Histone Variant H2A.B.3 Orchestrates a New Nuclear Pathway for Histone mRNA Decay

Replication-dependent (RD) histones are key proteins that ensure continuous DNA packaging during cell division. In dividing cells, RD histone mRNAs are produced during S phase and rapidly degraded afterwards in an UPF1-dependent manner. However, RD histone mRNA regulation in non-dividing cells has remained largely unclear. This study uncovers a new nuclear pathway controlling RD histone mRNA degradation in non-dividing, post-meiotic male spermatids. The process depends on the histone variant H2A.B.3, which is enriched at nucleosomes within histone gene clusters and interacts with UPF1 in an RNA-dependent manner. Loss of H2A.B.3 leads to abnormal stabilisation of histone mRNAs in haploid germ cells, revealing a unique post-meiotic mechanism for histone mRNA turnover. We demonstrate that H2A.B.3 binds the stem-loop structure of RD histone mRNA. This interaction facilitates the recruitment of active phosphorylated UPF1 (phUPF1) to RD histone mRNA in the nucleus, promoting its degradation by the nuclear exosome. Overexpression of H2A.B.3 enhances RD histone mRNA decay, while UPF1 depletion abolishes this effect. Collectively, these findings define a mechanism by which H2A.B.3 recognises the histone mRNA stem-loop and recruits UPF1, revealing a previously unrecognised nuclear function of UPF1 that links histone variant–mediated chromatin regulation to selective histone mRNA degradation required for histone–protamine exchange and male fertility. These findings uncover an alternative nuclear mechanism of histone mRNA degradation crucial for histone-protamine exchange and male fertility and may also have broader implications for malignancies in which H2A.B is upregulated.