Cited by 161Genomics and Chromatin DynamicsChromatin Remodeling and CancerEpigenetics and DNA Methylation

Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome

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Chen, Hebing, Tian, Yao, Shu, Wenjie, Bo, Xiaochen, Wang, Shengqi·2012·PLoS ONE

Abstract

Chromatin insulators are DNA elements that regulate the level of gene expression either by preventing gene silencing through the maintenance of heterochromatin boundaries or by preventing gene activation by blocking interactions between enhancers and promoters. CCCTC-binding factor (CTCF), a ubiquitously expressed 11-zinc-finger DNA-binding protein, is the only protein implicated in the establishment of insulators in vertebrates. While CTCF has been implicated in diverse regulatory functions, CTCF has only been studied in a limited number of cell types across human genome. Thus, it is not clear whether the identified cell type-specific differences in CTCF-binding sites are functionally significant. Here, we identify and characterize cell type-specific and ubiquitous CTCF-binding sites in the human genome across 38 cell types designated by the Encyclopedia of DNA Elements (ENCODE) consortium. These cell type-specific and ubiquitous CTCF-binding sites show uniquely versatile transcriptional functions and characteristic chromatin features. In addition, we confirm the insulator barrier function of CTCF-binding and explore the novel function of CTCF in DNA replication. These results represent a critical step toward the comprehensive and systematic understanding of CTCF-dependent insulators and their versatile roles in the human genome.

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Authors
Chen, H., Tian, Y., Shu, W., Bo, X., & Wang, S.
Affiliations
Beijing Radiation Center (CN)
Corresponding author
  • Shu, Wenjie
  • Bo, Xiaochen
  • Wang, Shengqi
Venue
PLoS ONE
Published
2012-07-19
Volume
7
Issue
7
Pages
e41374
ISSN
1932-6203 (ISSN-L)
OpenAlex
W2000626262
Cited by
161
References
96
Citations by year
2026: 4 · 2025: 13 · 2024: 19 · 2023: 11 · 2022: 15 · 2021: 9 · 2020: 16 · 2019: 3 · 2018: 13 · 2017: 8 · 2016: 12 · 2015: 17 · 2014: 13 · 2013: 7 · 2012: 1
FWCI
4.89
Type
journal article
Language
en
Open access
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
Funders
National Natural Science Foundation of China
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
CTCF, chromatin insulators, CTCF binding sites, cell type-specific binding, enhancer-promoter interactions, heterochromatin boundaries, DNA replication, transcriptional regulation, chromatin features, human genome
MeSH terms
CCCTC-Binding Factor, Binding Sites, Humans, Repressor Proteins, Genome, Human, Insulator Elements

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