Shedding light on three-dimensional gene regulation

Introduction

The orchestration of precise gene expression patterns during differentiation and development is dependent on the cis-regulatory elements of the genome, which interact and communicate in three-dimensional (3D) chromatin structures. It is not well understood how these interactions are formed and influence gene expression.

Challenges

Our ability to identify the molecular mechanisms involved is hampered by a lack of tools that provide control over the function of regulatory proteins with high temporal precision and that measure 3D chromatin interactions at high resolution.

Project Overview

In this project, we will overcome these hurdles by utilizing an ultra-fast optogenetic system that allows for efficient and reversible nuclear depletion of mammalian proteins upon blue light exposure. We will combine this approach with a range of high-resolution genomic tools to investigate the context-specific functions of:

1. Transcription factors
2. Co-activators
3. Architectural proteins

This investigation will be conducted throughout erythroid differentiation.

Methodology

Importantly, our set-up does not only allow for the characterization of acute protein depletion, but also enables us to map the molecular events triggered by the restoration of regulatory proteins to the nucleus. This unique approach will therefore provide detailed insight into their molecular functions.

Proteomics Approach

Moreover, to get a more complete overview of the proteins involved in gene activation, we will implement a locus-specific proteomics approach that enables unbiased identification of the proteome of regulatory regions.

Conclusion

This innovative integrated research program has strong potential to transform our understanding of the molecular mechanisms that shape the genome and drive gene activation during cellular differentiation. Furthermore, it will lead to the development of cutting-edge tools to analyze gene regulation in its 3D context at high temporal and spatial resolution.