Genome compartments guide protamine replacement and genome stability during spermiogenesis

Masashi, H.; Zhong, C.; Inoue, E.; Fukuda, Y.; Koga, C.; Hosokawa, M.; Chuma, S.-i.; Sato, S.; Kurumizaka, H.; Ikawa, M.; Baek, S. H.; Okada, Y.

doi:10.64898/2026.03.08.710361

bioRxiv · 10.64898/2026.03.08.710361

Genome compartments guide protamine replacement and genome stability during spermiogenesis

Masashi, H.·Zhong, C.·Inoue, E.·Fukuda, Y.·Koga, C.·Hosokawa, M.·Chuma, S.-i.·Sato, S.·Kurumizaka, H.·Ikawa, M.·Baek, S. H.·Okada, Y.

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Abstract

Compartment-scale genome organisation persists in mammalian sperm, yet how histone-protamine replacement is orchestrated in space and time during spermiogenesis remains unclear. Here we combine stage-resolved purification of mouse spermatids with spike-in-normalised ATAC-seq and PRM1 CUT&Tag to map chromatin accessibility and protamine incorporation across spermiogenesis. We uncover a transient, genome-wide hyper-accessible phase coincident with replacement that is uncoupled from transcription and suppressed in catalytic PHF7-mutant spermatids. PRM1 loading initiates within accessible A-compartment chromatin and later spreads across both A- and B-compartments, whereas protamine-null mice demonstrated that PRM1/ PRM2 deficiency selectively destabilises A-compartment closure. Sequencing of short DNA fragments from Prm1/Prm2 dosage-reduced epididymal sperm reveals early enrichment of breakage at protamine-targeted A-compartment regions, which dissipates as fragmentation becomes genome-wide during epididymal transit. Together, our data place histone-protamine replacement within a compartment-centred framework that links 3D genome domains to the timing, targeting and integrity of the sperm genome.

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Masashi, H., Zhong, C., Inoue, E., Fukuda, Y., Koga, C., Hosokawa, M., Chuma, S.-i., Sato, S., Kurumizaka, H., Ikawa, M., Baek, S. H., Okada, Y.. 2026-03-10. Genome compartments guide protamine replacement and genome stability during spermiogenesis. https://doi.org/10.64898/2026.03.08.710361

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