Sex differences in transcription-associated mutagenesis in the human germline

In humans, germline mutation rates are three- to four-fold higher in males than females for largely unknown reasons. We investigated whether transcription, a well-documented source of both DNA damage and repair in somatic tissues, is associated with sex differences in germline mutations. We used single-cell germline expression data from different stages of gametogenesis in males and females and phased de novo mutations from pedigrees. Focusing on protein-coding genes, we found no relationship between the male mutation rate and averaged gene expression levels during spermatogenesis despite evidence for transcription-asymmetry. Individual stages of spermatogenesis appear to vary in their contribution to mutation, however: expression levels in spermatogonial stem cells and sperm are significantly positively associated with paternal mutation rates, while those in primary spermatocytes are significantly negatively associated. Thus, transcription may have varying effects over male gametogenesis that are not visible from its cumulative effect on the total germline mutation rate. By contrast, the female mutation rate increases significantly with transcription levels averaged across different stages of folliculogenesis, with corresponding evidence for transcription-asymmetry. The difference between the sexes is also observed when using a smaller set of phased mutations from three-generation pedigrees and when relying on expression data from bulk gonadal tissues. These results indicate that transcription has distinct effects on the mutation rate in the two sexes, leading to more mutations in females but not males, in contrast to what one might expect from the overall paternal bias in germline mutations.