Transcription-induced mutation and gBGC at the Transcriptional Start Site impact the evolution of human protein-coding genes

In the human genome, mutation rates vary along genes, yet their fine-scale structure and causes have remained largely unexplored. Here, we map mutations at single-nucleotide resolution, and uncover a striking hypermutation peak at transcription start sites (TSSs). This pattern is observed both in population polymorphisms (gnomAD) and in de novo mutations from parent-offspring trios, and is dependent on transcriptional activity in testes. We also find a hypermutation peak at TSSs used to produce long noncoding RNAs and at intergenic RNA Polymerase II pause sites. We also identify distinct mutational signatures at exon-intron boundaries and in introns. By comparing the current nucleotide content to predicted equilibrium levels, inferred from mutation and fixation rates, we observe signals that are compatible with a low level of ongoing background GC-biased gene conversion (gBGC) throughout the region and ancestral gBGC occurring just downstream from the TSS. Using a forward-in-time simulation algorithm we demonstrate that the current nucleotide composition surrounding the TSS of protein-coding genes is best explained by local biases in the mutation rate coupled to gBGC, due to ongoing and ancestral crossover events. We then use the algorithm to model some of the features of these gBGC events. Overall, these findings indicate that the local nucleotide composition around TSSs is largely shaped by non-adaptive forces, such as mutation bias and gBGC.