Enhancer-promoter interactions and transcription are maintained upon acute loss of CTCF, cohesin, WAPL, and YY1

We use high-resolution Micro-C, ChIP-seq and nascent and total transcript profiling to show that Enhancer-Promoter (E-P) interactions are largely insensitive to acute depletion of CTCF, cohesin, WAPL and YY1. We performed ChIP-seq, RNA-seq, mNET-seq, and Micro-C in mESCs with either CTCF (clone C58), the cohesin subunit RAD21 (clone F1), the cohesin unloader WAPL (clone C40) or YY1 transcription factor (clone YD39) endogenously tagged with an auxin-inducible degron, 3 hours after treatment with either ethanol alone (UT) or ethanol-dissolved auxin (IAA, 500 mM). For ChIP-seq, we performed two biological replicates per each sample and condition, immunoprecipitating chromatin with antibodies against CTCF, the cohesin subunits RAD21, SMC1A and SMC3, and YY1 (4 cell types, 2 conditions, 5 antibodies + input in duplicate, for a total of 96 libraries). For RNA-seq, mNET-seq, and Micro-C, we also performed two biological replicates for each sample and condition.