3D chromatin compartment of round spermatids encodes the spatiotemporal program of histone-to-protamine exchange in spermiogenesis

Sperm formation requires a radical chromatin reorganization, where nucleosomes are replaced by transition proteins (TNPs) and subsequently by protamines (PRM1 and PRM2). Although essential for fertility, the regulatory logic governing this exchange is unknown, but it’s presumed to be stochastic and unregulated. Using endogenously tagged PRM mouse models and stage-resolved, genome-wide profiling, we revise the order of histone-to-protamine exchange and show that the chromatin remodeling process is highly programmed. Imaging and biochemical experiments reveal a direct histone-to-PRM1 exchange, while TNPs appear after PRM1 but precede PRM2 incorporation. This temporal uncoupling of PRM1 and PRM2 incorporation coincides with dynamic, region-specific chromatin remodeling that is not governed by histone acetylation but is instructed by the three-dimensional nuclear architecture of round spermatids. Therefore, by integrating ATAC-seq, CUT&Tag, and Hi-C, we define a compartment-encoded “blueprint” that prescribes the assembly of the mature sperm epigenome and establishes a complex molecular hierarchy for the histone-to-protamine exchange.