Interrogating the mesoscale chromatin domain organisation and function with super-resolution imaging

Abstract
Life on earth is thought to have begun with self-replicating molecules as the ancestors of DNA. The evolution of mechanisms to wrangle increasingly sophisticated functions out of genetic material is central to the development of complex, multicellular life. Cells have evolved to express a sub-set of genes which facilitate their specific function. Gene expression is intricately and dynamically regulated in time and space, with the 3D structure of the genome playing a crucial role. This project aims to test a recently developed model of genome structure and function. We envision the nucleus as a sponge, with the DNA forming a mesh-like network separated by channels containing RNA. We hypothesise that transcription occurs where the DNA compartment interfaces with the RNA compartment, and that mechanisms of gene regulation act to manipulate which genes are in contact with the RNA compartment and therefore accessible for transcription. We aim to test the model with super-resolution imaging, with which we can visualise genes and regulatory elements within this nuclear landscape. We plan to advance the techniques available for imaging DNA at high resolution, as well as perform perturbation experiments to gain mechanistic understanding of the significance of this genome structure. We aim to produce a refined model of the fundamental organisation of the interphase genome and mechanisms of gene regulation, grounded in the context of the nucleus and at the single cell level.
BBSRC Research Priorities
This project ties into the BBSRC research priorities of "Understanding the rules of life" through the study of the fundamental mechanisms of eukaryotic genome function and "Transformative technologies" by advancing super-resolution imaging and analysis methods.