Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling

Abstract

Pioneer transcription factors (PTFs) bind to inaccessible chromatin and recruit collaborating transcription factors to promote chromatin accessibility. However, mechanisms driving PTFs to specify collaborating transcription factor recruitment and chromatin remodeling remain unclear. Here, we utilize inducible expression of a PTF, GATA3, in a basal breast cancer cell line (SUM159PT) to mechanistically address the collaborating transcription factor requirements and the local chromatin architecture delineating GATA3-depenent chromatin accessibility and enhancer formation (productive sites) versus GATA3-bound inaccessible chromatin (unproductive sites). Transcription factor footprinting in productive sites illustrated enrichment of GATA3 with AP-1 transcription factor. Together, GATA3 and AP-1 colocalize at primed enhancers with p300 and BRG1 where nucleosome positioning is influenced by GATA3 binding. Although inhibition of AP-1 binding affects a small subset of productive sites, we demonstrate that inhibition of SWI/SNF ATPases results in dramatic loss of GATA3-dependent chromatin accessibility, binding, and alterations in local chromatin architecture. We conclude that GATA3-dependent gains in chromatin accessibility require chromatin remodeling and that accessibility at some loci is facilitated by collaborating transcription factors like AP-1.