Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl

We analysed the effect on the genomic localisation of cohesin (Stag1 and Scc1) and CTCF in CTCF, Smc3 and Wapl single depleted as well as CTCF Wapl double depleted mouse embryonic fibroblasts. Furthermore, we addressed the effect of CTCF and Smc3 depletion on gene expression as measured by RNA-Seq and the transcriptional activity in CTCF and Wapl double depleted cells by GRO-Seq. Overall design: ChIP-Seq profiles of CTCF, H3K4me2, H3K9ac, Nipbl, Scc1, Stag1 in wild-type mouse embryonic fibroblasts (MEFs, E13.5d), CTCF, Smc3 and Wapl depleted or CTCF Wapl double depleted MEFs; mRNA-seq profiles of wild-type MEFs as well as CTCF and Smc3 depleted MEFs; GRO-seq profiles of wild-type MEFs as well as CTCF Wapl double depleted MEFs.