HMGN1 and HMGN2 are recruited to acetylated and histone variant H2A.Z-containing nucleosomes to regulate chromatin state and transcription

The High Mobility Group Nucleosome-binding (HMGN) proteins are small, abundant nuclear proteins that directly bind nucleosomes and form a major component of chromatin. HMGN proteins localize to enhancers and actively transcribed genes across the genome; however, their roles in regulating chromatin structure and transcription remain poorly understood. Although it is well established that HMGN proteins bind to the H2A-H2B acidic patch on nucleosomes, other potential nucleosome targeting mechanisms, including histone post-translational modifications and histone variants, remain unclear. To investigate the nucleosomal binding preferences and function of HMGN proteins, we engineered mouse embryonic stem cells (mESCs) lacking HMGN1 and/or HMGN2 (Hmgn1^-/- mESCs, Hmgn2^-/- mESCs, and Hmgn1^-/-Hmgn2^-/- mESCs) and profiled gene expression and localization of architectural proteins. In the absence of these HMGN proteins, ∼1000 genes were differentially expressed, including cell identity genes, with most genes being downregulated. Nucleosome binding assays revealed preferential binding of HMGN1 and HMGN2 proteins to nucleosomes with acetylated H3 tail residues and nucleosomes containing the histone variant H2A.Z. In addition, in vitro acetylation assays demonstrated that binding of HMGN1 and HMGN2 to nucleosomes reduces p300-mediated acetylation of H3K18, H3K23, and H3K27 residues. An epiproteomic mass spectrometry analysis of histone tail modifications revealed that Hmgn1^-/-Hmgn2^-/- mESCs have increased steady-state levels of H3K27me2 and H3K27me3, but not H3 tail acetylation, relative to WT cells. Together, these findings show that HMGN proteins function as both sensors and modulators of the histone post-translational modification landscape inside cells, playing a critical role in the dynamic balance between active and repressive chromatin states.