Higher-order genome architecture of spermatids guides chromatin assembly in mature sperm

Differential packaging of vertebrate sperm and egg genomes is evolutionarily conserved for hundreds of millions of years. Unlike oocytes, post-meiotic spermatid nuclei are thought to uniformly replace histones with transition proteins (TNPs) and, ultimately, with protamines, the small non-histone structural proteins. Tracking of endogenously tagged protamines overturns the classical model of paternal chromatin remodeling, revealing a direct histone-to-protamine-1 transition that occurs independently of both TNPs and protamine-2. Stage-resolved chromatin profiling across 26 spermatid datasets reveals that chromatin compaction is a programmed process that requires H4-hyperacetylation but is not instructed by it. Rather, chromatin remodeling is guided by the pre-meiotic 3D-architecture of the spermatid nucleus: i.e., compaction of the A-compartment precedes B-compartment. This compartment-encoded template for sperm nuclear remodeling suggests that male-specific protamine patterns can transmit pre-meiotic structural information to the zygote and may impact embryonic development.