Single molecule footprinting measures low nucleosome occupancy in mature spermatozoa of mice and men

Nucleosomes are fundamental units of DNA packaging and gene regulation in eukaryotes. In mammalian sperm, most nucleosomes are replaced by protamines causing extreme chromatin compaction. Various epigenomic studies reported conflicting results on the distribution of residual nucleosomes in mammalian sperm, questioning their potential role in mediating intergenerational inheritance of paternal epigenetic information. Here we performed single-molecule footprinting through Nucleosome Occupancy and Methylome (NOMe) sequencing and applied the Bayesian statistical model nomeR to determine frequencies of nucleosome removal and retention at 103 specific genomic regions in thousands of developing haploid spermatids and mature spermatozoa of mice. While we readily detected footprints of nucleosomes and the transcription factor CTCF in round spermatids, chromatin became transiently highly accessible in elongating spermatids with loss of such footprints, indicating extensive chromatin reprogramming during spermiogenesis. In mature sperm, following nuclear decondensation with recombinant nucleoplasmin, we measured nucleosome occupancy frequencies ranging ~1.2 to 1.7% at mouse loci. In human sperm, nucleosome occupancy varied between ~2.3 to 4.5% at 163 genomic loci profiled. Contrasting mice, chromatin in ~25% of human sperm was accessible upon reducing disulfide bonds between protamines arguing for species specific protamine packaging. Our findings support a stochastic rather than programmed potential role of residual nucleosomes in mammalian sperm in regulating paternal gene expression during ensuing embryonic development.