Understanding cellular variation of 3D genome organization using novel Nanopore-sequencing-based Chromosome Conformation Capture assays. – Nanopore 4 3D-Genome

Below, my abstract as provided in my ERC-StG project is provided:

To understand the mechanisms of gene transcription and regulation, the essential functions of tridimensional (3D) genome organization in these processes need to be dissected. Our current knowledge of 3D organization is incomplete because the available technology provides incompatible data. High-resolution 3C-based assays (Chromosome Conformation Capture) indicate highly distinct patterns of 3D organization, whereas single-cell microscopy experiments reveal dramatic variation. To fully understand the functions of 3D organization, technology is needed that bridges the gap between these technologies.

In this project, I aim to develop two new technologies that combine 3C approaches with Nanopore sequencing and improved library preparation to study the variability in 3D organization at the level of individual cells and at unprecedented resolution. A Nanopore 3C-seq experiment quantifies the variation of 3D organization at defined genomic sites from thousands of individual cells. A Nanopore Hi-C experiment comprehensively determines the complete 3D interactome of individual cells at high resolution.

These technologies will be used to advance understanding of cell-to-cell variation in 3D genome organization and determine how this variation can influence cellular function. For the first time, naturally occurring variation in 3D genome organization will be determined at ultra-high resolution. Moreover, the importance of specific 3D structures in the stabilization of 3D genome organization will be established, focusing on the role of Topological Associated Domains (TADs). A diagnostics application to determine breast cancer tumor heterogeneity will be developed using Nanopore 3C- seq to quantitate the frequency of 3D remodeling.

Together, the data generated by Nanopore 3C-seq and Nanopore Hi-C are expected to revolutionize our understanding of natural cell-to-cell 3D genome variability and how defined 3D structures can influence the processes of gene transcription and regulation.