重新评估精子保留组蛋白的定位揭示了修饰依赖性在特定基因组区域的积累。

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

机构信息

Laboratory of Pathology and Development, the Institute for Quantitative Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-0032, Japan; Graduate School of Art and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan.

Laboratory of Pathology and Development, the Institute for Quantitative Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-0032, Japan; RIKEN BioResource Center, Ibaraki 305-0074, Japan.

出版信息

Cell Rep. 2018 Jun 26;23(13):3920-3932. doi: 10.1016/j.celrep.2018.05.094.

DOI:10.1016/j.celrep.2018.05.094

PMID:29949774

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.

摘要

精子基因组中组蛋白是否定位于基因编码区或基因荒漠一直存在争议。以前的矛盾观察结果可能是由于精子染色质对微球菌核酸酶（MNase）消化的非均匀敏感性造成的。精子染色质具有高度浓缩但异质的结构，由 90%∼99%的鱼精蛋白和 1%∼10%的组蛋白组成。在这项研究中，我们利用核质蛋白（NPM）在体外去除鱼精蛋白来提高精子染色质的溶解度。NPM 处理有效地溶解了组蛋白，同时保持了质量和数量。使用 NPM 处理的精子进行染色质免疫沉淀测序（ChIP-seq）分析表明，H4 主要定位于远端基因间区域，而修饰的组蛋白则表现出对特定基因组元件的修饰依赖性优先富集，例如富含 CpG 的启动子处的 H3K4me3 和卫星重复处的 H3K9me3，这表明存在保护修饰组蛋白免受驱逐的机制。