DNA methylation insulates exons from CTCF loops with nuclear speckles (RNA-Seq)

CTCF is necessary for the formation and maintenance of many DNA loops and Topologically Associating Domains, but the genomic features that influence CTCF looping are incompletely understood. We characterized the downstream effects of treating cells with a DNMT1 inhibitor and acute depletion of nuclear speckles to study the factors that influence CTCF looping. Overall design: Comparative gene expression profiling analysis of full-length RNA-seq data for K562 and HCT116 cells treated with a DNA methylation inhibitor (DNMT1i) and DMSO control. Also, comparative gene expression profiling analysis of full-length RNA-seq data for speckle dTAG knockin K562 cells treated with dTAG-13 for speckle depletion and DMSO control. All experiments were performed in biolocial triplicate.