Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries.
Journal
Genome research
ISSN: 1549-5469
Titre abrégé: Genome Res
Pays: United States
ID NLM: 9518021
Informations de publication
Date de publication:
01 2023
01 2023
Historique:
received:
26
01
2022
accepted:
10
11
2022
pubmed:
18
1
2023
medline:
4
2
2023
entrez:
17
1
2023
Statut:
ppublish
Résumé
Vertebrate genomes are partitioned into chromatin domains or topologically associating domains (TADs), which are typically bound by head-to-head pairs of CTCF binding sites. Transcription at domain boundaries correlates with better insulation; however, it is not known whether the boundary transcripts themselves contribute to boundary function. Here we characterize boundary-associated RNAs genome-wide, focusing on the disease-relevant
Identifiants
pubmed: 36650052
pii: gr.276643.122
doi: 10.1101/gr.276643.122
pmc: PMC9977152
doi:
Substances chimiques
Chromatin
0
CCCTC-Binding Factor
0
RNA
63231-63-0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1-17Subventions
Organisme : Wellcome Trust
Pays : United Kingdom
Informations de copyright
© 2023 Islam et al.; Published by Cold Spring Harbor Laboratory Press.
Références
Cell. 2018 Jul 26;174(3):744-757.e24
pubmed: 29887377
Nat Cell Biol. 2017 Jul 28;19(8):883-885
pubmed: 28752854
Nat Commun. 2020 Jul 29;11(1):3696
pubmed: 32728046
Cell. 2017 May 18;169(5):930-944.e22
pubmed: 28525758
Nat Genet. 2020 Apr;52(4):388-400
pubmed: 32203470
Methods Mol Biol. 2017;1543:187-193
pubmed: 28349427
Nat Genet. 2019 Aug;51(8):1263-1271
pubmed: 31358994
Mol Cell. 2017 Jan 5;65(1):25-38
pubmed: 28017589
Cell. 2019 Feb 7;176(4):816-830.e18
pubmed: 30595451
EMBO Rep. 2019 Oct 4;20(10):e48068
pubmed: 31448565
Nat Methods. 2012 Oct;9(10):969-72
pubmed: 22961246
Methods Mol Biol. 2017;1468:1-9
pubmed: 27662865
Nucleic Acids Res. 2017 Nov 2;45(19):11088-11105
pubmed: 28977633
Cell Rep. 2018 Apr 10;23(2):349-360
pubmed: 29641996
Science. 2015 Feb 27;347(6225):1017-21
pubmed: 25722416
Cell. 2017 Oct 5;171(2):305-320.e24
pubmed: 28985562
Nat Struct Mol Biol. 2018 Aug;25(8):687-697
pubmed: 30076409
Genome Biol. 2020 Jan 7;21(1):5
pubmed: 31910870
Elife. 2017 Jan 16;6:
pubmed: 28079019
Nucleic Acids Res. 2016 Jul 8;44(W1):W160-5
pubmed: 27079975
Nature. 2014 Mar 27;507(7493):455-461
pubmed: 24670763
Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):16175-80
pubmed: 24046371
PLoS One. 2009 Jul 01;4(7):e6109
pubmed: 19568426
Nature. 2016 Jan 7;529(7584):110-4
pubmed: 26700815
Cell. 2014 Dec 18;159(7):1665-80
pubmed: 25497547
Nat Rev Genet. 2016 Apr;17(4):207-23
pubmed: 26948815
Cell Syst. 2016 Jul;3(1):95-8
pubmed: 27467249
Nat Genet. 2019 Sep;51(9):1380-1388
pubmed: 31427791
Nucleic Acids Res. 2019 Jul 2;47(W1):W158-W165
pubmed: 31165883
Nature. 2017 Mar 23;543(7646):519-524
pubmed: 28273065
Cell Rep. 2016 May 31;15(9):2038-49
pubmed: 27210764
Elife. 2021 Nov 04;10:
pubmed: 34734806
Development. 2019 Sep 30;146(19):
pubmed: 31511252
Mol Cell. 2018 May 17;70(4):730-744.e6
pubmed: 29706538
Elife. 2018 May 14;7:
pubmed: 29757144
Nat Protoc. 2014 Sep;9(9):2045-60
pubmed: 25079428
Mol Cell. 2019 Nov 7;76(3):412-422.e5
pubmed: 31522988
Nucleic Acids Res. 2017 Sep 29;45(17):9837-9849
pubmed: 28973462
Nat Commun. 2018 Feb 7;9(1):542
pubmed: 29416042
EMBO J. 2017 Dec 15;36(24):3573-3599
pubmed: 29217591
Mol Cell. 2019 Jan 17;73(2):250-263.e5
pubmed: 30527662
Nat Commun. 2020 Jan 7;11(1):54
pubmed: 31911579
Cell. 2017 Apr 6;169(2):216-228.e19
pubmed: 28388407
J Virol. 2014 May;88(10):5256-62
pubmed: 24599991
Nat Methods. 2012 Mar 04;9(4):357-9
pubmed: 22388286
Genome Res. 2002 Jun;12(6):996-1006
pubmed: 12045153
Nat Genet. 2020 Oct;52(10):1076-1087
pubmed: 32868908
PLoS Comput Biol. 2016 Mar 03;12(3):e1004780
pubmed: 26938081
Cell Rep. 2021 Mar 23;34(12):108898
pubmed: 33761351
Proc Natl Acad Sci U S A. 2018 Jul 17;115(29):E6697-E6706
pubmed: 29967174
Mol Cell. 2010 May 28;38(4):576-89
pubmed: 20513432
Nat Genet. 2020 Jan;52(1):8-16
pubmed: 31925403
Nat Genet. 2020 Nov;52(11):1151-1157
pubmed: 33077913
Cell Rep. 2020 Jul 21;32(3):107929
pubmed: 32698000
Nucleus. 2020 Dec;11(1):132-148
pubmed: 32631111
Mol Cell. 2019 Nov 7;76(3):395-411.e13
pubmed: 31522987
Bioinformatics. 2020 May 1;36(10):2980-2985
pubmed: 32003791
Nat Methods. 2015 Apr;12(4):357-60
pubmed: 25751142
Nature. 2012 Apr 11;485(7398):376-80
pubmed: 22495300
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Nucleic Acids Res. 2020 Apr 17;48(7):3513-3524
pubmed: 32095812
Mol Cell. 2017 Sep 7;67(5):837-852.e7
pubmed: 28826674
Cell. 2017 Oct 19;171(3):557-572.e24
pubmed: 29053968
Nature. 2011 Feb 10;470(7333):264-8
pubmed: 21307941
Nat Cell Biol. 2017 Aug;19(8):952-961
pubmed: 28737770
Nature. 2017 Nov 2;551(7678):51-56
pubmed: 29094699
Nature. 2016 Jul 28;535(7613):575-9
pubmed: 27437574
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nat Commun. 2019 Apr 3;10(1):1519
pubmed: 30944321
Nature. 2013 Jun 27;498(7455):516-20
pubmed: 23728302
Mol Cell. 2020 May 7;78(3):539-553.e8
pubmed: 32213323
Cell. 2016 Mar 10;164(6):1110-1121
pubmed: 26967279