The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index.
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
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
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 1,449
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
Flagged first, then by citations
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)
Cited by
Sorted by citations
Items 401–500 of 1,018
CircRNA_101237 promotes NSCLC progression via the miRNA-490-3p/MAPK1 axis
Zhang, Z., Gao, X.-H., Ma, M.-Y., Zhao, C., Zhang, Y., & Guo, S. (2020) · Scientific Reports · doi:10.1038/s41598-020-65920-2 · Cited by 182
Su, Z., Fang, H., Hong, H., Shi, L. M., Zhang, W., Zhang, W., Zhang, Y., Dong, Z., Lancashire, L., Bessarabova, M., et al. (2014) · Genome biology · doi:10.1186/s13059-014-0523-y · Cited by 184
Epigenetic inactivation of the p53-induced long noncoding RNA TP53 target 1 in human cancer
Díaz‐Lagares, Á., Crujeiras, A. B., López-Serra, P., Soler, M., Setién, F., Goyal, A., Sandoval, J., Hashimoto, Y., Martínez‐Cardús, A., Gómez, A., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1608585113 · Cited by 179
Kang, M., Ren, M., Yan, L., Fu, Y., Deng, M., & Li, C. (2018) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-018-0845-9 · Cited by 180
RetractedIlluminating the dark side of the human transcriptome with long read transcript sequencing
Kuo, R. I., Cheng, Y., Zhang, R., Brown, J. W. S., Smith, J., Archibald, A. L., & Burt, D. W. (2020) · BMC Genomics · doi:10.1186/s12864-020-07123-7 · Cited by 171
Quiescence-induced LncRNAs trigger H4K20 trimethylation and transcriptional silencing
Bierhoff, H., Dammert, M. A., Brocks, D., Dambacher, S., Schotta, G., & Grummt, I. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.03.032 · Cited by 179
Inbar‐Feigenberg, M., Choufani, S., Butcher, D. T., Roifman, M., & Weksberg, R. (2013) · Fertility and Sterility · doi:10.1016/j.fertnstert.2013.01.117 · Cited by 193
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
The emerging role of lncRNAs in the regulation of cancer stem cells
Castro‐Oropeza, R., Meléndez-Zajgla, J., Maldonado, V., & Vázquez-Santillán, K. (2018) · Cellular Oncology · doi:10.1007/s13402-018-0406-4 · Cited by 178
Menschaert, G., Van Criekinge, W., Notelaers, T., Koch, A., Crappé, J., Gevaert, K., & Van Damme, P. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.027540 · Cited by 173
Creating reference gene annotation for the mouse C57BL6/J genome assembly
Mudge, J. M., & Harrow, J. (2015) · Mammalian Genome · doi:10.1007/s00335-015-9583-x · Cited by 173
Self-citationWerner, M. S., & Ruthenburg, A. J. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.07.033 · Cited by 180
Critical roles of long noncoding RNAs in Drosophila spermatogenesisPreprint
Wen, K., Yang, L., Xiong, T., Di, C., Ma, D., Wu, M., Xue, Z., Zhang, X., Li, L., Zhang, W., et al. (2016) · Genome Research · doi:10.1101/gr.199547.115 · Cited by 182
Efficient and Allele-Specific Genome Editing of Disease Loci in Human iPSCs
Smith, C. J., Abalde-Atristain, L., He, C., Brodsky, B. R., Braunstein, E. M., Chaudhari, P., Jang, Y.-Y., Cheng, L., & Ye, Z. (2014) · Molecular Therapy · doi:10.1038/mt.2014.226 · Cited by 180
Liao, Y., Shen, L., Zhao, H., Liu, Q., Fu, J., Guo, Y. G., Peng, R., & Cheng, L. (2017) · Journal of Cellular Biochemistry · doi:10.1002/jcb.25910 · Cited by 175
Cis- and trans-acting lncRNAs in pluripotency and reprogramming
Yan, P., Luo, S., Lu, J., & Shen, X. (2017) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2017.07.009 · Cited by 173
Influence of RNA extraction methods and library selection schemes on RNA-seq data
Sultan, M., Amstislavskiy, V. S., Risch, T., Schuette, M., Dökel, S., Ralser, M., Balzereit, D., Lehrach, H. R., & Yaspo, M. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-675 · Cited by 174
Noncoding RNA and its associated proteins as regulatory elements of the immune system
Turner, M., Galloway, A., & Vigorito, E. (2014) · Nature Immunology · doi:10.1038/ni.2887 · Cited by 174
The Role of Long Noncoding RNAs in Neurodegenerative Diseases
Wan, P., Su, W., & Zhuo, Y. (2016) · Molecular Neurobiology · doi:10.1007/s12035-016-9793-6 · Cited by 173
Systematic identification of silencers in human cells
Pang, B., & Snyder, M. P. (2020) · Nature Genetics · doi:10.1038/s41588-020-0578-5 · Cited by 183
Chujo, T., Yamazaki, T., & Hirose, T. (2015) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2015.05.007 · Cited by 174
The landscape of antisense gene expression in human cancersPreprint
Balbin, O. A., Malik, R., Dhanasekaran, S. M., Prensner, J. R., Cao, X., Wu, Y.-M., Robinson, D. R., Wang, R., Chen, G., Beer, D. G., et al. (2015) · Genome Research · doi:10.1101/gr.180596.114 · Cited by 174
Emerging roles of long non-coding RNAs in plant response to biotic and abiotic stresses
Nejat, N., & Mantri, N. L. (2017) · Critical Reviews in Biotechnology · doi:10.1080/07388551.2017.1312270 · Cited by 171
The Role of Transposable Elements in Health and Diseases of the Central Nervous System
Reilly, M. T., Faulkner, G. J., Dubnau, J., Ponomarev, I., & Gage, F. H. (2013) · The Journal of Neuroscience · doi:10.1523/jneurosci.3369-13.2013 · Cited by 175
Noncoding RNAs and myocardial fibrosis
Thum, T. (2014) · Nature Reviews Cardiology · doi:10.1038/nrcardio.2014.125 · Cited by 173
Osteosarcoma Genetics and Epigenetics: Emerging Biology and Candidate Therapies
Morrow, J. J., & Khanna, C. (2015) · Critical Reviews™ in Oncogenesis · doi:10.1615/critrevoncog.2015013713 · Cited by 176
Lnc RNA ‐ ATB : An indispensable cancer‐related long noncoding RNA
Li, J., Li, Z., Zheng, W., Li, X., Wang, Z., Cui, Y., & Jiang, X. (2017) · Cell Proliferation · doi:10.1111/cpr.12381 · Cited by 172
LncRNAs in vascular biology and disease
Simion, V., Haemmig, S., & Feinberg, M. W. (2018) · Vascular Pharmacology · doi:10.1016/j.vph.2018.01.003 · Cited by 174
Divergent Transcription: A Driving Force for New Gene Origination?
Wu, X., & Sharp, P. A. (2013) · Cell · doi:10.1016/j.cell.2013.10.048 · Cited by 180
Marques, A. C., Hughes, J. R., Graham, B., Kowalczyk, M. S., Higgs, D. R., & Ponting, C. P. (2013) · Genome biology · doi:10.1186/gb-2013-14-11-r131 · Cited by 178
Kornienko, A. E., Dotter, C. P., Guenzl, P. M., Gisslinger, H., Gisslinger, B., Cleary, C., Královics, R., Pauler, F. M., & Barlow, D. P. (2016) · Genome biology · doi:10.1186/s13059-016-0873-8 · Cited by 172
RNA editing in nascent RNA affects pre-mRNA splicingPreprint
Hsiao, Y.-H. E., Bahn, J. H., Yang, Y., Lin, X., Tran, S. S., Yang, E.-W., Quinones-Valdez, G., & Xiao, X. G. (2018) · Genome Research · doi:10.1101/gr.231209.117 · Cited by 166
Widespread purifying selection on RNA structure in mammals
Smith, M. A., Gesell, T., Stadler, P. F., & Mattick, J. S. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt596 · Cited by 178
Jeziorska, D. M., Murray, R. J. S., De Gobbi, M., Gaentzsch, R., Garrick, D., Ayyub, H., Chen, T., Li, E., Telenius, J., Lynch, M., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1703087114 · Cited by 166
Transcriptome-wide discovery of coding and noncoding RNA-binding proteins
Huang, R., Han, M., Meng, L., & Chen, X. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1718406115 · Cited by 163
Self-citationProgress Towards RNAi-Mediated Insect Pest Management
Baum, J. A., & Roberts, J. K. (2014) · Advances in insect physiology · doi:10.1016/b978-0-12-800197-4.00005-1 · Cited by 168
On the importance of cotranscriptional RNA structure formation
Lai, D., Proctor, J. R., & Meyer, I. M. (2013) · RNA · doi:10.1261/rna.037390.112 · Cited by 167
Physiological roles of long noncoding RNAs: insight from knockout mice
Li, L., & Chang, H. Y. (2014) · Trends in Cell Biology · doi:10.1016/j.tcb.2014.06.003 · Cited by 167
Epigenetics of breast cancer: Biology and clinical implication in the era of precision medicine
Pasculli, B., Barbano, R., & Parrella, P. (2018) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2018.01.007 · Cited by 174
Han, S., Liang, Y., Ma, Q., Xu, Y., Zhang, Y., Du, W., Wang, C., & Li, Y. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bby065 · Cited by 165
Multi-species annotation of transcriptome and chromatin structure in domesticated animals
Foissac, S., Djebali, S., Munyard, K., Vialaneix, N., Rau, A., Muret, K., Esquerré, D., Zytnicki, M., Derrien, T., Bardou, P., et al. (2019) · BMC Biology · doi:10.1186/s12915-019-0726-5 · Cited by 162
Self-citationUniform, optimal signal processing of mapped deep-sequencing data
Kumar, V., Muratani, M., Rayan, N. A., Kraus, P., Lufkin, T., Ng, H., & Prabhakar, S. (2013) · Nature Biotechnology · doi:10.1038/nbt.2596 · Cited by 161
A pathophysiological view of the long non-coding RNA world
Gesualdo, F. D., Capaccioli, S., & Lulli, M. (2014) · Oncotarget · doi:10.18632/oncotarget.2770 · Cited by 169
Regulation of pri-miRNA Processing by a Long Noncoding RNA Transcribed from an Ultraconserved Region
Liz, J., Portela, A., Soler, M., Gómez, A., Ling, H. Y., Michlewski, G., Călin, G. A., Guil, S., & Esteller, M. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.05.005 · Cited by 169
Farkas, M. H., Grant, G. R., White, J., Sousa, M. E., Consugar, M. B., & Pierce, E. A. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-486 · Cited by 169
How We Think about Targeting RNA with Small Molecules
Costales, M. G., Childs‐Disney, J. L., Haniff, H. S., & Disney, M. D. (2020) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.9b01927 · Cited by 164
Targeted sequencing for gene discovery and quantification using RNA CaptureSeq
Mercer, T. R., Clark, M. B., Crawford, J., Brunck, M. E. G., Gerhardt, D. J., Taft, R. J., Nielsen, L. K., Dinger, M. E., & Mattick, J. S. (2014) · Nature Protocols · doi:10.1038/nprot.2014.058 · Cited by 169
Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing
Clark, M. B., Mercer, T. R., Bussotti, G., Leonardi, T., Haynes, K., Crawford, J., Brunck, M. E. G., Cao, K. L., Thomas, G. P., Chen, W. Y., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3321 · Cited by 173
Epigenetic regulation: A new frontier for biomedical engineers
Chen, Z., Li, S., Subramaniam, S., Shyy, J. Y.-J., & Chien, S. (2017) · Annual Review of Biomedical Engineering · doi:10.1146/annurev-bioeng-071516-044720 · Cited by 163
Role of miRNA and lncRNAs in organ fibrosis and aging
Ghafouri‐Fard, S., Abak, A., Talebi, S. F., Shoorei, H., Branicki, W., Taheri, M. N., & Dilmaghani, N. A. (2021) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2021.112132 · Cited by 162
A meta-analysis of the genomic and transcriptomic composition of complex life
Liu, G., Mattick, J. S., & Taft, R. J. (2013) · Cell Cycle · doi:10.4161/cc.25134 · Cited by 171
Nascent RNA sequencing reveals distinct features in plant transcription
Hetzel, J., Duttke, S. H. C., Benner, C. W., & Chory, J. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1603217113 · Cited by 158
Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners?
Lee, H., Zhang, Z., & Krause, H. M. (2019) · Trends in Genetics · doi:10.1016/j.tig.2019.09.006 · Cited by 164
Gene regulatory network inference resources: A practical overview
Mercatelli, D., Scalambra, L., Triboli, L., Ray, F., & Giorgi, F. M. (2019) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2019.194430 · Cited by 169
Origins of De Novo Genes in Human and Chimpanzee
Ruiz-Orera, J., Hernandez-Rodriguez, J., Chiva, C., Sabidó, E., Kondova, I., Bontrop, R., Marqués-Bonet, T., & Albà, M. M. (2015) · PLOS Genetics · doi:10.1371/journal.pgen.1005721 · Cited by 160
Long noncoding RNAs: new insights into non-small cell lung cancer biology, diagnosis and therapy
Ricciuti, B., Mencaroni, C., Paglialunga, L., Paciullo, F., Crinò, L., Chiari, R., & Metro, G. (2016) · Medical Oncology · doi:10.1007/s12032-016-0731-2 · Cited by 157
The RNA Atlas expands the catalog of human non-coding RNAs
Lorenzi, L., Chiu, H.-S., Avila Cobos, F., Gross, S., Volders, P.-J., Cannoodt, R., Nuytens, J., Vanderheyden, K., Anckaert, J., Lefever, S., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-021-00936-1 · Cited by 163
Paulsen, M. T., Veloso, A., Prasad, J., Bedi, K., Ljungman, E. A., Tsan, Y.-C., Chang, C., Tarrier, B., Washburn, J. G., Lyons, R., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1219192110 · Cited by 162
Mapping RNA–RNA interactome and RNA structure in vivo by MARIO
Nguyen, T. C., Cao, X., Yu, P., Shu Dong, X. I. A. O., Lu, J., Biase, F. H., Sridhar, B., Huang, N., Zhang, K., & Zhong, S. (2016) · Nature Communications · doi:10.1038/ncomms12023 · Cited by 164
DNA methylation and microRNA biomarkers for noninvasive detection of gastric and colorectal cancer
Toiyama, Y., Okugawa, Y., & Goel, A. (2014) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2014.08.001 · Cited by 159
Universal Alternative Splicing of Noncoding Exons
Deveson, I. W., Brunck, M. E. G., Blackburn, J., Tseng, E., Hon, T., Clark, T. A., Clark, M. B., Crawford, J., Dinger, M. E., Nielsen, L. K., et al. (2018) · Cell Systems · doi:10.1016/j.cels.2017.12.005 · Cited by 155
The role of lncRNAs and circRNAs in the PD-1/PD-L1 pathway in cancer immunotherapy
Jiang, W., Pan, S., Chen, X., Wang, Z. P., & Zhu, X. (2021) · Molecular Cancer · doi:10.1186/s12943-021-01406-7 · Cited by 162
Self-citationNie, F., Yu, X., Huang, M., Wang, Y., Xie, M., Ma, H., Wang, Z., De, W., & Sun, M. (2016) · Oncotarget · doi:10.18632/oncotarget.9611 · Cited by 155
Controlling nuclear RNA levels
Schmid, M., & Jensen, T. H. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0013-2 · Cited by 154
When Long Noncoding Becomes Protein Coding
Hartford, C. C. R., & Lal, A. (2020) · Molecular and Cellular Biology · doi:10.1128/mcb.00528-19 · Cited by 160
Diversification of human plasmacytoid predendritic cells in response to a single stimulus
Alculumbre, S. G., Saint‐André, V., Domizio, J. D., Vargas, P., Sirven, P., Bost, P., Maurin, M., Maiuri, P., Wéry, M., Jouve, M. J., et al. (2017) · Nature Immunology · doi:10.1038/s41590-017-0012-z · Cited by 164
Anthrax Susceptibility: Human Genetic Polymorphisms Modulating ANTXR2 Expression
Zhang, Z., Zhang, Y., Shi, M., Ye, B., Shen, W., Li, P., Xing, L., Zhang, X., Hou, L., Xu, J., et al. (2015) · Toxins · doi:10.3390/toxins8010001 · Cited by 152
The lncRNA DEANR1 Facilitates Human Endoderm Differentiation by Activating FOXA2 Expression
Jiang, W., Liu, Y., Liu, R., Zhang, K., & Zhang, Y. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.03.008 · Cited by 153
Jadaliha, M., Gholamalamdari, O., Tang, W., Zhang, Y., Petracovici, A., Hao, Q., Tariq, A., Kim, T. G., Holton, S. E., Singh, D. K., et al. (2018) · PLoS Genetics · doi:10.1371/journal.pgen.1007802 · Cited by 154
Long Noncoding RNA and Epithelial Mesenchymal Transition in Cancer
Gugnoni, M., & Ciarrocchi, A. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20081924 · Cited by 149
The long non-coding RNA HNF1A-AS1 regulates proliferation and metastasis in lung adenocarcinoma
Wu, Y., Liu, H., Shi, X., Yao, Y., Yang, W., & Song, Y. (2015) · Oncotarget · doi:10.18632/oncotarget.3247 · Cited by 149
Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes
Huang, S., Chen, Z., Yan, X., Yu, T., Huang, G., Yan, Q., Pontarotti, P., Zhao, H., Li, J., Yang, P. S., et al. (2014) · Nature Communications · doi:10.1038/ncomms6896 · Cited by 156
Kishore, S., Gruber, A. R., Jedlinski, D., Syed, A. P., Jorjani, H., & Zavolan, M. (2013) · Genome biology · doi:10.1186/gb-2013-14-5-r45 · Cited by 150
A comprehensive overview of lncRNA annotation resources
Xu, J., Bai, J., Zhang, X., Lv, Y., Gong, Y., Liu, L., Zhao, H., Yu, F., Ping, Y., Zhang, G., et al. (2016) · Briefings in Bioinformatics · doi:10.1093/bib/bbw015 · Cited by 149
Misawa, A., Takayama, K., Urano, T., & Inoue, S. (2016) · Journal of Biological Chemistry · doi:10.1074/jbc.m116.718536 · Cited by 151
Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH)
Helwak, A., & Tollervey, D. W. (2014) · Nature Protocols · doi:10.1038/nprot.2014.043 · Cited by 160
Li, S., Huang, Y., Huang, Y., Fu, Y., Tang, D., Kang, R., Zhou, R., & Fan, X. (2017) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-017-0519-z · Cited by 149
The emerging role of lncRNAs in inflammatory bowel disease
Yarani, R., Mirza, A. H., Kaur, S., & Pociot, F. (2018) · Experimental & Molecular Medicine · doi:10.1038/s12276-018-0188-9 · Cited by 147
Huang, M., Hou, J., Wang, Y., Xie, M., Wei, C., Nie, F., Wang, Z., & Sun, M. (2017) · Molecular Therapy · doi:10.1016/j.ymthe.2017.01.017 · Cited by 147
RetractedA multiregional proteomic survey of the postnatal human brain
Carlyle, B. C., Kitchen, R. R., Kanyo, J. E., Voss, E. Z., Pletikos, M., Sousa, A. M. M., Lam, T. T., Gerstein, M. B., Sestan, N., & Nairn, A. C. (2017) · Nature Neuroscience · doi:10.1038/s41593-017-0011-2 · Cited by 143
Self-citationCryo-EM advances in RNA structure determination
Ma, H., Jia, X., Zhang, K., & Su, Z. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-00916-0 · Cited by 151
Rise of the RNA Machines: Exploring the Structure of Long Non-Coding RNAs
Novikova, I. V., Hennelly, S. P., Tung, C., & Sanbonmatsu, K. Y. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.02.030 · Cited by 153
Millan, M. J. (2017) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2017.03.004 · Cited by 151
Lin, C., Zhang, S., Wang, Y., Wang, Y., Nice, E. C., Guo, C., Zhang, E., Yu, L., Li, M., Liu, C., et al. (2017) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-17-1851 · Cited by 146
Efficient and accurate detection of splice junctions from RNA-seq with Portcullis
Mapleson, D., Venturini, L., Kaithakottil, G., & Swarbreck, D. (2018) · GigaScience · doi:10.1093/gigascience/giy131 · Cited by 141
Characterization and identification of long non-coding RNAs based on feature relationship
Wang, G., Yin, H., Li, B., Yu, C., Wang, F., Xu, X., Cao, J., Bào, Y., Wang, L., Abbasi, A. A., et al. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz008 · Cited by 146
A comprehensive profile of circulating RNAs in human serum
Umu, S. U., Langseth, H., Bucher-Johannessen, C., Fromm, B., Keller, A., Meese, E. U., Lauritzen, M., Leithaug, M., Lyle, R., & Rounge, T. B. (2017) · RNA Biology · doi:10.1080/15476286.2017.1403003 · Cited by 149
Ahmed, A. S. I., Dong, K., Liu, J., Wen, T., Yu, L., Xu, F., Kang, X., Osman, I., Hu, G., Bunting, K. M., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1803725115 · Cited by 145
Self-citationThe lncRNA lincNMR regulates nucleotide metabolism via a YBX1 - RRM2 axis in cancer
Gandhi, M., Groß, M., Holler, J. M., Coggins, S. A., Patil, N., Leupold, J. H., Munschauer, M., Schenone, M., Hartigan, C. R., Allgayer, H., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-17007-9 · Cited by 143
Spliced synthetic genes as internal controls in RNA sequencing experiments
Hardwick, S. A., Chen, W. Y., Wong, T., Deveson, I. W., Blackburn, J., Andersen, S. B., Nielsen, L. K., Mattick, J. S., & Mercer, T. R. (2016) · Nature Methods · doi:10.1038/nmeth.3958 · Cited by 144
High-throughput single-base resolution mapping of RNA 2΄-O-methylated residues
Incarnato, D., Anselmi, F., Morandi, E., Neri, F., Maldotti, M., Rapelli, S., Parlato, C., Basile, G., & Oliviero, S. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw810 · Cited by 145
Liu, T., Chi, H., Chen, J., Chen, C., Huang, Y., Xi, H., Xue, J. F., & Si, Y. (2017) · Gene · doi:10.1016/j.gene.2017.08.008 · Cited by 144
Shi, L., Zhang, Z., Yu, A. M., Wang, W., Wei, Z., Akhter, E., Maurer, K., Costa‐Reis, P., Song, L., Petri, M., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0093846 · Cited by 142
Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling
Raj, A., Wang, S. H., Shim, H., Harpak, A., Li, Y., Engelmann, B. W., Stephens, M., Gilad, Y., & Pritchard, J. K. (2016) · eLife · doi:10.7554/elife.13328 · Cited by 148
Ogami, K., Richard, P., Chen, Y., Hoque, M., Li, W., Moresco, J. J., Yates, J. R., Tian, B., & Manley, J. L. (2017) · Genes & Development · doi:10.1101/gad.302604.117 · Cited by 149
Knauss, J. L., & Sun, T. (2013) · Neuroscience · doi:10.1016/j.neuroscience.2013.01.022 · Cited by 144
Cai, B., Li, Z., Ma, M., Wang, Z., Han, P., Abdalla, B. A., Nie, Q., & Zhang, X. (2017) · Frontiers in Physiology · doi:10.3389/fphys.2017.00230 · Cited by 142
Regulation and signaling pathways in cancer stem cells: implications for targeted therapy for cancer
Zeng, Z., Fu, M., Hu, Y., Wei, Y., Wei, X., & Luo, M. (2023) · Molecular Cancer · doi:10.1186/s12943-023-01877-w · Cited by 155
Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity
Yao, F., Kausalya, J. P., Sia, Y. Y., Teo, A. S. M., Lee, W. H., Ong, A. G. M., Zhang, Z., Tan, J. H. J., Li, G., Bertrand, D., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.06.020 · Cited by 141
Self-citationPROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration
Crappé, J., Ndah, E., Koch, A., Steyaert, S., Fijałkowska, D., Keulenaer, S. D., Meester, E. D., Meyer, T. D., Criekinge, W. V., Damme, P. V., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1283 · Cited by 140
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
