Mutation rate determinants across cellular and evolutionary scales

Introduction

As individuals age, mutations accumulate inexorably in their cells, playing a key role in evolution, ageing, and disease. Despite their importance, we still have a poor understanding of how mutations originate, or why some cells accumulate more mutations than others. This proposal aims to address these fundamental questions by examining two axes of mutation rate variation: among cell types and across species.

Aim 1: Decoding Germline Mutation

In Aim 1, we will decode the rules of germline mutation during mammalian spermatogenesis.

Mutation Rates in Germline vs. Soma

Cells in the germline exhibit mutation rates significantly lower than those in the soma, through mechanisms that remain unknown.

Methodology

Leveraging recent breakthroughs in long-read DNA sequencing, we will track the accumulation of mutations from spermatogonial stem cells to mature spermatozoa in mice. By integrating this data with existing cell type-specific profiles of gene expression, epigenetic marks, and chromatin architecture, we will delineate how cellular processes influence mutation rates in the germline, aiming to reveal differences with patterns in the soma.

Aim 2: Characterising DNA Damage Response

In Aim 2, we will characterise the DNA damage response across primates.

Background on Somatic Mutation Rates

Recent findings suggest that longer-lived mammals have lower somatic mutation rates, but the underlying mechanisms remain elusive.

Experimental Approach

To tackle this question, we will experimentally expose primary fibroblasts of ten primates to UV radiation and a promoter of oxidative stress, quantifying the impacts on:

1. Cell viability
2. Gene expression
3. Genome accessibility
4. Mutation rates and spectra

With this comprehensive approach, we will disentangle the pathways leading to damage-induced mutations, as well as uncover molecular mechanisms that evolution has wielded to select for healthier, longer-lived primates.

Conclusion

In summary, this proposal aims to learn about how mutations occur—that is, how they originate mechanistically—as well as why their rate of appearance differs across cell types and species—namely, what selective pressures drive mutation rate evolution.