The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates [RNA-Seq]

When stem cells activate a member of the SOX family of pioneer factors, they bind their cognate sequences within condensed chromatin, not only evicting the associated nucleosome, but also recruiting H3K4-monomethylases, which modify flanking nucleosomes to open chromatin and activate one lineage program; simultaneously, pioneer factors also silence alternative fates, but in this case act indirectly, through competing for H3K4-monomethylases pre-existing at the original fate genes. FACS-sorted EdpSCs were directly sorted into TRI Reagent, and total RNA was purified using the Direct-zol RNA kit (Zymo Research) according to the kit protocol. RNA quality was determined by Agilent 2100 Bioanalyzer, and RNA libraries were generated using SMARTer RNA kit for low input RNA-seq and sequenced on Illumina HiSeq 4000 or NovaSeq SP 50PE.