Project description
Gene regulation and function of the 3D genome
The three-dimensional organisation of the genome inside the nucleus, referred to as the 3D genome (3DG), is crucial for gene regulation. The building blocks of the 3DG have been identified, but their contribution to gene regulation is not clear. The EU-funded FuncDis3D project aims to functionally dissect the 3DG to understand its effects on gene expression. The approach is to induce changes in the 3DG by acute protein depletion and evaluate these changes over time. The preliminary data show that by depleting regulators of the 3DG the changes occur within a few hours. Researchers will deplete a range of proteins in pluripotent and differentiated cells to determine their contribution to 3DG organisation. Simultaneous characterisation of the epigenome and transcriptome will allow them to determine the sequence of changes.
Objective
The three-dimensional organization of the genome inside the nucleus (3DG) is crucial for gene regulation. Although the fundamental building blocks of the 3DG have been identified, how they contribute to gene regulation is incompletely understood. In recent years my lab has started to functionally dissect the 3DG in order to understand the effects on gene expression. The current proposal intends to expand this work and aims to i) broaden the array of proteins that are known organize the 3DG, ii) determine how loss of these proteins affects the 3DG and iii) elucidate how this influences gene expression.
The key to this is to induce changes in the 3DG by acute protein depletion and measuring changes over time. We have preliminary data showing that by depleting regulators of the 3DG we can induce changes within a few hours. We will deplete a range of proteins in pluripotent and differentiated cells to determine their contribution to 3DG organization. Simultaneous characterization of the epigenome and transcriptome will allow us to determine the sequence of changes. In addition, we will perform Thousands of Reporters Integrated in Parallel (TRIP) after perturbation of the 3DG. TRIP reporters all have the same minimal promoter that acts as a sensor for promoter-enhancer (mis)-communication. By combining TRIP with 4C we can measure the changes in the reporter-enhancer interaction landscape. Our data will generate fundamental insight into the parameters that govern the interactions between promoters and regulatory elements, within the context of the 3DG, and their effects on gene expression. Furthermore, it allows us to determine the temporal order of changes in the 3DG, the epigenome and gene expression, which is essential for the establishment of cause-and-effect relationships. Collectively, our data will lead to a better appreciation of how distal and proximal regulatory regions cooperate to establish cell-type specific gene expression programs.
Fields of science
Programme(s)
Funding Scheme
ERC-COG - Consolidator GrantHost institution
1066 CX Amsterdam
Netherlands