Landscape of transcription in human cells

Sarah Djebali (1) , Carrie A. Davis (2) , Angelika Merkel (1) , Alex Dobin (2) , Timo Lassmann (3) , Ali Mortazavi (4, 5) , Andrea Tanzer (1) , Julien Lagarde (1) , Wei Lin (2) , Felix Schlesinger (2) , Chenghai Xue (2) , Georgi K. Marinov (4) , Jainab Khatun (6) , Brian A. Williams (4) , Chris Zaleski (2) , Joel Rozowsky (7, 8) , Maik Röder (1) , Felix Kokocinski (8) , Rehab F. Abdelhamid (3) , Tyler Alioto (9, 1) , Igor Antoshechkin (4) , Michael T. Baer (2) , Nadav S Bar (10) , Philippe Batut (2) , Kimberly Bell (2) , Ian Bell (11) , Sudipto Chakrabortty (2) , Xian Chen (12) , Jacqueline Chrast (13) , Joao Curado (1) , Thomas Derrien (1) , Jorg Drenkow (3) , Erica Dumais (11) , Jacqueline Dumais (11) , Radha Duttagupta (11) , Emilie Falconnet (14) , Meagan Fastuca (2) , Kata Fejes-Toth (2) , Pedro Ferreira (1) , Sylvain Foissac (15) , Melissa J Fullwood (16) , Hui Gao (11) , David Gonzalez (1) , Assaf Gordon (2) , Harsha Gunawardena (12) , Cedric Howald (13) , Sonali Jha (2) , Rory Johnson (1) , Philipp Kapranov (11, 17) , Brandon King (4) , Colin Kingswood (9, 1) , Oscar J Luo (18) , Eddie Park (5) , Kimberly Persaud (2) , Jonathan B. Preall (2) , Paolo Ribeca (9, 1) , Brian Risk (6) , Daniel Robyr (14) , Michael Sammeth (9, 1) , Lorian Schaffer (9, 1) , Lei-Hoon See (2) , Atif Shahab (18) , Jorgen Skancke (10, 1) , Ana Maria Suzuki (3) , Hazuki Takahashi (3) , Hagen Tilgner (1) , Diane Trout (4) , Nathalie Walters (13) , Huaien Wang (2) , John Wrobel (6) , Yanbao Yu (12) , Xiaoan Ruan (18) , Yoshihide Hayashizaki (3) , Jennifer Harrow (8) , Mark Gerstein (7, 8, 19) , Tim Hubbard (8) , Alexandre Reymond (13) , Stylianos E Antonarakis (14) , Gregory Hannon (2) , Morgan C Giddings (6, 12) , Yijun Ruan (18) , Barbara Wold (4) , Piero Carninci (3) , Roderic Guigó (20, 1) , Thomas R Gingeras (2, 11)

1 CRG - Centre for Genomic Regulation - Centre de Regulació Genòmica [Barcelona]
2 UPF - Universitat Pompeu Fabra [Barcelona]
3 Cold Spring Harbor Laboratory
4 Riken Yokohama Institute
5 CALTECH - California Institute of Technology
6 UC Irvine - University of California [Irvine]
7 Boise State University
8 Yale University [New Haven]
9 The Wellcome Trust Sanger Institute [Cambridge]
10 CNAG - Centro Nacional de Analisis Genomico [Barcelona]
11 NTNU - Norwegian University of Science and Technology [Trondheim]
12 Affymetrix Inc.
13 UNC - University of North Carolina [Chapel Hill]
14 UNIL - Université de Lausanne = University of Lausanne
15 LGC - Laboratoire de Génétique Cellulaire
16 UNIGE - Université de Genève = University of Geneva
17 IGE3 Inst Genet & Genom Geneva -
18 University of Geneva Medical School
19 GIS - Genome Institute of Singapore
20 St Laurent Institut

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.

Mots clés: map; expression; identification; enhancer; genome; small rnas

Domaines: Sciences du Vivant [q-bio]

Sarah Djebali, Carrie A. Davis, Angelika Merkel, Alex Dobin, Timo Lassmann, et al.. Landscape of transcription in human cells. Nature, 2012, 489 (7414), pp.101-108. ⟨10.1038/nature11233⟩. ⟨hal-01216755⟩