CoChat
Sign Up
Cited by 492Genomics and Chromatin DynamicsGene Regulatory Network AnalysisRNA Research and Splicing

Transcription factor trapping by RNA in gene regulatory elements

Open access
Sigova, Alla A., Abraham, Brian J., Ji, Xiong, Molinie, Benoit, Hannett, Nancy M., Guo, Yang Eric, Jangi, Mohini, Giallourakis, Cosmas C. +2 more·2015·Science
DOI 10.1126/science.aad3346PMC PMC4720525
Open this paper in CoChat — free account

Abstract

Noncoding RNA helps protein binding: Besides reading the coding regions of genes, RNA polymerase generates RNA at promoter-proximal and -distal DNA elements, but the function of these molecules is largely unknown. Sigova et al. show that these RNAs facilitate interactions between gene regulators and the regulatory elements they occupy. Nascent RNA associates with the transcription factor YY1 and increases its ability to bind DNA. Thus, transcription at active regulatory elements may provide a positive feedback loop that reinforces regulatory elements contributing to the stability of gene expression programs. Science , this issue p. 978

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.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1126/science.aad3346

Cites

9 of 9 references verified0 citation errors · 0 not checkable

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.

A few free checks a day · papers already verified open instantly · results are public

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?

  • eRNA can capture various transcription factors, thereby increasing their local concentration on the enhancer.

    “In addition, eRNA can capture various transcription factors [65], thereby increasing their local concentration on the enhancer.”

    From Enhancer Function in the 3D Genome (2023) · cites this paper as [65]

    The passages labeled Abstract (page not provided) report that RNA tethered near enhancers increases YY1 occupancy and propose that nascent RNA traps dissociating YY1. The paper suggests other transcription factors may behave similarly, but it does not establish that enhancer RNA captures various transcription factors. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Current theories propose liquid-liquid phase separation and some form of transcription factor trapping or engagement of transcription factors in multivalent interactions independent of assembly into phase-separated liquid-like droplets.

    “current theories propose liquid-liquid phase separation18,64–66 and some form of TF trapping22,67 or engagement of TFs in multivalent interactions independent of assembly into phase-separated liquid-like droplets.68”

    From Super-enhancers include classical enhancers and facilitators to fully activate gene expression (2023) · cites this paper as [67]

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

Flagged first, then by citations

Research works printed but not linked: 52

  1. [1]Core LJ Waterfall JJ Lis JT Science 2008 322 1845 1848 19056941 PMC2833333
  2. [2]Seila AC Science 2008 322 1849 1851 19056940 PMC2692996
  3. [3]Sigova AA Proc Natl Acad Sci U S A 2013 110 2876 2881 23382218 PMC3581948
  4. [4]Kim TK Nature 2010 465 182 187 20393465 PMC3020079
  5. [5]Wang D Nature 2011 474 390 394 21572438 PMC3117022
  6. [6]Melo CA Mol Cell 2013 49 524 535 23273978
  7. [7]Lai F Nature 2013 494 497 501 23417068 PMC4109059
  8. [8]Lam MT Nature 2013 498 511 515 23728303 PMC3839578
  9. [9]Li W Nature 2013 498 516 520 23728302 PMC3718886
  10. [10]Kaikkonen MU Mol Cell 2013 51 310 325 23932714 PMC3779836
  11. [11]Mousavi K Mol Cell 2013 51 606 617 23993744 PMC3786356
  12. [12]Di Ruscio A Nature 2013 503 371 376 24107992 PMC3870304
  13. [13]Schaukowitch K Mol Cell 2014 56 29 42 25263592 PMC4186258
  14. [14]Cassiday LA Maher LJ 3rd Nucleic Acids Res 2002 30 4118 4126 12364590 PMC140532
  15. [15]Jeon Y Lee JT Cell 2011 146 119 133 21729784 PMC3150513
  16. [16]Gordon S Akopyan G Garban H Bonavida B Oncogene 2006 25 1125 1142 16314846
  17. [17]Flynn RA Almada AE Zamudio JR Sharp PA Proc Natl Acad Sci U S A 2011 108 10460 10465 21670248 PMC3127934
  18. [18]Preker P Science 2008 322 1851 1854 19056938
  19. [19]Houbaviy HB Usheva A Shenk T Burley SK Proc Natl Acad Sci U S A 1996 93 13577 13582 8942976 PMC19349
  20. [20]Hnisz D Cell 2013 155 934 947 24119843 PMC3841062
  21. [21]Lubas M Cell Rep 2015 10 178 192 25578728
  22. [22]Maurano MT Science 2012 337 1190 1195 22955828 PMC3771521
  23. [23]Whyte WA Cell 2013 153 307 319 23582322 PMC3653129
  24. [24]Wang L Nature 2015 523 621 625 26123024 PMC4521995
  25. [25]Vella P Barozzi I Cuomo A Bonaldi T Pasini D Nucleic Acids Res 2012 40 3403 3418 22210892 PMC3333890
  26. [26]Kim J Chu J Shen X Wang J Orkin SH Cell 2008 132 1049 1061 18358816 PMC3837340
  27. [27]Boyer LA Nature 2006 441 349 353 16625203
  28. [28]Schmieder R Edwards R Bioinformatics 2011 27 863 864 21278185 PMC3051327
  29. [29]Kim J Cantor AB Orkin SH Wang J Nature Protocols 2009 4 506 517 19325547
  30. [30]Langmead B Trapnell C Pop M Salzberg SL Genome Biol 2009 10 R25 19261174 PMC2690996
  31. [31]Zhang Y Genome biology 2008 9 R137 18798982 PMC2592715
  32. [32]Kent WJ Genome research 2002 12 996 1006 12045153 PMC186604
  33. [33]Grant CE Bailey TL Noble WS Bioinformatics 2011 27 1017 1018 21330290 PMC3065696
  34. [34]Bryne JC Nucleic acids research 2008 36 D102 D106 18006571 PMC2238834
  35. [35]Jolma A Cell 2013 152 327 339 23332764
  36. [36]Trapnell C Pachter L Salzberg SL Bioinformatics 2009 25 1105 1111 19289445 PMC2672628
  37. [37]Wang L Wang S Li W Bioinformatics 2012 28 2184 2185 22743226
  38. [38]Loven J Cell 2012 151 476 482 23101621 PMC3505597
  39. [39]Lin CY Cell 2012 151 56 67 23021215 PMC3462372
  40. [40]Quinlan AR Hall IM Bioinformatics 2010 26 841 842 20110278 PMC2832824
  41. [41]Sigova AA Proc Natl Acad Sci U S A 2013 110 2876 2881 23382218 PMC3581948
  42. [42]Wang D Nature 2011 474 390 394 21572438 PMC3117022
  43. [43]Kopylova E Noe L Touzet H Bioinformatics 2012 28 3211 3217 23071270
  44. [44]Kent WJ Zweig AS Barber G Hinrichs AS Karolchik D Bioinformatics 2010 26 2204 2207 20639541 PMC2922891
  45. [45]Jangi M Boutz PL Paul P Sharp PA Genes & development 2014 28 637 651 24637117 PMC3967051
  46. [46]Martin M EMBnet journal 2011 17 10 12
  47. [47]Langmead B Salzberg SL Nature Methods 2012 9 357 359 22388286 PMC3322381
  48. [48]Li H Bioinformatics 2009 25 2078 2079 19505943 PMC2723002
  49. [49]Cernilogar FM Nature 2011 480 391-U151 22056986 PMC4082306
  50. [50]Mullen AC Cell 2011 147 565 576 22036565 PMC3212730
  51. [51]Wang H Cell 2013 153 910 918 23643243 PMC3969854
  52. [52]Kearns NA Development 2014 141 219 223 24346702 PMC3865759

Cited by

Sorted by citations

Authors
Sigova, A. A., Abraham, B. J., Ji, X., Molinie, B., Hannett, N. M., Guo, Y. E., Jangi, M., Giallourakis, C. C., Sharp, P. A., & Young, R. A.
Affiliations
  • Whitehead Institute for Biomedical Research (US)
  • Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
  • Koch Institute for Integrative Cancer Research At MIT (US)
  • Harvard University (US)
Corresponding author
Young, Richard A.
ORCID
Venue
Science
Publisher
American Association for the Advancement of Science (AAAS)
Published
2015-11-20
Volume
350
Issue
6263
Pages
978-981
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
DOI
10.1126/science.aad3346
PMC
PMC4720525
OpenAlex
W2618657542
Cited by
492
References
9
Citations by year
2026: 18 · 2025: 30 · 2024: 62 · 2023: 55 · 2022: 52 · 2021: 53 · 2020: 52 · 2019: 39 · 2018: 44 · 2017: 42 · 2016: 44 · 2015: 1
FWCI
18.97
Type
journal article
Language
en
Open access
Licence
www.sciencemag.org/about/science-licenses-journal-article-reuse (vor, 366 d)
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion)
Funders
  • NIH (HG002668)
  • Cancer Research Institute
  • Biogen
  • Hope Funds for Cancer Research
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords
RNA transcription, gene regulatory elements, distal regulatory elements, YY1, transcription factor occupancy, positive feedback loop, gene expression stability, transcriptional regulation
MeSH terms
Animals, Base Sequence, Binding Sites, Cell Line, DNA, Enhancer Elements, Genetic, Gene Expression Regulation, Promoter Regions, Genetic, RNA, Messenger, Transcription, Genetic, Consensus Sequence, YY1 Transcription Factor, Mice, Embryonic Stem Cells

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