Re-evaluating the Localization of Sperm-Retained Histones Revealed the Modification-Dependent Accumulation in Specific Genome Regions
Kosuke Yamaguchi,
Masashi Hada,
Yuko Fukuda,
Erina Inoue,
Yoshinori Makino,
Yuki Katou,
Katsuhiko Shirahige,
Yuki Okada
Affiliations
Kosuke Yamaguchi
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
Masashi Hada
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
Yuko Fukuda
Laboratory of Pathology and Development, the Institute for Quantitative Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-0032, Japan
Erina Inoue
Laboratory of Pathology and Development, the Institute for Quantitative Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-0032, Japan
Yoshinori Makino
Laboratory of Pathology and Development, the Institute for Quantitative Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-0032, Japan
Yuki Katou
Laboratory of Genome Structure and Function, the Institute for Quantitative Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-0032, Japan
Katsuhiko Shirahige
Laboratory of Genome Structure and Function, the Institute for Quantitative Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-0032, Japan
Yuki Okada
Laboratory of Pathology and Development, the Institute for Quantitative Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-0032, Japan; Corresponding author
Summary: 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. : 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. Keywords: sperm, histone, ChIP-seq, nucleoplasmin, NPM
