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Landscape of transcription in human cells.

TitleLandscape of transcription in human cells.
Publication TypeJournal Article
Year of Publication2012
AuthorsDjebali-Quelen, S, Davis, CA, Merkel, A, Dobin, A, Lassmann, T, Mortazavi, A, Tanzer, A, Lagarde, J, Lin, W, Schlesinger, F, Xue, C, Marinov, GK, Khatun, J, Williams, BA, Zaleski, C, Rozowsky, J, Röder, M, Kokocinski, F, Abdelhamid, RF, Alioto, T, Antoshechkin, I, Baer, MT, Bar, NS, Batut, P, Bell, K, Bell, I, Chakrabortty, S, Chen, X, Chrast, J, Curado, J, Derrien, T, Drenkow, J, Dumais, E, Dumais, J, Duttagupta, R, Falconnet, E, Fastuca, M, Fejes-Toth, K, Ferreira, P, Foissac, S, Fullwood, MJ, Gao, H, Gonzalez, D, Gordon, A, Gunawardena, H, Howald, C, Jha, S, Johnson, R, Kapranov, P, King, B, Kingswood, C, Luo, OJ, Park, E, Persaud, K, Preall, JB, Ribeca, P, Risk, B, Robyr, D, Sammeth, M, Schaffer, L, See, L-H, Shahab, A, Skancke, J, Suzuki, AMaria, Takahashi, H, Tilgner, H, Trout, D, Walters, N, Wang, H, Wrobel, J, Yu, Y, Ruan, X, Hayashizaki, Y, Harrow, J, Gerstein, M, Hubbard, T, Reymond, A, Antonarakis, SE, Hannon, G, Giddings, MC, Ruan, Y, Wold, B, Carninci, P, Guigó, R, Gingeras, TR
JournalNature
Volume489
Issue7414
Pagination101-8
Date Published2012 Sep 06
ISSN1476-4687
KeywordsAlleles, Cell Line, DNA, DNA, Intergenic, Encyclopedias as Topic, Enhancer Elements, Genetic, Exons, Gene Expression Profiling, Genes, Genome, Human, Genomics, Humans, Molecular Sequence Annotation, Polyadenylation, Protein Isoforms, Regulatory Sequences, Nucleic Acid, Repetitive Sequences, Nucleic Acid, RNA, RNA Editing, RNA Splicing, Sequence Analysis, RNA, Transcription, Genetic, Transcriptome
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.

DOI10.1038/nature11233
Alternate JournalNature
PubMed ID22955620
PubMed Central IDPMC3684276
Grant ListU54HG004558 / HG / NHGRI NIH HHS / United States
U01 HG003147 / HG / NHGRI NIH HHS / United States
RC2 HG005591 / HG / NHGRI NIH HHS / United States
U54 HG007004 / HG / NHGRI NIH HHS / United States
U54 HG004558 / HG / NHGRI NIH HHS / United States
U54HG004557 / HG / NHGRI NIH HHS / United States
U54 HG004557 / HG / NHGRI NIH HHS / United States
249968 / / European Research Council / International
R01HG003700 / HG / NHGRI NIH HHS / United States
P30 CA045508 / CA / NCI NIH HHS / United States
U54 HG004576 / HG / NHGRI NIH HHS / United States
062023 / / Wellcome Trust / United Kingdom
1RC2HG005591 / HG / NHGRI NIH HHS / United States
R37 GM062534 / GM / NIGMS NIH HHS / United States
U54HG004576 / HG / NHGRI NIH HHS / United States
R01 HG003700 / HG / NHGRI NIH HHS / United States
U54HG004555 / HG / NHGRI NIH HHS / United States
U54 HG004555 / HG / NHGRI NIH HHS / United States