Gcn5-mediated histone acetylation governs nucleosome dynamics in spermiogenesis [ATAC-seq]

During mammalian spermatogenesis, male germ cells undergo dramatic reorganization of chromatin, whereby 90-99% of histones are evicted and replaced by protamines. This reorganization prominently features histone acetylation to loosen chromatin structure. Given the potential role of retained histones in fertility and early embryonic development, the genomic location of retained nucleosomes is of great interest. However, the ultimate position and mechanisms underlying nucleosome eviction/retention are poorly understood, including several studies utilizing MNase-seq methodologies, but reporting remarkably dissimilar locations. Here, we utilized ATAC-seq to determine the location of retained nucleosomes in mouse sperm and found enrichment at promoters, but also retention at inter- and intragenic regions, and repetitive elements. We further investigated nucleosome eviction/retention by generating pre-meiotic, germ cell specific, conditional knockout mice for the histone acetyltransferase Gcn5, a key histone acetyltransferase. Gcn5cKO germ cells exhibited abnormal chromatin dynamics during spermiogenesis, including diminished nucleosome eviction leading to increased histone retention in sperm. These mice exhibited severe reproductive phenotypes: abnormal sperm production, sperm morphology, and ultimately, male infertility. Our findings demonstrate Gcn5 mediated histone acetylation promotes chromatin accessibility and nucleosome eviction in spermiogenesis, and that loss of histone acetylation leads to defects that disrupt male fertility and potentially, early embryogenesis. Includes paired-end ATAC-seq from four stages of spermatogenesis (meiotic spermatid, round spermatid, elongating spermatid, and mature sperm) in three separate genetic backgrounds: SV129 mice (two technical repeats of two biological replicates for meiotic, round, and elongating spermatids and six biological replicates for mature sperm), C57BL6 GCN5+/+ mice (2 biological replicates each) and C57BL6 GCN5-/- mice (Stra8-CRE homozygous flox'd alleles) (2 biological replicates each)