Pioneering new enhancers by GATA3: role of facilitating transcription factors and chromatin remodeling [ATAC-seq]

The mechanistic details by which pioneer transcription factors interact with partner transcription factors and chromatin modification/remodeling enzymes to activate enhancers remains an emerging area of study. Here, we utilize inducible expression of the pioneer factor GATA3 and study cofactor association and structural alterations in local chromatin. ATAC-seq analysis and footprinting revealed co-occurrence of GATA3 with other transcription factors, including AP-1, in newly accessible chromatin. GATA3 and AP-1 co-localize at primed enhancers with p300 and BRG1 where nucleosome positioning is responsive to GATA3 location, not to AP-1. Genetic inhibition of AP-1 binding alters chromatin opening at some, but not most, GATA3-bound loci. Pharmacologic inhibition of SWI/SNF ATPase function results in 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 a partner transcription factor, in this case AP-1. Overall design: Doxycycline (dox) inducible wildtype (wt; 1-444aa) and TA1del (ta1; 126-444aa) GATA3 cell lines were generated in SUM159PT basal breast cancer cell line. ATAC-seq was performed for accesible chromatin in +/- DOX conditions and +/- inhibitiors of transcription factor binding (AFOS) or chromatin remodeling (BRM014).