On Evolution of Gene Regulation in Mus

Abstract

What constitutes the genetic basis of adaptation is a fundamental question in evolutionary biology. Evolution of gene regulation is a major contributor to phenotypic variation and as such plays a critical role in adaptation. In general, regulatory changes can be facilitated through genetic changes in either cis-regulatory elements (CREs), which modify gene expression of local genes on their own allele, or in trans-regulatory factors such as transcription factors, which can affect any gene in the genome. Pinpointing genetic variation facilitating expression changes is challenging, but current evidence points to cis-regulatory changes being the main contributor to regulatory evolution, though this is debated. However, much remains unknown about how gene regulation at the chromatin, transcript and cellular level evolves in mammals, especially at the crucial transition from individual to species-level differences. In this thesis, I investigated cell-type specific regulatory evolution between several Mus species with particular focus on the role of CREs. In the first chapter, I developed easySHARE-seq, a single-cell technique simultaneously measuring gene expression and chromatin accessibility. I show that easySHARE-seq generates high-quality datasets and removes cost-prohibitive barriers, allowing diverse and flexible study design. I further demonstrate how the simultaneous measurements can be exploited to survey the cis-regulatory landscape of cell types and link CREs to their target gene. In the second chapter, I apply easySHARE-seq to four different species and their F1 hybrids from Mus to investigate how gene regulation evolved across them. I find that in all cell types cis-regulatory changes become pervasive with increasing evolutionary divergence. However, between closer related species the majority of regulatory changes occur in trans. Furthermore, I argue that some cell types might follow common evolutionary trajectories independent of species, possibly due to similar selective pressures. Lastly, I link CREs to their target gene in each species and cell type and show that these linked CREs are generally under purifying selection yet those linked to cis-regulated genes show signatures of adaptive evolution. These results contribute to uncovering the genetic basis of adaptation by demonstrating that CREs are the dominant driver of regulatory evolution across Mus. They also provide a novel approach in identifying genetic variants underlying regulatory changes in CREs.