DNA methylation insulates exons from CTCF loops with nuclear speckles (CUT&TAG)

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: SON Cut&Tag for K562 and HCT116 cells treated with a DNA methylation inhibitor (DNMT1i) and DMSO control.