Genome binding/occupancy profiling by high throughput sequencing Other Expression profiling by high throughput sequencing
Summary
Few transcription factors have been examined for their direct roles in physically connecting enhancers and promoters. Here acute degradation of Yin Yang 1 (YY1) in erythroid cells revealed its requirement for the maintenance of numerous enhancer-promoter loops, but not compartments or domains. Despite its reported ability to interact with cohesin, the formation of YY1-dependent enhancer-promoter loops does not involve stalling of cohesin-mediated loop extrusion. Integrating mitosis-to-G1-phase dynamics, we observed partial retention of YY1 on mitotic chromatin, predominantly at gene promoters, followed by rapid rebinding during mitotic exit, coinciding with enhancer-promoter loop establishment. YY1 degradation during the mitosis-to-G1-phase interval revealed a set of enhancer-promoter loops that require YY1 for establishment during G1-phase entry but not for maintenance in interphase, suggesting that cell cycle stage influences YY1's architectural function. Thus, as revealed here for YY1, chromatin architectural functions of transcription factors can vary in their interplay with CTCF and cohesin as well as by cell cycle stage.
Overall design
We performed ChIP-seq (YY1, CTCF, RAD21, LDB1, H3K27ac, and total Pol2) and Micro-C in asynchronous YY1-AID cells treated with auxin for 4h. RNA-seq and TT-seq were also performed in asynchronous YY1-AID cells. Additional Pol2 ChIP-seqs and Micro-C were performed on synchronized and FACS-purified YY1-AID cells (nocodazole treatment for 7h with simultaneous auxin treatment for 4h). YY1 ChIP-seq was also performed on synchronized and FACS-purified G1E-ER4 MD-mCherry cells at mitosis-to-G1 stages (nocodazole treatment for 7h).
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