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Very proud to present the lab’s first bioRxiv preprint: biorxiv.org/cgi/content/sh… Great collaboration between @benoitbruneau and @ElphegeNoraLab. Main gist is that WAPL is important for maintaining dynamic cohesin to bring promoters and enhancers together. Digest in the thread.
@benoitbruneau @ElphegeNoraLab 1/9 Using the auxin inducible degron (AID) system we acute depleted the cohesin release factor WAPL from mouse ESCs. Within 1 hour WAPL is lost. This leads to morphological changes that suggest differentiation. Alkaline phosphatase staining suggests a loss of pluripotency. 
@benoitbruneau @ElphegeNoraLab 2/9 RNAseq confirms upregulation of developmental pathways and downregulation of pluripotency related genes. Interestingly, ChIPseq suggests very limited changes in H3K4me3, H3K27ac and H3K27me3.
@benoitbruneau @ElphegeNoraLab 3/9 WAPL releases cohesin from chromatin. In WAPL KO and depleted cells there is hardly any turnover. Paradoxically, cohesin is lost from certain regions in the genome in WAPL depletion. Is there anything special about these regions.
@benoitbruneau @ElphegeNoraLab 4/9 Since these regions are only found in situations where cohesin is dynamic, we refer to these regions as Regions of Dynamic Cohesin. These RDCs are enriched for enhancer marks and pluripotency TF binding sites and found in proximity to genes expressed in early embryo.
@benoitbruneau @ElphegeNoraLab 5/9 We performed Hi-C to look at changes in the 3D genome. Consistent with our earlier results loss of WAPL leads to longer loops. RDCs show a high degree of self-interaction, compared to the rest of the genome, which is diminished after WAPL loss. 4Cseq confirms this.
@benoitbruneau @ElphegeNoraLab 6/9 What about expression? Genes down-regulated after WAPL loss are enriched close to RDCs. So is cohesin involved? Well, a cohesin degron experiments phenocopies WAPL loss with respect to expression and promoter-enhancer contacts.
@benoitbruneau @ElphegeNoraLab 7/9 What brings cohesin to RDCs? We employed an OCT4 and NANOG degron line to determine what happens to cohesin after loss of of these TFs. Conclusion: OCT4 loss affects cohesin binding, but NANOG loss does not.
@benoitbruneau @ElphegeNoraLab 8/9 Is this specific for pluripotent cells? We in vitro differentiated our WAPL-AID cells and found a similar redistribution of cohesin after WAPL loss. Lost binding sites were enriched for motifs of lineage specific TFs. This seems to be general regulatory principle!
@benoitbruneau @ElphegeNoraLab 9/9 Conclusion: transcription factors + cohesin == loops + expression.
