FOXA1 Directs H3K4 Monomethylation at Enhancers via Recruitment of the Methyltransferase MLL3

Summary FOXA1 is a pioneer factor that binds to enhancer regions that are enriched in H3K4 mono- and dimethylation (H3K4me1 and H3K4me2). We performed a FOXA1 rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) screen in ERα-positive MCF-7 breast cancer cells and found histone-lysine N-methyltransferase (MLL3) as the top FOXA1-interacting protein. MLL3 is typically thought to induce H3K4me3 at promoter regions, but recent findings suggest it may contribute to H3K4me1 deposition. We performed MLL3 chromatin immunoprecipitation sequencing (ChIP-seq) in breast cancer cells, and MLL3 was shown to occupy regions marked by FOXA1 occupancy and H3K4me1 and H3K4me2. MLL3 binding was dependent on FOXA1, indicating that FOXA1 recruits MLL3 to chromatin. MLL3 silencing decreased H3K4me1 at enhancer elements but had no appreciable impact on H3K4me3 at enhancer elements. We propose a mechanism whereby the pioneer factor FOXA1 recruits the chromatin modifier MLL3 to facilitate the deposition of H3K4me1 histone marks, subsequently demarcating active enhancer elements.
Graphical Abstract
Highlights • Mass spectrometry of chromatin-associated proteins with FOXA1 identifies MLL3 • FOXA1 recruits MLL3 to deposit H3K4me1 on FOXA1-bound enhancers • MLL3 promotes ERα-dependent gene transcription and proliferation • GRHL2 co-occupies regions of ERα, FOXA1, and MLL3 on enhancers
Jozwik et al. demonstrate that FOXA1 can activate enhancers by recruiting the chromatin-associated histone methyltransferase MLL3 to mediate monomethylation on enhancers. This identifies FOXA1 as an upstream regulatory element in the establishment of enhancers that regulates active chromatin marks.