DNA methylation insulates genic regions from CTCF loops near nuclear speckles

Abstract

AbstractCTCF occupancy is inhibited by DNA methylation, but the effects of methylation-sensitive CTCF binding on chromatin structure and transcription are poorly understood. Here, we use a selective DNMT1 inhibitor to demethylate the genome and investigate the features and functions of the resulting ’reactivated’ CTCF peaks. We reveal a tendency for reactivated CTCF peaks to form chromatin loops on gene bodies and to interact with highly-looping partner peaks located in active chromatin regions near architectural stripe anchors. To dissect the potential functions of reactivated CTCF peaks, we combine DNMT1 inhibition with acute CTCF depletion and identify a subset of genes that are upregulated in a CTCF-dependent manner. These genes, as well as reactivated peaks and their highly-looping partners, are located in close proximity to nuclear speckles, prompting us to investigate whether CTCF looping and speckles are functionally linked. We find that despite the prevalence of CTCF reactivation and looping near nuclear speckles, acute depletion of speckles affects transcription with minimal disruption to CTCF binding or looping. Taken together, these findings suggest a model in which DNA methylation prevents genic CTCF occupancy and spurious interactions with regulatory elements near nuclear speckles, while CTCF looping is robust towards speckle disruption.