Landscape of transcription in human cells

Sarah Djebali, Carrie A. Davis, Angelika Merkel, Alex Dobin, Timo Lassmann, Ali Mortazavi, Andrea Tanzer, Julien Lagarde, Wei Lin, Felix Schlesinger, Chenghai Xue, Georgi K. Marinov, Jainab Khatun, Brian A. Williams, Chris Zaleski, Joel Rozowsky, Maik Röder, Felix Kokocinski, Rehab F. Abdelhamid, Tyler Alioto, Igor Antoshechkin, Michael T. Baer, Nadav S. Bar, Philippe Batut, Kimberly Bell, Ian Bell, Sudipto Chakrabortty, Xian Chen, Jacqueline Chrast, Joao Curado, Thomas Derrien, Jorg Drenkow, Erica Dumais, Jacqueline Dumais, Radha Duttagupta, Emilie Falconnet, Meagan Fastuca, Kata Fejes-Toth, Pedro Ferreira, Sylvain Foissac, Melissa J. Fullwood, Hui Gao, David Gonzalez, Assaf Gordon, Harsha Gunawardena, Cedric Howald, Sonali Jha, Rory Johnson, Philipp Kapranov, Brandon King, Colin Kingswood, Oscar J. Luo, Eddie Park, Kimberly Persaud, Jonathan B. Preall, Paolo Ribeca, Brian Risk, Daniel Robyr, Michael Sammeth, Lorian Schaffer, Lei-Hoon See, Atif Shahab, Jorgen Skancke, Ana Maria Suzuki, Hazuki Takahashi, Hagen Tilgner, Diane Trout, Nathalie Walters, Huaien Wang, John Wrobel, Yanbao Yu, Xiaoan Ruan, Yoshihide Hayashizaki, Jennifer Harrow, Mark Gerstein, Tim Hubbard, Alexandre Reymond, Stylianos E. Antonarakis, Gregory Hannon, Morgan C. Giddings, Yijun Ruan, Barbara Wold, Piero Carninci, Roderic Guigó () and Thomas R. Gingeras ()
Additional contact information
Sarah Djebali: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Carrie A. Davis: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Angelika Merkel: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Alex Dobin: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Timo Lassmann: RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Ali Mortazavi: California Institute of Technology, 2 Beckman Institute
Andrea Tanzer: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Julien Lagarde: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Wei Lin: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Felix Schlesinger: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Chenghai Xue: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Georgi K. Marinov: California Institute of Technology, 2 Beckman Institute
Jainab Khatun: Boise State University, College of Arts & Sciences, 1910 University Drive
Brian A. Williams: California Institute of Technology, 2 Beckman Institute
Chris Zaleski: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Joel Rozowsky: Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
Maik Röder: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Felix Kokocinski: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Rehab F. Abdelhamid: RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Tyler Alioto: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Igor Antoshechkin: California Institute of Technology, 2 Beckman Institute
Michael T. Baer: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Nadav S. Bar: Norwegian University of Science and Technology, Trondheim NO-7491, Norway
Philippe Batut: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Kimberly Bell: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Ian Bell: Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA
Sudipto Chakrabortty: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Xian Chen: University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, USA
Jacqueline Chrast: University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne 1015, Switzerland
Joao Curado: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Thomas Derrien: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Jorg Drenkow: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Erica Dumais: Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA
Jacqueline Dumais: Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA
Radha Duttagupta: Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA
Emilie Falconnet: University of Geneva Medical School, 1 rue Michel-Servet, Geneva 1211, Switzerland
Meagan Fastuca: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Kata Fejes-Toth: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Pedro Ferreira: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Sylvain Foissac: Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA
Melissa J. Fullwood: Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore
Hui Gao: Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA
David Gonzalez: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Assaf Gordon: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Harsha Gunawardena: University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, USA
Cedric Howald: University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne 1015, Switzerland
Sonali Jha: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Rory Johnson: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Philipp Kapranov: Affymetrix, Inc, 3380 Central Expressway, Santa Clara, California 95051, USA
Brandon King: California Institute of Technology, 2 Beckman Institute
Colin Kingswood: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Oscar J. Luo: Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore
Eddie Park: University of California Irvine, 2300 Biological Sciences III, Irvine, California 92697, USA
Kimberly Persaud: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Jonathan B. Preall: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Paolo Ribeca: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Brian Risk: Boise State University, College of Arts & Sciences, 1910 University Drive
Daniel Robyr: University of Geneva Medical School, 1 rue Michel-Servet, Geneva 1211, Switzerland
Michael Sammeth: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Lorian Schaffer: California Institute of Technology, 2 Beckman Institute
Lei-Hoon See: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Atif Shahab: Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore
Jorgen Skancke: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Ana Maria Suzuki: RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Hazuki Takahashi: RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Hagen Tilgner: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Diane Trout: California Institute of Technology, 2 Beckman Institute
Nathalie Walters: University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne 1015, Switzerland
Huaien Wang: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
John Wrobel: Boise State University, College of Arts & Sciences, 1910 University Drive
Yanbao Yu: University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, North Carolina 27599, USA
Xiaoan Ruan: Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore
Yoshihide Hayashizaki: RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Jennifer Harrow: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Mark Gerstein: Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, Connecticut 06520, USA
Tim Hubbard: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Alexandre Reymond: University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne 1015, Switzerland
Stylianos E. Antonarakis: University of Geneva Medical School, 1 rue Michel-Servet, Geneva 1211, Switzerland
Gregory Hannon: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA
Morgan C. Giddings: Boise State University, College of Arts & Sciences, 1910 University Drive
Yijun Ruan: Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, 02-01, Genome, Singapore 138672, Singapore
Barbara Wold: California Institute of Technology, 2 Beckman Institute
Piero Carninci: RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
Roderic Guigó: Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain
Thomas R. Gingeras: Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Road, Cold Spring Harbor, New York 11742, USA

Nature, 2012, vol. 489, issue 7414, 101-108

Abstract: Abstract 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.

Date: 2012
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DOI: 10.1038/nature11233

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