Genetic Determinants and Epigenetic Effects of Pioneer Factor Occupancy

Abstract

Transcription factors (TFs) are the core drivers of gene regulatory networks that control developmental transitions and a complete understanding of how they access, alter and maintain specific gene expression patterns remains an important goal. To begin a systematic dissection of the molecular components that either enable or constrain TF activity, we investigated the genomic occupancy of a set of previously defined pioneer factors, FOXA2, GATA4 and OCT4 in both endogenous and ectopic settings. We find that all three factors display cell type specific occupancy even with super-physiological expression conditions, but only FOXA2 and GATA4 display, in both endogenous and ectopic conditions, low enrichment sampling of additional loci that are occupied in alternative lineages. Ectopic co-expression of FOXA2 and GATA4 can stabilize sites that were previously only sampled. In general, we observe little influence of the chromatin state on FOXA2 or GATA4 enrichment, but a bias towards open chromatin for ectopic OCT4 targets. Finally, we demonstrate that FOXA2 occupancy and changes to DNA accessibility at silent cis-regulatory elements can occur when the cell cycle is halted in G1, but surprisingly, subsequent changes in DNA methylation require DNA replication. Taken together, our results provide several new molecular insights that contribute to our basic understanding of gene regulation and pave the way for a more rational use of ectopic TFs for cellular reprogramming.