Genetic determinants and epigenetic effects of pioneer factor occupancy

Transcription factors are the core drivers of gene regulatory networks that control developmental transitions, therefore a more complete understanding of how they access, alter and maintain tissue-specific gene expression patterns remains an important goal. To systematically dissect molecular components that enable or constrain their activity, we investigated the genomic occupancy of FOXA2, GATA4 and OCT4 in several cell types. Despite a classification as pioneer factors, all three factors demonstrate cell type specific enrichment even under super-physiological expression. However, only FOXA2 and GATA4 display, in both endogenous and ectopic conditions, a low enrichment sampling of additional loci that are occupied in alternative cell types. Co-factor expression can lead to increased pioneer factor binding at subsets of previously sampled target sites. 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 subsequent loss of DNA methylation requires DNA replication.