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 1,451
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)
Cited by
Sorted by citations
Items 701–800 of 1,018
Long Non-Coding RNAs: A Novel Paradigm for Toxicology
Dempsey, J. L., & Cui, J. Y. (2016) · Toxicological Sciences · doi:10.1093/toxsci/kfw203 · Cited by 105
Sequence Determinants for Nuclear Retention and Cytoplasmic Export of mRNAs and lncRNAs
Palazzo, A. F., & Lee, E. S. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00440 · Cited by 107
Regulatory roles of long noncoding RNAs implicated in cancer hallmarks
Wang, J., Zhang, X., Chen, W., Hu, X., Li, J., & Liu, C. (2019) · International Journal of Cancer · doi:10.1002/ijc.32277 · Cited by 102
Long non-coding RNAs in innate and adaptive immunity
Aune, T. M., & Spurlock, C. F. (2015) · Virus Research · doi:10.1016/j.virusres.2015.07.003 · Cited by 105
Paradigm shifts in genomics through the FANTOM projects
de Hoon, M., Shin, J. W., & Carninci, P. (2015) · Mammalian Genome · doi:10.1007/s00335-015-9593-8 · Cited by 101
Self-citationSun, L., Li, Y., & Yang, B. (2016) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2016.05.031 · Cited by 100
Understanding the Functions of Long Non-Coding RNAs through Their Higher-Order Structures
Li, R., Zhu, H., & Luo, Y. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17050702 · Cited by 100
Co-regulation of paralog genes in the three-dimensional chromatin architecture
Ibn-Salem, J., Muro, E. M., & Andrade-Navarro, M. A. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw813 · Cited by 101
LncRNA MALAT1 promotes development of mantle cell lymphoma by associating with EZH2
Wang, X., Sehgal, L., Jain, N. K., Khashab, T., Mathur, R., & Samaniego, F. (2016) · Journal of Translational Medicine · doi:10.1186/s12967-016-1100-9 · Cited by 101
Sun, Y., Wei, G., Luo, H., Wu, W., Skogerbø, G., Luo, J., & Chen, R. (2017) · Oncogene · doi:10.1038/onc.2017.286 · Cited by 101
Dong, P., Xiong, Y., Yue, J., Hanley, S. J. B., Kobayashi, N., Todo, Y., & Watari, H. (2019) · Cancers · doi:10.3390/cancers11020234 · Cited by 102
Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome
Martinez-Ara, M., Comoglio, F., van Arensbergen, J., & van Steensel, B. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.04.009 · Cited by 101
Zucchelli, S., Fasolo, F., Russo, R., Cimatti, L., Patrucco, L., Takahashi, H., Jones, M. H., Santoro, C., Sblattero, D., Cotella, D., et al. (2015) · Frontiers in Cellular Neuroscience · doi:10.3389/fncel.2015.00174 · Cited by 101
Self-citationMicroRNAs in platelet production and activation
Edelstein, L. C., McKenzie, S. E., Shaw, C. A., Holinstat, M. A., Kunapuli, S. P., & Bray, P. F. (2013) · Journal of Thrombosis and Haemostasis · doi:10.1111/jth.12214 · Cited by 103
Unveiling the hidden function of long non-coding RNA by identifying its major partner-protein
Yang, Y., Wen, L., & Zhu, H. (2015) · Cell & Bioscience · doi:10.1186/s13578-015-0050-x · Cited by 101
Long Non-Coding RNAs: New Players in Hematopoiesis and Leukemia
Morlando, M., Ballarino, M., & Fatica, A. (2015) · Frontiers in Medicine · doi:10.3389/fmed.2015.00023 · Cited by 100
Wang, W., Gao, Z., Wang, H., Li, T., He, W., Lv, W., & Zhang, J. (2016) · Scientific Reports · doi:10.1038/srep26604 · Cited by 101
Self-citationNon-coding RNAs in homeostasis, disease and stress responses: an evolutionary perspective
Amaral, P., Dinger, M. E., & Mattick, J. S. (2013) · Briefings in Functional Genomics · doi:10.1093/bfgp/elt016 · Cited by 103
Long noncoding RNAs in spermatogenesis: insights from recent high-throughput transcriptome studies
Luk, A. C. S., Chan, W., Rennert, O. M., & Lee, T. (2014) · Reproduction · doi:10.1530/rep-13-0594 · Cited by 99
Yamanaka, Y., Faghihi, M. A., Magistri, M., Álvarez-García, Ó., Lotz, M., & Wahlestedt, C. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.04.011 · Cited by 100
Doose, G., Haake, A., Bernhart, S. H., López, C., Duggimpudi, S., Wojciech, F., Bergmann, A. K., Borkhardt, A., Burkhardt, B., Claviez, A., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1505753112 · Cited by 100
LncRNA-ID: Long non-coding RNA IDentification using balanced random forests
Achawanantakun, R., Chen, J., Sun, Y., & Zhang, Y. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv480 · Cited by 102
Roles for long non-coding RNAs in physiology and disease
Melissari, M., & Grote, P. (2016) · Pflügers Archiv - European Journal of Physiology · doi:10.1007/s00424-016-1804-y · Cited by 103
MechRNA: prediction of lncRNA mechanisms from RNA–RNA and RNA–protein interactions
Gawronski, A., Uhl, M., Zhang, Y., Lin, Y., Niknafs, Y. S., Ramnarine, V. R., Malik, R., Feng, F. Y.-C., Chinnaiyan, A. M., Collins, C. C., et al. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty208 · Cited by 99
A myriad of roles of miR-25 in health and disease
Sárközy, M., Kahán, Z., & Csont, T. (2018) · Oncotarget · doi:10.18632/oncotarget.24662 · Cited by 99
Long noncoding RNAs: a missing link in osteoporosis
da Silva, A. M., Moura, S. R., Teixeira, J. H., Barbosa, M. A., Santos, S. G., & Almeida, M. I. (2019) · Bone Research · doi:10.1038/s41413-019-0048-9 · Cited by 99
Saeinasab, M., Bahrami, A. R., González, J., Marchese, F. P., Martínez, D., Mowla, S. J., Matin, M. M., & Huarte, M. (2019) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-019-1169-0 · Cited by 99
Single-molecule fluorescence in situ hybridization: Quantitative imaging of single RNA molecules
Kwon, S. (2013) · BMB Reports · doi:10.5483/bmbrep.2013.46.2.016 · Cited by 98
Epigenetics, chromatin and genome organization: recent advances from the ENCODE project
Siggens, L., & Ekwall, K. (2014) · Journal of Internal Medicine · doi:10.1111/joim.12231 · Cited by 105
Gao, W., Xiao, R.-Q., Zhang, W., Hu, Y., Peng, B., Li, W., He, Y., Shen, H., Ding, J., Huang, Q.-X., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.03.006 · Cited by 101
The Role of Long Noncoding RNAs in Central Nervous System and Neurodegenerative Diseases
Wei, C.-W., Luo, T., Zou, S.-S., & Wu, A. (2018) · Frontiers in Behavioral Neuroscience · doi:10.3389/fnbeh.2018.00175 · Cited by 104
MaTAR25 lncRNA regulates the Tensin1 gene to impact breast cancer progression
Chang, K.-C., Diermeier, S. D., Yu, A. T., Brine, L., Russo, S., Bhatia, S., Alsudani, H., Kostroff, K. M., Bhuiya, T. A., Brogi, E., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-20207-y · Cited by 98
Adoptive Immunotherapy beyond CAR T-Cells
Titov, A., Zmievskaya, E., Ganeeva, I., Valiullina, A., Petukhov, A., Rakhmatullina, A., Рифкатовна, М. Р., Fainshtein, M., Rizvanov, A. A., & Bulatov, E. (2021) · Cancers · doi:10.3390/cancers13040743 · Cited by 101
Casanova, M., Pasternak, M., Marjou, F. E., Baccon, P. L., Probst, A. V., & Almouzni, G. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.08.015 · Cited by 106
Long noncoding RNA EWSAT1-mediated gene repression facilitates Ewing sarcoma oncogenesis
Marques, M. R., Simpson, D. R., Ngok, S. P., Nieves, B., Ron, C., Siprashvili, Z., Vaka, D., Breese, M. R., Crompton, B. D., Alexe, G., et al. (2014) · Journal of Clinical Investigation · doi:10.1172/jci72124 · Cited by 102
Cui, M., Zheng, M., Sun, B., Wang, Y., Ye, L., & Zhang, X. (2015) · Neoplasia · doi:10.1016/j.neo.2014.11.004 · Cited by 97
Long noncoding RNAs and prostate carcinogenesis: the missing ‘linc’?
Walsh, A. L., Tuzova, A. V., Bolton, E. M., Lynch, T. H., & Perry, A. S. (2014) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2014.03.005 · Cited by 101
Expression of androgen receptor splice variants in clinical breast cancers
Hickey, T. E., Irvine, C. M., Dvinge, H., Tarulli, G. A., Hanson, A. R., Ryan, N. K., Pickering, M. A., Birrell, S. N., Hu, D. G., Mackenzie, P. I., et al. (2015) · Oncotarget · doi:10.18632/oncotarget.6296 · Cited by 99
Zang, C., Nie, F., Wang, Q., Sun, M., Li, W., He, J., Zhang, M., & Lu, K. (2016) · Oncotarget · doi:10.18632/oncotarget.7077 · Cited by 97
Major Tumor Suppressor and Oncogenic Non-Coding RNAs: Clinical Relevance in Lung Cancer
Inamura, K. (2017) · Cells · doi:10.3390/cells6020012 · Cited by 100
Small non‐coding RNA and colorectal cancer
Chen, H., Xu, Z., & Liu, D. (2019) · Journal of Cellular and Molecular Medicine · doi:10.1111/jcmm.14209 · Cited by 97
MicroRNAs: Biological Regulators in Pathogen–Host Interactions
Acuña, S. M., Floeter‐Winter, L. M., & Muxel, S. M. (2020) · Cells · doi:10.3390/cells9010113 · Cited by 96
Understanding Celiac Disease by Genomics
Withoff, S., Li, Y., Jonkers, I. H., & Wijmenga, C. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.02.003 · Cited by 96
Functional significance of aberrantly expressed microRNAs in prostate cancer
Goto, Y., Kurozumi, A., Enokida, H., Ichikawa, T., & Seki, N. (2015) · International Journal of Urology · doi:10.1111/iju.12700 · Cited by 97
MOURAVIEV, V. B., Lee, B., Patel, V., Albala, D., Johansen, T. E. B., Partin, A. W., Ross, A. E., & Perera, R. J. (2015) · Prostate Cancer and Prostatic Diseases · doi:10.1038/pcan.2015.48 · Cited by 96
Evaluating risks of insertional mutagenesis by DNA transposons in gene therapy
Hackett, P. B., Largaespada, D. A., Switzer, K. C., & Cooper, L. J. N. (2013) · Translational research · doi:10.1016/j.trsl.2012.12.005 · Cited by 97
Distinct lncRNA transcriptional fingerprints characterize progressive stages of multiple myeloma
Ronchetti, D., Agnelli, L., Taìana, E., Galletti, S., Manzoni, M., Todoerti, K., Musto, P., Strozzi, F., & Neri, A. (2016) · Oncotarget · doi:10.18632/oncotarget.7442 · Cited by 96
Yu, B., Ye, X., Du, Q., Zhu, B., & Zhai, Q. (2017) · Cellular Physiology and Biochemistry · doi:10.1159/000475941 · Cited by 96
Hah, N., & Kraus, W. L. (2013) · Molecular and Cellular Endocrinology · doi:10.1016/j.mce.2013.06.021 · Cited by 101
Short-term memory of danger signals and environmental stimuli in immune cells
Monticelli, S., & Natoli, G. (2013) · Nature Immunology · doi:10.1038/ni.2636 · Cited by 92
A FTH1 gene:pseudogene:microRNA network regulates tumorigenesis in prostate cancer
Chan, J. J., Kwok, Z. H., Chew, X. H., Zhang, B., Liu, C., Soong, T. W., Yang, H. H., & Tay, Y. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1248 · Cited by 98
Silla, T., Karadoulama, E., Mąkosa, D., Lubas, M., & Jensen, T. H. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.04.061 · Cited by 95
Dong, X., Liao, Z., Gritsch, D., Hadzhiev, Y., Bai, Y., Locascio, J. J., Guennewig, B., Liu, G., Blauwendraat, C., Wang, T., et al. (2018) · Nature Neuroscience · doi:10.1038/s41593-018-0223-0 · Cited by 97
Ferreira, R. G., Cardoso, M. V., Furtado, K. M. D. S., Espíndola, K. M. M., Amorim, R. P., & Monteiro, M. C. (2018) · Translational research · doi:10.1016/j.trsl.2018.09.001 · Cited by 95
Long Non-Coding RNA and Breast Cancer
Zhang, T., Hu, H., Ge, Y., Wu, T., Liu, S., Chen, W., Ning, Y., & Lu, Z. (2019) · Technology in Cancer Research & Treatment · doi:10.1177/1533033819843889 · Cited by 98
Κhan, P., Siddiqui, J. A., Kshirsagar, P., Venkata, R. C., Maurya, S. K., Mirzapoiazova, T., Perumal, N., Chaudhary, S., Kanchan, R. K., Fatima, M., et al. (2023) · Molecular Cancer · doi:10.1186/s12943-022-01695-6 · Cited by 96
Noncoding RNAs and Atherosclerosis
Aryal, B. K., Rotllán, N., & Fernandez-Hernando, C. F. (2014) · Current Atherosclerosis Reports · doi:10.1007/s11883-014-0407-3 · Cited by 94
The splicing landscape is globally reprogrammed during male meiosis
Schmid, R., Grellscheid, S. N., Ehrmann, I. E., Dalgliesh, C., Danilenko, M., Paronetto, M. P., Pedrotti, S., Grellscheid, D., Dixon, R. J., Sette, C., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt811 · Cited by 94
Transcriptional gene silencing in humans
Weinberg, M. S., & Morris, K. V. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw139 · Cited by 95
Reverse-genetics studies of lncRNAs—what we have learnt and paths forward
Gao, F., Cai, Y., Kapranov, P., & Xu, D. (2020) · Genome biology · doi:10.1186/s13059-020-01994-5 · Cited by 95
Self-citationRegulation of the ESC transcriptome by nuclear long noncoding RNAsPreprint
Bergmann, J. H., Li, J., Eckersley-Maslin, M. A., Rigo, F., Freier, S. M., & Spector, D. L. (2015) · Genome Research · doi:10.1101/gr.189027.114 · Cited by 93
Circulating DNA of HOTAIR in serum is a novel biomarker for breast cancer
Zhang, L., Song, X., Wang, X., Xie, Y., Wang, Z., Xu, Y., You, X., Liang, Z., & Cao, H. (2015) · Breast Cancer Research and Treatment · doi:10.1007/s10549-015-3431-2 · Cited by 93
Ballarino, M., Cazzella, V., D’Andrea, D., Grassi, L., Bisceglie, L., Cipriano, A., Santini, T., Pinnarò, C., Morlando, M., Tramontano, A. L., et al. (2014) · Molecular and Cellular Biology · doi:10.1128/mcb.01394-14 · Cited by 93
Leveraging the complementary nature of RNA‐Seq and shotgun proteomics data
Wang, X., Liu, Q., & Zhang, B. (2014) · PROTEOMICS · doi:10.1002/pmic.201400184 · Cited by 95
The role and possible mechanism of lncRNA U90926 in modulating 3T3-L1 preadipocyte differentiation
Chen, J., Liu, Y., Lu, S., Yin, L., Zong, C., Cui, S., Qin, D., Yang, Y., Guan, Q., Li, X., et al. (2016) · International Journal of Obesity · doi:10.1038/ijo.2016.189 · Cited by 93
The role of microRNAs in heart failure
Wang, H., & Cai, J. (2016) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2016.11.034 · Cited by 97
Self-citationCircular RNAs of the nucleophosmin (NPM1) gene in acute myeloid leukemia
Lux, S., Blätte, T. J., Grasedieck, S., Cocciardi, S., ROUHI, A. M., Jongen‐Lavrencic, M., Paschka, P., Krönke, J., Gaidzik, V. I., Döhner, H., et al. (2017) · Haematologica · doi:10.3324/haematol.2017.172866 · Cited by 93
Guo, J., Fang, W., Sun, L., Lu, Y., Dou, L., Huang, X., Tang, W., Yu, L., & Li, J. (2018) · Nature Communications · doi:10.1038/s41467-018-03072-8 · Cited by 94
Long non-coding RNA-dependent mechanism to regulate heme biosynthesis and erythrocyte development
Liu, J., Li, Y., Tong, J., Gao, J., Guo, Q., Zhang, L., Wang, B., Zhao, H., Wang, H., Jiang, E., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06883-x · Cited by 93
Self-citationRui, X., Xu, Y., Jiang, X., Ye, W., Huang, Y., & Jiang, J. (2018) · Cell Death and Disease · doi:10.1038/s41419-018-1228-z · Cited by 93
Xiao, J., Lin, L., Luo, D., Shi, L., Chen, W., Fan, H., Li, Z., Ma, X., Ni, P., Yang, L., et al. (2020) · Oncogenesis · doi:10.1038/s41389-020-0215-2 · Cited by 95
Reverse Remodeling With Left Ventricular Assist Devices
Burkhoff, D., Topkara, V. K., Sayer, G., & Uriel, N. (2021) · Circulation Research · doi:10.1161/circresaha.121.318160 · Cited by 98
Gao, Y., Wang, F., Wang, R., Kutschera, E., Xu, Y., Xie, S., Wang, Y., Kadash-Edmondson, K. E., Lin, L., & Xing, Y. (2023) · Science Advances · doi:10.1126/sciadv.abq5072 · Cited by 93
Coexpression networks identify brain region–specific enhancer RNAs in the human brain
Yao, P., Lin, P., Gokoolparsadh, A., Assareh, A. A., Thang, M. W. C., & Voineagu, I. (2015) · Nature Neuroscience · doi:10.1038/nn.4063 · Cited by 94
Databases for lncRNAs: a comparative evaluation of emerging tools
Fritah, S., Niclou, S. P., & Azuaje, F. J. (2014) · RNA · doi:10.1261/rna.044040.113 · Cited by 90
Tombácz, D., Csabai, Z., Oláh, P., Balázs, Z., Likó, I., Zsigmond, L., Sharon, D., Snyder, M. P., & Boldogkői, Z. (2016) · PLoS ONE · doi:10.1371/journal.pone.0162868 · Cited by 88
Long non-coding RNAs in osteosarcoma
Chen, R., Wang, G., Zheng, Y., Hua, Y., & Cai, Z. (2017) · Oncotarget · doi:10.18632/oncotarget.14726 · Cited by 93
Long noncoding RNA HAS2‐AS1 mediates hypoxia‐induced invasiveness of oral squamous cell carcinoma
Zhu, G., Wang, S., Chen, J., Wang, Z., Liang, X., Wang, X., Jiang, J., Lang, J., & Li, L. (2017) · Molecular Carcinogenesis · doi:10.1002/mc.22674 · Cited by 92
Du, Y., Weng, X., Wang, L., Liu, X., Zhu, H., Guo, J., Ning, J., & Xiao, C. (2017) · Oncotarget · doi:10.18632/oncotarget.21719 · Cited by 92
Luo, X., Qiu, Y., Jiang, Y., Chen, F., Jiang, L., Zhou, Y. J., Dan, H., Zeng, X. Y., Lei, Y. L., & Chen, Q. (2018) · Molecular Cancer · doi:10.1186/s12943-018-0763-7 · Cited by 92
SNHG5 Promotes Breast Cancer Proliferation by Sponging the miR-154-5p/PCNA Axis
Chi, J., Yu, Z., Liu, B., Zhang, D., Ge, J., Yu, Y., & Cao, X. (2019) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2019.05.013 · Cited by 92
Self-citationProduction of Spliced Long Noncoding RNAs Specifies Regions with Increased Enhancer Activity
Gil, N., & Ulitsky, I. (2018) · Cell Systems · doi:10.1016/j.cels.2018.10.009 · Cited by 88
Nuclear microenvironment in cancer: Control through liquid‐liquid phase separation
Nozawa, R., Yamamoto, T., Takahashi, M., Tachiwana, H., Maruyama, R., Hirota, T., & Saitoh, N. (2020) · Cancer Science · doi:10.1111/cas.14551 · Cited by 90
The role of ferroptosis in intervertebral disc degeneration
Fan, C., Chu, G., Yu, Z., Ji, Z., Kong, F., Yao, L., Wang, J., Geng, D., Wu, X., & Mao, H. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1219840 · Cited by 94
Ribosome-omics of the human ribosome
Gupta, V., & Warner, J. R. (2014) · RNA · doi:10.1261/rna.043653.113 · Cited by 101
SASP regulation by noncoding RNA
Panda, A. C., Abdelmohsen, K., & Gorospe, M. (2017) · Mechanisms of Ageing and Development · doi:10.1016/j.mad.2017.05.004 · Cited by 86
Laying a solid foundation for Manhattan – ‘setting the functional basis for the post-GWAS era’
Zhang, X., Bailey, S. D., & Lupien, M. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.02.006 · Cited by 95
Using microRNA Networks to Understand Cancer
Dragomir, M. P., Mafra, A. C. P., Dias, S. M. G., Vasilescu, C., & Călin, G. A. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19071871 · Cited by 93
The emerging role of noncoding RNAs in colorectal cancer chemoresistance
Wei, L., Wang, X., Lv, L., Zheng, Y., Zhang, N., & Yang, M. (2019) · Cellular Oncology · doi:10.1007/s13402-019-00466-8 · Cited by 88
Comprehensive Mechanism of Gene Silencing and Its Role in Plant Growth and Development
El‐Sappah, A. H., Yan, K., Huang, Q., Islam, M. M., Li, Q., Wang, Y., Khan, M. S., Xianming, Z., Mir, R. R., Li, J., et al. (2021) · Frontiers in Plant Science · doi:10.3389/fpls.2021.705249 · Cited by 95
Hamdy, N. Μ., Zaki, M. B., Rizk, N. I., Abdelmaksoud, N. M., Abd‐Elmawla, M. A., Abdelhamid, R., & Abulsoud, A. I. (2024) · Life Sciences · doi:10.1016/j.lfs.2024.122946 · Cited by 92
Self-citationSystematic classification of non-coding RNAs by epigenomic similarity
Dozmorov, M. G., Giles, C. B., Koelsch, K. A., & Wren, J. D. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-s14-s2 · Cited by 94
The dark matter rises: the expanding world of regulatory RNAs
Clark, M. B., Choudhary, A., Smith, M. A., Taft, R. J., & Mattick, J. S. (2013) · Essays in Biochemistry · doi:10.1042/bse0540001 · Cited by 96
De novo DNA demethylation and noncoding transcription define active intergenic regulatory elementsPreprint
Schlesinger, F. J., Smith, A. D., Gingeras, T., Hannon, G. J., & Hodges, E. C. (2013) · Genome Research · doi:10.1101/gr.157271.113 · Cited by 96
Self-citationZhang, H., Zhang, N., Liu, Y., Su, P., Liang, Y., Li, Y., Wang, X., Chen, T., Song, X., Sang, Y., et al. (2021) · Cancer Research · doi:10.1158/0008-5472.can-21-1188 · Cited by 92
From “Cellular” RNA to “Smart” RNA: Multiple Roles of RNA in Genome Stability and Beyond
Michelini, F., Jalihal, A. P., Francia, S., Meers, C., Neeb, Z. T., Rossiello, F., Gioia, U., Aguado, J., Jones-Weinert, C., Luke, B., et al. (2018) · Chemical Reviews · doi:10.1021/acs.chemrev.7b00487 · Cited by 85
Self-citationColombo, M., Blok, M. J., Whiley, P. J., Santamariña, M., Gutiérrez‐Enríquez, S., Romero, A., Garré, P., Becker, A. A., Smith, L., Vecchi, G. D., et al. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu075 · Cited by 97
Kelley, D. R., Hendrickson, D. G., Tenen, D. E., & Rinn, J. L. (2014) · Genome biology · doi:10.1186/s13059-014-0537-5 · Cited by 87
Zhang, R., Jin, H., & Lou, F. (2017) · Journal of Cellular Biochemistry · doi:10.1002/jcb.26021 · Cited by 89
Sun, X., Ali, M. S. S. H., & Moran, M. (2017) · Biochemical Journal · doi:10.1042/bcj20170280 · Cited by 90
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
