Spermatid-specific linker histone HILS1 is a poor condenser of DNA and chromatin and preferentially associates with LINE-1 elements

Abstract

BackgroundLinker histones establish and maintain higher-order chromatin structure. Eleven linker histone subtypes have been reported in mammals. HILS1 is a spermatid-specific linker histone, and its expression overlaps with the histone–protamine exchange process during mammalian spermiogenesis. However, the role of HILS1 in spermatid chromatin remodeling is largely unknown.ResultsIn this study, we demonstrate using circular dichroism spectroscopy that HILS1 is a poor condenser of DNA and chromatin compared to somatic linker histone H1d. Genome-wide occupancy study in elongating/condensing spermatids revealed the preferential binding of HILS1 to the LINE-1 (L1) elements within the intergenic and intronic regions of rat spermatid genome. We observed specific enrichment of the histone PTMs like H3K9me3, H4K20me3 and H4 acetylation marks (H4K5ac and H4K12ac) in the HILS1-bound chromatin complex, whereas H3K4me3 and H3K27me3 marks were absent.ConclusionsHILS1 possesses significantly lower α-helicity compared to other linker histones such as H1t and H1d. Interestingly, in contrast to the somatic histone variant H1d, HILS1 is a poor condenser of chromatin which demonstrate the idea that this particular linker histone variant may have distinct role in histone to protamine replacement. Based on HILS1 ChIP-seq analysis of elongating/condensing spermatids, we speculate that HILS1 may provide a platform for the structural transitions and forms the higher-order chromatin structures encompassing LINE-1 elements during spermiogenesis.Electronic supplementary materialThe online version of this article (10.1186/s13072-018-0214-0) contains supplementary material, which is available to authorized users.

Genome-Wide Occupancy Reveals The Localization of H1T2 (H1fnt) To Repeat Regions and A Subset of Transcriptionally Active Chromatin Domains in Mammalian Spermatids

“…An interesting observation from this study is the association of H1T2 to a subset of promoter-TSS chromatin domains in spermatids (~3% of total CHIPseq reads). In contrast, only 0.6% and 0.08% of the ChIP-seq reads were associated with promoter regions by H1t and HILS1 respectively (22,23). Detailed annotation of the H1T2 bound LINE repeats revealed the major association to a particular class of LINE repeat, LINE L1 Rn (Fig 3F; Additional le 6: Table S6) similar to our previous observation with respect to HILS1 (22).…”

“…In contrast, only 0.6% and 0.08% of the ChIP-seq reads were associated with promoter regions by H1t and HILS1 respectively (22,23). Detailed annotation of the H1T2 bound LINE repeats revealed the major association to a particular class of LINE repeat, LINE L1 Rn (Fig 3F; Additional le 6: Table S6) similar to our previous observation with respect to HILS1 (22). Full-length rat L1s (L1Rn) with intact open reading frames (ORFs) is considered as the functional master copies for retrotransposition.…”

“…Numerous studies have identi ed H1T2 as a critical testes speci c histone H1 for spermiogenesis, lack of which results in reduced fertility because of delayed nuclear condensation and aberrant elongation characterized by acrosome detachment and fragmented DNA (20). With this background, we were curious to gain more insights into the genomic functions of H1T2 in the context of our recent studies on the other two testes speci c histone variants, H1t and HILS1 (22,23).…”

“…In pacheytene spermatocytes, H1t decorates the methylated LINE and LTR repeats in addition to heterochromatin repressive marks (23). As the sperm differentiation progresses through histone hyper acetyaltion and incorporartion of other histone variants, HILS1 gets incorporated to provide a more loosened chromatin to facilitate the histone replacement, still maintaining the repressed chromatin architecture of the majorly bound LINE repeats (22). An interesting observation from this study is the association of H1T2 to a subset of promoter-TSS chromatin domains in spermatids (~3% of total CHIPseq reads).…”

“…More recently, focused studies have been initiated to understand how the sequence diversity of H1 proteins leads to distinct chromatin structures associated with different functional properties. Studies from our laboratory recently focused on the mechanism by which testes speci c H1 variants contributes to diverse chromatin function by studying the genomic localization, PTMs and chromatin loci speci c interacting proteins (22,23). Linker histone H1t constituting about 50-60% of total H1 content induces local chromatin relaxation to recruit the appropriate protein machinery for establishing closed chromatin repressed structures (23).…”