High-Resolution Mapping of H1 Linker Histone Variants in Embryonic Stem Cells

Abstract

H1 linker histones facilitate higher-order chromatin folding and are essential for mammalian development. To achieve high-resolution mapping of H1 variants H1d and H1c in embryonic stem cells (ESCs), we have established a knock-in system and shown that the N-terminally tagged H1 proteins are functionally interchangeable to their endogenous counterparts in vivo. H1d and H1c are depleted from GC- and gene-rich regions and active promoters, inversely correlated with H3K4me3, but positively correlated with H3K9me3 and associated with characteristic sequence features. Surprisingly, both H1d and H1c are significantly enriched at major satellites, which display increased nucleosome spacing compared with bulk chromatin. While also depleted at active promoters and enriched at major satellites, overexpressed H1⁰ displays differential binding patterns in specific repetitive sequences compared with H1d and H1c. Depletion of H1c, H1d, and H1e causes pericentric chromocenter clustering and de-repression of major satellites. These results integrate the localization of an understudied type of chromatin proteins, namely the H1 variants, into the epigenome map of mouse ESCs, and we identify significant changes at pericentric heterochromatin upon depletion of this epigenetic mark. Embryonic stem cells (ESCs) possess unique chromatin and epigenetic signatures, which are important in defining the identity and genome plasticity of pluripotent stem cells. Although ESC epigenomes have been extensively characterized, the genome localization of histone H1 variants, the chromatin structural proteins facilitating higher-order chromatin folding, remains elusive. Linker histone H1 is essential for mammalian development and regulates the expression of specific genes in ESCs. Here, by using a knock-in system coupled with ChIP–seq, we first achieve the high resolution mapping of two H1 variants on a genome-wide scale in mouse ESCs. Our study reveals the correlations of this underexplored histone family with other epigenetic marks and genome attributes. Surprisingly, we identify a dramatic enrichment of H1d and H1c at major satellite sequences. H1⁰, mapped using an overexpressing ESC line, shows similar features at active promoters but differential binding at repetitive sequences compared with H1d and H1c. Furthermore, using mutant ESCs that are deficient for multiple H1 variants, we demonstrate the role of H1 in chromocenter clustering and transcriptional repression of major satellites. Thus, these results connect this important repressive mark with the well understood ESC epigenome and identify novel functions of H1 in mammalian genome organization.