Dissecting the evolution of 3D genome structure with Pore-C nanopore sequencing

点击翻译按钮获取中文摘要

Aim: The aim of this project is to investigate how high-order genome structure evolves and corelates withlow-level genomic features (repeat content, heterozygosity and DNA methylation) using as proxy annelidworms and exploiting ONT Pore-C methodology.Objectives: To address this aim, we will implement three main experimental and computational objectives:- Objective 1: Reconstruct high-order genome structure in adults of the annelids Owenia fusiformis andCapitella teleta.- Objective 2: Profile genome-wide DNA methylation patterns (5mC) in adult O. fusiformis and C. teleta inrelation to chromatin comformation and functionally explore the impact of DNA methylation in chromatinstructure.- Objective 3: Develop new software solutions to reconstruct high-order genome structure from Pore-Cnanopore data in cases of high heterozygosity and high repeat content, simultaneously calling methylation.Fit into BBSRC remit: This academy-industry collaboration aligns with and addresses core BBSRC researchpriorities: "Systems Biology" (understanding high-order DNA structure through computational biology), "DataDriven Biology" and "Technology Development for the Biosciences" (generation of new software applicationsfor 'omics' technologies, in particular to resolve chromosome-scale DNA structure under confoundinggenomic contexts).Project impact: This project will (i) provide fundamental understanding of the principles of 3D genomestructure; (ii) generate novel software solutions to the study of genome structure; and (iii) foster academyindustrycollaborations that strengthen the leading position of UK biosciences in the 'omics' field.The PhD student will have weekly one-to-one meetings with the academic and non-academic mainsupervisors to monitor progress. The PhD student will participate in weekly lab meetings where there will bethe opportunity to share data and get feedback with other members of the main academic and non-academiclab, and the student will also engage with the secondary academic supervisors on a regular basis (fortnightlyor monthly). The PhD student will actively participate in the meetings of the QMUL Epigenomics Hub, a groupof 13 researchers united by their common interest on genomic regulation, and in the SBCS departmentalseminar series, where once per year PhD students and postdocs present their projects to a wider audienceand gain feedback from different expertises. In addition, the student and main academic and non-academicsupervisors will communicate on a daily basis either on-site or remotely via team-working apps.