The pioneer factor SOX9 competes for epigenetic factors to switch stem cell fates [ATAC-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. Overall design: ATAC-seq was performed as described before in Buenrostro et al., 2013. Briefly, FACS sorted cells were lysed with ATAC lysis buffer on ice for 1 minute. Lysed cells were then tagmented with Tn5 transposase (Illumina) at 37C for 30min. Cleaned up fragments were PCR amplified (NEB) and size selected with 1.8X SPRI beads (Beckman Coulter). All libraries were sequenced on Illumina NextSeq 500 with 40-bp paired-end settings.