esBAF chromatin remodeling complexes promote spacing of nucleosomes flanking pluripotency factor binding sites

We showed that topoisomerase II synergizes with BAF (mSWI/SNF) ATP-dependent chromatin remodeling complexes genome-wide to resolve facultative heterochromatin to accessible chromatin. To study the consequences of this on transcription factors, we performed MNase-seq on light digest of native chromatin in Brg1 conditional knockout embryonic stem (ES) cells. We found that spacing of nucleosomes flanking pluripotency factor binding sites specifically partially collapsed upon Brg1 deletion, indicating that pluripotency factor binding is likely lost. We grew Brg1 conditional knockout ES cells (Brg1fl/fl; Actin-CreER) ES cells on gelatin-coated plates in serum-LIF media, treated them with ethanol or 0.8 µM tamoxifen for 24 hours, and then grew in fresh media without ethanol or tamoxifen for another 48 hours before harvesting the cells for nucleosome profiling by MNase-seq.