Re-evaluating the Localization of Sperm-Retained Histones Revealed the Modification-Dependent Accumulation in Specific Genome Regions

The question of whether retained histones in the sperm genome localize to gene-coding regions or gene deserts has been debated for years. Previous contradictory observations are likely caused by the non-uniform sensitivity of sperm chromatin to micrococcal nuclease (MNase) digestion. Sperm chromatin has a highly condensed but heterogeneous structure and is composed of 90%∼99% protamines and 1%∼10% histones. In this study, we utilized nucleoplasmin (NPM) to improve the solubility of sperm chromatin by removing protamines in vitro. NPM treatment efficiently solubilized histones while maintaining quality and quantity. Chromatin immunoprecipitation sequencing (ChIP-seq) analyses using NPM-treated sperm demonstrated the predominant localization of H4 to distal intergenic regions, whereas modified histones exhibited a modification-dependent preferential enrichment in specific genomic elements, such as H3K4me3 at CpG-rich promoters and H3K9me3 in satellite repeats, respectively, implying the existence of machinery protecting modified histones from eviction. [Display omitted] •Nucleoplasmin efficiently removes protamines from sperm chromatin in vitro•Protamine removal improves the solubility of sperm chromatin•Sperm histones are mainly retained in distal intergenic regions•Modified histones are preferentially retained in specific genomic elements Sperm chromatin is tightly packed by protamines, preventing unbiased solubilization by physical or enzymatic digestions. Here, Yamaguchi et al. successfully utilize nucleoplasmin in vitro to remove protamines and increase solubility. ChIP-seq demonstrates the predominant localization of sperm histones to intergenic regions, whereas modified histones are enriched in specific genomic elements.