Designing synthetic regulatory domains to understand gene expression

Introduction

How the genome controls precise, cell-type specific gene expression is crucial for cell identity and differentiation. Short cis-regulatory elements, such as enhancers, are distributed in extended regulatory domains surrounding their target gene, which in mammals typically span hundreds of kilobases.

Current Understanding

Although all evidence indicates that gene regulation is controlled by the combined action of large domains, our current understanding mostly focuses on enhancers. If and how intervening DNA sequences, enhancer order, or spacing within regulatory domains contribute to gene regulation is unknown. The reason for this largely unexplored aspect lies in our limited ability to systematically alter large genomic regions.

Study Objectives

In this study, we will use recent advances in synthetic biology to overcome this limitation. From synthetic DNA, we will create variants of entire gene regulatory domains and integrate these into mouse embryonic stem cells.

Methodology

We will test synthetic regulatory domain function in tailored gene expression analyses using:

• Cell culture
• Organoid models
• In vivo models

By investigating regulatory elements with respect to their surrounding regulatory domain, we will uncover hidden rules of gene regulation.

Parameters to be Assayed

In variant regulatory domains, we will systematically assay understudied parameters, such as:

1. Enhancer spacing
2. Enhancer order
3. Inter-enhancer sequences

Techniques Used

We will use single-molecule methods to measure gene expression levels, employ organoid and in vivo systems to profile cell-type specific changes in expression patterns, and utilize the unique potential of synthetic DNA to understand the fundamental link between DNA sequence and chromatin composition of regulatory domains.

Conclusion

With this interdisciplinary approach, we aim to uncover previously hidden layers of genomic information. The insights generated from this work will provide a novel and unique view on the organization of the non-coding genome, with the potential to expand our ability to read and write genomic DNA sequences.