Gene Network Transitions in Embryos Depend Upon Interactions between a Pioneer Transcription Factor and Core Histones [ATAC-Seq]

Gene network transitions in embryos and fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. But a gap has remained in understanding how molecular interactions with the nucleosome, beyond interactions with the DNA helix, contribute to the chromatin opening phenomenon. Here we identified a short alpha-helical region, conserved among FoxA pioneer factors and separated from the DNA binding domain, that interacts with core histones and is necessary for chromatin opening in vitro. The same domain is necessary for chromatin opening in early mouse embryos and for normal embryonic development and viability. Thus, local opening of chromatin by interactions between pioneer factors and core histones is crucial for genetic programming. Overall design: Paired-end ATAC-seq of mouse embryo cells (E7.5) which were FACS-sorted on FoxA2-tag-RFP into RFP-high, RFP-middle, and RFP-negative cell populations. FoxA2 WT mice were compared to mice with a homozygous DHx mutation that removes an alpha helix from FoxA2 critical for the activation of gene targets. Two replicates were sequenced for each (genetic background, RFP level) condition.