ISSN 1355-8382

EDITOR IN CHIEF REVIEWS EDITOR Timothy W. Nilsen Thomas R. Cech Case Western Reserve University Howard Hughes Medical Institute

EDITORS Brenton R. Graveley Erik Sontheimer University of Connecticut Health Center Northwestern University Javier F. Caceres MRC Human Unit Rachel Green Johns Hopkins University Peter F. Stadler Kathleen Collins Leipzig University University of California, Berkeley Elisa Izaurralde Max Planck Institute for Developmental Biology, Tuebingen Gisela Storz Elena Conti National Institute of Child Health and Max Planck Institute of Biochemistry, Daniel Kolakofsky Human Development Martinsried University of Geneva Adrian R. Ferré-D’Amaré Rob Singer National Heart, Lung and Blood Institute Albert Einstein School of Medicine CNRS, Strasbourg

EDITORIAL BOARD John N. Abelson Martha J. Fedor Thomas Maniatis Phillip A. Sharp California Institute of Technology The Scripps Research Institute Harvard University Massachusetts Institute of Technology Sidney Altman Witold Filipowicz James Manley Joan A. Steitz Yale University Friedrich Miescher Institute Columbia University Yale University Mariano A. Garcia-Blanco Scott Strobel Manuel Ares Lynne E. Maquat Yale University University of California, Santa Cruz Duke University University of Rochester David Tollervey David P. Bartel Christine Guthrie Iain W. Mattaj University of Edinburgh Massachusetts Institute of Technology University of California, San Francisco EMBL, Heidelberg Thomas Tuschl Brenda L. Bass Matthias W. Hentze William H. McClain The University of Utah EMBL, Heidelberg University of Wisconsin, Madison Olke C. Uhlenbeck Daniel Herschlag Northwestern University Philip C. Bevilacqua Stanford University Andrew Newman Pennsylvania State University MRC Laboratory of Juan Valcárcel Allan Jacobson ICREA and Centre de Regulació Genòmica Douglas L. Black University of Massachusetts Harry F. Noller University of California, Los Angeles University of California, Santa Cruz Alan M. Weiner Walter Keller University of Washington Thomas Blumenthal University of Basel Norman R. Pace University of Colorado University of Colorado Marvin Wickens Adrian R. Krainer University of Wisconsin, Madison Ronald R. Breaker Cold Spring Harbor Laboratory Richard A. Padgett Yale University Lerner Research Institute, Cleveland Clinic James R. Williamson Alan M. Lambowitz The Scripps Research Institute Chris Burge University of Texas at Austin Roy Parker Massachusetts Institute of Technology University of Colorado, Boulder Sandra L. Wolin David M.J. Lilley Yale University James E. Dahlberg University of Dundee Marina V. Rodnina Sarah A. Woodson University of Wisconsin, Madison Universität Witten/Herdecke Reinhard Lührmann Johns Hopkins University David R. Engelke Max Planck Institute for Biophysical Michael Rosbash Robert Zimmermann University of Michigan Chemistry, Göttingen Brandeis University University of Massachusetts

PRODUCTION MANAGER PRODUCTION EDITOR ASSISTANT PRODUCTION EDITORIAL ASSISTANT Linda Sussman Michael Henigman EDITOR Mary Mulligan Ann Marie Micenmacher Cold Spring Harbor Laboratory Press Cold Spring Harbor Laboratory Press Cold Spring Harbor Laboratory Press Case Western Reserve University

Editorial Office: RNA, Center for RNA Molecular Biology, Room W127, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4973, USA. Telephone: 216-368-1852; fax: 216-368-2010; e-mail: [email protected]. Publishing and Advertising Offices: Cold Spring Harbor Laboratory Press, 1 Bungtown Road, Cold Spring Harbor, New York 11724-2203. For advertising rates and data, contact Marcie Siconolfi, Advertising Manager, at 516-422-4010 (telephone) or 516-422-4092 (fax). Instructions for Authors: Instructions for authors are published in each issue of RNA and are available online (http://www.rnajournal.org). Books for Review: Publications should be sent to Timothy Nilsen, Center for RNA Molecular Biology, Room W127, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4973, USA. Readers are encouraged to draw to his attention publications that may be of interest to other readers of RNA. Subscriptions: Published monthly. Subscribers have a choice of “online only” or “print + online” subscriptions for this journal. For 2014 institutional pricing, visit http:// rnajournal.cshlp.org/site/subscriptions/cost.dtl. Personal rate (must be paid by check, credit card, or money order): Online only: $245; Print + Online: U.S. $320, Canada and Mexico $405, R.O.W. $435. Contact Kathleen Cirone, Subscription Manager, Fulfillment Department, 500 Sunnyside Boulevard, Woodbury, New York 11797-2924. Telephone: Continental U.S. and Canada 1-800-843-4388; all other locations 516-422-4100. Fax: 516-422-4097. Claims for missing issues must be received within four months of issue date. Member Subscriptions: Members of the RNA Society automatically receive RNA as part of their annual membership dues. The RNA Society: Membership information and application forms may be obtained from: The RNA Society, 9650 Rockville Pike, Bethesda, MD 20814-3998, USA. Telephone: 301-530-7120; fax: 301-530-7049; e-mail: @faseb.org.

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RNA (ISSN 1355-8382) is published monthly by Cold Spring Harbor Laboratory Press, 500 Sunnyside Blvd.,Woodbury, NY 11797-2924. Periodicals paid at Woodbury, NY, and additional mailing offices. POSTMASTER: Send address changes to Cold Spring Harbor Laboratory Press, Journals Fulfillment Dept., 500 Sunnyside Blvd., Woodbury, NY 11797-2924.

Copyright © 2014 The RNA Society FORTHCOMING PAPERS

Hypothesis The RIDL hypothesis: transposable elements as functional domains of lncRNA Rory Johnson and Roderic Guigo

Letter to the Editor 3′-biotin-tagged microRNA-27 does not associate with Argonaute proteins in cells Yang Eric Guo and Joan A. Steitz

Bioinformatics RAID: a comprehensive resource for human RNA-associated (RNA–RNA/RNA–protein) interaction Xiaomeng Zhang, Deng Wu, Liqun Chen, Xiang Li, Jinxurong Yang, Dandan Fan, Tingting Dong, Mingyue Liu, Puwen Tan, Jintian Xu, Ying Yi, Yuting Wang, Hua Zou, Yongfei Hu, Kaili Fan, Juanjuan Kang, Yan Huang, Zhengqiang Miao, Miaoman Bi, Nana Jin, Kongning Li, Xia Li, Jianzhen Xu, and Dong Wang

Report The prolyl isomerase, FKBP25, interacts with RNA-engaged nucleolin and the pre-60S ribosomal subunit Geoff Gudavicius, David Dilworth, Jason J. Serpa, Nicole Sessler, Evgeniy V. Petrotchenko, Christoph H. Borchers, and Christopher J. Nelson

Articles A central role for the primary microRNA stem in guiding the position and efficiency of Drosha processing of a viral pri-miRNA James M. Burke, Demetra P. Kelenis, Rodney P. Kincaid, and Christopher S. Sullivan

Climbing the vertebrate branch of U1A/U2B′′ protein evolution Kimberly J. Delaney, Sandra G. Williams, Mariah Lawler, and Kathleen B. Hall

The SBP2 protein central to selenoprotein synthesis contacts the human ribosome at expansion segment 7L of the 28S rRNA Olga Kossinova, Alexey Malygin, Alain Krol, and Galina Karpova

Adjustments, extinction, and remains of selenocysteine incorporation machinery in the nematode lineage Lucía Otero, Laura Romanelli-Cedrez, Anton A. Turanov, Vadim N. Gladyshev, Antonio Miranda-Vizuete, and Gustavo Salinas