A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing

Pablo Landgraf,1 Mirabela Rusu,2 Robert Sheridan,3 Alain Sewer,2,19,29 Nicola Iovino,1,27 Alexei Aravin,1,26 Sébastien Pfeffer,1,25 Amanda Rice,1 Alice O. Kamphorst,1 Markus Landthaler,1 Carolina Lin,1 Nicholas D. Socci,3 Leandro Hermida,2 Valerio Fulci,4 Sabina Chiaretti,4 Robin Foà,4 Julia Schliwka,5 Uta Fuchs,6 Astrid Novosel,6,28 Roman-Ulrich Müller,1,7 Bernhard Schermer,7 Ute Bissels,8 Jason Inman,9 Quang Phan,10 Minchen Chien,11 David B. Weir,11 Ruchi Choksi,11 Gabriella De Vita,12 Daniela Frezzetti,12 Hans-Ingo Trompeter,13 Veit Hornung,23,24 Grace Teng,14 Gunther Hartmann,18 Miklos Palkovits,15 Roberto Di Lauro,12,20 Peter Wernet,13 Giuseppe Macino,4 Charles E. Rogler,16 James W. Nagle,22 Jingyue Ju,11,21 F. Nina Papavasiliou,14 Thomas Benzing,7 Peter Lichter,5 Wayne Tam,17 Michael J. Brownstein,10 Andreas Bosio,8 Arndt Borkhardt,6,28 James J. Russo,11 Chris Sander,3 Mihaela Zavolan,2,19, and Thomas Tuschl1,

1 Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
2 Biozentrum, University of Basel, CH-4056 Basel, Switzerland
3 Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
4 Dipartimento di Biotecnologie Cellulari ed Ematologia, Università di Roma “La Sapienza,” 00185 Roma, Italy
5 Division of Molecular Genetics B060, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
6 Oncology and Hematology Department, Dr. v. Hauner Children's Hospital, University of Munich, 80337 Munich, Germany
7 Renal Division, University Hospital Freiburg, 79106 Freiburg, Germany
8 Miltenyi Biotec GmbH, 50829 Cologne, Germany
9 TIGR (The Institute for Genomic Research), Rockville, MD 20850, USA
10 J. Craig Venter Institute, Functional Genomics, Rockville, MD 20850, USA
11 Columbia Genome Center, Russ Berrie Pavilion, New York, NY 10032, USA
12 Dipartimento di Biologia e Patologia Cellulare e Molecolare, Universita' di Napoli Federico II, 80131 Napoli, Italy
13 Institute for Transplantation Diagnostics and Cell Therapeutics, Heinrich Heine University Medical Center, 40225 Düsseldorf, Germany
14 Laboratory of Lymphocyte Biology, The Rockefeller University, New York, NY 10021, USA
15 Laboratory of Neuromorphology, Hungarian Academy of Sciences-Semmelweis University, Budapest, Hungary
16 Ullman Bldg Room 509, Albert Einstein College of Medicine, Bronx, NY 10461, USA
17 Department of Pathology and Laboratory Medicine, the Joan and Sanford I. Weill Medical College of Cornell University, New York, NY 10021, USA
18 Division of Clinical Pharmacology, University Hospital, University of Bonn, 53105 Bonn, Germany
19 Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
20 IRGS, Biogem s.c.ar.l., 83031, Ariano Irpino (AV), Italy
21 Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
22 DNA Sequencing Facility, NINDS, NIH, Bethesda, MD 20892, USA
23 Division of Clinical Pharmacology, Department of Internal Medicine, University of Munich, 80366 Munich, Germany

Corresponding author
Mihaela Zavolan
mihaela.zavolan@unibas.ch

Corresponding author
Thomas Tuschl
ttuschl@rockefeller.edu

MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequence-complementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ systems and cell types of human and rodents that were enriched in neuronal as well as normal and malignant hematopoietic cells and tissues. We present expression profiles derived from clone count data and provide computational tools for their analysis. Unexpectedly, a relatively small set of miRNAs, many of which are ubiquitously expressed, account for most of the differences in miRNA profiles between cell lineages and tissues. This broad survey also provides detailed and accurate information about mature sequences, precursors, genome locations, maturation processes, inferred transcriptional units, and conservation patterns. We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses.

全文链接：

http://www.cell.com/content/article/fulltext?uid=PIIS0092867407006046