A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers
Open accessAbstract
Mammalian genomes are pervasively transcribed outside mapped protein-coding genes. One class of extragenic transcription products is represented by long non-coding RNAs (lncRNAs), some of which result from Pol_II transcription of bona-fide RNA genes. Whether all lncRNAs described insofar are products of RNA genes, however, is still unclear. Here we have characterized transcription sites located outside protein-coding genes in a highly regulated response, macrophage activation by endotoxin. Using chromatin signatures, we could unambiguously classify extragenic Pol_II binding sites as belonging to either canonical RNA genes or transcribed enhancers. Unexpectedly, 70% of extragenic Pol_II peaks were associated with genomic regions with a canonical chromatin signature of enhancers. Enhancer-associated extragenic transcription was frequently adjacent to inducible inflammatory genes, was regulated in response to endotoxin stimulation, and generated very low abundance transcripts. Moreover, transcribed enhancers were under purifying selection and contained binding sites for inflammatory transcription factors, thus suggesting their functionality. These data demonstrate that a large fraction of extragenic Pol_II transcription sites can be ascribed to cis-regulatory genomic regions. Discrimination between lncRNAs generated by canonical RNA genes and products of transcribed enhancers will provide a framework for experimental approaches to lncRNAs and help complete the annotation of mammalian genomes.
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
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 majority of active enhancers are themselves transcribed, producing enhancer RNAs in a bi-directional manner.
“The majority of active enhancers are themselves transcribed, producing enhancer RNAs (eRNAs) in a bi-directional manner [73–77].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [76]
The Discussion says that non-transcribed enhancers greatly outnumber transcribed ones, contrary to the claim that a majority are transcribed. The Introduction also gives an example of unidirectional enhancer-region transcription; this paper does not establish bidirectional production as the general pattern. No page numbers are available in our copy. (LLM, conf=0.90)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredEnhancers are sites for the assembly of a complete Pol II preinitiation complex and bidirectional transcription of short-lived enhancer RNA (eRNA).
“Relatively recently, enhancers have been shown to be sites for the assembly of a complete Pol II preinitiation complex and bidirectional transcription of short-lived enhancer RNA (eRNA) [57,58,59].”
From Enhancer Function in the 3D Genome (2023) · cites this paper as [57]
The Results section on inducible upstream transcripts reports Pol II-associated enhancer transcription and very unstable noncoding RNAs; the Discussion links transcriptional directionality to control of preinitiation-complex formation. But the paper does not establish assembly of a complete preinitiation complex. Its characterized Ccl5 transcripts are strand-specific, with no signal from the opposite strand, rather than bidirectional (page numbers unavailable in our copy). (LLM, conf=0.88)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386 · see citing works
Long non-coding RNAs: insights into functions
Mercer, T. R., Dinger, M. E., & Mattick, J. S. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2521 · Cited by 5,654 · see citing works
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223 · see citing works
Evolution and Functions of Long Noncoding RNAs
Ponting, C. P., Oliver, P. L., & Reik, W. (2009) · Cell · doi:10.1016/j.cell.2009.02.006 · Cited by 4,917 · see citing works
Shared Principles in NF-κB Signaling
Hayden, M. S., & Ghosh, S. (2008) · Cell · doi:10.1016/j.cell.2008.01.020 · Cited by 4,814 · see citing works
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 4,408 · cited 1× · see citing works
“mammals [62] to measure the degree of conservation in the”
BackgroundFunctional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs
Rinn, J. L., Kertesz, M., Wang, J. K., Squazzo, S. L., Xu, X. H., Brugmann, S. A., Goodnough, L. H., Helms, J. A., Farnham, P., Segal, E., et al. (2007) · Cell · doi:10.1016/j.cell.2007.05.022 · Cited by 4,246 · see citing works
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129 · see citing works
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D., Huarte, M., Zuk, O., Carey, B. W., Cassady, J. P., et al. (2009) · Nature · doi:10.1038/nature07672 · Cited by 4,098 · see citing works
Capturing Chromosome Conformation
Dekker, J., Rippe, K., Dekker, M., & Kleckner, N. (2002) · Science · doi:10.1126/science.1067799 · Cited by 3,652 · see citing works
The Transcriptional Landscape of the Mammalian Genome
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M. C., Maeda, N., Oyama, R., Ravasi, T., Lenhard, B., Wells, C. A., et al. (2005) · Science · doi:10.1126/science.1112014 · Cited by 3,492 · see citing works
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · cited 3× · see citing works
“Conversely, enhancers display high levels of H3K4me1, usually distributed over several kilobases, associated with low or no H3K4me3 (H3K4me1/H3K4me3 domains) [52,53].”
BackgroundHistone modifications at human enhancers reflect global cell-type-specific gene expression
Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature · doi:10.1038/nature07829 · Cited by 2,533 · see citing works
RNA 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
Long noncoding RNAs: functional surprises from the RNA worldPreprint
Wilusz, J. E., Sunwoo, H., & Spector, D. L. (2009) · Genes & Development · doi:10.1101/gad.1800909 · Cited by 2,298 · see citing works
A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells
Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R., & Young, R. A. (2007) · Cell · doi:10.1016/j.cell.2007.05.042 · Cited by 1,946 · see citing works
JASPAR: an open-access database for eukaryotic transcription factor binding profiles
Sandelin, A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh012 · Cited by 1,763 · see citing works
Antisense Transcription in the Mammalian Transcriptome
Katayama, S., Tomaru, Y., Kasukawa, T., Waki, K., Nakanishi, M., Nakamura, M., Nishida, H., Yap, C.-S., Suzuki, M., Kawai, J., et al. (2005) · Science · doi:10.1126/science.1112009 · Cited by 1,661 · see citing works
IRF Family of Transcription Factors as Regulators of Host Defense
Taniguchi, T., Ogasawara, K., Takaoka, A., & Tanaka, N. (2001) · Annual Review of Immunology · doi:10.1146/annurev.immunol.19.1.623 · Cited by 1,658 · see citing works
Requirement of transcription factor PU.1 in the development of multiple hematopoietic lineages
Scott, E. W., Simon, M. C., Anastasi, J., & Singh, H. (1994) · Science · doi:10.1126/science.8079170 · Cited by 1,532 · see citing works
Saxonov, S., Berg, P., & Brutlag, D. L. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510310103 · Cited by 1,401 · see citing works
Genome-wide analysis of mammalian promoter architecture and evolution
Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C. A. M., Taylor, M. S., Engström, P. G., Frith, M. C., et al. (2006) · Nature Genetics · doi:10.1038/ng1789 · Cited by 1,350 · see citing works
Carrozza, M. J., Li, B., Florens, L. A., Suganuma, T., Swanson, S. K., Lee, K. K., Shia, W.-J., Anderson, S., Yates, J. R., Washburn, M. P., et al. (2005) · Cell · doi:10.1016/j.cell.2005.10.023 · Cited by 1,297 · see citing works
Requirement for Xist in X chromosome inactivation
Penny, G. D., Kay, G. F., Sheardown, S. A., Rastan, S., & Brockdorff, N. (1996) · Nature · doi:10.1038/379131a0 · Cited by 1,254 · see citing works
Pandey, R. R., Mondal, T., Mohammad, F., Enroth, S., Redrup, L., Komorowski, J., Nagano, T., Mancini‐DiNardo, D., & Kanduri, C. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.08.022 · Cited by 1,192 · see citing works
Controlling the elongation phase of transcription with P-TEFb
Peterlin, B. M., & Price, D. H. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.06.014 · Cited by 1,144 · see citing works
Shilatifard, A. (2006) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.75.103004.142422 · Cited by 1,099 · see citing works
The non-coding Air RNA is required for silencing autosomal imprinted genes
Sleutels, F., Zwart, R., & Barlow, D. P. (2002) · Nature · doi:10.1038/415810a · Cited by 1,071 · see citing works
Diversity and Complexity in DNA Recognition by Transcription Factors
Badis, G., Berger, M., Philippakis, A. A., Talukder, S., Gehrke, A. R., Jaeger, S., Chan, E. T., Metzler, G., Vedenko, A., Chen, X., et al. (2009) · Science · doi:10.1126/science.1162327 · Cited by 1,031 · see citing works
Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription
Wang, X., Arai, S., Song, X., Reichart, D. R., Du, K., Pascual, G., Tempst, P., Rosenfeld, M. G., Glass, C. K., & Kurokawa, R. (2008) · Nature · doi:10.1038/nature06992 · Cited by 988 · see citing works
Requirement for Xist in X chromosome inactivation
(1996) · Trends in Genetics · doi:10.1016/0168-9525(96)81414-4 · Cited by 982 · see citing works
Divergent transcription from active promoters
Seila, A. C., Calabrese, J. M., Levine, S., Yeo, G. W., Rahl, P., Flynn, R. A., Young, R., & Sharp, P. (2008) · Science · doi:10.1126/science.1162253 · Cited by 923 · see citing works
The Air Noncoding RNA Epigenetically Silences Transcription by Targeting G9a to Chromatin
Nagano, T., Mitchell, J. A., Sanz, L. A., Pauler, F. M., Ferguson‐Smith, A. C., Feil, R., & Fraser, P. (2008) · Science · doi:10.1126/science.1163802 · Cited by 907 · see citing works
FACT Facilitates Transcription-Dependent Nucleosome Alteration
Belotserkovskaya, R., Oh, S., Bondarenko, V. A., Orphanides, G., Studitsky, V. M., & Reinberg, D. (2003) · Science · doi:10.1126/science.1085703 · Cited by 869 · see citing works
IRF3 Mediates a TLR3/TLR4-Specific Antiviral Gene Program
Doyle, S. E., Vaidya, S. A., O’Connell, R. M., Dadgostar, H., Dempsey, P. W., Wu, T., Rao, G., Sun, R., Haberland, M. E., Modlin, R. L., et al. (2002) · Immunity · doi:10.1016/s1074-7613(02)00390-4 · Cited by 845 · see citing works
Wyers, F., Rougemaille, M., Badis, G., Rousselle, J.-C., Dufour, M., Boulay, J., Regnault, B., Devaux, F., Namane, A., Séraphin, B., et al. (2005) · Cell · doi:10.1016/j.cell.2005.04.030 · Cited by 843 · see citing works
RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters
Preker, P., Nielsen, J. S., Kammler, S., Lykke‐Andersen, S., Christensen, M. S., Mapendano, C. K., Schierup, M. H., & Jensen, T. H. (2008) · Science · doi:10.1126/science.1164096 · Cited by 777 · see citing works
Regulation of B lymphocyte and macrophage development by graded expression of PU.1
DeKoter, R. P., & Singh, H. (2000) · Science · doi:10.1126/science.288.5470.1439 · Cited by 749 · see citing works
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAsPreprint
Ponjavic, J., Ponting, C. P., & Lunter, G. A. (2007) · Genome Research · doi:10.1101/gr.6036807 · Cited by 731 · see citing works
Genome-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
Feng, J., Bi, C., Clark, B. S., Mady, R., Shah, P., & Kohtz, J. D. (2006) · Genes & Development · doi:10.1101/gad.1416106 · Cited by 712 · see citing works
Ghisletti, S., Barozzi, I., Mietton, F., Polletti, S., De Santa, F., Venturini, E., Gregory, L., Lonie, L., Chew, A., Wei, C.-L., et al. (2010) · Immunity · doi:10.1016/j.immuni.2010.02.008 · Cited by 666 · see citing works
Self-citationTranscriptional noise and the fidelity of initiation by RNA polymerase II
Struhl, K. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb0207-103 · Cited by 643 · see citing works
Zhao, X. D., Han, X., Chew, J. L., Liu, J., Chiu, K. P., Choo, A. B. H., Orlov, Y. L., Sung, W.-K. K., Shahab, A., Kuznetsov, V. A., et al. (2007) · Cell stem cell · doi:10.1016/j.stem.2007.08.004 · Cited by 616 · see citing works
Self-citationIntergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene
Martens, J. A., Laprade, L., & Winston, F. (2004) · Nature · doi:10.1038/nature02538 · Cited by 594 · see citing works
Ramirez-Carrozzi, V. R., Braas, D., Bhatt, D. M., Cheng, C. S., Hong, C., Doty, K. R., Black, J. C., Hoffmann, A., Carey, M., & Smale, S. T. (2009) · Cell · doi:10.1016/j.cell.2009.04.020 · Cited by 581 · see citing works
The genomic landscape of histone modifications in human T cells
Roh, T., Cuddapah, S., Cui, K., & Zhao, K. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0607617103 · Cited by 496 · see citing works
A Novel Histone Acetyltransferase Is an Integral Subunit of Elongating RNA Polymerase II Holoenzyme
Wittschieben, B. Ø., Otero, G., de Bizemont, T., Fellows, J., Erdjument‐Bromage, H., Ohba, R., Li, Y., Allis, C. D., Tempst, P., & Svejstrup, J. Q. (1999) · Molecular Cell · doi:10.1016/s1097-2765(00)80194-x · Cited by 463 · see citing works
Sharp, P. A. (2009) · Cell · doi:10.1016/j.cell.2009.02.007 · Cited by 452 · see citing works
PU.1 induces myeloid lineage commitment in multipotent hematopoietic progenitors
Nerlov, C., & Graf, T. (1998) · Genes & Development · doi:10.1101/gad.12.15.2403 · Cited by 449 · see citing works
Detection of functional DNA motifs via statistical over-representation
Frith, M. C. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh299 · Cited by 424 · see citing works
Jmjd3 contributes to the control of gene expression in LPS‐activated macrophages
Santa, F. D., Narang, V., Yap, Z. H., Tusi, B. K., Burgold, T., Austenaa, L. M. I., Bucci, G., Cagánová, M., Notarbartolo, S., Casola, S. S., et al. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.271 · Cited by 422 · see citing works
Self-citationElongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genesPreprint
Mancini‐DiNardo, D., Steele, S. J., Levorse, J. M., Ingram, R. S., & Tilghman, S. M. (2006) · Genes & Development · doi:10.1101/gad.1416906 · Cited by 421 · see citing works
Transcription Regulation Through Promoter-Proximal Pausing of RNA Polymerase II
Core, L. J., & Lis, J. T. (2008) · Science · doi:10.1126/science.1150843 · Cited by 406 · see citing works
Eukaryotic regulatory RNAs: an answer to the ‘genome complexity’ conundrumPreprint
Prasanth, K. V., & Spector, D. L. (2007) · Genes & Development · doi:10.1101/gad.1484207 · Cited by 398 · see citing works
Transcription factories: gene expression in unions?
Sutherland, H. G. E., & Bickmore, W. A. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2592 · Cited by 380 · see citing works
Ponjavic, J., Oliver, P. L., Lunter, G. A., & Ponting, C. P. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000617 · Cited by 368 · see citing works
RNA Polymerase II Holoenzyme Contains SWI/SNF Regulators Involved in Chromatin Remodeling
Wilson, C. J., Chao, D. M., Imbalzano, A. N., Schnitzler, G. R., Kingston, R. E., & Young, R. A. (1996) · Cell · doi:10.1016/s0092-8674(00)80978-2 · Cited by 364 · see citing works
Camblong, J., Iglesias, N., Fickentscher, C., Dieppois, G., & Stutz, F. (2007) · Cell · doi:10.1016/j.cell.2007.09.014 · Cited by 354 · see citing works
Intergenic transcription and transinduction of the human beta-globin locus.Preprint
Ashe, H. L., Monks, J., Wijgerde, M., Fraser, P. J., & Proudfoot, N. (1997) · Genes & Development · doi:10.1101/gad.11.19.2494 · Cited by 350 · see citing works
Gribnau, J. H., Diderich, K. E. M., Pruzina, S., Calzolari, R., & Fraser, P. (2000) · Molecular Cell · doi:10.1016/s1097-2765(00)80432-3 · Cited by 338 · see citing works
A Human RNA Polymerase II Complex Containing Factors That Modify Chromatin Structure
Cho, H. K., Orphanides, G., Sun, X., Yang, X., Ogryzko, V. V., Lees, E. M., Nakatani, Y., & Reinberg, D. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.9.5355 · Cited by 277 · see citing works
Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs
Hirota, K., Miyoshi, T., Kugou, K., Hoffman, C. S., Shibata, T., & Ohta, K. (2008) · Nature · doi:10.1038/nature07348 · Cited by 275 · see citing works
Petruk, S., Sedkov, Y., Riley, K. M., Hodgson, J. W., Schweisguth, F., Hirose, S., Jaynes, J. B., Brock, H. W., & Mazo, A. (2006) · Cell · doi:10.1016/j.cell.2006.10.039 · Cited by 273 · see citing works
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness
Marques, A. C., & Ponting, C. P. (2009) · Genome biology · doi:10.1186/gb-2009-10-11-r124 · Cited by 255 · see citing works
Ripples from neighbouring transcription
Ebisuya, M., Yamamoto, T., Nakajima, M., & Nishida, E. (2008) · Nature Cell Biology · doi:10.1038/ncb1771 · Cited by 253 · see citing works
Interactions of NF-κB with chromatin: the art of being at the right place at the right time
Natoli, G., Saccani, S., Bosisio, D., & Marazzi, I. (2005) · Nature Immunology · doi:10.1038/ni1196 · Cited by 250 · see citing works
Self-citationIntergenic transcription through a Polycomb group response element counteracts silencingPreprint
Schmitt, S., Prestel, M., & Paro, R. (2005) · Genes & Development · doi:10.1101/gad.326205 · Cited by 230 · see citing works
Sehgal, P. B., Darnell, J. E., Jr., & Tamm, I. (1976) · Cell · doi:10.1016/0092-8674(76)90092-1 · Cited by 203 · see citing works
Grove, M., & Plumb, M. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.9.5276 · Cited by 174 · see citing works
Promoter-associated Pausing in Promoter Architecture and Postinitiation Transcriptional RegulationPreprint
Lis, J. T. (1998) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1998.63.347 · Cited by 172 · see citing works
Chromatin remodeling and extragenic transcription at the MHC class II locus control region
Masternak, K., Peyraud, N., Krawczyk, M., Barras, E., & Reith, W. (2003) · Nature Immunology · doi:10.1038/ni883 · Cited by 157 · see citing works
A role for noncoding transcription in activation of the yeast PHO5 gene
Uhler, J. P., Hertel, C. B., & Svejstrup, J. Q. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0702431104 · Cited by 155 · see citing works
Lefevre, P., Witham, J., Lacroix, C., Cockerill, P. N., & Bonifer, C. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.07.023 · Cited by 137 · see citing works
Noncoding transcription controls downstream promoters to regulate T‐cell receptor α recombination
Abarrategui, I., & Krangel, M. S. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601866 · Cited by 126 · see citing works
Eichbaum, Q. G., Iyer, R., Raveh, D., Mathieu, C., & Ezekowitz, R. A. B. (1994) · The Journal of Experimental Medicine · doi:10.1084/jem.179.6.1985 · Cited by 119 · see citing works
Chromatin modification by DNA tracking
TRAVERS, A. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.24.13634 · Cited by 93 · see citing works
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation
Kawaji, H., Severin, J., Lizio, M., Waterhouse, A. M., Katayama, S., Irvine, K. M., Hume, D. A., Forrest, A. R. R., Suzuki, H., Carninci, P., et al. (2009) · Genome biology · doi:10.1186/gb-2009-10-4-r40 · Cited by 85 · see citing works
Jak-STAT signaling pathways in cells of the immune system.
Ivashkiv, L. B. (2000) · PubMed · Cited by 65 · see citing works
Ling, J., Baibakov, B. A., Pi, W., Emerson, B. M., & Tuan, D. Y. H. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.05.039 · Cited by 51 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Gene regulation by long non-coding RNAs and its biological functions
Statello, L., Guo, C.-J., Chen, L.-L., & Huarte, M. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-00315-9 · Cited by 4,991 · see citing works
The M1 and M2 paradigm of macrophage activation: Time for reassessment
Martinez, F. O., & Gordon, S. (2014) · F1000Prime Reports · doi:10.12703/p6-13 · Cited by 4,689 · see citing works
Genome Regulation by Long Noncoding RNAs
Rinn, J. L., & Chang, H. Y. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-051410-092902 · Cited by 4,011 · 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
Cabili, M. N., Trapnell, C., Goff, L. A., Koziol, M. J., Tazón‐Vega, B., Regev, A., & Rinn, J. L. (2011) · Genes & Development · doi:10.1101/gad.17446611 · Cited by 3,473 · see citing works
Mapping and analysis of chromatin state dynamics in nine human cell types
Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898 · 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
Long 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
Modular regulatory principles of large non-coding RNAs
Guttman, M., & Rinn, J. L. (2012) · Nature · doi:10.1038/nature10887 · Cited by 2,257 · see citing works
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
Wang, K., Yang, Y. W., Liu, B., Sanyal, A., Corces, M. R., Chen, Y., Lajoie, B. R., Protacio, A., Flynn, R. A., Gupta, R. A., et al. (2011) · Nature · doi:10.1038/nature09819 · Cited by 1,963 · see citing works
lincRNAs act in the circuitry controlling pluripotency and differentiation
Guttman, M., Donaghey, J., Carey, B. W., Garber, M. G., Grenier, J. K., Munson, G., Young, G., Lucas, A. B., Ach, R. A., Bruhn, L., et al. (2011) · Nature · doi:10.1038/nature10398 · Cited by 1,845 · see citing works
Transcriptional enhancers: from properties to genome-wide predictions
Shlyueva, D., Stampfel, G., & Stark, A. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3682 · Cited by 1,356 · see citing works
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards
Fishilevich, S., Nudel, R., Rappaport, N., Hadar, R., Plaschkes, I., Stein, T. I., Rosen, N., Kohn, A., Twik, M., Safran, M., et al. (2017) · Database · doi:10.1093/database/bax028 · Cited by 1,219 · see citing works
Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters
Hung, T., Wang, Y., Lin, M. F., Koegel, A. K., Kotake, Y., Grant, G. D., Horlings, H. M., Shah, N., Umbricht, C. B., Wang, P., et al. (2011) · Nature Genetics · doi:10.1038/ng.848 · Cited by 1,165 · see citing works
Charting histone modifications and the functional organization of mammalian genomes
Zhou, V. W., Goren, A., & Bernstein, B. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2905 · Cited by 1,147 · see citing works
Linking Long Noncoding RNA Localization and Function
Chen, L. (2016) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2016.07.003 · Cited by 1,042 · see citing works
The selection and function of cell type-specific enhancers
Heinz, S., Romanoski, C. E., Benner, C., & Glass, C. K. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3949 · Cited by 1,010 · see citing works
RNA-mediated epigenetic regulation of gene expression
Holoch, D., & Moazed, D. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3863 · Cited by 994 · see citing works
The multidimensional mechanisms of long noncoding RNA function
Marchese, F. P., Raimondi, I., & Huarte, M. (2017) · Genome biology · doi:10.1186/s13059-017-1348-2 · Cited by 966 · see citing works
No-Nonsense Functions for Long Noncoding RNAs
Nagano, T., & Fraser, P. (2011) · Cell · doi:10.1016/j.cell.2011.03.014 · Cited by 877 · see citing works
Latent Enhancers Activated by Stimulation in Differentiated Cells
Ostuni, R., Piccolo, V., Barozzi, I., Polletti, S., Termanini, A., Bonifacio, S., Curina, A., Prosperini, E., Ghisletti, S., & Natoli, G. (2013) · Cell · doi:10.1016/j.cell.2012.12.018 · Cited by 867 · see citing works
Self-citationActivating RNAs associate with Mediator to enhance chromatin architecture and transcription
Lai, F., Ørom, U. A., Cesaroni, M., Beringer, M., Taatjes, D. J., Blobel, G. A., & Shiekhattar, R. (2013) · Nature · doi:10.1038/nature11884 · Cited by 857 · see citing works
Functional and Mechanistic Diversity of Distal Transcription Enhancers
Bulger, M., & Groudine, M. (2011) · Cell · doi:10.1016/j.cell.2011.01.024 · Cited by 803 · see citing works
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesisPreprint
Pauli, A., Valen, E., Lin, M. F., Garber, M. G., Vastenhouw, N. L., Levin, J. Z., Fan, L., Sandelin, A., Rinn, J. L., Regev, A., et al. (2011) · Genome Research · doi:10.1101/gr.133009.111 · Cited by 776 · see citing works
Non-coding RNAs as regulators of gene expression and epigenetics
Kaikkonen, M. U., Lam, M. T. Y., & Glass, C. K. (2011) · Cardiovascular Research · doi:10.1093/cvr/cvr097 · Cited by 764 · see citing works
Eukaryotic core promoters and the functional basis of transcription initiation
Haberle, V., & Stark, A. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0028-8 · Cited by 737 · see citing works
Xiang, J., Yin, Q.-F., Chen, T., Zhang, Y., Zhang, X.-O., Wu, Z., Zhang, S., Wang, H., Ge, J., Lu, X., et al. (2014) · Cell Research · doi:10.1038/cr.2014.35 · Cited by 729 · see citing works
Determinants of enhancer and promoter activities of regulatory elements
Andersson, R., & Sandelin, A. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0173-8 · Cited by 713 · see citing works
Regulation of gene expression by cis-acting long non-coding RNAs
Gil, N., & Ulitsky, I. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0184-5 · Cited by 712 · 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
Kaikkonen, M. U., Spann, N. J., Heinz, S., Romanoski, C. E., Allison, K. A., Stender, J. D., Chun, H. B., Tough, D. F., Prinjha, R. K., Benner, C., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.07.010 · Cited by 672 · see citing works
Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions
Zentner, G. E., Tesar, P. J., & Scacheri, P. C. (2011) · Genome Research · doi:10.1101/gr.122382.111 · Cited by 564 · see citing works
eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription
Melo, C. A., Drost, J., Wijchers, P. J., van de Werken, H., de Wit, E., Vrielink, J. A. F. O., Elkon, R., Melo, S. A., Léveillé, N., Kalluri, R., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2012.11.021 · Cited by 544 · see citing works
Molecular control of activation and priming in macrophages
Glass, C. K., & Natoli, G. (2015) · Nature Immunology · doi:10.1038/ni.3306 · Cited by 522 · see citing works
Self-citationKarmodiya, K., Krebs, A. R., Oulad‐Abdelghani, M., Kimura, H., & Tora, L. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-424 · Cited by 506 · see citing works
eRNAs Promote Transcription by Establishing Chromatin Accessibility at Defined Genomic Loci
Mousavi, K., Zare, H., Dell’Orso, S., Grøntved, L., Gutierrez-Cruz, G., Derfoul, A., Hager, G. L., & Sartorelli, V. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.07.022 · Cited by 503 · see citing works
Enhancer RNAs and regulated transcriptional programs
Lam, M. T. Y., Li, W., Rosenfeld, M. G., & Glass, C. K. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.02.007 · Cited by 502 · see citing works
Bonn, S., Zinzen, R. P., Girardot, C., Gustafson, E. H., Perez-Gonzalez, A., Delhomme, N., Ghavi-Helm, Y., Wilczyński, B., Riddell, A., & Furlong, E. E. M. (2012) · Nature Genetics · doi:10.1038/ng.1064 · Cited by 502 · see citing works
Histone modifications for human epigenome analysis
Kimurâ, H. (2013) · Journal of Human Genetics · doi:10.1038/jhg.2013.66 · Cited by 479 · see citing works
A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics
Rapicavoli, N. A., Qu, K., Zhang, J., Mikhail, M. E., Laberge, R.-M., & Chang, H. Y. (2013) · eLife · doi:10.7554/elife.00762 · Cited by 477 · see citing works
Enhancer transcripts mark active estrogen receptor binding sitesPreprint
Hah, N., Murakami, S., Nagari, A., Danko, C. G., & Kraus, W. L. (2013) · Genome Research · doi:10.1101/gr.152306.112 · Cited by 475 · see citing works
Enhancer RNA Facilitates NELF Release from Immediate Early Genes
Schaukowitch, K., Joo, J., Liu, X., Watts, J. K., Martinez, C., & Kim, T.-K. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.08.023 · Cited by 445 · see citing works
RNA Binding to CBP Stimulates Histone Acetylation and Transcription
Bose, D. A., Donahue, G., Reinberg, D., Shiekhattar, R., Bonasio, R., & Berger, S. L. (2017) · Cell · doi:10.1016/j.cell.2016.12.020 · Cited by 426 · see citing works
Regulation of Transcription by Long Noncoding RNAs
Bonasio, R., & Shiekhattar, R. (2014) · Annual Review of Genetics · doi:10.1146/annurev-genet-120213-092323 · Cited by 424 · see citing works
Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics
Nojima, T., & Proudfoot, N. J. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00447-6 · Cited by 424 · see citing works
Transcriptional regulatory functions of nuclear long noncoding RNAs
Vance, K. W., & Ponting, C. P. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.06.001 · Cited by 423 · see citing works
Long non-coding RNAs in the regulation of the immune response
Heward, J. A., & Lindsay, M. A. (2014) · Trends in Immunology · doi:10.1016/j.it.2014.07.005 · Cited by 418 · see citing works
Ozsolak, F., Kapranov, P., Foissac, S., Kim, S. W., Fishilevich, E., Monaghan, A. P., John, B., & Milos, P. M. (2010) · Cell · doi:10.1016/j.cell.2010.11.020 · Cited by 400 · see citing works
Hsieh, C.-L., Fei, T., Chen, Y., Li, T., Gao, Y., Wang, X., Sun, T., Sweeney, C. J., Lee, G.-S. M., Chen, S., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1324151111 · Cited by 398 · see citing works
Towards a comprehensive catalogue of validated and target-linked human enhancers
Gasperini, M., Tome, J. M., & Shendure, J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0209-0 · Cited by 396 · see citing works
Epigenetic regulation of macrophage polarization and function
Ivashkiv, L. B. (2012) · Trends in Immunology · doi:10.1016/j.it.2012.11.001 · Cited by 396 · see citing works
Noncoding Transcription at Enhancers: General Principles and Functional Models
Natoli, G., & Andrau, J. (2012) · Annual Review of Genetics · doi:10.1146/annurev-genet-110711-155459 · Cited by 395 · see citing works
Self-citationMicroRNAs activate gene transcription epigenetically as an enhancer trigger
Xiao, M., Li, J., Li, W., Wang, Y., Wu, F., Xi, Y., Zhang, L., Ding, C., Luo, H., Li, Y., et al. (2016) · RNA Biology · doi:10.1080/15476286.2015.1112487 · Cited by 378 · see citing works
The Diversity of Long Noncoding RNAs and Their Generation
Wu, H., Yang, L. C., & Chen, L. (2017) · Trends in Genetics · doi:10.1016/j.tig.2017.05.004 · Cited by 378 · see citing works
Enhancer RNAs are an important regulatory layer of the epigenome
Sartorelli, V., & Lauberth, S. M. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0446-0 · Cited by 367 · see citing works
H3K4 tri‐methylation provides an epigenetic signature of active enhancers
Pękowska, A., Benoukraf, T., Cabeza, J. Z., Belhocine, M., Koch, F., Holota, H., Imbert, J., Andrau, J., Ferrier, P., & Spicuglia, S. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.295 · Cited by 365 · see citing works
Cis-regulatory sequences in plants: Their importance, discovery, and future challenges
Schmitz, R. J., Grotewold, E., & Stam, M. E. (2021) · The Plant Cell · doi:10.1093/plcell/koab281 · Cited by 358 · see citing works
Mechanisms of enhancer action: the known and the unknown
Panigrahi, A., & O’Malley, B. W. (2021) · Genome biology · doi:10.1186/s13059-021-02322-1 · Cited by 351 · see citing works
Widespread transcriptional pausing and elongation control at enhancers
Henriques, T., Scruggs, B. S., Inouye, M. O., Muse, G. W., Williams, L. H., Burkholder, A. B., Lavender, C. A., Fargo, D. C., & Adelman, K. (2018) · Genes & Development · doi:10.1101/gad.309351.117 · Cited by 350 · see citing works
Technological Developments in lncRNA Biology
Jathar, S., Kumar, V., Srivastava, J. P., & Tripathi, V. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-981-10-5203-3_10 · Cited by 348 · see citing works
Transcription regulation by long non-coding RNAs: mechanisms and disease relevance
Ferrer, J. P., & Dimitrova, N. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-023-00694-9 · Cited by 346 · see citing works
Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters
Koch, F., Fenouil, R., Gut, M., Cauchy, P., Albert, T., Cabeza, J. Z., Spicuglia, S., de la Chapelle, A. L., Heidemann, M., Hintermair, C., et al. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2085 · Cited by 333 · see citing works
Architectural and Functional Commonalities between Enhancers and Promoters
Kim, T.-K., & Shiekhattar, R. (2015) · Cell · doi:10.1016/j.cell.2015.08.008 · Cited by 331 · see citing works
Qiao, Y., Giannopoulou, E. G., Chan, C. H., Park, S.-H., Gong, S., Chen, J., Hu, X., Elemento, O., & Ivashkiv, L. B. (2013) · Immunity · doi:10.1016/j.immuni.2013.08.009 · Cited by 330 · see citing works
Long non-coding RNAs as emerging regulators of differentiation, development, and disease
Dey, B. K., Mueller, A. C., & Dutta, A. (2014) · Transcription · doi:10.4161/21541272.2014.944014 · Cited by 324 · see citing works
Integrator mediates the biogenesis of enhancer RNAs
Lai, F., Gardini, A., Zhang, A., & Shiekhattar, R. (2015) · Nature · doi:10.1038/nature14906 · Cited by 316 · see citing works
Enhancer biology and enhanceropathies
Smith, E. R., & Shilatifard, A. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2784 · Cited by 310 · see citing works
Regulation of mammalian cell differentiation by long non‐coding RNAs
Hu, W., Alvarez‐Dominguez, J. R., & Lodish, H. F. (2012) · EMBO Reports · doi:10.1038/embor.2012.145 · Cited by 308 · see citing works
Sun, C., Yin, J., Fang, Y., Chen, J., Jeong, K. J., Chen, X., Vellano, C. P., Ju, Z., Zhao, W., Zhang, D., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.01.019 · Cited by 302 · see citing works
A Pan-Cancer Analysis of Enhancer Expression in Nearly 9000 Patient Samples
Chen, H., Li, C., Peng, X., Zhou, Z., Weinstein, J. N., Johnson, R., Demchok, J. A., Felau, I., Kasapi, M., Ferguson, M. L., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.027 · Cited by 298 · see citing works
Ilott, N. E., Heward, J. A., Roux, B. T., Tsitsiou, E., Fenwick, P. S., Lenzi, L., Goodhead, I., Hertz‐Fowler, C., Heger, A., Hall, N., et al. (2014) · Nature Communications · doi:10.1038/ncomms4979 · Cited by 294 · see citing works
Mikhaylichenko, O., Bondarenko, V., Harnett, D., Schor, I. E., Males, M., Viales, R. R., & Furlong, E. E. M. (2018) · Genes & Development · doi:10.1101/gad.308619.117 · Cited by 293 · see citing works
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications
Kapusta, A., & Feschotte, C. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.08.004 · Cited by 291 · see citing works
Bell, R. D., Long, X., Lin, M., Bergmann, J. H., Nanda, V., Cowan, S. L., Zhou, Q., Han, Y., Spector, D. L., Zheng, D., et al. (2014) · Arteriosclerosis Thrombosis and Vascular Biology · doi:10.1161/atvbaha.114.303240 · Cited by 290 · see citing works
Dealing with Pervasive Transcription
Jensen, T. H., Jacquier, A., & Libri, D. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.10.032 · Cited by 284 · see citing works
Ounzain, S., Micheletti, R., Beckmann, T., Schroen, B. L. M., Alexanian, M., Pezzuto, I., Crippa, S., Nemir, M., Sarre, A., Johnson, R., et al. (2014) · European Heart Journal · doi:10.1093/eurheartj/ehu180 · Cited by 281 · see citing works
Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation
Lee, J.-H., Wang, R., Xiong, F., Krakowiak, J., Liao, Z., Nguyen, P. T.-M., Moroz, E., Shao, J., Zhu, X., Bolt, M. J., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.07.024 · Cited by 275 · see citing works
Update of the FANTOM web resource: expansion to provide additional transcriptome atlases
Lizio, M., Abugessaisa, I., Noguchi, S., Kondo, A., Hasegawa, A., Hon, C.-C., de Hoon, M., Severin, J., Oki, S., Hayashizaki, Y., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky1099 · Cited by 273 · see citing works
Clouaire, T., Webb, S., Skene, P., Illingworth, R. S., Kerr, A. R. W., Andrews, R., Lee, J., Skalnik, D. G., & Bird, A. P. (2012) · Genes & Development · doi:10.1101/gad.194209.112 · Cited by 273 · see citing works
Intragenic Enhancers Act as Alternative Promoters
Kowalczyk, M. S., Hughes, J. R., Garrick, D., Lynch, M. D., Sharpe, J. A., Sloane-Stanley, J. A., McGowan, S. J., De Gobbi, M., Hosseini, M., Vernimmen, D., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2011.12.021 · Cited by 267 · see citing works
Long Noncoding RNAs in Cardiovascular Pathology, Diagnosis, and Therapy
Bär, C., Chatterjee, S., & Thum, T. (2016) · Circulation · doi:10.1161/circulationaha.116.023686 · Cited by 267 · see citing works
Diversity and Emerging Roles of Enhancer RNA in Regulation of Gene Expression and Cell Fate
Arnold, P. R., Wells, A. D., & Li, X. C. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2019.00377 · Cited by 247 · see citing works
Enhancer Function: Mechanistic and Genome-Wide Insights Come Together
Plank, J. L., & Dean, A. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.06.015 · Cited by 246 · see citing works
Transcription Factories: Genome Organization and Gene Regulation
Papantonis, A., & Cook, P. R. (2013) · Chemical Reviews · doi:10.1021/cr300513p · Cited by 246 · see citing works
Long Noncoding RNAs Usher In a New Era in the Biology of Enhancers
Ørom, U. A., & Shiekhattar, R. (2013) · Cell · doi:10.1016/j.cell.2013.08.028 · Cited by 243 · see citing works
Berghe, W. V. (2012) · Pharmacological Research · doi:10.1016/j.phrs.2012.03.007 · Cited by 241 · see citing works
Hierarchies of NF-κB target-gene regulation
Smale, S. T. (2011) · Nature Immunology · doi:10.1038/ni.2070 · Cited by 239 · see citing works
A transcriptional switch governs fibroblast activation in heart disease
Alexanian, M., Przytycki, P. F., Micheletti, R., Padmanabhan, A., Ye, L., Travers, J. G., Gonzalez-Teran, B., Silva, A. C., Duan, Q., Ranade, S. S., et al. (2021) · Nature · doi:10.1038/s41586-021-03674-1 · Cited by 238 · see citing works
Transcription in Living Cells: Molecular Mechanisms of Bursting
Rodriguez, J., & Larson, D. R. (2020) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-011520-105250 · Cited by 224 · see citing works
U1 snRNP regulates chromatin retention of noncoding RNAs
Yin, Y., Lu, J., Zhang, X., Shao, W., Xu, Y., Li, P., Hong, Y., Cui, L., Shan, G., Tian, B., et al. (2020) · Nature · doi:10.1038/s41586-020-2105-3 · Cited by 224 · see citing works
Scruggs, B. S., Gilchrist, D. A., Nechaev, S., Muse, G. W., Burkholder, A., Fargo, D. C., & Adelman, K. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.04.006 · Cited by 218 · see citing works
Evaluating Enhancer Function and Transcription
Field, A. R., & Adelman, K. (2020) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-011420-095916 · Cited by 218 · see citing works
Long non‐coding RNA modifies chromatin
Saxena, A., & Carninci, P. (2011) · BioEssays · doi:10.1002/bies.201100084 · Cited by 211 · see citing works
A unified architecture of transcriptional regulatory elements
Andersson, R., Sandelin, A., & Danko, C. G. (2015) · Trends in Genetics · doi:10.1016/j.tig.2015.05.007 · Cited by 211 · see citing works
Chromatin Contributions to the Regulation of Innate Immunity
Smale, S. T., Tarakhovsky, A., & Natoli, G. (2014) · Annual Review of Immunology · doi:10.1146/annurev-immunol-031210-101303 · Cited by 209 · see citing works
Self-citationBarozzi, I., Simonatto, M., Bonifacio, S., Yang, L., Rohs, R., Ghisletti, S., & Natoli, G. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.04.006 · Cited by 209 · see citing works
Self-citationThe long non‐coding RNA Paupar regulates the expression of both local and distal genes
Vance, K. W., Sansom, S. N., Lee, S., Chalei, V., Kong, L., Cooper, S., Oliver, P. L., & Ponting, C. P. (2014) · The EMBO Journal · doi:10.1002/embj.201386225 · Cited by 208 · see citing works
Widespread Inducible Transcription Downstream of Human Genes
Vilborg, A., Passarelli, M. C., Yario, T. A., Tycowski, K. T., & Steitz, J. A. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.06.016 · Cited by 206 · see citing works
Catarino, R. R., & Stark, A. (2018) · Genes & Development · doi:10.1101/gad.310367.117 · Cited by 205 · see citing works
Kashi, K., Henderson, L., Bonetti, A., & Carninci, P. (2015) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2015.10.010 · Cited by 204 · see citing works
- Authors
- De Santa, F., Barozzi, I., Mietton, F., Ghisletti, S., Polletti, S., Tusi, B. K., Muller, H., Ragoussis, J., Wei, C.-L., & Natoli, G.
- Affiliations
- IFOM (IT)
- Centre for Human Genetics (GB)
- Genome Institute of Singapore (SG)
- Corresponding author
- Natoli, Gioacchino
- ORCID
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2010-05-11
- Volume
- 8
- Issue
- 5
- Pages
- e1000384
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- PMC
- PMC2867938
- OpenAlex
- W1978901723
- Cited by
- 934
- References
- 80
- Citations by year
- 2026: 23 · 2025: 46 · 2024: 40 · 2023: 57 · 2022: 61 · 2021: 81 · 2020: 70 · 2019: 45 · 2018: 57 · 2017: 63 · 2016: 67 · 2015: 75 · 2014: 73 · 2013: 73 · 2012: 49
- FWCI
- 22.68
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Figshare (submittedVersion, cc-by)
- Funders
- Wellcome Trust (075491, 075491/Z/04,)
- European Commission (222008)
- Ministry of Education, Culture, Sports, Science and Technology
- Associazione Italiana per la Ricerca sul Cancro
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- RNA polymerase II, long non-coding RNA, transcribed enhancers, macrophage activation, lipopolysaccharide response, purifying selection, cis-regulatory elements, genome annotation, chromatin signatures
- MeSH terms
- Animals, Binding Sites, Female, Gene Expression Regulation, Humans, Lipopolysaccharides, Macrophage Activation, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid, RNA Polymerase II, Transcription, Genetic, RNA, Untranslated, Mice
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
