Paternal chromatin undergoes extensive structural and epigenetic changes during mammalian spermatogenesis, producing sperm that contain an epigenome optimal for the transition to embryogenesis. Histone modifiers play an important role in this process by encoding specialized regulatory information in the sperm epigenome. Lysine demethylase 6a (KDM6A) promotes gene activation via demethylation of H3K27me3, a developmentally important repressive modification abundant throughout the epigenome of

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... rm and embryonic stem cells. Despite its developmental importance in pluripotent cells and germ cell progenitors, the function of KDM6A during spermatogenesis has not been described. Here, we show that Kdm6a is transiently expressed in the male germline in late spermatogonia and during the early stages of meiotic entry. Deletion of Kdm6a in the male mouse germline (Kdm6a cKO) yielded a modest increase in sperm head defects but did not affect fertility or the overall progression of spermatogenesis. However, hundreds of genes were deregulated upon loss of Kdm6a in spermatogenic cells and in an immortalized spermatogonia cell line (GC-1 spg) with a strong bias towards downregulation. Single cell RNA-seq revealed that most of these genes were deregulated in spermatogenic cells at the same stage when Kdm6a is expressed and encode epigenetic factors involved in chromatin organization and modification. A subset of these genes was persistently deregulated in the male germ line across two generations of offspring of Kdm6a cKO males. Our findings highlight KDM6A as a transcriptional activator in the mammalian male germline that is dispensable for spermatogenesis but important for safeguarding gene regulatory state intergenerationally.