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Landscape of transcription in human cells
Open accessAbstract
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. A description is given of the ENCODE effort to provide a complete catalogue of primary and processed RNAs found either in specific subcellular compartments or throughout the cell, revealing that three-quarters of the human genome can be transcribed, and providing a wealth of information on the range and levels of expression, localization, processing fates and modifications of known and previously unannotated RNAs. These authors describe the ENCODE (Encyclopedia of DNA Elements) effort to provide a complete catalogue of primary and processed RNAs found either in specific sub-cellular compartments or throughout the cell. They show that three-quarters of the human genome can be transcribed, and provide a wealth of information about the range and levels of expression, localization, processing fates and modifications of both known and previously unannotated RNAs. Collectively, these observations suggest that the current concept of a gene should be revisited.
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“Almost all human multi-exon genes exhibit alternative splicing, and spliced human genes have on average over nine alternative transcribed forms.”
From A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium (2014) · cites this paper as [7]
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“The human genome now has >55,000 well-validated genes, and the majority of them are not protein coding.”
From A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium (2014) · cites this paper as [7]
Experimental — accuracy not yet measuredIn the citing paper
“Efforts including ENCODE71 and others91, have reported that more than 75% of genomic DNA is at some point transcribed to primary (un-spliced) RNA.”
From Decoding neuroproteomics: integrating the genome, translatome and functional anatomy (2014) · cites this paper as [71]
In the citing paper
“A recent result that has a potentially significant impact on interpretation of proteomic data is the finding that most genes, in a given cell-type, likely express only a single ‘dominant’ transcript70,71.”
From Decoding neuroproteomics: integrating the genome, translatome and functional anatomy (2014) · cites this paper as [71]
In the citing paper
“RNA deep-sequencing (RNA-seq) provides a powerful tool to decipher global gene expression patterns far beyond the limitations of microarrays, including an unprecedented capability to discover novel genes, alternative transcript variants, chimeric transcripts, and expressed sequence variants as well as allele-specific expression [8–12].”
From Comparison of RNA-seq and microarray-based models for clinical endpoint prediction (2015) · cites this paper as [9]
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An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
Self-citationMapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696
Self-citationThe ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
Self-citationGENCODE: The reference human genome annotation for The ENCODE Project
Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research · doi:10.1101/gr.135350.111 · Cited by 4,585
Self-citationThe accessible chromatin landscape of the human genome
Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., et al. (2012) · Nature · doi:10.1038/nature11232 · Cited by 2,679
Self-citationRNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
Kapranov, P., Cheng, J., Dike, S., Nix, D. A., Duttagupta, R., Willingham, A. T., Stadler, P. F., Jana Hertel, A., Jörg Hackermüller, A., Hofacker, I. L., et al. (2007) · Science · doi:10.1126/science.1138341 · Cited by 2,519
Self-citationWidespread transcription at neuronal activity-regulated enhancers
Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450
The ENCODE (ENCyclopedia Of DNA Elements) Project
(2004) · Science · doi:10.1126/science.1105136 · Cited by 2,390
Architecture of the human regulatory network derived from ENCODE data
Gerstein, M., Kundaje, A. B., Hariharan, M., Landt, S. G., Yan, K., Cheng, C., Mu, X. J., Khurana, E., Rozowsky, J. S., Alexander, R. P., et al. (2012) · Nature · doi:10.1038/nature11245 · Cited by 1,451
Self-citationTranscriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution
Cheng, J., Kapranov, P., Drenkow, J., Dike, S., Brubaker, S., Patel, S. A., Long, J. C., Stern, D., Tammana, H., Helt, G. A., et al. (2005) · Science · doi:10.1126/science.1108625 · Cited by 1,192
Self-citation
Research works printed but not linked: 2
- Tilgner, H. et al. Genomic analysis of ENCODE data reveals widespread links between epigenetic chromatin marks and alternative splicing. Genome Res. (in the press)
- Miller, B. Pre-programming of chromatin structure across the cell cycle. Genome Res. (in the press)
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Wéry, M., Descrimes, M., Vogt, N., Dallongeville, A.-S., Gautheret, D., & Morillon, A. (2016) · Molecular Cell · doi:10.1016/j.molcel.2015.12.020 · Cited by 120
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Ouyang, H., Chen, X., Wang, Z., Yu, J., Jia, X., Li, Z., Luo, W., Abdalla, B. A., Jebessa, E., Nie, Q., et al. (2017) · DNA Research · doi:10.1093/dnares/dsx039 · Cited by 119
Self-citationIdentification of genetic variants associated with alternative splicing using sQTLseekeR
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Qu, H., & Fang, X. (2013) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2013.05.001 · Cited by 124
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Chen, L., Zhang, P., Fan, Y., Huang, J., Li, Q., Li, Q., JianBing, Y. A. N., Muehlbauer, G. J., Schnable, P. S., Dai, M., et al. (2017) · New Phytologist · doi:10.1111/nph.14901 · Cited by 119
Long non-coding RNAs and their implications in cancer epigenetics
Beckedorff, F., Amaral, M. S., DeOcesano-Pereira, C., & Verjovski‐Almeida, S. (2013) · Bioscience Reports · doi:10.1042/bsr20130054 · Cited by 114
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Cloonan, N. (2015) · BioEssays · doi:10.1002/bies.201400191 · Cited by 118
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Liu, K., Hou, Y., Liu, Y., & Zheng, J. (2017) · Journal of Biomedical Science · doi:10.1186/s12929-017-0353-9 · Cited by 113
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Zhou, W., Chen, X., Hu, Q., Chen, X., Chen, Y., & Huang, L. (2018) · BMC Cancer · doi:10.1186/s12885-018-4461-z · Cited by 112
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Tang, Y. M., Jin, X., Yin, X., Chen, Y., Shen, C., Zhang, Y., & Li, Y. (2015) · FEBS Letters · doi:10.1016/j.febslet.2015.08.046 · Cited by 111
Serghiou, S., Kyriakopoulou, A., & Ioannidis, J. P. A. (2016) · Molecular Cancer · doi:10.1186/s12943-016-0535-1 · Cited by 112
Sun, X., Li, M., Sun, Y., Cai, H., Lan, X., Huang, Y., Bai, Y., Qi, X., & Chen, H. (2016) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2016.08.014 · Cited by 115
Qian, K., Liu, G., Tang, Z., Hu, Y., Yu, F., Chen, Z., & Xu, X. (2016) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2016.12.011 · Cited by 112
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RetractedHe, F., Song, Z., Chen, H., Chen, Z., Yang, P., Li, W., Yang, Z. H., Zhang, T., Wang, F., Wei, J., et al. (2018) · Oncogene · doi:10.1038/s41388-018-0432-8 · Cited by 114
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Conservation and tissue-specific transcription patterns of long noncoding RNAs
Ward, M., McEwan, C., Mills, J. D., & Janitz, M. (2015) · Journal of Human Transcriptome · doi:10.3109/23324015.2015.1077591 · Cited by 114
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Hrdličková, B., Kumar, V., Kanduri, K., Zhernakova, D. V., Tripathi, S. K., Karjalainen, J. M., Lund, R., Li, Y., Ullah, U., Modderman, R., et al. (2014) · Genome Medicine · doi:10.1186/preaccept-4701398771324073 · Cited by 109
Xu, T., Ma, P., Wang, W., Shuai, Y., Wang, Y., Yu, T., Xia, R., & Shu, Y. (2019) · Cell Death and Differentiation · doi:10.1038/s41418-018-0236-y · Cited by 110
Caudron‐Herger, M., Rusin, S. F., Adamo, M. E., Seiler, J., Schmid, V., Barreau, E., Kettenbach, A. N., & Diederichs, S. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.04.018 · Cited by 110
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Ghosal, S., Das, S., & Chakrabarti, J. (2013) · Stem Cells and Development · doi:10.1089/scd.2013.0014 · Cited by 109
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Poliseno, L., Marranci, A., & Pandolfi, P. P. (2015) · Frontiers in Medicine · doi:10.3389/fmed.2015.00068 · Cited by 109
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Lorenzen, J. M., Schauerte, C., Kielstein, J. T., Hübner, A., Martino, F., Fiedler, J., Gupta, S. K., Faulhaber‐Walter, R., Kumarswamy, R., Hafer, C., et al. (2014) · Clinical Chemistry · doi:10.1373/clinchem.2014.230359 · Cited by 109
Long non-coding RNAs: An emerging powerhouse in the battle between life and death of tumor cells
Xiong, X.-D., Ren, X., Cai, M., Yang, J. W., Liu, X., & Yang, J. (2016) · Drug Resistance Updates · doi:10.1016/j.drup.2016.04.001 · Cited by 109
Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs
Ribeiro, D. M., Zanzoni, A., Cipriano, A., Ponti, R. D., Spinelli, L., Ballarino, M., Bozzoni, I., Tartaglia, G. G., & Brun, C. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1169 · Cited by 112
MALAT1: A long non‑coding RNA highly associated with human cancers (Review)
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Sun, Y., & Chen, Y.-Q. (2020) · Journal of Hematology & Oncology · doi:10.1186/s13045-020-00945-8 · Cited by 114
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Ilott, N. E., & Ponting, C. P. (2013) · Methods · doi:10.1016/j.ymeth.2013.03.019 · Cited by 110
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Xie, W., Chu, M., Song, G., Zuo, Z., Han, Z., Chen, C., Li, Y., & Wang, Z. P. (2020) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2020.11.004 · Cited by 108
Jayakodi, M., Jung, J. W., Park, D., Ahn, Y.-J., Lee, S.-C., Shin, S., Shin, C., Yang, T., & Kwon, H. W. (2015) · BMC Genomics · doi:10.1186/s12864-015-1868-7 · Cited by 106
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White, E. J., Matsangos, A. E., & Wilson, G. M. (2016) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1393 · Cited by 109
Wang, H., Shen, Q., Zhang, X., Yang, C.-L., Cui, S., Sun, Y., Wang, L., Fan, X., & Xu, S. (2017) · Cellular Physiology and Biochemistry · doi:10.1159/000475637 · Cited by 107
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Self-citationMichel, B. Y., Dziuba, D., Benhida, R., Demchenko, A. P., & Burger, A. (2020) · Frontiers in Chemistry · doi:10.3389/fchem.2020.00112 · Cited by 111
Sequencing Degraded RNA Addressed by 3' Tag Counting
Sigurgeirsson, B., Emanuelsson, O., & Lundeberg, J. (2014) · PLoS ONE · doi:10.1371/journal.pone.0091851 · Cited by 107
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Metadata
- Authors
- Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., Xue, C., Marinov, G. K., Khatun, J., Williams, B. A., Zaleski, C., Rozowsky, J., Röder, M., Kokocinski, F., Abdelhamid, R. F., Alioto, T., Antoshechkin, I., Baer, M. T., Bar, N. S., 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, M. J., Gao, H., Gonzalez, D., Gordon, A., Gunawardena, H., Howald, C., Jha, S., Johnson, R., Kapranov, P., King, B., Kingswood, C., Luo, O. J., Park, E., Persaud, K., Preall, J. B., Ribeca, P., Risk, B., Robyr, D., Sammeth, M., Schaffer, L., See, L.-H., Shahab, A., Skancke, J., Suzuki, A. M., 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, S. E., Hannon, G., Giddings, M. C., Ruan, Y., Wold, B., Carninci, P., Guigó, R., & Gingeras, T. R.
- Affiliations
- Centre for Genomic Regulation (ES)
- Universitat Pompeu Fabra (ES)
- Cold Spring Harbor Laboratory (US)
- California Institute of Technology (US)
- Boise State University (US)
- Wellcome Sanger Institute (GB)
- Norwegian University of Science and Technology (NO)
- University of North Carolina at Chapel Hill (US)
- University of Geneva (CH)
- Laboratoire de Génétique Cellulaire (FR)
- Corresponding author
- Guigó, Roderic
- Gingeras, Thomas R.
- ORCID
- Djebali, Sarah
- Merkel, Angelika
- Lassmann, Timo
- Mortazavi, Ali
- Lagarde, Julien
- Lin, Wei
- Marinov, Georgi K.
- Williams, Brian A.
- Rozowsky, Joel
- Kokocinski, Felix
- Abdelhamid, Rehab F.
- Alioto, Tyler
- Antoshechkin, Igor
- Bar, Nadav S.
- Batut, Philippe
- Bell, Kimberly
- Chen, Xian
- Derrien, Thomas
- Ferreira, Pedro
- Foissac, Sylvain
- Fullwood, Melissa J.
- Gao, Hui
- Gunawardena, Harsha
- Johnson, Rory
- Kapranov, Philipp
- Luo, Oscar J.
- Park, Eddie
- Preall, Jonathan B.
- Ribeca, Paolo
- Sammeth, Michael
- Shahab, Atif
- Takahashi, Hazuki
- Tilgner, Hagen
- Trout, Diane
- Wrobel, John
- Yu, Yanbao
- Hayashizaki, Yoshihide
- Harrow, Jennifer
- Gerstein, Mark
- Hubbard, Tim
- Reymond, Alexandre
- Antonarakis, Stylianos E.
- Hannon, Gregory
- Ruan, Yijun
- Wold, Barbara
- Carninci, Piero
- Guigó, Roderic
- Gingeras, Thomas R.
- Venue
- Nature
- Published
- 2012-09
- Volume
- 489
- Issue
- 7414
- Pages
- 101-108
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3684276
- OpenAlex
- W2166810745
- Cited by
- 5,187
- References
- 42
- Citations by year
- 2026: 102 · 2025: 217 · 2024: 347 · 2023: 332 · 2022: 372 · 2021: 487 · 2020: 523 · 2019: 421 · 2018: 440 · 2017: 429 · 2016: 392 · 2015: 357 · 2014: 389 · 2013: 323 · 2012: 49
- FWCI
- 143.23
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Research Portal (King's College London) (publishedVersion, other-oa)
- RECERCAT (Consorci de Serveis Universitaris de Catalunya) (publishedVersion, other-oa)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- SERVAL (Université de Lausanne) (acceptedVersion, other-oa)
- Archive ouverte UNIGE (University of Geneva) (acceptedVersion, other-oa)
- Scholar Works (Boise State University) (submittedVersion, cc-by-nc-sa)
- HAL (submittedVersion, other-oa)
- eScholarship (California Digital Library) (submittedVersion, cc-by-nc-sa)
- IRIS (submittedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion, cc-by-nc-sa)
- Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Repositori digital de la UPF (Universitat Pompeu Fabra) (submittedVersion, cc-by-nc-sa)
- Archive ouverte UNIGE (University of Geneva) (submittedVersion, cc-by)
- Funders
- National Science Foundation
- Wellcome Trust (062023)
- Ministry of Education, Culture, Sports, Science and Technology
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (26205, 127375, 249968)
- National Institutes of Health (5u54hg004555-04, 5p30ca045508-35)
- RIKEN
- National Human Genome Research Institute (U54HG007004, R01HG003700, U54HG004576, U54-HG004555, U54HG004558, U01HG003147, RC2HG005591, U54HG004557, U24HG007234)
- National Cancer Institute (P30-CA045508)
- National Institute of General Medical Sciences (R37GM062534)
- FP7 Ideas: European Research Council (249968)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- transcription, human genome, RNA processing, RNA localization, RNA modification, gene definition, ENCODE, RNA expression levels, genome annotation
- MeSH terms
- Alleles, Cell Line, DNA, Encyclopedias as Topic, Enhancer Elements, Genetic, Exons, Genes, Humans, Regulatory Sequences, Nucleic Acid, Repetitive Sequences, Nucleic Acid, RNA, RNA Splicing, Transcription, Genetic, Genome, Human, RNA Editing, Sequence Analysis, RNA, Protein Isoforms, Gene Expression Profiling, DNA, Intergenic, Genomics, Polyadenylation, Molecular Sequence Annotation, Transcriptome
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