Elucidate TE Impact On Sex Chromosome Regulatory Evolution

Objective

Understanding sex chromosome evolution is crucial in evolutionary biology. In eukaryotes with separate sexes, sex determination often involves heteromorphic sex chromosomes that have diverged after recombination arrest. The Y(/W) chromosome loses protein-coding genes over time, causing gene dosage imbalance between sexes and Dosage Compensation (DC) mechanisms' evolution. The first steps of DC evolution are still unclear. Recent theoretical work suggests a gradual coevolution of X(/Z)-upregulation and Y(/W)-downregulation through cis-regulators divergence. In agreement, positive selection on Y-cis regulators drives Y-downregulation in stickleback. Yet, while it loses genes, the Y(/W) chromosome also accumulates Transposable Elements (TEs). This accumulation is generally considered as a source of deleterious mutations contributing to Y(/W) degeneration, however it could also actively contribute to the silencing of Y-linked genes, as the silencing mechanisms controlling TEs proliferation can spread to nearby genes. So far, this dual role of TEs has not been fully appreciated. The proposed project will fill this knowledge gap by examining three pairs of ant-cricket neo-sex chromosomes undergoing regulatory evolution. I will assess TE dynamics, its impact on cis-regulators chromatin structure and gene expression, and especially if TEs actively silence Y-protein accumulating deleterious mutations. This project will use a multi-disciplinary approach that combines comparative genomics, transcriptomics, epigenetics, and population genetics and portray sex chromosome regulatory evolution with an unprecedented level of detail. I will acquire new skills in epigenetics, deepen my knowledge of theoretical population genetics, and improve my management and writing skills. In exchange, I will share my expertise in bioinformatics and TEs, as well as my knowledge of a promising new biological model, which will certainly spark new research ideas and collaborations.