Widespread Transcriptional Scanning in the Testis Modulates Gene Evolution Rates

The testis expresses the largest number of genes of any mammalian organ, a finding that has long puzzled molecular biologists. Our single-cell transcriptomic data of human and mouse spermatogenesis provide evidence that this widespread transcription maintains DNA sequence integrity in the male germline by correcting DNA damage through a mechanism we term transcriptional scanning. We find that genes expressed during spermatogenesis display lower mutation rates on the transcribed strand and have low diversity in the population. Moreover, this effect is fine-tuned by the level of gene expression during spermatogenesis. The unexpressed genes, which in our model do not benefit from transcriptional scanning, diverge faster over evolutionary timescales and are enriched for sensory and immune-defense functions. Collectively, we propose that transcriptional scanning shapes germline mutation signatures and modulates mutation rates in a gene-specific manner, maintaining DNA sequence integrity for the bulk of genes but allowing for faster evolution in a specific subset. [Display omitted] •Genes expressed in the testis have reduced germline mutation rates•Germline mutational signature is tuned by spermatogenesis-gene expression levels•Genes not expressed during spermatogenesis are enriched for fast-evolving functions•A germline mutational signature generated by TCR follows a “3′-pyrimidine rule” The male germline cells in human and mice balance the protection of genomic integrity and the evolutionary benefit of genetic mutations through transcriptional scanning, a mechanism that preferentially couples efficient DNA damage repair with high transcription activity.