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

Laxmi Narayan Mishra,Nikhil Gupta,Utsa Bhaduri,Krittika Ghosh,M R Satyanarayana Rao,Neeraj Suthar,Vasantha Shalini

doi:10.1186/s13072-018-0214-0

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.

Highlights

Linker histones establish and maintain higher-order chromatin structure
Linker histone HILS1 possesses less α‐helicity compared to H1t and H1d Recombinant rat Hils1 gene is located on chromosome 10, within the 9th intron of the α-sarcoglycan gene and codes for 169 amino acid protein
Sequence comparison with chicken linker histone H5, for which the globular domain structure is known, indicates the presence of N-terminal basic domain (NTD) comprising of 1st to 42nd amino acids, GD spanning from 43rd to 116th amino acids, and a highly basic C-terminal domain (CTD) consisting of 117th to 169th amino acids (Fig. 1a)

Summary

Introduction

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. Linker histones are lysine-rich proteins associated with the DNA entering and exiting the nucleosomes sealing two turns of DNA around the core histone octamer. Linker histone binding to the nucleosome protects extra 20 bp of DNA and the structure is called chromatosome. Linker histones help in the formation and stabilization of 30 nm fiber [2] and facilitate the self-association of fibers into oligomeric tertiary chromatin structures [3]. Eleven linker histone variants have been reported, of which, seven are somatic subtypes like H1a (H1.1), H1b (H1.5), H1c (H1.2), H1d (H1.3), H1e (H1.4), H1x (H1.10), and H10 (H1.0); three are testis-specific

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