Role of three-dimensional genome architecture on innovation through gene duplication in chordates

forthcoming

Inside the nucleus of each eukaryotic cell, DNA is intricately packed into a three-dimensional (3D) structure essential for gene regulation. However, its role in genome evolution, particularly in gene function innovation, remains largely unexplored. Gene duplication is the primary evolutionary path to gene function innovation. This project aims to investigate the interplay between gene duplication evolution and 3D genome structure in chordate genomes by comparing zebrafish to amphioxus, a non-vertebrate marine chordate that diverged from the rest of chordates about 500 million years ago. By generating, for the first time, 3D genome structure maps for several amphioxus organs, I will construct an atlas of gene duplications in zebrafish and amphioxus, encompassing sequence, synteny, gene expression, and 3D genome structure information. Leveraging the information encompassed in this atlas, I will investigate the intricate dynamics between the origin and evolutionary fate of chordate duplicated genes, emerged either by whole-genome or small-scale duplication, and the 3D genome structure around them. By combining my expertise in evolution of gene duplications and amphioxus genomics, with my host group’s experience in 3D genomic architecture and its evolution, we will be able to provide deep insight into the spatial mechanisms of gene innovation through duplication. Studying the effect of 3D genome structure across amphioxus and zebrafish organs in the context of gene duplications, will position me at the forefront of this emerging field within the comparative genomics community. Altogether, the results obtained will enhance our understanding of the evolution of new gene functions, and open new avenues for structural and evolutionary genomics.