Single-nucleus transcriptomics and phosphoproteomics identify misregulated sperm components in mice carrying a selfish supergene

The t-haplotype is a selfish variant of the mouse chromosome 17. It reaches 90-100% transmission rates in heterozygous (+/t) males through a poison-antidote system that disables sperm carrying the homologous (+) haplotype. While several poisons and one antidote have been identified, how these mediate drive, and what additional molecular players are involved, is not fully understood. Here, we characterized patterns of gene expression throughout spermatogenesis in +/t versus +/+ males using single nucleus RNA sequencing. Genes differentially expressed in early spermatogenesis, when poisons are likely to be expressed, were enriched for key regulators of sperm motility. These included dyneins, which provide the motor function of sperm flagella, and protein phosphatase 1 (PP1) complex genes, which regulate protein activity through dephosphorylation. Phosphoproteomics of +/t versus +/+ testes revealed changes in phosphorylation levels of several spermatogenesis proteins, supporting a contribution of dysregulated phosphorylation to the biology of the t-haplotype. In particular, the PP1 component PPP1CC2 itself showed significantly decreased phosphorylation in +/t testes. Further, we found that dyneins located on both the t-haplotype and the corresponding standard version of chromosome 17 have undergone large increases in spermatocyte expression in the house mouse lineage. We argue that this may result from an ongoing arms race between the homologs for transmission rates. Together, these results extend our understanding of the molecular changes associated with the t-haplotype, and highlight the value of integrating various OMICS approaches to investigate the mechanisms and evolutionary consequences of transmission distortion.