MACMIC Reveals A Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes
Autor: | Min Gyu Lee, Yiwen Bu, Dongyu Zhao, Kaifu Chen, Man Zhou, Guangyu Wang, Yanqiang Li, Xin Wang, Lili Zhang, Qi Cao, John P. Cooke, Bo Xia, Jie Lv |
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Jazyk: | angličtina |
Rok vydání: | 2021 |
Předmět: |
Cell type
H3K27me3 Method Computational biology Biology Biochemistry Genome Epigenesis Genetic 03 medical and health sciences 0302 clinical medicine Genetics Humans Epigenetics Molecular Biology Gene Psychological repression 030304 developmental biology Epigenomics 0303 health sciences Colocalization Genomics H3K27ac CCCTC-binding factor Chromatin Correlation Mutual information Computational Mathematics Enhancer Elements Genetic CTCF 030217 neurology & neurosurgery |
Zdroj: | Genomics, Proteomics & Bioinformatics |
ISSN: | 2210-3244 1672-0229 |
Popis: | Numerous studies of relationship between epigenomic features have focused on their strong correlation across the genome, likely because such relationship can be easily identified by many established methods for correlation analysis. However, two features with little correlation may still colocalize at many genomic sites to implement important functions. There is no bioinformatic tool for researchers to specifically identify such feature pairs. Here, we develop a method to identify feature pairs in which two features have maximal colocalization minimal correlation (MACMIC) across the genome. By MACMIC analysis of 3306 feature pairs in 16 human cell types, we reveal a dual role of CCCTC-binding factor (CTCF) in epigenetic regulation of cell identity genes. Although super-enhancers are associated with activation of target genes, only a subset of super-enhancers colocalized with CTCF regulate cell identity genes. At super-enhancers colocalized with CTCF, CTCF is required for the active marker H3K27ac in cell types requiring the activation, and also required for the repressive marker H3K27me3 in other cell types requiring repression. Our work demonstrates the biological utility of the MACMIC analysis and reveals a key role for CTCF in epigenetic regulation of cell identity. The code for MACMIC is available at https://github.com/bxia888/MACMIC. |
Databáze: | OpenAIRE |
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