RIKEN Omics Science Center OSC Newsletter No. 12

24 APRIL 2009

Events

RIKEN Advisory Council (RAC)

RIKEN Advisory Council (RAC), in which external reviewers evaluate the RIKEN’s scientific activities and contributions to society, was held at the Intercontinental Tokyo Bay Hotel April 22-24, 2009. OSC’s director, Dr. Hayashizaki, gave the reviewers a presentation on the OSC’s activities. Dr. Allan Bradley, the director of the Wellcome Trust Sanger Institute in U.K., also reported the evaluation of OSC’s activities that were under review at the Cluster of Lifescience Platform Advisory Council (CLAC) on January 26 and 27, 2009 as the chairperson of the CLAC. He mentioned that OSC is internationally Dr. Allan Bradley and Dr. recognized for its research activities. Its unique management system, in which Yoshihide Hayashizaki researchers with different expertise cooperate, was also reported as a good answering questions from RAC members model for such a genome center.

The report is posted on the RIKEN web site: http://www.riken.go.jp/engn/r-world/info/report/rac/pdf/7report.pdf

RAC members

Zach W. Hall（RAC Emeritus Vice Chancellor, University California Chairperson）

Yuan Tseh Lee President Emeritus and Distinguished Research

Fellow, Academia Sinica (1986 Nobel Laureate)

Hiroo Imura Chairman, Foundation for Biomedical Research and

Innovation

Howard Alper Distinguished University Professor, University of

Ottawa

Teruhiko Beppu Professor, Advanced Research Institute for the

Sciences and Humanities, Nihon University

Colin Blakemore Professor of Neuroscience, University of Oxford

Rita R. Colwell Distinguished University Professor,

University of Maryland at College Park

Mitiko Go Executive Director, Research Organization of

Information and Systems

Toshiaki Ikoma Executive Vice President, Canon Inc.

Biao Jiang Director, Shanghai institute of Organic Chemistry,

Chinese Academy of Sciences

Paul Kienle Professor Emeritus, Department of Physics, Munich

University of Technology

Karin Markides President, Chalmers University of Technology

Rainer E. Metternich Vice President, Basic Research and Site Head West

Point, Merck & Co., Inc.

Hans L. R. Wigzell Senior Strategic Advisor/Professor, MTC, Karolinska

Institutet

Allan Bradley Director, Wellcome Trust Sanger Institute

Max D. Cooper Professor, Department of Pathology and Laboratory,

Medicine, Emoy University

Hidetoshi Fukuyama Professor, Tokyo University of Science

Sydney Gales Director, Grand Acceleraeur National D’lons Lourds

Sten Grillner Professor and Director, Nobel Institute for

Neurophysiology, Karolinska Institutet

Wilhelm Gruissem Professor, ETH Zurich, Institute of Plant sciences Jean-Louis Guenet Director, Unite de Genetique des Mammiferes, Institut Pasteur Jerome Hastings Professor, Photon Science, SLAC National Accelerator Laboratory Bengt Langstrom Professor, Uppsala University Mark Lathrop Director General, Center National de Genogypage Austin Smith MRC Professor and Director, Wellcome Trust Center for Stem Cell Research University of Cambridge

OSC News Letter with an article about CLAC: http://134.160.84.27/osc/english/newsletter/pdf/OSC_newsletter_200901_EN.pdf

The CLAC report:

http://www.yokohama.riken.jp/outline/advisory/pdf/2008CLACreportE.pdf

Topics

Publication of three milestone papers from the FANTOM4 Consortium

How can a specific cell play a specific role at a specific site in an organism even though most of the cells in an organism have an identical genome? Different

gene expressions in the different state of cells are one of the mechanisms.

Omics Science Center (OSC) published three milestone papers about the Press release for the network of key genomic elements that control growth arrest and differentiation in publication of three milestone the human monocytic cell line THP-1 in the prestigious journal, Nature Genetics, papers from the FANTOM4 from the FANTOM (Functional Annotation of the Mammalian Genome) project. Consortium. FANTOM is an international consortium organized by OSC with many excellent From right side, Drs. collaborating scientists in 15 countries around the world. They depicted the Yoshihide Hayashizaki, network based only on experimental data, and this is the first such achievement Harukazu Suzuki, Piero in the world. Understanding the regulatory networks of the key elements of the Carninci, Carsten Daub, Jun Kawai. gene expression at a specific state of cell is important for the development of a technique to control cell differentiation and to improve regenerative medicine.

Related papers: http://fantom.gsc.riken.jp/4/publications/

Second-generation sequencing center

In fiscal year 2009, Omics Science Center was selected by the Ministry of

Education, Culture, Sports, Science and Technology to participate in the "Cell Innovation” project as the “Second-generation sequencer center.” This establishes OSC at the forefront of second-generation sequencing.

The goal of “Cell Innovation” project is to understand the program of life in order to contribute to medical and industrial fields using genome-wide analytical tools provided by innovative DNA sequencers and cell imaging technologies. The platforms to be established in this project, such as the DNA sequencing center and data analysis center, will be open to academia and industriy for life science promotion in Japan.OSC will update and expand its sequencing infrastructure and capacity with the grant and assume the role of Japan's primary national sequencing center.

Book publication “Interesting stories of genes”

“DNA holds all the information needed to generate an organism and it produces proteins that play critical roles for maintaining the life. RNA is a copy of DNA and acts as intermediary to make proteins.” This is the central dogma of molecular biology that people have believed so far. However, the FANTOM consortium that Omics Science Center (OSC) organized has found that tmore than half of RNA present in a cell is non-coding RNA that has functions and does not code for proteins. This work made it necessary for scientists to reexamine RNA’s functions.

A book newly released on April 16, 2009 titled “Interesting stories of genes” (Jitsugyo no Nohon sya), which was overseen by the OSC’s director, Dr. Yoshihide Hayashizaki, is written for readers who do not have scientific background. This book tells the recent knowledge in genome research using the history and findings in OSC. You can find an answer to the simple question “what is a gene?” and learn a mystical hypothesis “RNA world” in this book.

Lab Tours

2009/4/3 Evaluation committee of Independent Administrative Institution 2009/4/9 Tokyo College of Medical Sports 2009/4/9 Russian Perm medical inspection group 2009/4/21 Committee members of RAC

Publications

1. Shannon Davis, Mary Anne Potok, Michelle Brinkmeier, Piero Carninci, Robert Lyons, James MacDonald, Michelle Fleming, Amanda Mortensen, Noboru Egashira, Karen Steel, Robert Osamura, Yoshihide Hayashizaki, Sally Camper. Genetics, gene expression, and bioinformatics of the pituitary gland, Hormone Research, 71 (Suppl. 2), 101-115 (2009) 2. Yoshihide Hayashizaki. 教科書ではわからない遺伝子のおもしろい話, 実業 之日本社, 東京, (2009) 3. Jessica Severin, Andrew Waterhouse, Hideya Kawaji, Timo Lassmann, Erik van Nimwegen, Piotr Balwierz, Michiel De Hoon, David Hume, Piero Carninci, Yoshihide Hayashizaki, Harukazu Suzuki, Carsten Daub, Alistair Forrest. FANTOM4 EdgeExpressDB: an integrated database of genes, microRNAs, their promoters, expression dynamics and regulatory interactions, Genome Biology, 10:R39, 1-9 (2009) 4. Harukazu Suzuki, Alistair Forrest, Erik van Nimwegen, Carsten Daub, Piotr Balwierz, Katharine Irvine, Timo Lassmann, Timothy Ravasi, Yuki Hasegawa, Michiel De Hoon, Shintaro Katayama, Kate Schroder, Piero Carninci, Yasuhiro Tomaru, Mutsumi Kanamori, Atsutaka Kubosaki, Altuna Akalin, Yoshinari Ando, Erik Arner, Maki Asada, Hiroshi Asahara, Timothy Bailey, Vladimir Bajic, Denis Bauer, Anthony Beckhouse, Nicolas Bertin, Johan Bjo¨rkegren, Frank Brombacher, Erika Bulger, Alistair Chalk, Joe Chiba, Nicole Cloonan, Adam Dawe, Josee Dostie, Par Engstrom, Magbubah Essack, Geoffrey Faulkner, J Lynn Fink, David Fredman, Ko Fujimori, Masaaki Furuno, Takashi Gojyobori, Julian Gough, Sean Grimmond, Mika Gustafsson, Megumi Hashimoto, Takehiro Hashimoto, Mariko Hatakeyama, Susanne Heinzel, Winston Hide, Oliver Hofmann, Michael Hornquist, Lukasz Huminiecki, Kazuho Ikeo, Naoko Imamoto, Satoshi Inoue, Yusuke Inoue, Ryoko Ishihara, Takao Iwayanagi, Anders Jacobsen, Mandeep Kaur, Hideya Kawaji, Markus Kerr, Ryuichiro Kimura, Syuhei Kimura, Yasumasa Kimura, Hiroaki Kitano, Hisashi Koga, Toshio Kojima, Shinji Kondo, Takeshi Konno, Anders Krogh, Adele Kruger, Ajit Kumar, Boris Lenhard, Andreas Lennartsson, Morten Lindow, Marina Lizio, Cameron MacPherson, Norihiro Maeda, Christopher Maher, Monique Maqungo, Jessica Mar, Nick Matigian, Hideo Matsuda, John Mattick, Stuart Meier, Sei Miyamoto, Etsuko Miyamoto-Sato, Kazuhiko Nakabayashi, Yutaka Nakachi, Mika Nakano, Sanne Nygaard, Toshitsugu Okayama, Yasushi Okazaki, Haruka Okuda-Yabukami, Valerio Orlando, Jun Otomo, Mikhail Pachkov, Nikolai Petrovsky, Charles Plessy, John Quackenbush, Aleksandar Radovanovic, Michael Rehli, Rintaro Saito, Albin Sandelin, Sebastian Schmeier, Christian Schonbach, Ariel Schwartz, Colin Semple, Miho Sera, Jessica Severin, Katsuhiko Shirahige, Cas Simons, George St. Laurent, Masanori Suzuki, Takahiro Suzuki, Matthew Sweet, Ryan Taft, Shizu Takeda, Yoichi Takenaka, Kai Tan, Martin Taylor, Rohan Teasdale, Jesper Tegnér, Sarah Teichmann, Eivind Valen, Claes Wahlestedt, Kazunori Waki, Andrew Waterhouse, Christine Wells, Ole Winther, Linda Wu, Kazumi Yamaguchi, Hiroshi Yanagawa, Jun Yasuda, Mihaela Zavolan, David Hume, Takahiro Arakawa, Shiro Fukuda, Kengo Imamura, Chikatoshi Kai, Ai Kaiho, Tsugumi Kawashima, Chika Kawazu, Yayoi Kitazume, Miki Kojima, Hisashi Miura, Kayoko Murakami, Mitsuyoshi Murata, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Chihiro Ogawa, Takuma Sano, Cristophe Simon, Michihira Tagami, Yukari Takahashi, Jun Kawai, Yoshihide Hayashizaki. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line, Nat Genet, 41(5), 553-562 (2009) 5. Ryan Taft, Evgeny Glazov, Nicole Cloonan, Cas Simons, Stuart Stephen, Geoffrey Faulkner, Timo Lassmann, Alistair Forrest, Sean Grimmond, Kate Schroder, Katharine Irvine, Takahiro Arakawa, Mari Nakamura, Atsutaka Kubosaki, Kengo Hayashida, Chika Kawazu, Mitsuyoshi Murata, Hiromi Nishiyori, Shiro Fukuda, Jun Kawai, Carsten Daub, David Hume, Harukazu Suzuki, Valerio Orlando, Piero Carninci, Yoshihide Hayashizaki, John Mattick. Tiny RNAs associated with transcription start sites in animals, Nat Genet, 41:5, 572-578 (2009) 6. Hideya Kawaji, Jessica Severin, Marina Lizio, Andrew Waterhouse, Shintaro Katayama, Katharine Irvine, David Hume, Alistair Forrest, Harukazu Suzuki, Piero Carninci, Yoshihide Hayashizaki, Carsten Daub. The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation, Genome Biology, 10:R40, 1-8 (2009) 7. Atsutaka Kubosaki, Yasuhiro Tomaru, Michihira Tagami, Erik Arner, Hisashi Miura, Takahiro Suzuki, Masanori Suzuki, Harukazu Suzuki, Yoshihide Hayashizaki. Genome-wide investigation of in vivo EGR-1 binding sites in monocytic differentiation, Genome Biology, 10:R41, 1-14 (2009) 8. Altuna Akalin, David Fredman, Erik Arner, Xianjun Dong, Jan Bryne, Harukazu Suzuki, Carsten Daub, Yoshihide Hayashizaki, Boris Lenhard. Transcriptional Features of Genomic Regulatory Blocks, Genome Biology, 10:R38, 1-13 (2009) 9. Geoffrey Faulkner, Yasumasa Kimura, Carsten Daub, Shivangi Wani, Charles Plessy, Katharine Irvine, Kate Schroder, Nicole Cloonan, Anita Steptoe, Timo Lassmann, Kazunori Waki, Nadine Hornig, Takahiro Arakawa, Hazuki Takahashi, Jun Kawai, Alistair Forrest, Harukazu Suzuki, Yoshihide Hayashizaki, David Hume, Valerio Orlando, Sean Grimmond, Piero Carninci. The regulated retrotransposon transcriptome of mammalian cells, Nat Genet, 41(5), 563-571 (2009) 10. James Fraser, Mathieu Rousseau, Solomon Shenker, Maria Ferraiuolo, Yoshihide Hayashizaki, Mathieu Blanchette, Josee Dostie. Chromatin conformation signatures of cellular differentiation, Genome Biology, 10:R37, 1-18 (2009) 11. Jessica Mar, Yasumasa Kimura, Kate Schroder, Katharine Irvine, Harukazu Suzuki, David Hume, John Quackenbush, Yoshihide Hayashizaki. Data-driven Normalization Strategies for High-throughput Quantitative RT-PCR, BMC Bioinformatics, 10:110, 1-32 (2009) 12. Yu Toyoda, Aki Sakurai, Yasumasa Mitani, Masahiro Nakashima, Koh- ichiro Yoshiura, Hiroshi Nakagawa, Yasuo Sakai, Ikuko Ota, Alexander Lezhava, Yoshihide Hayashizaki, Norio Niikawa, Toshihisa Ishikawa. Earwax, osmidrosis, and breast cancer: why does one SNP (538G>A) in the human ABC transporter ABCC11 gene determine earwax type?, FASEB J, 23(6), 2001-2013 (2009) 13. Yasumasa Kimura, Atsuko Oguchi-Katayama, Yuki Kawai, Kana Naito, Yasumasa Mitani, Morlighem Jean-Étienne, Yoshihide Hayashizaki, Alexander Lezhava. Tail variation of the folding primer affects the SmartAmp2 process differently, Biochem Biophys Res Commun, 383, 455-459 (2009)

Presentations

English

1. Daub C. Novel Regulatory Mechanisms in the Mammalian Transcriptome, 2nd annual illumina asia pacific and Japan user meeting: Illumina User Group Meeting (UGM), Shangri-La's Rasa Ria Resort, Kota Kinabalu, Malaysia, April 7, 2009 2. De Hoon M. Cross-mapping in short RNA sequencing libraries, 2nd annual illumina asia pacific and Japan user meeting: Illumina User Group Meeting, Shangri-La's Rasa Ria Resort, Kota Kinabalu, Malaysia, April 9, 2009 3. De Hoon M. Genome-wide analysis of the transcriptome and promoter activity during differentiation of a human leukemia cell line., Seminar at the University of Tokyo, University of Tokyo, Institute of Medical Science, Human Genome Center, Tokyo, Japan, April 17, 2009

Japanese

1. Tunekawa K., yanagigawa m., aoki t., morimura g., ogiwara t., Mitani Y., Hayashizaki Y., murakami m. 2 型甲状腺ホルモン脱ヨード酵素遺伝子多型 の糖代謝に及ぼす影響, 日本内分泌学会, 群馬, April 23, 2009

Editors & Writers: Emi Ito, Thomas Rodgers, Miki Nishikawa