullerova et al.), 631–642 analysis of a 39-translational enhancer in RNA structural motifs and IRES activity Pcf11–RNA interaction (Hollingworth TBSV (tomato bushy stunt virus) (Fabian (Ferna´ndez-Miragall et al.), 223–232 et al.), 555–559 and White), 1304–1313 solution structure of REF2-1 (Golovanov restoration in vivo of defective hepatitis FMDV IRES and (Ferna´ndez-Miragall et al.), et al.), 1933–1946 delta virus RNA genomes (Gudima 223–232 structure of a poorly functional et al.), 1061–1072 frequency in a model of the RNA World frameshifting pseudoknot (Cornish et al.), RNA processing (Striggles et al.), 353–358 1959–1967 composition of the human RNase MRP and mRNA 59-UTR and regulatory tRNA Tetrahymena telomerase RNA stem–loop RNase P complexes (Welting et al.), (Nelson et al.), 1254–1260 IV domain (Richards et al.), 1475–1484 1373–1381 structure probing of a gRNA bound to its thermostability (Baird et al.), 598–608 Penn State Symposium in Plant Physiology mRNA (Yu and Koslowsky), 1050–1059 translational control by mRNA structure (Bove et al.), 2039–2041 RNA secondary structure. See Secondary near caps (Babendure et al.), 851–860 RNAProfile, IRES prediction with (Baird structure RNA surveillance et al.), 1774–1775 RNase III nuclear in Saccharomyces cerevisiae RNA–protein interactions Dicer-like1 protein of Trypanosoma brucei (Kadaba et al.), 508–519 analysis of Cbf5p binding to a box (Shi et al.), 2063–2070 stabilization of RSV RNA by 39 UTR H/ACA snoRNA (Normand et al.), polyadenylation-dependent RNA (Weil and Beemon), 102–109 1868–1880 processing (Egecioglu et al.), 26–31 RNA switches (Zhang et al.), 147–161 CUG-BP (Moraes et al.), 1084–1091 T. brucei RNase III editosomes (Panigrahi RNA synthesis editing complex interactions with site for et al.), 1038–1048 general two-step lariat (Wang and full-round U deletion in Trypanosoma RNase MRP Silverman), 313–320 brucei (Sacharidou et al.), 1219–1226 differential association of protein subunits open and closed RdRp complexes eEF1a binding to perinuclear mRNA with (Welting et al.), 1373–1381 (Ranjith-Kumar and Kao), 303–311 localization signal (Mickleburgh et al.), Pop1p, mutational analysis of (Xiao et al.), RNA topology, of three-way junctions in 1397–1406 1023–1036 folded RNAs (Lescoute and Westhof), high-affinity binding of RDE-4 homodimer RNA (Zhu et al.), 699–705 83–91 (Parker et al.), 807–816 RNA sensors, natural (Bove et al.), 2041–2042 RNA transfection, liposome-mediated L22 binding to EBER 1 (Fok et al.), 872–881 RNase P (Barreau et al.), 1790–1793 p53 recognition of RNA (Riley et al.), differential association of protein subunits RNA virus, 39-translational enhancer in TBSV 620–629 with (Welting et al.), 1373–1381 (tomato bushy stunt virus) (Fabian and Pcf11–RNA interactions (Hollingworth as a gene-targeting agent (Li et al.), White), 1304–1313 et al.), 555–559 63–71 RNA World in poliovirus replication (Melchers et al.), mitochondrial in jakobids (Seif et al.), RNA catalysis induced by freezing and 1671–1681 1661–1668 dehydration (Kazakov et al.), 446–454 prediction of RNA binding sites in proteins P4 metal binding site in RNase P RNA RNA interaction frequency (Striggles et al.), (Terribilini et al.), 1450–1461 (Christian et al.), 1463–1467 353–358 PTB1 binding to RNA (Clerte and Hall), Pop1p, mutational analysis of (Xiao et al.), RNP. See Ribonucleoprotein (RNP) 457–473 1023–1036 RNPase (Bowers et al.), 903–911 RNA binding cyclophilin (Gullerova et al.), RNAs lacking P18 in the Aquificales Rnt1p (Egecioglu et al.), 26–31 631–642 (Marszalkowski et al.), 1915–1920 Rolling circle amplification, microRNA RNA interactions of splicing factor prp8 RNAse PH domain, RNA binding by detection system based on (Jonstrup (Turner et al.), 375–384 (Anderson et al.), 1810–1814 et al.), 1747–1751 small Hfq-binding RNAs in Listeria RNase P RNA Rotavirus, RNA replication in (Tortorici et al.), monocytogenes (Christiansen et al.), RNase MRP RNA origination from 133–145 1383–1394 (Zhu et al.), 699–705 Rous sarcoma virus, stabilization of RNA by structures and interaction of U65 snoRNA tRNA 39-CCA contact with (Wegscheid 39 UTR (Weil and Beemon), 102–109 and Nop10 (Khanna et al.), 40–50 and Hartmann), 2135–2147 rRIP-Chip (Townley-Tilson et al.), 1853–1866 three-hybrid screen identification of RNase probing, footprint analysis of the RRM. See RNA recognition motif (RRM) mRNAs controlled by a regulatory Cbf5D p-snR5 interactions by (Normand rRNA protein (Seay et al.), 1594–1599 et al.), 1873–1876, 1880 compositional patterns in rRNA secondary RNA:pseudouridine synthases, modification RNA silencing, transitive of Arabidopsis structure (Smit et al.), 1–13 of U2 snRNA and tRNAs (Behm-Ansmant endogenes (Bleys et al.), 1633–1638 depurination of sarcin/ricin loop (Mansouri et al.), 1583–1592 RNA splicing. See Splicing et al.), 1683–1691 RNA recognition motif (RRM) RNA stability. See Stability fluorescence and solution NMR study of AtCyp59 cyclophilin (Gullerova et al.), RNA structure the active site of a 160-kDa group II 631–635, 639–640 39 untranslated region in the tomato intron ribozyme (Gumbs et al.), Bacillus subtilis DEAD-box helicase bushy stunt virus genome (Na et al.), 1693–1704 (Wang et al.), 959–966 2199–2209 modification by KsgA/Dim1 domain of REF2-1 (Golovanov et al.), analysis of a 39-translational enhancer in dimethyltransferases (O’Farrell et al.), 1933–1946 TBSV (tomato bushy stunt virus) (Fabian 725–731 p14 (Spadaccini et al.), 410–420 and White), 1304–1313 modifications, ligation-based approach to role of RNA structure in U1A/U1hpII bunyavirus (Mir and Panganiban), study (Saikia et al.), 2025–2032 binding (Law et al.), 1168–1176 272–281 pseudouridylation, by yeast Cbf5p RNA repair, T4 RNA ligase and (Wang et al.), conformational switch in virus replication (Normand et al.), 1868–1880 2126–2133 (Zhang et al.), 147–161 Rrp5p (de Boer et al.), 263–270

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Rrp6p, polyadenylation-dependent RNA scPus1p, modification of U2 snRNA RNA structure prediction form (Bindewald processing and (Egecioglu et al.), 26–31 and tRNAs (Behm-Ansmant et al.), and Shapiro), 342–351 RSEARCH, IRES prediction with (Baird et al.), 1583–1592 RsmE family protein sequences (Basturea 1775–1776 Screening et al.), 430 RsmE RNA methyltransferase (Basturea et al.), amplified sensitivity of a splicing reporter Slx9p and yeast homologs (Bax et al.), 2006 426–433 (Levinson et al.), 925–929 UPF1 proteins, 1818 RTBV (Rice tungro bacilliform virus) (Pooggin three-hybrid screen identification of Sequence analysis, of RNase MRP RNA et al.), 841–849 mRNAs controlled by a regulatory revealing its origination from eukaryotic RUST (regulated unproductive splicing and protein (Seay et al.), 1594–1599 RNase P RNA (Zhu et al.), 699–705 translation), of spermidine/spermine Secondary structure Sequence scanning, for microRNA promoter N1-acetyltransferase (Hyvo¨nen et al.), compositional patterns in rRNA element discovery in Arabidopsis 1569–1580 (Smit et al.), 1–13 (Megraw et al.), 1612–1618 IRES (Baird et al.), 1755–1777 SF2/ASF binding site, in GFB gene (Spena mitochondrial RNase P RNAs in jakobids et al.), 948–956 S (Seif et al.), 1661–1668 SF3b155-p14-U2AF–RNA interaction S1, enhancement of transcriptional cycling p53 recognition of RNA (Riley et al.), (Spadaccini et al.), 410–424 by (Trippe et al.), 1505–1512 620–629 SF-A complex (Liang and Lutz), 111–120 S1 RNA binding motifs, in Rrp5p (de Boer RNase MRP and RNase P RNAs Short hairpin RNA (shRNA) et al.), 263–270 (Zhu et al.), 699–705 regulation of RNAi (An et al.), 710–715 S5 protein, ram mutant (Kirthi et al.), RNA structure prediction from sequence siRNA seed region-mediated off-target 2080–2090 alignments (Bindewald and Shapiro), transcript silencing (Jackson et al.), S15 (ribosomal protein) (Bubunenko et al.), 342–351 1179–1186 1229–1238 role of a metastable RNA secondary Short interspersed elements (SINEs), mouse Saccharomyces cerevisiae structure in hepatitis delta virus genotype genome (Neeman et al.), 1802–1808 39 end formation in yeast NMD (Baker III RNA editing (Linnstaedt et al.), Short open reading frame (ORF), inhibition and Parker), 1441–1445 1521–1532 of nonsense-mediated mRNA-decay and antizyme mRNA (Ivanov et al.), 332–336 rotavirus (Tortorici et al.), 133–145 (Silva et al.), 2160–2169 blocked in vivo splicing complexes statistical methods for RNA folding (Ding), Short RNA (Tardiff and Rosbash), 968–978 323–330 bound by the P19 suppressor of RNA critical 59 monophosphate group for Secondary studies, of translational control by silencing in mouse embryonic stem cells aminoacylation of histidine tRNAs mRNA structure near caps (Babendure (Calabrese and Sharp), 2092–2100 (Rosen et al.), 1315–1320 et al.), 851–860 cloning (Calabrese and Sharp), 2092–2100 La protein (Copela et al.), 644–652 Seed region, effect on siRNA off-target Shuttling, nucleocytoplasmic of DAZAP1 (Lin Mer1p-dependent intron requirement for transcript silencing (Jackson et al.), and Yen), 1486–1492 Bud13p (Scherrer and Spingola), 1179–1188 Signal recognition particle (SRP), 7SL RNA 1361–1370 Selection, in compositional patterns in rRNA incorporation (Onafuwa-Nuga et al.), nuclear RNA surveillance in (Kadaba secondary structure (Smit et al.), 1–13 542–545 et al.), 508–519 SELEX (systematic evolution of ligands by Silencing nucleo-cytoplasmic shuttling in (Belaya exponential enrichment) reduction of off-target silencing by et al.), 921–924 aptamer isolation for FMDV RNA- chemical modification of siRNAs Pcf11 (Hollingworth et al.), 555–559 dependent RNA polymerase (Ellingham (Jackson et al.), 1197–1204 regulation of YRA1 expression (Preker et al.), 1970–1978 siRNA mediation in human cells (Weinberg and Guthrie), 994–1005 aptamers binding the double-stranded et al.), 256–261 RNA-hybrid system for the detection of RNA-binding domain (dsRBD) siRNA seed region-mediated off-target RNA-RNA interactions in vivo (Piganeau (Hallegger et al.), 1993–2003 transcript silencing (Jackson et al.), et al.), 177–183 GCUA tetranucleotide loop in poliovirus 1179–1186 role of Brr5/Ysh1 C-terminal domain and oriL (Melchers et al.), 1671–1681 transitive of Arabidopsis endogenes (Bleys homolog Syc1 in mRna 39-end inhibitory RNA aptamer to eIF4G et al.), 1633–1638 processing in (Zhelkovsky et al.), (Miyakawa et al.), 1825–1833 Single nucleotide polymorphism (SNP), 435–443 RNA interaction frequency (Striggles et al.), U1snRNAs (Kyriakopoulou et al.), Rrp5p and ribosome biogenesis (de Boer 353–358 1603–1609 et al.), 263–270 to select aptamers that recognize Sinorhizobium meliloti, potential for scPus1p (Behm-Ansmant et al.), 1583–1592 cytoplasmic tail of BACE (B1-CT) alternative intron–exon pairings in group Slx9p and pre-rRNA processing, 2005–2011 (Rentmeister et al.), 1650–1659 II intron RmInt1 from (Costa et al.), telomerase levels in (Mozdy and Cech), Selfish genes, tRNA (Withers et al.), 338–340 1721–1736 933–941 siRISC (Liu et al.), 1514–1520 translation-independent inhibition of Self-organization, in compositional patterns siRNArules 1.0 (Holen), 1620–1625 mRNA deadenylation during stress in in rRNA secondary structure (Smit et al.), siRNAs (Hilgers et al.), 1835–1844 1–13 29-OMe-mediated RNAi (Kraynack and Ty3 stimulator effect on translation Self-splicing, of alternative group II intron- Baker), 163–175 initiation (Raman et al.), 1154–1160 exon pairings (Costa et al.), 338–340 Dicer-2 and R2D2 coordination in binding Sampling, in statistical and Bayesian Sequence alignment siRNA (Liu et al.), 1514–1520 approaches to RNA secondary structure 39hExo/ERI-1 family of exonucleases human Ago2 expression (Shi et al.), prediction (Ding), 323–330 (Kupsco et al.), 2105 943–946 SARS-associated coronavirus (Plant and dimethyltransferases (O’Farrell et al.), 727 induction of interferon response (Reynolds Dinman), 666–672 glmS ribozymes (Roth et al.), 609 et al.), 988–993 Satellite RNAs, and conformational switch in Nop56/58 core proteins (Zhang et al.), interacting endogenous and exogenous virus replication (Zhang et al.), 147–161 1099 RNAi pathways in Caenorhabditis scaRNPs (Hoareau-Aveilla et al.), 832–839 Pop1 RNase P subunit (Xiao et al.), 1025 elegans (Lee et al.), 589–596 scaRNPs, hNaf1 and (Hoareau-Aveilla et al.), RNA m7G methyltransferase (Hall and Ho), predicting effective siRNAs with 832–839 489, 495 siRNArules 1.0 (Holen), 1620–1625 Schmidtea mediterranea, microRNAs from RNA Ontology Consortium (Leontis et al.), RDE-4 production of (Parker et al.), (Palakodeti et al.), 1640–1647 533–540 807–815

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reduction of off-target silencing by Specificity domain, RNase MRP and RNase P dual color fluorescent (Newman et al.), chemical modification of siRNAs RNAs (Zhu et al.), 699–705 1129–1139 (Jackson et al.), 1197–1204 Spectinomycin resistance, of S5 ram mutant Splint, use in RNA-ligase mediated creation seed region-mediated off-target (Jackson protein (Kirthi et al.), 2080–2090 of synthetic RNAs (Stark et al.), et al.), 1179–1186 Spermidine/spermine N1-acetyltransferase 2014–2019 short RNAs bound by P19 in ES cells (SSAT), alternative splicing of (Hyvo¨nen sRNAs (small RNAs) (Calabrese and Sharp), 2092–2100 et al.), 1569–1580 C/D-box methylation guide (Omer et al.), stearylated octaarginine and artificial Spinocerebellar axtaxia 3, ribosomal 1708–1719 virus-like particles for transfection of frameshifting and (Wills and Atkins), enrichment and analysis of RNA siRNA into primary rat neurons (To¨nges 1149–1152 centered on ion pair reverse phase et al.), 1431–1438 Splice leader RNA cap modification (Arhin methodology (Dickman and Hornby), toxicity of off-target effects (Federov et al.), et al.), 53–61 691–695 1188–1195 Spliceosomal snRNAs, heterogeneity in in Listeria monocytogenes (Christiansen transcriptional gene silencing (TGS) in (Kyriakopoulou et al.), 1603–1609 et al.), 1383–1394 human cells (Weinberg et al.), 256–261 Spliceosome Penn State Symposium in Plant Physiology transitive RNA silencing of Arabidopsis assembly of Snu114 into U5 snRNP (Bove et al.), 2035–2043 endogenes (Bleys et al.), 1633–1638 (Brenner and Guthrie), 862–869 regulation of RNAi (An et al.), 710–715 Site-directed random mutagenesis, of Pop1p efficiency of U12-type intron removal sRNP methylation (Zhang et al.), (Xiao et al.), 1023–1036 (Pessa et al.), 1883–1891 1092–1102 SLBP. See Stem–loop binding protein (SLBP) in vitro assembly of functional A complexes SR proteins, AtCyp50 cyclophilin interaction Slippery site, effects of heptameric (Behzadnia et al.), 1738–1744 with (Gullerova et al.), 631–642 composition on frameshifting (Plant and protein-protein interactions in human SRP (signal recognition particle), 7SL RNA Dinman), 666–672 tri-snRNPs (Liu et al.), 1418–1429 incorporation (Onafuwa-Nuga et al.), SL RNA, Trypanosoma brucei TbMT57 recycling, and Prp19-associated complex 542–545 protein (Arhin et al.), 53–61 and U4/U6 biogenesis (Chen et al.), SSAT (spermidine/spermine N1- Slx9p, facilitation of processing of pre-rRNA 765–773 acetyltransferase), alternative splicing of in Saccharomyces cerevisiae (Bax et al.), RNA interactions of splicing factor prp8 (Hyvo¨nen et al.), 1569–1580 2005–2011 (Turner et al.), 375–384 Stability Small Cajal body (sca)RNPs (Hoareau-Aveilla stepwise snRNP recruitment (Tardiff and arginine methylation regulation of et al.), 832–839 Rosbash), 968–978 mitochondrial gene expression in Small interfering RNAs. See siRNAs ubiquitin binding by the Prp8p Jab1/MPN Trypanosoma brucei (Goulah et al.), Small RNAs. See sRNAs (small RNAs) domain (Bellare et al.), 292–300 1545–1554 SmpB (Mehta et al.), 2188 Splicing evolution of ribozyme stability (Guo et al.), Snipper (Kupsco et al.), 2103–2116 alternative splice-site activation in human 387–394 snoRNA genomes (Dou et al.), 2047–2055 La protein and tRNA modification, effect of analysis of Cbf5p binding to a box H/ACA amplified sensitivity of a splicing reporter (Copela et al.), 644–652 snoRNA (Normand et al.), 1868–1880 (Levinson et al.), 925–929 partitioning of native and misfolded RNA modifications, ligation-based approach to Bud13p effects on Mer1p-activated splicing populations in yeast (Jackson et al.), study (Saikia et al.), 2025–2032 (Scherrer and Spingola), 1361–1370 2149–2157 structures and interaction of U65 snoRNA cryptic splice site usage in the FGB gene structural basis of RNA thermostability and Nop10 (Khanna et al.), 40–50 (Spena et al.), 948–956 (Baird et al.), 598–608 snoRNP distal effects of b-casein splicing enhancer translational control by mRNA structure composition of the human RNase MRP and (Lenasi et al.), 498–506 near caps (Babendure et al.), 851–860 RNase P complexes (Welting et al.), distal regulation by splicing enhancer in Staphylococcus aureus, use of targetrons in 1373–1381 equine b-casein intron 1 (Lenasi et al.), (Yao et al.), 1271–1280 H/ACA RNP proteins (Kittur et al.), 498–506 Steady-state kinetics, of Pop1 RNase P subunit 2057–2061 efficiency of U12-type intron removal (Xiao et al.), 1031–1032 SNP (single nucleotide polymorphism), (Pessa et al.), 1883–1891 Stearylated octaarginine (Stearyl-R8), for U1snRNAs (Kyriakopoulou et al.), gene insertion within the Lactococcus transfection of siRNA into rat neurons 1603–1609 lactis Ll.LtrB group II intron (Plante and (To¨nges et al.), 1431–1438 snRNA, interaction with Prp8 protein Cousineau), 1980–1991 Stem cells (Turner et al.), 375–383 identification of RNA-binding proteins that alternative splicing of (SSAT) spermidine/ snRNP regulate FGFR2 splicing through spermine N1-acetyltransferase (Hyvo¨nen abundance of the spliceosomal (Pessa sensitive and specific dual color et al.), 1569–1580 et al.), 1883–1891 fluorescence minigene assays (Newman planaria as model system (Palakodeti et al.), in vitro assembly of functional A complexes et al.), 1640–1647 (Behzadnia et al.), 1738–1744 1129–1139 short RNAs bound by P19 in (Calabrese protein interactions within human 25S imaging in vivo (Bonano et al.), 2073–2080 and Sharp), 2092–2100 U4/U6.U5 tri-snRNP (Liu et al.), in vitro assembly of functional A complexes Stem–loop binding protein (SLBP) 1418–1429 (Behzadnia et al.), 1738–1744 histone pre-mRNA processing and Snu114p (Boon et al.), 199–203 P-element somatic inhibitor protein (Godfrey et al.), 396–407 stepwise recruitment during in vivo (Chmiel et al.), 283–290 interaction with ZFP100 (zinc finger spliceosome assembly (Tardiff and Prp8 protein dissection (Boon et al.), protein) (Wagner et al.), 1206–1217 Rosbash), 968–978 198–205 RIP-Chip analysis of mRNAs bound to U1-like (Kyriakopoulou et al.), 1603–1609 spermidine/spermine N1-acetyltransferase (Townley-Tilson et al.), 1853–1866 Snu114p (Hyvo¨nen et al.), 1569–1580 Stem–loop, FMDV IRES and (Ferna´ndez- assembly into U5 snRNP (Brenner and U1 snRNA variants and (Kyriakopoulou Miragall et al.), 223–232 Guthrie), 862–869 et al.), 1603–1609 Streptosporangium cinnabarinum, GE82832 Prp8p association (Boon et al.), 199–203 Splicing enhancer, distal effects of b-casein as 30S inhibitor of translocation Solid phase extraction, for enrichment and (Lenasi et al.), 498–506 (Brandi et al.), 1262–1269 analysis of RNA (Dickman and Hornby), Splicing reporter Stress granules, RNA-associated protein 55 691–695 amplified sensitivity of (Levinson et al.), (RAP55) localization to (Yang et al.), SORF, RTBV (Pooggin et al.), 841–848 925–929 547–554

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Stress, inhibition of deadenylation of yeast hNaf1 and (Hoareau-Aveilla et al.), structural insight into RNA (Baird et al.), mRNAs by (Hilgers et al.), 1835–1844 832–839 598–605 Stress responses, small RNAs involved in levels in yeast (Mozdy and Cech), topological stabilization of kinase plant (Bove et al.), 2038–2039 1721–1736 ribozyme (Cho and Burke), 2118–2124 Structure. See RNA structure stimulation by hnRNP A1 (Zhang et al.), translational control by mRNA structure Structure-function analysis 1116–1126 near caps (Babendure et al.), 851–860 of Plasmodium RNA triphosphatase Telomerase reverse transcriptase (TERT), Thermostable DNA polymerases, in (Gong et al.), 1468–1473 Tetrahymena telomerase RNA stem–loop fluorescent assay for RNA editing of sno-like RNAs (Omer et al.), 1708–1719 IV domain (Richards et al.), 1475–1484 (Roberson and Rosenthal), 1907–1911 Subcellular localization, La and tRNA Telomere Thermus thermophilus, RNase P RNA modification and tRNA biogenesis hnRNP A1 and (Zhang et al.), 1116–1126 thermostability in (Baird et al.), 598–605 (Copela et al.), 644, 649–652 length regulation, in yeast (Mozdy and THOS complex, Yra1p and (Preker and Substrate binding affinity, of Drosophila Cech), 1721–1736 Guthrie), 994–1002 P-element somatic inhibitor protein Temperature-gradient gel electrophoresis Three-hybrid system (Chmiel et al.), 283–290 conformational switch in virus replication for identification of mRNAs controlled Substrate positioning, P4 metal binding site in (Zhang et al.), 147–161 by regulatory protein (Seay et al.), RNase P RNA affects active site metal stabilizing mutations in Tetrahymena 1594–1599 affinity through (Christian et al.), ribozyme (Guo et al.), 387–394 p53 recognition of RNA (Riley et al.), 1463–1467 Temperature sensitivity, of LI.LtrB group II 620–629 Substrate recognition, at P4 metal binding site intron splicing (Yao et al.), 1271–1280 Tissue-specific expression, and post- in RNase P RNA (Christian et al.), Template switching, hepatitis delta virus RNA transcriptional regulation of miRNA 1463–1467 genomes (Gudima et al.), 1061–1072 expression (Obernosterer et al.), Sugarcane yellow leaf virus (ScYLV) (Cornish Terminal uridylyl transferase (TUTase) 1161–1166 et al.), 1959–1967 action in U-deletion (Zhelonkina et al.), TLC1 (Mozdy and Cech), 1721–1736 Sulfolobus acidocaldarius, sRNA is (Omer 476–485 tmRNA et al.), 1708–1719 human U6 snRNA-specific (Trippe et al.), role in nonstop mRNA decay (Mehta et al.), Sulfolobus solfataricus 1494–1503 2187–2198 aIF1 translation initiation factor from Ternary complex, open and closed RdRp tagging at rare codons (Li et al.), (Haseno¨hrl et al.), 674–681 (Ranjith-Kumar and Kao), 303–311 248–255 sRNA in (Omer et al.), 1708–1719 Tertiary interactions Tn5, insertion sites within Ll.LtrB (Plante and Sulfurihydrogenibium azorense, RNAse P between conserved motifs involved in Cousineau), 1984–1990 RNA (Marszalkowski et al.), organizing RNA structure essential TNFa, and CUG-BP role in mRNA decay 1915–1920 for internal initiation of translation (Moraes et al.), 1084–1090 Surface plasmon resonance, of Pcf11-RNA (Ferna´ndez-Miragall et al.), 223–232 Tomato bushy stunt virus (TBSV) interactions (Hollingworth et al.), stabilizing mutations in Tetrahymena 39 UTR of (Na et al.), 2199–2209 555–559 ribozyme (Guo et al.), 387–394 analysis of 39-translational enhancer in Surveillance complex (Kadlec et al.), topology of three-way junctions in folded (Fabian and White), 1304–1313 1817–1823 RNAs (Lescoute and Westhof), 83–91 Tombusvirus Syc1 (Zhelkovsky et al.), 435–443 Tertiary structure 39 untranslated region in the tomato Systematic evolution of ligands by 39 untranslated region in the tomato bushy stunt virus genome (Na et al.), exponential enrichment. See SELEX bushy stunt virus genome (Na et al.), 2199–2209 2199–2209 analysis of 39-translational enhancer in T Kin.46 ribozyme (Cho and Burke), (Fabian and White), 1304–1313 2118–2124 Total RNA, enrichment and analysis of RNA T4 DNA ligase Testis centered on ion pair reverse phase for RNA 59-adenylation (Wang and molecular interaction between FMRP and methodology (Dickman and Hornby), Silverman), 1142–1146 NXF2 (Lai et al.), 1446–1449 691–695 systematic, ligation-based approach to nucleocytoplasmic shuttling of DAZAP1 Toxicity, induction by siRNA off-target effects study RNA modifications (Saikia et al.), (Lin and Yen), 1486–1492 (Federov et al.), 1188–1195 2025–2032 Tethering, function of hUpf3 protein (Kunz Toyocamycin, ribozyme self-cleavage T4 RNA ligase et al.), 1015–1020 inhibition by (Yen et al.), 797–805 lariat RNA synthesis (Wang and Silverman), Tetrahymena ribozyme, stabilizing mutations Trans-acting factor, Rrp5p (de Boer et al.), 313–320 in (Guo et al.), 387–394 263–270 method for efficient creation of Tetrahymena telomerase RNA (TER) Transcription large, synthetic RNAs (Stark et al.), stem–loop IV domain (Richards et al.), enhancement of transcriptional cycling by 2014–2019 1475–1484 S1 (Trippe et al.), 1505–1512 structure-guided mutational analysis of Tetraloop motifs RNA polymerase II interaction with (Wang et al.), 2126–2133 GCUA tetranucleotide loop in poliovirus cyclophilin (Gullerova et al.), 631–642 T loop, tRNA (Kapp et al.), 751–762 oriL (Melchers et al.), 1671–1681 Transcription factor binding motifs (Megraw Tandem affinity purification mitochondrial RNase P RNAs in jakobids et al.), 1612–1618 identification of proteins interacting with (Seif et al.), 1661–1668 Transcription factor, p53 recognition of RNA U1A by (Liang and Lutz), 112–113, 119 TEV protease sites, insertion into Prp8 (Riley et al.), 620–629 of Prp8p complexes (Boon et al.), (Turner et al.), 376–384 Transcriptional gene silencing (TGS). See 200–201 Theophylline, regulation of RNAi by Silencing TarBase (Sethupathy et al.), 192–195 (An et al.), 710–715 Transcriptional pausing, AAUAAA hexamer of Targeting, mitochondrial of ATP6 protein Thermophiles poly(A) signal direction of (Nag et al.), (Kaltimbacher et al.), 1408–1417 RNase P RNA thermostability (Baird et al.), 1534–1543 Targetron, use in Staphylococcus aureus 598–605 Transcriptional synergy, use to augment (Yao et al.), 1271–1280 structural basis of RNA thermostability sensitivity of a splicing reporter assay TBSV. See Tomato bushy stunt virus (TBSV) (Baird et al.), 598–608 (Levinson et al.), 925–929 Telomerase Thermostability Transcriptional termination dynamics of H/ACA RNP proteins (Kittur evolution of ribozyme stability (Guo et al.), Pcf11–RNA interactions (Hollingworth et al.), 2057–2061 387–394 et al.), 555–559

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Subject index

sequences in the mouse serum albumin Translation termination Dicer-like1 protein of (Shi et al.), gene (West et al.), 655–664 39 end formation in yeast NMD (Baker and 2063–2070 Transcript isoforms, intergenic Parker), 1441–1445 human Argonaute2 expression in (Shi polyadenylation sites and (Lopez et al.), ribosome and mRNA release from et al.), 943–946 1794–1799 endoplasmic reticulum (Lerner and KREPA4 (Salavati et al.), 819–829 Transcriptome, ADAR targets in Drosophila, Nicchitta), 775–785 mitochondria gene expression regulation 1922–1930 stabilization of RSV RNA by 39 UTR (Weil by arginine methylation (Goulah et al.), Transfection, of siRNA, stearylated and Beemon), 102–109 1545–1554 octaarginine and artificial virus-like Translocation RBP16 stimulation of RNA editing in vitro particles for (To¨nges et al.), 1431–1438 29-deoxy-substituted P-tRNA (Feinberg and (Miller et al.), 1292–1302 Transfer RNA. See tRNA Joseph), 580–587 RNA cap (guanine N-7) methyltransferase Transgenic mouse (Hyvo¨nen et al.), GE82832 as 30S inhibitor of translocation (Hall and Ho), 488–496 1569–1580 (Brandi et al.), 1262–1269 RNA editing complex interactions with Transitive RNA silencing of Arabidopsis inhibition by pokeweed antiviral protein a site for full-round U deletion in endogenes (Bleys et al.), 1633–1638 (PAP) (Mansouri et al.), 1683–1691 (Sacharidou et al.), 1219–1226 Translation Transposon mutagenesis, Prp8 protein (Boon RNase III editosomes (Panigrahi et al.), analysis of a 39-translational enhancer in et al.), 198–205 1038–1048 TBSV (tomato bushy stunt virus) (Fabian Trans-splicing, Trypanosoma brucei TbMT57 structure probing of a gRNA bound to its and White), 1304–1313 protein (Arhin et al.), 53–61 mRNA (Yu and Koslowsky), 1050–1059 efficiency, function of hUpf3a and hUpf3b Trans-translation (Mehta et al.), TUTase action in U-deletion (Zhelonkina in (Kunz et al.), 1015–1021 2187–2198 et al.), 476–485 elongation inhibition by pokeweed Trf4p- and Trf5p-dependent polyadenylation tRNAHis antiviral protein (PAP) (Mansouri et al.), (Egecioglu et al.), 26–31 anticodon recognition by tRNAHis 1683–1691 Trf4p (Kadaba et al.), 508–519 guanylyltransferase (Jackman and enhancement of transcriptional cycling by Triphosphatase, structure-function analysis of Phizicky), 1007–1013 S1 (Trippe et al.), 1505–1512 Plasmodium (Gong et al.), 1468–1473 guanylyltransferase, anticodon recognition fidelity, S5 ram mutant and (Kirthi et al.), Triplet repeat expansions diseases, ribosomal by (Jackman and Phizicky), 1007–1013 2080–2090 frameshifting and (Wills and Atkins), tRNase Z, modulation of activity (Zareen GE82832 as 30S inhibitor of translocation 1149–1152 et al.), 1104–1114 (Brandi et al.), 1262–1269 tRNA Trypanosome in HCV (Lancaster et al.), 894–901 39-CCA, contact with E. coli RNase P in arginine methylation regulation of inhibition by chlorolissoclimides (Robert vivo (Wegscheid and Hartmann), mitochondrial gene expression in et al.), 717–723 2135–2147 Trypanosoma brucei (Goulah et al.), initiator tRNA identity elements (Kapp critical 59 monophosphate group for 1545–1554 et al.), 751–762 aminoacylation of histidine tRNAs human Ago2 expression T. brucei (Shi miRNA-microarray based on LNA (Rosen et al.), 1315–1320 et al.), 943–946 technology (Castoldi et al.), 913–919 evolution as a selfish process (Withers Turnip crinkle virus (TCV) (Zhang et al.), role of cap and poly(A) tail in (Meaux and et al.), 933–941 147–161 Hoof), 1323–1335 functional conformations of the L11-rRNA Turnip yellow mosaic virus (TYMV), stress inhibition of mRNA deadenylation in complex and tRNA accommodation dicistronic mRNA from proximal AUG yeast (Hilgers et al.), 1835–1844 (Li et al.), 1240–1252 codons (Matsuda and Dreher), three-hybrid screen identification of La and tRNA modification and tRNA 1338–1348 mRNAs controlled by a regulatory biogenesis (Copela et al.), 644–652 TUTase. See Terminal uridylyl transferase protein (Seay et al.), 1594–1599 modification by mPus1p and scPus1p (TUTase) translational control by mRNA (Behm-Ansmant et al.), 1583–1592 Ty3 structure near caps (Babendure et al.), modification enzymes (Copela et al.), interaction with P-bodies (Beliakova- 851–860 644–652 Bethell et al.), 94–100 Translation initiation modulation of tRNase Z activity (Zareen stimulator (Raman et al.), 1154–1160 39-UTR-mediated translation starting at et al.), 1104–1114 the 59-end (Rakotondrafara et al.), processing, by RNaseP RNAs lacking P18 U 1893–1905 in the Aquificales (Marszalkowski et al.), affinity purification of 48S complexes 1915–1920 U1-like snRNAs, lacking complementarity to (Locker et al.), 683–690 recognition, by histidyl-tRNA synthetases canonical 59 splice sites (Kyriakopoulou AUF1 interaction with eIF4G and PABP (Rosen et al.), 1315–1320 et al.), 1603–1609 (Lu et al.), 883–891 regulation of gene expression (Nelson U1 snRNP context effect on initiation codon et al.), 1254–1260 dissociation and displacement (Bowers discrimination (Raman et al.), repair (Wang et al.), 2126–2133 et al.), 903–911 1154–1160 role of A-loop:tRNA interaction in peptidyl in vitro assembly of functional A complexes dicistronic mRNA from proximal transfer (Brunelle et al.), 33–39 (Behzadnia et al.), 1738–1744 AUG codons (Matsuda and Dreher), tmRNA tagging at rare codons (Li et al.), U1A protein 1338–1348 248–255 changing levels (Ma et al.), 122–131 inhibitory RNA aptamer to eIF4G translocation of 29-deoxy-substituted role of RNA structure in U1A/U1hpII (Miyakawa et al.), 1825–1833 P-tRNA (Feinberg and Joseph), 580–587 binding (Law et al.), 1168–1176 IRES activity in HIF-1a and other 59 UTRs tRNA synthetase, anticodon recognition by SF-A complex and roles in polyadenylation (Bert et al.), 1074–1082 tRNAHis guanylyltransferase (Jackman (Liang and Lutz), 111–120 ribosome shunting in Rice tungro and Phizicky), 1007–1013 U2AF–RNA–Sf3b155-p14 interaction bacilliform virus (Pooggin et al.), tRNA turnover, nuclear RNA surveillance (Spadaccini et al.), 410–424 841–849 (Kadaba et al.), 508–519 U2 snRNA, modification by mPus1p and Sulfolobus solfataricus translation initiation Trypanosoma brucei scPus1p (Behm-Ansmant et al.), factor 1 (Haseno¨hrl et al.), 674–681 59!39 exoribonuclease (Li et al.), 1583–1592 Translation reinitiation, inhibition of 2171–2184 U2snRNP, in vitro assembly of functional nonsense-mediated mRNA-decay and cap 4 modification in (Arhin et al.), A complexes (Behzadnia et al.), (Silva et al.), 2160–2169 53–61 1738–1744

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Subject index

U4atac snRNA (Pessa et al.), 1883–1891 barley yellow dwarf virus class of anticodon recognition by tRNAHis U4 snRNP, Prp19-associated complex and cap-independent translation elements guanylyltransferase (Jackman and U4/U6 biogenesis (Chen et al.), (BTE) (Rakotondrafara et al.), 1893–1905 Phizicky), 1007–1013 765–773 beet western yellows virus (BWYV) blocked in vivo splicing complexes U4/U6.U5 tri-snRNP, protein-protein (Cornish et al.), 1959–1967 (Tardiff and Rosbash), 968–978 interactions (Liu et al.), 1418–1429 bunyavirus RNA chaperone (Mir and critical 59 monophosphate group for U5 snRNA, interaction with Prp8 protein Panganiban), 272–281 aminoacylation of histidine tRNAs (Turner et al.), 377–379 comparative study of the effects of (Rosen et al.), 1315–1320 U5 snRNP heptameric slippery site composition genetic selection, p53 recognition of RNA assembly of Snu114 into (Brenner and on frameshifting (Plant and Dinman), (Riley et al.), 620–629 Guthrie), 862–869 666–672 histidine-tRNA synthetase (Rosen et al.), Snu114p (Boon et al.), 199–203 conformational switch involved in virus 1315–1320 ubiquitin binding by the Prp8p Jab1/MPN replication (Zhang et al.), 147–161 initiator tRNA identity elements (Kapp domain (Bellare et al.), 292–300 dicistronic mRNA from proximal et al.), 751–762 U6atac RNA (Trippe et al.), 1494–1503 AUG codons (Matsuda and Dreher), La protein (Copela et al.), 644–652 U6 snRNA 1338–1348 Mer1p-dependent intron requirement interaction with Prp8 protein (Turner et al.), foot-and-mouth disease virus (FMDV), IRES for Bud13p (Scherrer and Spingola), 376–377 (Ferna´ndez-Miragall et al.), 223–231 1361–1370 specific terminal uridylyl transferase identification of gamma-herpesvirus mutational analysis of the Pop1 RNase P (Trippe et al.), 1494–1503 microRNAs (Grundhoff et al.), 733–749 subunit (Xiao et al.), 1023–1036 U6 snRNP, Prp19-associated complex IRESes (Baird et al.), 1755–1777 nucleo-cytoplasmic shuttling in (Belaya and U4/U6 biogenesis (Chen et al.), mRNA translation at the endoplasmic et al.), 921–924 765–773 reticulum (Lerner and Nicchitta), partitioning of native and misfolded RNA U7 snRNA, genetic analysis of Drosophila 775–787 populations in (Jackson et al.), (Godfrey et al.), 396–407 open and closed RdRp complexes (Ranjith- 2149–2157 U7 snRNP, interaction with ZFP100 Kumar and Kao), 303–311 polyadenylation-dependent RNA (zinc finger protein) (Wagner et al.), ribosome shunting mechanism (Pooggin processing (Egecioglu et al.), 26–31 1206–1217 et al.), 841–849 Prp8 protein dissection (Boon et al.), U12-type introns, efficiency of removal (Pessa translation in HCV, effect on (Lancaster 198–205 et al.), 1883–1891 et al.), 894–901 regulation of YRA1 expression (Preker and U65 snoRNA (Khanna et al.), 40–50 Virus assembly, Ty3 interaction with P-bodies Guthrie), 994–1005 UBB+1, role in neurodegenerative diseases (Beliakova-Bethell et al.), 94–100 RNA-hybrid system for the detection of (Wills and Atkins), 1149–1152 Virus-like particles, for transfection of RNA-RNA interactions in vivo (Piganeau Ubiquitin siRNA into rat neurons (To¨nges et al.), et al.), 177–183 aberrant form UBB+1 in neurodegenerative 1431–1438 role of the Brr5/Ysh1 C-terminal domain diseases (Wills and Atkins), 1149–1152 and its homolog Syc1 in mRna 39-end binding by a variant Jab1/MPN domain in W processing in (Zhelkovsky et al.), the essential pre-mRNA splicing factor 435–443 Prp8p (Bellare et al.), 292–300 Weak exon (Lenasi et al.), 498 Rrp5p and ribosome biogenesis (de Boer Ubiquitination, of Paip2B (Berlanga et al.), et al.), 263–270 1556–1567 X scPus1p (Behm-Ansmant et al.), 1583–1592 U-deletion, TUTase action in (Zhelonkina Slx9p and pre-rRNA processing, 2005–2011 et al.), 476–485 X2S, IRES prediction with (Baird et al.), telomerase levels in (Mozdy and Cech), Unadenylated mRNA, study on translation 1773–1774 1721–1736 and decay of (Meaux and Hoof), Xenopus, 40LoVe interaction with Vg1LE three-hybrid screen identification of 1323–1335 binding proteins in (Czaplinski and mRNAs controlled by a regulatory Uncapped mRNA, study on translation and Mattaj), 213–220 protein (Seay et al.), 1594–1599 decay of (Meaux and Hoof), 1323–1335 Xlrbpa, double-stranded RNA-binding translation and decay of uncapped or UPF1 domain (dsRBD) (Hallegger et al.), unadenylated mRNA (Meaux and Hoof), crystal structure of the UPF2-interacting 1993–2003 1323–1335 domain (Kadlec et al.), 1817–1823 X-ray crystallography translation-independent inhibition of dependent nonsense-mediated mRNA Bacillus subtilis DEAD-box helicase mRNA deadenylation during stress in decay and AUG-proximity effect (Silva (Wang et al.), 959–966 (Hilgers et al.), 1835–1844 et al.), 2160–2169 hUPF1 cysteine-histidine-rich domain Ty3 stimulator effect on translation Upf3 (Kunz et al.), 1015–1021 structure (Kadlec et al.), 1817–1823 initiation (Raman et al.), 1154–1160 Uridylytransferase, human U6 snRNA-TUTase XRN1 Yeast three-hybrid system (Trippe et al.), 1494–1503 Trypanosoma brucei homolog (Li et al.), for detection of RNA–RNA interactions UV cross-linking studies, of L22 binding to 2171–2184 (Piganeau et al.), 177–183 EBER 1 (Fok et al.), 872–881 Yra1p and (Preker and Guthrie), 999–1000, p53 recognition of RNA (Riley et al.), 1003 620–629 YNMG tetraloop (Melchers et al.), 1671–1681 V YOL047c (Stark et al.), 2014–2019 Y VEGF, assessing IRES activity in (Bert et al.), Yra1p (Preker and Guthrie), 994–1005 1074–1082 Y14, eIF4AIII interaction (Shibuya et al.), 361, YxiN RNA binding domain structure (Wang Vg1LE binding proteins, 40LoVe interaction 369–371 et al.), 959–966 with (Czaplinski and Mattaj), 213–220 Y-box protein, RBP16 stimulator of Virus trypanosome RNA editing in vitro (Miller Z 39 untranslated region in the tomato et al.), 1292–1302 bushy stunt virus genome (Na et al.), Yeast ZFP100, role in histone pre-mRNA processing 2199–2209 39 end formation in yeast NMD (Baker and (Wagner et al.), 1206–1217 analysis of a 39-translational enhancer in Parker), 1441–1445 Zinc finger protein, ZFP100 in histone TBSV (tomato bushy stunt virus) (Fabian analysis of Cbf5p binding to a box H/ACA pre-mRNA processing (Wagner et al.), and White), 1304–1313 snoRNA (Normand et al.), 1868–1880 1206–1217

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2234 RNA (2006), 12:2234. Published by Cold Spring Harbor Laboratory Press. Copyright Ó 2006 RNA Society.

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