Systematical identification of cell-specificity of CTCF-gene binding based on epigenetic modifications.

Systematical identification of cell-specificity of CTCF-gene binding based on epigenetic modifications. Brief Bioinform. 2020 Feb 05;: Authors: Wu J, Zhang L, Song Q, Yu L, Wang S, Zhang B, Wang W, Xia P, Chen X, Xiao Y, Xu C Abstract The CCCTC-binding factor (CTCF) mediates transcriptional regulation and implicates epigenetic modifications in cancers. However, the systematically unveiling inverse regulatory relationship between CTCF and epigenetic modifications still remains unclear, especially the mechanism by which histone modification mediates CTCF binding. Here, we developed a systematic approach to investigate how epigenetic changes affect CTCF binding. Through integration analysis of CTCF binding in 30 cell lines, we concluded that CTCF generally binds with higher intensity in normal cell lines than that in cancers, and higher intensity in genome regions closed to transcription start sites. To facilitate the better understanding of their associations, we constructed linear mixed-effect models to analyze the effects of the epigenetic modifications on CTCF binding in four cancer cell lines and six normal cell lines, and identified seven epigenetic modifications as potential epigenetic patterns that influence CTCF binding intensity in promoter regions and six epigenetic modifications in enhancer regions. Further analysis of the effects in different locations revealed that the epigenetic regulation of CTCF binding was location-spe...
Source: Briefings in Bioinformatics - Category: Bioinformatics Authors: Tags: Brief Bioinform Source Type: research