MacroH2A histone variants modulate enhancer activity to repress oncogenic programs and cellular reprogramming

Abstract

Considerable efforts have been made to characterize active enhancer elements, which can be annotated by accessible chromatin and H3 lysine 27 acetylation (H3K27ac). However, apart from poised enhancers that are observed in early stages of development and putative silencers, the functional significance of cis-regulatory elements lacking H3K27ac is poorly understood. Here we show that macroH2A histone variants mark a subset of enhancers in normal and cancer cells, which we coined ‘macro-Bound Enhancers’, that modulate enhancer activity. We find macroH2A variants localized at enhancer elements that are devoid of H3K27ac in a cell type-specific manner, indicating a role for macroH2A at inactive enhancers to maintain cell identity. In following, reactivation of macro-bound enhancers is associated with oncogenic programs in breast cancer and their repressive role is correlated with the activity of macroH2A2 as a negative regulator of BRD4 chromatin occupancy. Finally, through single cell epigenomic profiling of normal mammary stem cells derived from mice, we show that macroH2A deficiency facilitates increased activity of transcription factors associated with stem cell activity.

MacroH2A restricts inflammatory gene expression in melanoma cancer-associated fibroblasts by coordinating chromatin looping

“…Traditional enhancers (TEs) and superenhancers (SEs) are emerging regulators of NF-κB-driven inflammatory gene transcription 63 – 67 . Moreover, macroH2A regulates specific promoter–enhancer contacts 68 and suppresses a subset of enhancers 69 . Therefore, we performed chromatin immunoprecipitation with sequencing (ChIP–seq) for H3K27ac, which marks active promoters (Extended Data Fig.…”

“…Together with changes in enhancer activity, this finding suggests that macroH2A may enforce the position of enhancers relative to nuclear compartments or the ability of enhancers to interact with their cognate promoters. Accordingly, previous studies have suggested that macroH2A affects 3D chromatin organization at several scales, including stabilizing nucleosome–DNA contacts to limit the mobility of the chromatin fibre 73 , 76 , associating with the boundaries of lamina-associated domains and promoting heterochromatin 74 , 75 , blocking BRD4 binding at macroH2A-bound enhancers 69 , and changing contact frequency of promoter–enhancer pairs, the activity of which is affected by macroH2A1 or macroH2A2 depletion 68 . Interestingly, however, changes in chromatin accessibility were minimal, which suggests that macroH2A loss does not affect chromatin remodelling, as previously reported 79 .…”

Combinatorial targeting of a specific EMT/MET network by macroH2A variants safeguards mesenchymal identity

“…Previous studies have provided evidence for a regulatory role of mH2A nucleosomes bound at proximal DNA regulatory regions or at the gene bodies of their targeted genes [ 22 , 37 ]. Therefore, we performed Average Binding Analysis to test for the binding of mH2As at the regions located 5 kb upstream from TSS and at gene bodies of the mH2A MET/EMT genes.…”

Roles of Histone H2A Variants in Cancer Development, Prognosis, and Treatment

“…In glioblastoma, the tumor-suppressive function of macroH2A2 is mediated through repression of genes associated with stemness and self-renewal. Depletion of macroH2A2 significantly promoted the self-renewal properties in cancer cells, while overexpression antagonized self-renewal [ 143 , 158 ]. In anal neoplasm, high macroH2A2 expression is associated with low-grade neoplasm and delayed recurrence.…”