Systematic identification of Y-chromosome gene functions in mouse spermatogenesis [10x]

The mammalian Y chromosome is essential for male fertility, but how individual Y genes regulate spermatogenesis is poorly understood. To resolve this question, we generate a deletion series of the mouse Y chromosome, creating thirteen Y-deletant mouse models and conducting exhaustive reproductive phenotyping. Eight Y genes, including several that are deeply conserved and exhibit testis-specific expression, are dispensable for spermatogenesis. For others, we uncover novel functions, including a role for Uty in establishment and differentiation of spermatogonia, and for Zfy2 in ensuring meiotic pairing and reciprocal recombination between the sex chromosomes. We also generate the first mouse equivalent of the human infertility AZFa deletion, revealing cumulative detrimental effects of Y-gene loss on spermatogenesis. We use single nuclei RNAseq to identify candidate mechanisms by which Y genes regulate the germ cell transcriptome and reveal an unexpected impact of Y genes on testis supporting cells. Our study represents a paradigm for the complete functional dissection of a mammalian Y chromosome and advances our knowledge of human infertility and Y-chromosome evolution. To gain deeper molecular insights into each spermatogenic defect, we performed single nuclei RNA sequencing on Eif2s3y-KO, Uty-KO, AZFa-KO, Zfy2-KO, and Zfy1&2-DKO males. P10 testes from Eif2s3y and Uty-KOs were used to enrich for spermatogonia, since this was where the phenotypes manifested, and adult testes were used for Zfy1, Zfy2, Zfy1&2, and AZFa-KOs to capture all cell types.