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

Abstract

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.

Histone Post-Translational Modifications and CircRNAs in Mouse and Human Spermatozoa: Potential Epigenetic Marks to Assess Human Sperm Quality

“…As described above, the distribution of sperm derived histone PTMs on zygotic genome is not random, but follows a specific pattern [209,210]. In detail, sperm retained histones are enriched at development-related loci, including imprinted gene clusters, binding sites of chromatin insulator protein CCCTC-binding factor (CTCF) and promoters of developmental transcription and signaling factors [37,174,182,187,206,211,212].…”

“…In detail, sperm retained histones are enriched at development-related loci, including imprinted gene clusters, binding sites of chromatin insulator protein CCCTC-binding factor (CTCF) and promoters of developmental transcription and signaling factors [37,174,182,187,206,211,212]. Most of them have unmethylated CpG-rich promoters and are enriched of H3K4me2/3 or H3K27me3 [111,174,182,194,205,206,209,212,213]. Actually, H3K4me3 marks promoters of microRNA clusters, transcription and signaling factors (i.e., STAT3, KLF4/5, SOX7/9), developmental genes and paternally expressed imprinted genes (i.e., MEST, BEGAIN, DLK1, RTL).…”

Maternal DNMT3A-dependent de novo methylation of the zygotic paternal genome inhibits gene expression in the early embryo

“…In addition, CGIs retain nucleosomes in spermatozoa, foregoing the exchange for protamines [28][29][30] . These retained nucleosomes include canonical H3 or its variant H3.3, which are enriched for di-and/or tri-methylation on lysine 4 (H3K4me2/3) 30,34,35 .…”

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“…Some studies found sperm histones enriched next to promoter regions of genes related to embryo development, miRNA, HOX genes, imprinted genes and chromatin binding sites like CCCTC-binding factor (ARPANAHI et al, 2009;BRYKCZYNSKA et al, 2010;. On the opposite side, other studies found nucleosome structures enriched at intergenic regions or gene deserts (SAITOU; YAMAGUCHI et al, 2018). These divergent results may be partially explained due to differences in experimental details and technical process used to map the nucleosome over the sperm DNA.…”

“…In this process, it is possible to increase the chances of somatic cells contaminations or immature cells in the sample, which could explain the difference find between species. Recently, ChIP-Seq comparison of mice sperm samples submitted only to swim-up and swim-up and percoll verified some differences between sequencing data suggesting swim-up sperm samples could contain non-sperm cells contamination, which could have impacted the ChIP-seq results (YAMAGUCHI et al, 2018). Then, the sperm process can also be a bias to different results between experiments.…”