Project Title: Dissecting the evolution of 3D genome structure with Pore-C nanopore sequencing
Summary: 3D genome structure is fundamental for gene regulation. However, how genome structure evolves and is influenced by other genomic features such as DNA modifications, repeats, or heterozygosity is still unclear. Our current understanding of this biological phenomenon is limited by relying mostly on distantly related model organisms with highly dissimilar genomic organisations and genome regulatory features. Current methods to reconstruct 3D genome structure such as Hi-C rely on short-read sequencing, which makes resolving highly repetitive regions and phasing high-order haplotype blocks in heterozygous genomes challenging, both experimentally and computationally. In late 2019, Oxford Nanopore Technologies (ONT) released Pore-C, a method to apply nanopore long-read sequencing to reconstruct 3D genome structure that overcomes current limitations in chromatin conformation approaches. To date Pore-C has only been used in mammalian samples.
In my PhD project we will expand the use of Pore-C to study the 3D genome architecture in non-mammalian genomes. We will benchmark Pore-C for chromosome scaffolding outside of mammalian/vertebrate genomes. This will include invertebrates with a range of differing genomic features, protist and plant genomes. Additionally, we will attempt to benchmark Pore-C to call topologically associated domains (TADs) in Owenia fusiformis. We will also explore 3D genome architecture in different annelid species at different life stages, focusing on the segmented worms established in the Martin-Duran lab; Owenia fusiformis, Capitella teleta and Dimorphilus gyrocilliatus. Altogether my PhD will establish ONT Pore-C methodology in non-mammals and investigate high-order genome structure and its role in evolution