DNA methylation insulates genic regions from CTCF loops near nuclear speckles.

ABSTRACT: The insulator protein CTCF is essential for mediating chromatin loops and regulating gene expression. While it is established that DNA methylation hinders CTCF binding, the impacts of this methylation-sensitive CTCF binding on chromatin architecture and transcription are poorly defined. Here, we used a selective DNMT1 inhibitor (DNMT1i) to investigate the characteristics and functions of 'DNMT1i-specific' CTCF peaks resulting from global DNA demethylation. We found that DNMT1i-specific peaks preferentially form chromatin loops on gene bodies and interact with highly looping partner peaks located in regions of active chromatin. Notably, both DNMT1i-specific CTCF peaks and their highly looping partners are enriched near nuclear speckles - condensate bodies implicated in transcription and spl

SUBMITTER: Roseman SA 

PROVIDER: S-EPMC12408068 | biostudies-literature | 2025 Sep

REPOSITORIES: biostudies-literature