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. To this end, we used expression data from male and female germline cells and phased de novo germline mutations from pedigrees. Focusing on protein-coding genes, we found no relationship between the male mutation rate and gene expression levels in the fetal germline or in adult testis tissue, despite evidence for transcriptional asymmetry. Individual stages of spermatogenesis differ in their contribution to mutation, however: expression levels in spermatogonial stem cells 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 readily detected from its cumulative effect on the total germline mutation rate. In females, by contrast, mutation rates increase significantly with transcription levels in the fetal germline, adult oocytes and adult ovary tissues, consistent with widespread transcription asymmetry. We confirm the difference between the sexes by analyzing phased mutations from three-generation pedigrees and the lack of an association in males by analyzing paternal mutations from seminiferous tubules and sperm. Thus, transcription has distinct effects on the mutation rate in the two sexes, leading to an increase in mutations in females but not males, in contrast to what one might expect from the overall paternal bias in germline mutations.