The epigenetic reader Phf2 is positioned in the genome by cohesin

Eukaryotic genomes are assembled into chromatin by histones and extruded into loops by cohesin. These mechanisms control important genomic functions, but whether histones and cohesin cooperate in genome regulation is poorly understood. Here we identify Phf2, a member of the Jumonji-C family of histone demethylases, as a cohesin-interacting protein. Phf2 binds to H3K4me3 nucleosomes at active transcription start sites (TSSs) but also co-localizes with cohesin. Cohesin depletion reduces Phf2 binding at sites lacking H3K4me3, and depletion of Wapl and CTCF re-positions Phf2 together with cohesin in the genome, resulting in the accumulation of both proteins in vermicelli and cohesin islands. Conversely, Phf2 depletion reduces cohesin binding at TSSs lacking CTCF, decreases the number of short cohesin loops, but increases the length of heterochromatic B compartments. These results suggest that Phf2 is an 'epigenetic reader', which is translocated through the genome by cohesin-mediated DNA loop extrusion, and which recruits cohesin to active TSSs and limits the size of B compartments. These findings reveal an unexpected degree of cooperativity between epigenetic and architectural mechanisms of eukaryotic genome regulation. Overall design: This study investigates the role of Phf2 in gene regulation by performing RNA-Seq analysis on samples with and without Phf2 expression. Experimental samples included wild-type and Phf2 KO in mouse embryonic fibroblast cells (MEFs), allowing us to compare transcriptional profiles and identify genes potentially regulated by Phf2. Total RNA was extracted from 2 replicates for each condition, followed by library preparation and sequencing to provide insights into the differential gene expression patterns associated with Phf2 function.