Systematic screening of CTCF binding partners identifies that BHLHE40 regulates CTCF genome-wide distribution and long-range chromatin interactions

Hu，Gongcheng1,2,3,4,5; Dong，Xiaotao1,2,3,4,5; Gong，Shixin1,2,3,4,5; Song，Yawei1,2,3,4; Hutchins，Andrew P.6; Yao，Hongjie1,2,3,4,5

2020-09-25

10.1093/nar/gkaa705

NUCLEIC ACIDS RESEARCH   影响因子和分区

0305-1048

1362-4962

CTCF plays a pivotal role in mediating chromatin interactions, but it does not do so alone. A number of factors have been reported to co-localize with CTCF and regulate CTCF loops, but no comprehensive analysis of binding partners has been performed. This prompted us to identify CTCF loop participants and regulators by co-localization analysis with CTCF. We screened all factors that had ChIP-seq data in humans by co-localization analysis with human super conserved CTCF (hscCTCF) binding sites, and identified many new factors that overlapped with hscCTCF binding sites. Combined with CTCF loop information, we observed that clustered factors could promote CTCF loops. After in-depth mining of each factor, we found that many factors might have the potential to promote CTCF loops. Our data further demonstrated that BHLHE40 affected CTCF loops by regulating CTCF binding. Together, this study revealed that many factors have the potential to participate in or regulate CTCF loops, and discovered a new role for BHLHE40 in modulating CTCF loop formation.

SCI

英语

其他

National Natural Science Foundation of China[31925009][3200040294] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDA16010502] ; National Key R&D Program of China[2016YFA0100400] ; Science and Technology Planning Project of Guangdong Province of China[2019B020234004] ; Key Research & Development Program of Guangzhou Regenerative Medicine andHealth Guangdong Laboratory[2018GZR110104007] ; Science and Technology Program of Guangzhou, China[201807010101][201707020042] ; Guangdong Basic and Applied Basic Research Foundation[2019A1515110028] ; National Mega-project of China for Innovative Drugs[2018ZX09201002-005]

Biochemistry & Molecular Biology

Biochemistry & Molecular Biology

WOS:000593122300019

OXFORD UNIV PRESS

BIOLOGY & BIOCHEMISTRY

2-s2.0-85091668202

Scopus

1.CAS Key Laboratory of Regenerative Biology,Joint School of Life Sciences,State Key Laboratory of Respiratory Disease,Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences,Guangzhou Medical University,Guangzhou,510530,China
2.Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine,Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences,Guangzhou,510530,China
3.Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory),Guangzhou,510005,China
4.Institute of Stem Cell and Regeneration,Chinese Academy of Sciences,100101,China
5.University of Chinese Academy of Sciences,100049,China
6.Department of Biology,Southern University of Science and Technology,Shenzhen,518055,China

Hu，Gongcheng,Dong，Xiaotao,Gong，Shixin,et al. Systematic screening of CTCF binding partners identifies that BHLHE40 regulates CTCF genome-wide distribution and long-range chromatin interactions[J]. NUCLEIC ACIDS RESEARCH,2020,48(17):9606-9620.

Hu，Gongcheng,Dong，Xiaotao,Gong，Shixin,Song，Yawei,Hutchins，Andrew P.,&Yao，Hongjie.(2020).Systematic screening of CTCF binding partners identifies that BHLHE40 regulates CTCF genome-wide distribution and long-range chromatin interactions.NUCLEIC ACIDS RESEARCH,48(17),9606-9620.

Hu，Gongcheng,et al."Systematic screening of CTCF binding partners identifies that BHLHE40 regulates CTCF genome-wide distribution and long-range chromatin interactions".NUCLEIC ACIDS RESEARCH 48.17(2020):9606-9620.