Chromatin architecture and regulation

In human cells, DNA, our genetic blueprint, is precisely folded with proteins in a complex called chromatin. This serves two purposes, to protect DNA from damage and to regulate how DNA is read by molecular machines, in a process called transcription; mistakes in reading DNA lead to altered proteins and change cell function. The regions of our genomes that need to be read are called genes and despite many years research we do not understand how DNA is folded up inside cells, particularly at the specialised regions in front of genes called promoters and enhancers. In this programme we will develop new tools to map the 3D structures of DNA/proteins in human cells and create a high resolution map of our genomes. We will then focus on mapping the structure of specific promoters and enhancers for genes that are well known to be important for human disease and identify the molecular mechanisms for controlling promoter folding and function. This project will provide fundamental insight into how DNA is packaged and regulated in human cells. This information will subsequently enable us to investigate how chromatin folding is altered in disease and to develop new therapies to correct these changes.

Characterising and investigating the 3D architecture of regulatory features (promoters, and enhancers) is fundamental to understanding how these components function. Based on our previous studies and evidence in the literature we hypothesise that chromatin architecture of local genomic features form discrete structural states that regulate activity. These states are further modulated by genetic variants and mutations, which influence gene expression and phenotypic variation. This idea moves away from the notion that local chromatin is merely a structural phenomenon but is instead a gatekeeper for determining regulation. To test our hypothesis we will investigate local chromatin architecture of genomic features (promoters and enhancers) and define their structural states. We will then modulate local chromatin architecture to understand how this affects transcription. Finally we will investigate how sequence variants and mutations can alter local chromatin architecture and transcription. This study will provide new insight into the structural organisation of the human genome and enable us to understand the molecular basis for critical aspects of gene regulation. Importantly it will also provide a framework for generating the first high-resolution chromatin fibre map of the human genome. To achieve these goals we will study three inter-related aims: 1. Develop chromatin interaction analysis (CIA) to investigate the 3D architecture of the higher-order chromatin fibre. 2. Investigate distinct classes of promoter chromatin architecture. 3. Analyse the 3D chromatin architecture of specific regulatory elements (at Pax6 and Pou5F1).