Systematic characterization of the genome-wide and nuclear distribution of six linker histone H1 variants in human cancer cells

Abstract

[eng] The histone H1 family comprises up to seven members in human somatic cells. However, H1 studies have been limited by the lack of specific ChIP-grade antibodies. Here, we have mapped six endogenous H1 variants in T47D breast cancer cells, which represent the whole somatic H1 complement in this cell line. ChIP-Seq experiments indicate that H1 variants are categorized into two large groups depending on the local GC content: H1.0, H1.2, H1.3 and H1.5 are enriched at low-GC regions while H1.4 and H1X are more abundant at high-GC genomic regions. Data also uncovers common features for H1 variants, highlighting the existing balance between redundancy and specificity.

Examination of H1 variants abundance within repetitive elements classes denoted that H1.0, H1.2, H1.3 and H1.5 are enriched within Satellite, LINE, LTR or DNA classes while H1.4 and H1X are enriched within SINE or ‘Other’ classes. This last category comprises SVA retrotransposons, which emerged along hominoid evolution. Interestingly, we have determined that H1X abundance gradually increases from older SVA_A to humanrestricted SVA_F families. This unprecedented association of H1 variants abundance and transposable elements (TEs) evolutionary age is also observed across different TE classes. Both H1X and H1.4 are enriched within the most recently evolved TEs along primate evolution, including not only SVAs but also younger Alu, LINE-L1 or LTR repeats. Conversely, H1.2, H1.3, H1.5, H1.0 are enriched in older TEs.

Confocal and super-resolution microscopy experiments further confirm the differential distribution of H1 variants and their distinct contribution to chromatin structure. H1.2, H1.3 and H1.5 are enriched towards the nuclear periphery or lamina-associated domains. H1.4 and H1X show a punctuated pattern throughout the nucleus, with H1X being particularly enriched at nucleoli. H1.0 forms enrichment territories that tend to be peripheral. Moreover, depletion of H1.2, either alone or in combination with H1.4, leads to a general chromatin decompaction that is not observed upon single H1.4 or H1X depletion.

Extensive analysis of multiple cell lines revealed the existence of certain universal distribution features despite variations in the H1 somatic repertoire. Specifically, H1.2, H1.3 and H1.5 consistently show enrichments towards the nuclear periphery in all cell lines examined, suggesting their universal role as components of lamina-associated domains. H1X, whose nucleolar presence is evident in all cell lines, is enriched at high- GC regions and younger SVA and Alu elements, as observed in T47D cells.

In conclusion, we provide the first systematic comparison of six endogenous H1 variants within a mammalian cell type, while also addressing their differential distribution among multiple cell lines. Altogether, our results support H1 variants heterogeneity and highlight their significance as key organizers and regulators of chromatin.