دورية أكاديمية
Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes.
العنوان: | Building regulatory landscapes reveals that an enhancer can recruit cohesin to create contact domains, engage CTCF sites and activate distant genes. |
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المؤلفون: | Rinzema NJ; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Sofiadis K; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Tjalsma SJD; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Verstegen MJAM; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Oz Y; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Valdes-Quezada C; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Felder AK; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Filipovska T; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., van der Elst S; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., de Andrade Dos Ramos Z; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Han R; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., Krijger PHL; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands., de Laat W; Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands. w.laat@hubrecht.eu. |
المصدر: | Nature structural & molecular biology [Nat Struct Mol Biol] 2022 Jun; Vol. 29 (6), pp. 563-574. Date of Electronic Publication: 2022 Jun 16. |
نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't |
اللغة: | English |
بيانات الدورية: | Publisher: Nature Pub. Group Country of Publication: United States NLM ID: 101186374 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1545-9985 (Electronic) Linking ISSN: 15459985 NLM ISO Abbreviation: Nat Struct Mol Biol Subsets: MEDLINE |
أسماء مطبوعة: | Original Publication: New York : Nature Pub. Group, c2004- |
مواضيع طبية MeSH: | Cell Cycle Proteins*/genetics , Cell Cycle Proteins*/metabolism , Chromosomal Proteins, Non-Histone*/genetics , Chromosomal Proteins, Non-Histone*/metabolism, Binding Sites ; CCCTC-Binding Factor/genetics ; CCCTC-Binding Factor/metabolism ; Chromatin/genetics ; Enhancer Elements, Genetic/genetics ; Cohesins |
مستخلص: | Developmental gene expression is often controlled by distal regulatory DNA elements called enhancers. Distant enhancer action is restricted to structural chromosomal domains that are flanked by CTCF-associated boundaries and formed through cohesin chromatin loop extrusion. To better understand how enhancers, genes and CTCF boundaries together form structural domains and control expression, we used a bottom-up approach, building series of active regulatory landscapes in inactive chromatin. We demonstrate here that gene transcription levels and activity over time reduce with increased enhancer distance. The enhancer recruits cohesin to stimulate domain formation and engage flanking CTCF sites in loop formation. It requires cohesin exclusively for the activation of distant genes, not of proximal genes, with nearby CTCF boundaries supporting efficient long-range enhancer action. Our work supports a dual activity model for enhancers: its classic role of stimulating transcription initiation and elongation from target gene promoters and a role of recruiting cohesin for the creation of chromosomal domains, the engagement of CTCF sites in chromatin looping and the activation of distal target genes. (© 2022. The Author(s).) |
References: | Nat Biotechnol. 2015 Feb;33(2):198-203. (PMID: 25580597) Cell. 2017 May 18;169(5):930-944.e22. (PMID: 28525758) Mol Cell. 2019 Nov 7;76(3):473-484.e7. (PMID: 31494034) Dev Cell. 2016 Dec 5;39(5):529-543. (PMID: 27867070) Cell. 2014 Aug 14;158(4):849-860. (PMID: 25126789) Nat Methods. 2008 Nov;5(11):955-7. (PMID: 18953349) Nat Biotechnol. 2014 Oct;32(10):1019-25. (PMID: 25129690) Elife. 2019 May 24;8:. (PMID: 31124784) Nature. 2013 Oct 24;502(7472):499-506. (PMID: 24153303) Nature. 2022 Apr;604(7906):571-577. (PMID: 35418676) Mol Cell. 2005 Feb 4;17(3):453-62. (PMID: 15694345) Mol Cell. 2021 Aug 5;81(15):3082-3095.e6. (PMID: 34197738) Methods. 2020 Jan 1;170:17-32. (PMID: 31351925) Nat Struct Mol Biol. 2020 Nov;27(11):1032-1040. (PMID: 32958948) Science. 2019 Dec 13;366(6471):1338-1345. (PMID: 31753851) Cell. 2017 Oct 5;171(2):305-320.e24. (PMID: 28985562) Cell. 1987 Dec 24;51(6):975-85. (PMID: 3690667) Genome Res. 2015 Apr;25(4):504-13. (PMID: 25677180) Nature. 2016 Jan 7;529(7584):110-4. (PMID: 26700815) Cell. 2014 Dec 18;159(7):1665-80. (PMID: 25497547) Nat Genet. 2018 Feb;50(2):238-249. (PMID: 29335546) Genes Dev. 2016 Jun 15;30(12):1357-82. (PMID: 27340173) Science. 2018 Jul 27;361(6400):. (PMID: 29930091) Nat Commun. 2019 Jul 2;10(1):2908. (PMID: 31266948) Nature. 2010 Sep 23;467(7314):430-5. (PMID: 20720539) Physiol Genomics. 2004 Sep 16;19(1):117-30. (PMID: 15252187) Cell Rep. 2016 May 31;15(9):2038-49. (PMID: 27210764) Cell. 2019 Mar 7;176(6):1518. (PMID: 30849377) Cell. 2018 Dec 13;175(7):1842-1855.e16. (PMID: 30449618) Cell. 2015 May 21;161(5):1012-1025. (PMID: 25959774) Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):E6456-65. (PMID: 26499245) Nat Genet. 2018 Sep;50(9):1296-1303. (PMID: 30038397) J Biol Chem. 2004 Feb 13;279(7):5480-7. (PMID: 14660636) EMBO J. 2017 Dec 15;36(24):3573-3599. (PMID: 29217591) Cell. 2017 May 4;169(4):693-707.e14. (PMID: 28475897) Mol Cell. 2002 Dec;10(6):1453-65. (PMID: 12504019) Science. 2016 Mar 25;351(6280):1454-1458. (PMID: 26940867) FASEB J. 2021 Jun;35(6):e21669. (PMID: 34033138) Elife. 2017 Mar 23;6:. (PMID: 28332981) Genome Res. 2019 Mar;29(3):472-484. (PMID: 30737237) Mol Cell. 1997 Dec;1(1):131-9. (PMID: 9659910) Nature. 2020 Feb;578(7795):472-476. (PMID: 31905366) Nature. 2012 Sep 6;489(7414):57-74. (PMID: 22955616) Nat Struct Mol Biol. 2019 Jun;26(6):471-480. (PMID: 31133702) Nature. 2021 Jul;595(7865):125-129. (PMID: 34108683) Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21771-6. (PMID: 19959666) Nat Immunol. 2018 Sep;19(9):932-941. (PMID: 30127433) Science. 2019 Dec 13;366(6471):1345-1349. (PMID: 31780627) Mol Cell. 2017 Sep 21;67(6):1037-1048.e6. (PMID: 28890333) Cell. 2019 Aug 22;178(5):1145-1158.e20. (PMID: 31402173) Elife. 2016 Sep 23;5:. (PMID: 27661255) Nature. 1989 Mar 23;338(6213):352-5. (PMID: 2922063) Cell Rep. 2020 Jul 21;32(3):107929. (PMID: 32698000) Nature. 1999 Mar 25;398(6725):344-8. (PMID: 10192336) Nat Genet. 2021 Jan;53(1):100-109. (PMID: 33318687) Nature. 2021 Jul;595(7869):735-740. (PMID: 34040254) Science. 2002 Feb 15;295(5558):1306-11. (PMID: 11847345) Elife. 2021 Jul 09;10:. (PMID: 34240703) Mol Cell Biochem. 2006 Nov;292(1-2):155-67. (PMID: 16786195) Cell. 2018 Sep 20;175(1):292-294. (PMID: 30241609) Cell. 2017 Oct 19;171(3):557-572.e24. (PMID: 29053968) PLoS Comput Biol. 2014 Oct 23;10(10):e1003867. (PMID: 25340767) Nature. 2021 May;593(7858):238-243. (PMID: 33828297) Nature. 2017 Nov 2;551(7678):51-56. (PMID: 29094699) |
المشرفين على المادة: | 0 (CCCTC-Binding Factor) 0 (Cell Cycle Proteins) 0 (Chromatin) 0 (Chromosomal Proteins, Non-Histone) |
تواريخ الأحداث: | Date Created: 20220617 Date Completed: 20220621 Latest Revision: 20231213 |
رمز التحديث: | 20240628 |
مُعرف محوري في PubMed: | PMC9205769 |
DOI: | 10.1038/s41594-022-00787-7 |
PMID: | 35710842 |
قاعدة البيانات: | MEDLINE |
تدمد: | 1545-9985 |
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DOI: | 10.1038/s41594-022-00787-7 |