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.
“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]
The “Patterns of splicing” section says genes tend to express many isoforms and that the number of expressed isoforms plateaus at about 10–12 per gene. It does not say that almost all multi-exon genes undergo alternative splicing or that spliced genes average more than nine alternative forms; a plateau is not an average. (LLM, conf=0.85)
Experimental — accuracy not yet measuredThe human genome now has >55,000 well-validated genes, and the majority of them are not protein coding.
“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]
In “Detection of annotated and novel transcripts” (page unavailable), the paper predicts 41,204 novel genes in addition to Gencode annotations and says most novel transcripts appear to lack protein-coding capacity. But it validates only a tested subset of approximately 3,000 transcript models and cautions that some unspliced transcripts could be artifacts. It does not establish that more than 55,000 genes are well validated or that a majority of those genes are non-protein-coding. (LLM, conf=0.86)
Experimental — accuracy not yet measuredEfforts including ENCODE and others have reported that more than 75% of genomic DNA is at some point transcribed to primary unspliced RNA.
“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]
Most genes, in a given cell type, likely express only a single dominant transcript.
“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]
RNA-seq provides a powerful tool to decipher global gene expression patterns far beyond the limitations of microarrays.
“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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Cites
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works
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 · see citing works
Self-citationThe ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
The ENCODE (ENCyclopedia Of DNA Elements) Project
(2004) · Science · doi:10.1126/science.1105136 · Cited by 2,390 · see citing works
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 1,418 · see citing works
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 1,175 · see citing works
Self-citationA novel class of small RNAs: tRNA-derived RNA fragments (tRFs)
Lee, Y. S., Shibata, Y., Malhotra, A., & Dutta, A. (2009) · Genes & Development · doi:10.1101/gad.1837609 · Cited by 1,066 · see citing works
Measuring reproducibility of high-throughput experiments
Li, Q., Brown, J. B., Huang, H., & Bickel, P. J. (2011) · The Annals of Applied Statistics · doi:10.1214/11-aoas466 · Cited by 1,008 · see citing works
Measuring reproducibility of high-throughput experiments
Li, Q., Brown, J. B., Huang, H., & Bickel, P. J. (2010) · UC Berkeley · Cited by 915 · see citing works
Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA
Wang, D., García-Bassets, I., Benner, C. W., Li, W., Su, X. B., Zhou, Y., Qiu, J., Liu, W., Kaikkonen, M. U., Ohgi, K. A., et al. (2011) · Nature · doi:10.1038/nature10006 · Cited by 820 · see citing works
Wang, J., Zhuang, J., Iyer, S., Lin, X.-Y., Whitfield, T. W., Greven, M. C., Pierce, B. G., Dong, X., Kundaje, A. B., Cheng, Y., et al. (2012) · Genome Research · doi:10.1101/gr.139105.112 · Cited by 820 · see citing works
The regulated retrotransposon transcriptome of mammalian cells
Faulkner, G. J., Kimura, Y., Daub, C. O., Wani, S., Plessy, C., Irvine, K. M., Schroder, K., Cloonan, N., Steptoe, A. L., Lassmann, T., et al. (2009) · Nature Genetics · doi:10.1038/ng.368 · Cited by 819 · see citing works
Self-citationGenome-wide transcription and the implications for genomic organization
Kapranov, P., Willingham, A. T., & Gingeras, T. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2083 · Cited by 720 · see citing works
Self-citationGENCODE: producing a reference annotation for ENCODE
Harrow, J., Denoeud, F., Frankish, A., Reymond, A., Chen, C.-K., Chrast, J., Lagarde, J., Gilbert, J. G., Storey, R., Swarbreck, D., et al. (2006) · Genome Biology · doi:10.1186/gb-2006-7-s1-s4 · Cited by 648 · see citing works
Self-citationCole, C., Sobala, A., Lu, C. C., Thatcher, S., Bowman, A. J., Brown, J. W., Green, P. J., Barton, G. J., & Hutvágner, G. (2009) · RNA · doi:10.1261/rna.1738409 · Cited by 647 · see citing works
Integrative annotation of chromatin elements from ENCODE data
Hoffman, M. M., Ernst, J., Wilder, S. P., Kundaje, A. B., Harris, R. S., Libbrecht, M., Giardine, B. M., Ellenbogen, P. M., Bilmes, J. A., Birney, E., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1284 · Cited by 521 · see citing works
Tilgner, H., Knowles, D. G., Johnson, R., Davis, C., Chakrabortty, S. K., Djebali, S., Curado, J., Snyder, M. P., Gingeras, T., & Guigó, R. (2012) · Genome Research · doi:10.1101/gr.134445.111 · Cited by 463 · see citing works
Self-citationWidespread RNA and DNA Sequence Differences in the Human Transcriptome
Li, M., Wang, I. X., Li, Y., Bruzel, A., Richards, A. L., Toung, J. M., & Cheung, V. G. (2011) · Science · doi:10.1126/science.1207018 · Cited by 459 · see citing works
CAGE: cap analysis of gene expression
Kodzius, R., Kojima, M., Nishiyori, H., Nakamura, M., Fukuda, S., Tagami, M., Sasaki, D., Imamura, K., Kai, C., Harbers, M., et al. (2006) · Nature Methods · doi:10.1038/nmeth0306-211 · Cited by 444 · see citing works
Self-citationPost-transcriptional processing generates a diversity of 5′-modified long and short RNAs
Tóth, K. F., Sotirova, V. N., Sachidanandam, R., Gordon, A., Hannon, G. J., Gingeras, T., Kapranov, P., Foissac, S., Willingham, A. T., Duttagupta, R., et al. (2009) · Nature · doi:10.1038/nature07759 · Cited by 428 · see citing works
Self-citationEGASP: the human ENCODE Genome Annotation Assessment Project.
Guigó, R., Flicek, P., Abril, J. F., Reymond, A., Lagarde, J., Denœud, F., Antonarakis, S. E., Ashburner, M., Bajić, V. B., Birney, E., et al. (2006) · Genome biology · doi:10.1186/gb-2006-7-s1-s2 · Cited by 341 · see citing works
Self-citationAmeur, A., Zaghlool, A., Halvardson, J., Wetterbom, A., Gyllensten, U., Cavelier, L., & Feuk, L. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2143 · Cited by 323 · see citing works
AlleleSeq: analysis of allele-specific expression and binding in a network framework.
Rozowsky, J., Abyzov, A., Wang, J., Alves, P., Raha, D., Harmanci, A., Leng, J., Bjornson, R., Kong, Y., Kitabayashi, N., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.54 · Cited by 316 · see citing works
Self-citationThe metabolism of a poly(A) minus mRNA fraction in HeLa cells
Milcarek, C., Price, R. P., & Penman, S. (1974) · Cell · doi:10.1016/0092-8674(74)90030-0 · Cited by 315 · see citing works
Hidden layers of human small RNAs
Kawaji, H., Nakamura, M., Takahashi, Y., Sandelin, A., Katayama, S., Fukuda, S., Daub, C. O., Kai, C., Kawai, J., Yasuda, J., et al. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-157 · Cited by 296 · see citing works
Self-citationFu, Y., Sun, Y., Li, Y., Li, J., Rao, X., Chen, C., & Xu, A. (2011) · Genome Research · doi:10.1101/gr.115295.110 · Cited by 270 · see citing works
Ng, P., Wei, C., Sung, W.-K. K., Chiu, K. P., Lipovich, L., Ang, C. C., Gupta, S. M., Shahab, A., Ridwan, A. B. M., Wong, C., et al. (2005) · Nature Methods · doi:10.1038/nmeth733 · Cited by 247 · see citing works
Self-citationYip, K. Y.-L., Cheng, C., Bhardwaj, N., Brown, J., Leng, J., Kundaje, A. B., Rozowsky, J. S., Birney, E., Bickel, P. J., Snyder, M. P., et al. (2012) · Genome biology · doi:10.1186/gb-2012-13-9-r48 · Cited by 244 · see citing works
Self-citationSequence and chromatin determinants of cell-type–specific transcription factor bindingPreprint
Arvey, A. J., Agius, P., Noble, W. S., & Leslie, C. S. (2012) · Genome Research · doi:10.1101/gr.127712.111 · Cited by 216 · see citing works
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements
Kundaje, A., Kyriazopoulou-Panagiotopoulou, S., Libbrecht, M., Smith, C. L., Raha, D., Winters, E. E., Johnson, S. M., Snyder, M., Batzoglou, S., & Sidow, A. (2012) · Genome Research · doi:10.1101/gr.136366.111 · Cited by 178 · see citing works
RNA editing in the human ENCODE RNA-seq dataPreprint
Park, E., Williams, B. A., Wold, B. J., & Mortazavi, A. (2012) · Genome Research · doi:10.1101/gr.134957.111 · Cited by 161 · see citing works
Self-citationLong noncoding RNAs in cell and developmental biology
Mattick, J. S. (2011) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2011.05.002 · Cited by 75 · see citing works
The GENCODE exome: sequencing the complete human exome
Coffey, A. J., Kokocinski, F., Calafato, M., Scott, C., Palta, P., Drury, E., Joyce, C. J., LeProust, E. M., Harrow, J., Hunt, S. E., et al. (2011) · European Journal of Human Genetics · doi:10.1038/ejhg.2011.28 · Cited by 64 · see citing works
Self-citationSalditt-Georgieff, M., Harpold, M. M., Wilson, M. C., & Darnell, J. E., Jr. (1981) · Molecular and Cellular Biology · doi:10.1128/mcb.1.2.179 · Cited by 64 · see citing works
Khatun, J., Yu, Y., Wrobel, J. A., Risk, B. A., Gunawardena, H. P., Secrest, A., Spitzer, W. J., Xie, L., Wang, L., Chen, X., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-141 · Cited by 60 · see citing works
Self-citationWang, J., Zhuang, J., Iyer, S., Lin, X., Whitfield, T. W., Greven, M. C., Pierce, B. G., Dong, X., Kundaje, A. B., Cheng, Y., et al. (2013) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2013.786511 · Cited by 50 · see citing works
Non‐polyadenylated mRNAs from eukaryotes
Katinakis, P. K., Slater, R. J., & Burdon, R. H. (1980) · FEBS Letters · doi:10.1016/0014-5793(80)80515-1 · Cited by 40 · see citing works
Ren, B. (2010) · Nature · doi:10.1038/465173a · Cited by 38 · see citing works
Salditt-Georgieff, M., Harpold, M. M., Wilson, M. C., et al. (1981) · Molecular and Cellular Biology · doi:10.1128/mcb.1.2.179-187.1981 · Cited by 22 · see citing works
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STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709 · see citing works
Self-citationAn integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works
Self-citationvoom: precision weights unlock linear model analysis tools for RNA-seq read counts
Law, C. W., Chen, Y., Shi, W., & Smyth, G. K. (2014) · Genome Biology · doi:10.1186/gb-2014-15-2-r29 · Cited by 6,155 · see citing works
GENCODE: 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 · see citing works
Self-citationDerrien, T., Johnson, R., Bussotti, G., Andrea Tanzer, A., Djebali, S., Tilgner, H., Guernec, G., Martin, D., Merkel, A., Knowles, D. G., et al. (2012) · Genome Research · doi:10.1101/gr.132159.111 · Cited by 5,017 · see citing works
Self-citationDifferential analysis of gene regulation at transcript resolution with RNA-seq
Trapnell, C., Hendrickson, D. G., Sauvageau, M., Goff, L., Rinn, J. L., & Pachter, L. (2013) · Nature Biotechnology · doi:10.1038/nbt.2450 · Cited by 3,492 · see citing works
Unique features of long non-coding RNA biogenesis and function
Quinn, J. J., & Chang, H. Y. (2015) · Nature Reviews Genetics · doi:10.1038/nrg.2015.10 · Cited by 3,653 · see citing works
Functional Classification and Experimental Dissection of Long Noncoding RNAs
Kopp, F. B., & Mendell, J. T. (2018) · Cell · doi:10.1016/j.cell.2018.01.011 · Cited by 3,522 · see citing works
Long non-coding RNAs: new players in cell differentiation and development
Fatica, A., & Bozzoni, I. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3606 · Cited by 2,980 · see citing works
Long Noncoding RNAs in Cancer Pathways
Schmitt, A. M., & Chang, H. Y. (2016) · Cancer Cell · doi:10.1016/j.ccell.2016.03.010 · Cited by 2,991 · see citing works
The 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 · see citing works
Self-citationThe landscape of long noncoding RNAs in the human transcriptome
Iyer, M. K., Niknafs, Y. S., Malik, R., Singhal, U., Sahu, A., Hosono, Y., Barrette, T. R., Prensner, J. R., Evans, J. R., Zhao, S., et al. (2015) · Nature Genetics · doi:10.1038/ng.3192 · Cited by 2,738 · see citing works
Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation
Gilbert, L. A., Horlbeck, M. A., Adamson, B., Villalta, J. E., Chen, Y., Whitehead, E. H., Guimaraes, C., Panning, B., Ploegh, H. L., Bassik, M. C., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.029 · Cited by 2,728 · see citing works
The emerging role of lncRNAs in cancer
Huarte, M. (2015) · Nature Medicine · doi:10.1038/nm.3981 · Cited by 2,686 · see citing works
lincRNAs: Genomics, Evolution, and Mechanisms
Ulitsky, I., & Bartel, D. P. (2013) · Cell · doi:10.1016/j.cell.2013.06.020 · Cited by 2,596 · see citing works
An atlas of active enhancers across human cell types and tissues
The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550 · see citing works
Self-citationLong Noncoding RNAs: Cellular Address Codes in Development and Disease
Batista, P. J., & Chang, H. Y. (2013) · Cell · doi:10.1016/j.cell.2013.02.012 · Cited by 2,531 · see citing works
Expanded encyclopaedias of DNA elements in the human and mouse genomes
The ENCODE Project Consortium, Abascal, F., Acosta, R., Addleman, N. J., Adrian, J., Afzal, V., Ai, R., Aken, B., Akiyama, J. A., Jammal, O. A., et al. (2020) · Nature · doi:10.1038/s41586-020-2493-4 · Cited by 2,378 · see citing works
Self-citationTranscriptome and genome sequencing uncovers functional variation in humans
The Geuvadis Consortium, Lappalainen, T., Sammeth, M., Friedländer, M. R., ‘t Hoen, P. A. C., Monlong, J., Rivas, M. A., Gonzàlez-Porta, M., Kurbatova, N., Griebel, T., et al. (2013) · Nature · doi:10.1038/nature12531 · Cited by 1,888 · see citing works
Self-citationUtilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts
Sun, L. D., Luo, H., Bu, D., Zhao, G., Yu, K., Zhang, C., Liu, Y., Chen, R., & Zhao, Y. C. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt646 · Cited by 2,110 · see citing works
A comparative encyclopedia of DNA elements in the mouse genome
Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., et al. (2014) · Nature · doi:10.1038/nature13992 · Cited by 1,781 · see citing works
Self-citationRNA sequencing: the teenage years
Stark, R., Grzelak, M., & Hadfield, J. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0150-2 · Cited by 1,906 · see citing works
Non-coding RNA networks in cancer
Anastasiadou, E., Jacob, L. S., & Slack, F. J. (2017) · Nature reviews. Cancer · doi:10.1038/nrc.2017.99 · Cited by 1,901 · see citing works
Long noncoding RNAs: past, present, and future
Kung, J. T. Y., Colognori, D., & Lee, J. T. (2013) · Genetics · doi:10.1534/genetics.112.146704 · Cited by 1,874 · see citing works
Mass-spectrometry-based draft of the human proteome
Wilhelm, M., Schlegl, J., Hahne, H., Gholami, A. M., Lieberenz, M., Savitski, M. M., Ziegler, E., Butzmann, L., Gessulat, S., Marx, H., et al. (2014) · Nature · doi:10.1038/nature13319 · Cited by 1,820 · see citing works
The role of non-coding RNAs in oncology
Slack, F. J., & Chinnaiyan, A. M. (2019) · Cell · doi:10.1016/j.cell.2019.10.017 · Cited by 1,619 · see citing works
Transcriptional Regulation and Its Misregulation in Disease
Lee, T. I., & Young, R. A. (2013) · Cell · doi:10.1016/j.cell.2013.02.014 · Cited by 1,588 · see citing works
Expanded identification and characterization of mammalian circular RNAs
Guo, J. U., Agarwal, V., Guo, H., & Bartel, D. P. (2014) · Genome biology · doi:10.1186/s13059-014-0409-z · Cited by 1,578 · see citing works
LNCcation: lncRNA localization and function
Bridges, M. C., Daulagala, A. C., & Kourtidis, A. (2021) · Journal of Cell Biology · doi:10.1083/jcb.202009045 · Cited by 1,556 · see citing works
The long-range interaction landscape of gene promoters
Sanyal, A., Lajoie, B. R., Jain, G., & Dekker, J. (2012) · Nature · doi:10.1038/nature11279 · Cited by 1,489 · see citing works
Feng, Y., Spezia, M., Huang, S., Yuan, C., Zeng, Z., Zhang, L., Ji, X., Liu, W., Huang, B., Luo, W., et al. (2018) · Genes & Diseases · doi:10.1016/j.gendis.2018.05.001 · Cited by 1,538 · see citing works
Modification of Enhancer Chromatin: What, How, and Why?
Calo, E., & Wysocka, J. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.038 · Cited by 1,457 · see citing works
MicroRNAs and other non-coding RNAs as targets for anticancer drug development
Ling, H. Y., Fabbri, M., & Călin, G. A. (2013) · Nature Reviews Drug Discovery · doi:10.1038/nrd4140 · Cited by 1,465 · see citing works
RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts
Geisler, S., & Coller, J. (2013) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3679 · Cited by 1,451 · see citing works
The human transcriptome across tissues and individuals
Melé, M., Ferreira, P. G., Reverter, F., DeLuca, D. S., Monlong, J., Sammeth, M., Young, T. R., Goldmann, J. M., Pervouchine, D. D., Sullivan, T. J., et al. (2015) · Science · doi:10.1126/science.aaa0355 · Cited by 1,304 · see citing works
Self-citationStructure and function of long noncoding RNAs in epigenetic regulation
Mercer, T. R., & Mattick, J. S. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2480 · Cited by 1,436 · see citing works
Sequencing depth and coverage: key considerations in genomic analyses
Sims, D., Sudbery, I. M., Ilott, N. E., Heger, A., & Ponting, C. P. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3642 · Cited by 1,403 · see citing works
Morris, K. V., & Mattick, J. S. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3722 · Cited by 1,389 · see citing works
Cellular functions of long noncoding RNAs
Yao, R.-W., Wang, Y., & Chen, L. (2019) · Nature Cell Biology · doi:10.1038/s41556-019-0311-8 · Cited by 1,381 · see citing works
High-Throughput Sequencing Technologies
Reuter, J., Spacek, D. V., & Snyder, M. P. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.05.004 · Cited by 1,330 · see citing works
The functions and unique features of long intergenic non-coding RNA
Ransohoff, J. D., Wei, Y., & Khavari, P. A. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.104 · Cited by 1,337 · see citing works
Epigenetic Regulation by Long Noncoding RNAs
Lee, J. T. (2012) · Science · doi:10.1126/science.1231776 · Cited by 1,258 · see citing works
Alternative polyadenylation of mRNA precursors
Tian, B., & Manley, J. L. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.116 · Cited by 1,179 · see citing works
The Landscape of long noncoding RNA classification
Laurent, G. S., Wahlestedt, C., & Kapranov, P. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.03.007 · Cited by 1,192 · see citing works
Self-citationThe STAT3-Binding Long Noncoding RNA lnc-DC Controls Human Dendritic Cell Differentiation
Wang, P., Xue, Y., Han, Y., Li, L., Wu, C., Xu, S., Jiang, Z., Xu, J., Liu, Q., & Cao, X. (2014) · Science · doi:10.1126/science.1251456 · Cited by 1,106 · see citing works
SEQC/MAQC-III Consortium (2014) · Nature Biotechnology · doi:10.1038/nbt.2957 · Cited by 983 · see citing works
Self-citationMechanisms of long noncoding RNA function in development and disease
Schmitz, S. U., Grote, P., & Herrmann, B. G. (2016) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-016-2174-5 · Cited by 1,088 · see citing works
ROS, Cell Senescence, and Novel Molecular Mechanisms in Aging and Age‐Related Diseases
Davalli, P., Mitic, T., Caporali, A., Lauriola, A., & D’Arca, D. (2016) · Oxidative Medicine and Cellular Longevity · doi:10.1155/2016/3565127 · Cited by 1,059 · see citing works
Roles, Functions, and Mechanisms of Long Non-Coding RNAs in Cancer
Fang, Y., & Fullwood, M. J. (2016) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2015.09.006 · Cited by 1,068 · see citing works
Self-citationNoncoding RNA:RNA Regulatory Networks in Cancer
Chan, J. J., & Tay, Y. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19051310 · Cited by 1,030 · see citing works
Non-coding RNAs as drug targets
Matsui, M., & Corey, D. R. (2016) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2016.117 · Cited by 1,036 · see citing works
Diverse alternative back-splicing and alternative splicing landscape of circular RNAsPreprint
Zhang, X.-O., Dong, R., Zhang, Y., Zhang, J., Luo, Z. D., Zhang, J., Chen, L., & Yang, L. C. (2016) · Genome Research · doi:10.1101/gr.202895.115 · Cited by 1,022 · see citing works
An atlas of human long non-coding RNAs with accurate 5′ ends
Hon, C.-C., Ramilowski, J. A., Harshbarger, J., Bertin, N., Rackham, O. J. L., Gough, J., Denisenko, E., Schmeier, S., Poulsen, T. M., Severin, J., et al. (2017) · Nature · doi:10.1038/nature21374 · Cited by 1,007 · see citing works
Self-citationNeoantigens: promising targets for cancer therapy
Xie, N., Shen, G., Gao, W., Huang, Z., Huang, C., & Fu, L. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01270-x · Cited by 1,020 · see citing works
Regulation of mammalian nucleotide metabolism and biosynthesis
Lane, A. N., & Fan, T. W.-M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv047 · Cited by 959 · see citing works
Next-Generation Machine Learning for Biological Networks
Camacho, D. M., Collins, K. M., Powers, R. K., Costello, J. C., & Collins, J. J. (2018) · Cell · doi:10.1016/j.cell.2018.05.015 · Cited by 974 · see citing works
Non-coding RNAs: Classification, Biology and Functioning
Hombach, S., & Kretz, M. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-42059-2_1 · Cited by 959 · see citing works
Single-cell RNA-seq: advances and future challenges
Saliba, A.-E., Westermann, A. J., Gorski, S. A., & Vogel, J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku555 · Cited by 847 · see citing works
Transcriptional and Post-Transcriptional Gene Regulation by Long Non-Coding RNA
Dykes, I. M., & Emanueli, C. (2017) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2016.12.005 · Cited by 909 · see citing works
Non-coding RNA: what is functional and what is junk?
Palazzo, A. F., & Lee, E. S. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00002 · Cited by 891 · see citing works
Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients
Kahles, A., Lehmann, K.-V., Toussaint, N. C., Hüser, M., Stark, S. G., Sachsenberg, T. T., Stegle, O., Kohlbacher, O., Sander, C., Johnson, R., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.07.001 · Cited by 892 · see citing works
Self-citationHistory, Discovery, and Classification of lncRNAs
Jarroux, J., Morillon, A., & Pinskaya, M. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-981-10-5203-3_1 · Cited by 873 · see citing works
Ballgown bridges the gap between transcriptome assembly and expression analysis
Frazee, A. C., Pertea, G. M., Jaffe, A. E., Langmead, B., Salzberg, S. L., & Leek, J. T. (2015) · Nature Biotechnology · doi:10.1038/nbt.3172 · Cited by 853 · see citing works
Pal, S., & Tyler, J. K. (2016) · Science Advances · doi:10.1126/sciadv.1600584 · Cited by 860 · see citing works
Gateways to the FANTOM5 promoter level mammalian expression atlas
Lizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T., Sahin, S., Abugessaisa, I., Fukuda, S., Hori, F., Ishikawa-Kato, S., et al. (2015) · Genome Biology · doi:10.1186/s13059-014-0560-6 · Cited by 871 · see citing works
Self-citationceRNA Cross-Talk in Cancer: When ce-bling Rivalries Go Awry
Karreth, F. A., & Pandolfi, P. P. (2013) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0202 · Cited by 851 · see citing works
Wang, J., Zhuang, J., Iyer, S., Lin, X.-Y., Whitfield, T. W., Greven, M. C., Pierce, B. G., Dong, X., Kundaje, A. B., Cheng, Y., et al. (2012) · Genome Research · doi:10.1101/gr.139105.112 · Cited by 820 · see citing works
The complex transcriptional landscape of the anucleate human platelet
Bray, P. F., McKenzie, S. E., Edelstein, L. C., Nagalla, S., Delgrosso, K., Ertel, A., Kupper, J., Jing, Y., Londin, E., Loher, P., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-1 · Cited by 802 · see citing works
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
Rapaport, F., Khanin, R., Liang, Y., Pirun, M., Krek, A., Zumbo, P., Mason, C. E., Socci, N. D., & Betel, D. (2013) · Genome Biology · doi:10.1186/gb-2013-14-9-r95 · Cited by 733 · see citing works
Assessment of transcript reconstruction methods for RNA-seq
The RGASP Consortium, Steijger, T., Abril, J. F., Engström, P. G., Kokocinski, F., Hubbard, T. J., Guigó, R., Harrow, J., & Bertone, P. (2013) · Nature Methods · doi:10.1038/nmeth.2714 · Cited by 699 · see citing works
Self-citationENCODE Data in the UCSC Genome Browser: year 5 update
Rosenbloom, K., Sloan, C. A., Malladi, V., Dreszer, T. R., Learned, K., Kirkup, V. M., Wong, M., Maddren, M., Fang, R.-H., Heitner, S. G., et al. (2012) · Nucleic Acids Res. · doi:10.1093/nar/gks1172 · Cited by 827 · see citing works
Principles for targeting RNA with drug-like small molecules
Warner, K. D., Hajdin, C. E., & Weeks, K. M. (2018) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2018.93 · Cited by 742 · see citing works
CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells
Liu, S. J., Horlbeck, M. A., Cho, S. W., Birk, H. S., Malatesta, M., He, D. X., Attenello, F. J., Villalta, J. E., Cho, M. Y., Chen, Y., et al. (2016) · Science · doi:10.1126/science.aah7111 · Cited by 734 · see citing works
Systematic mapping of functional enhancer–promoter connections with CRISPR interference
Fulco, C. P., Munschauer, M., Anyoha, R., Munson, G., Grossman, S. R., Perez, E. M., Kane, M., Cleary, B., Lander, E. S., & Engreitz, J. M. (2016) · Science · doi:10.1126/science.aag2445 · Cited by 643 · see citing works
Hangauer, M. J., Vaughn, I. W., & McManus, M. T. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003569 · Cited by 738 · see citing works
Diversity and dynamics of the Drosophila transcriptome
Brown, J., Boley, N. P., Eisman, R. C., May, G. E., Stoiber, M. H., Duff, M. O., Booth, B. W., Wen, J., Park, S. H., Suzuki, A. M., et al. (2014) · Nature · doi:10.1038/nature12962 · Cited by 700 · see citing works
Self-citationPoly(A)-tail profiling reveals an embryonic switch in translational control
Subtelny, A. O., Eichhorn, S. W., Chen, G. R., Sive, H., & Bartel, D. P. (2014) · Nature · doi:10.1038/nature13007 · Cited by 664 · see citing works
Gene regulation by the act of long non-coding RNA transcription
Kornienko, A. E., Guenzl, P. M., Barlow, D. P., & Pauler, F. M. (2013) · BMC Biology · doi:10.1186/1741-7007-11-59 · Cited by 716 · see citing works
Evolutionary conservation of long non-coding RNAs; sequence, structure, function
Johnsson, P., Lipovich, L., Grandér, D., & Morris, K. V. (2013) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2013.10.035 · Cited by 707 · see citing works
Revealing protein–lncRNA interaction
Ferrè, F., Colantoni, A., & Helmer‐Citterich, M. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv031 · Cited by 702 · see citing works
A single-molecule long-read survey of the human transcriptome
Sharon, D., Tilgner, H., Grubert, F., & Snyder, M. (2013) · Nature Biotechnology · doi:10.1038/nbt.2705 · Cited by 701 · see citing works
Self-citationGene regulation in the immune system by long noncoding RNAs
Chen, Y. G., Satpathy, A. T., & Chang, H. Y. (2017) · Nature Immunology · doi:10.1038/ni.3771 · Cited by 686 · see citing works
Defining functional DNA elements in the human genome
Kellis, M., Wold, B. J., Snyder, M. P., Bernstein, B., Kundaje, A. B., Marinov, G. K., Ward, L. D., Birney, E., Crawford, G. E., Dekker, J., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1318948111 · Cited by 692 · see citing works
Self-citationCore, L. J., Martins, A. L., Danko, C. G., Waters, C. T., Siepel, A., & Lis, J. T. (2014) · Nature Genetics · doi:10.1038/ng.3142 · Cited by 693 · see citing works
RNA splicing factors as oncoproteins and tumour suppressors
Dvinge, H., Kim, E. H., Abdel-Wahab, O. I., & Bradley, R. K. (2016) · Nature reviews. Cancer · doi:10.1038/nrc.2016.51 · Cited by 684 · see citing works
Enhancers as non-coding RNA transcription units: recent insights and future perspectives
Li, W., Notani, D., & Rosenfeld, M. G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.4 · Cited by 710 · see citing works
Non-Coding RNAs and their Integrated Networks
Zhang, P., Wu, W., Chen, Q., & Chen, M. (2019) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2019-0027 · Cited by 691 · see citing works
Kapusta, A., Kronenberg, Z., Lynch, V. J., Zhuo, X., Ramsay, L., Bourque, G., Yandell, M., & Feschotte, C. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003470 · Cited by 687 · see citing works
Targeting noncoding RNAs in disease
Adams, B. D., Parsons, C., Walker, L., Zhang, W. C., & Slack, F. J. (2017) · Journal of Clinical Investigation · doi:10.1172/jci84424 · Cited by 672 · see citing works
NONCODE 2016: an informative and valuable data source of long non-coding RNAs
Zhao, Y., Li, H., Fang, S., Kang, Y., wu, W., Hao, Y., Li, Z., Bu, D., Sun, N., Zhang, M. Q., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1252 · Cited by 643 · see citing works
Atlas of Subcellular RNA Localization Revealed by APEX-Seq
Fazal, F. M., Han, S., Parker, K. R., Kaewsapsak, P., Xu, J., Boettiger, A. N., Chang, H. Y., & Ting, A. Y. (2019) · Cell · doi:10.1016/j.cell.2019.05.027 · Cited by 648 · see citing works
Long Noncoding RNA in Prostate, Bladder, and Kidney Cancer
Martens‐Uzunova, E. S., Böttcher, R., Croce, C. M., Jenster, G. W., Visakorpi, T., & Călin, G. A. (2013) · European Urology · doi:10.1016/j.eururo.2013.12.003 · Cited by 656 · see citing works
Long noncoding RNAs in cancer metastasis
Liu, S. J., Dang, H. X., Lim, D. A., Feng, F. Y.-C., & Maher, C. A. (2021) · Nature reviews. Cancer · doi:10.1038/s41568-021-00353-1 · Cited by 645 · see citing works
Long Non-Coding RNAs in the Regulation of Gene Expression: Physiology and Disease
Fernandes, J. C. R., Acuña, S. M., Aoki, J. I., Floeter‐Winter, L. M., & Muxel, S. M. (2019) · Non-Coding RNA · doi:10.3390/ncrna5010017 · Cited by 647 · see citing works
Gene regulation by antisense transcription
Pelechano, V., & Steinmetz, L. M. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3594 · Cited by 628 · see citing works
Discovery and annotation of long noncoding RNAs
Mattick, J. S., & Rinn, J. L. (2015) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2942 · Cited by 624 · see citing works
Towards a complete map of the human long non-coding RNA transcriptome
Uszczyńska-Ratajczak, B., Lagarde, J., Frankish, A., Guigó, R., & Johnson, R. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0017-y · Cited by 611 · see citing works
Self-citationThe RNA modification landscape in human disease
Jonkhout, N., Tran, J., Smith, M. A., Schönrock, N., Mattick, J. S., & Novoa, E. M. (2017) · RNA · doi:10.1261/rna.063503.117 · Cited by 606 · see citing works
Single-nucleus and single-cell transcriptomes compared in matched cortical cell types
Bakken, T. E., Hodge, R. D., Miller, J. A., Yao, Z., Nguyen, T. N., Aevermann, B., Barkan, E., Bertagnolli, D., Casper, T., Dee, N., et al. (2018) · PLoS ONE · doi:10.1371/journal.pone.0209648 · Cited by 608 · see citing works
Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis
Soumillon, M., Necşulea, A., Weier, M., Brawand, D., Zhang, X., Gu, H., Barthès, P., Kokkinaki, M., Nef, S., Gnirke, A., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.05.031 · Cited by 607 · see citing works
- 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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