ArticleNucleic acids research2016
Defining the multivalent functions of CTCF from chromatin state and three-dimensional chromatin interactions.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 19 citations in OpenAlex.
- Topoisomerase VI participates in an insulator-like function that prevents H3K9me2 spreading.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- CTCF: A misguided jack-of-all-trades in cancer cells.Computational and structural biotechnology journal · 2022Review
- CGGBP1-dependent CTCF-binding sites restrict ectopic transcription.Cell cycle (Georgetown, Tex.) · 2021Article
- Multivariable regulation of gene expression plasticity in metazoans.Open biology · 2019Article
- Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis.BMC bioinformatics · 2019Article
- Article
- Poly(ADP-ribosyl)ation associated changes in CTCF-chromatin binding and gene expression in breast cells.Biochimica et biophysica acta. Gene regulatory mechanisms · 2018Article
- CommonClinical cancer research : an official journal of the American Association for Cancer Research · 2017Article
- Functional assessment of CTCF sites at cytokine-sensing mammary enhancers using CRISPR/Cas9 gene editing in mice.Nucleic acids research · 2017Article
- 3DSNP: a database for linking human noncoding SNPs to their three-dimensional interacting genes.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
CCCTC-binding factor (CTCF) is a multi-functional protein that is assigned various, even contradictory roles in the genome. High-throughput sequencing-based technologies such as ChIP-seq and Hi-C provided us the opportunity to assess the multivalent functions of CTCF in the human genome. The location of CTCF-binding sites with respect to genomic features provides insights into the possible roles of this protein. Here we present the first genome-wide survey and characterization of three important functions of CTCF: enhancer insulator, chromatin barrier and enhancer linker. We developed a novel computational framework to discover the multivalent functions of CTCF based on chromatin state and three-dimensional chromatin architecture. We applied our method to five human cell lines and identified ∼46 000 non-redundant CTCF sites related to the three functions. Disparate effects of these functions on gene expression were found and distinct genomic features of these CTCF sites were characterized in GM12878 cells. Finally, we investigated the cell-type specificities of CTCF sites related to these functions across five cell types. Our study provides new insights into the multivalent functions of CTCF in the human genome.
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