Protein binding as a selective filter for new mutations at regulatory sites in the germline and in cancers

Abstract

Genetic mutations provide the raw material for evolution, they are responsible for heritable disease and drive the development of cancer. It has been previously shown that the binding of chromatin and regulatory proteins to DNA can interfere with replication, surveillance and repair processes but the proposed mechanisms presume the loading of sequence-specific binding factors over nucleotide mismatches and other lesions. This seems paradoxical for binders that recognise their docking sites by motif with defined sequence. In this work I propose the biased mask model where the binding of some transcription factors can tolerate mismatch substitutions or other lesions strand specifically at some sites, acting as a selective filter of new mutations. I provide electrophoretic mobility shift assay support for the biased mask, and illustrate how it is shaping the mutation patterns of both cancers and the human germline. Being replication associated, the mutational burden of this biased mask predicts that the protein binding sites occupied during germline replication are hotspots for functionally important mutations, which will be exacerbated by increased paternal age. Exploring this, in collaboration with other group we have isolated and applied chromatin accessibility assay, ATAC-seq, to primary human and mouse spermatogonial cells, which account for up to 80% of human and 30% of mouse germline DNA replication. I have used this data to develop a custom ATAC-seq processing pipeline and map protein binding landscape of the germline, and also of a number of somatic tissues for which ATAC-seq data was available. By combining this map with human and mouse population variation data I confirm sequence specific binding sites in germline as hotspots of deleterious mutations, and provide evidence that this mutational effect is dependent on protein binding.