Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos

Introduction

During mammalian embryogenesis, key events involving DNA and regulatory molecules over seconds and nanometers affect and are affected by a major reorganization of the genetic material in the nucleus over hours and micrometers. How these scales are spanned and integrated into the course of development remains a major unresolved challenge.

Challenges in Current Research

Progress in this quest is difficult for several reasons:

1. Current model systems suffer from severe technical limitations.
2. Existing analytical approaches probe individual spatial or temporal scales, thus ignoring their evolving interactions.
3. Traditional live imaging lacks the spatial resolution to accurately delineate chromosome organization at the scale of genes.
4. Bulk molecular assays are ill-suited for studying development over time.

Proposed Approach

Here, we propose a multi-disciplinary approach to the dynamics of developmental gene regulation to understand the details of the underlying mechanisms and their deployment over time.

Methodology

We combine and apply optical, molecular-genomic, and theoretical tools to recently available mammalian pseudo-embryos, allowing:

• Unprecedented precision in developmental staging.
• A large amount of material.
• Easy optical access.

By focusing on select gene loci, we track transcriptional activation and the interactions of distal DNA elements in real-time along with the associated chromatin dynamics using interaction profiles.

Data Analysis

Our datasets are iteratively distilled into mathematical models of increasing scope, converging towards an integrative dynamic polymer model that simultaneously captures:

• Long-timescale chromatin rearrangements.
• Short-timescale motions of genetic regulatory elements and transcriptional activity.

Experimental Validation

We then challenge these models via genome editing and temporally defined interventions by building light-controlled tools to affect the chromosome landscape.

Conclusion

This project aims to reshape our view of how genes are regulated during mammalian development.