Spatio-temporal Organization and Expression of the Genome

Project Information

4D-GenEx

Grant agreement ID: 757956

DOI

10.3030/757956

Project closed

EC signature date 25 September 2017

Start date 1 April 2018

End date 31 March 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 499 750,00

EU contribution

€ 1 499 750,00

Coordinated by

CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE CNRS
France

Periodic Reporting for period 5 - 4D-GenEx (Spatio-temporal Organization and Expression of the Genome)

Reporting period: 2024-04-01 to 2025-03-31

Summary of the context and overall objectives of the project

Every cell in our body contains the same genome — a vast ensemble of over 20,000 genes packed into long DNA molecules inside the nucleus. Yet different cells activate different subsets of genes, allowing them to perform specialized functions. Disruptions in this tightly regulated process can lead to diseases such as cancer, where a cell may inappropriately express certain genes and become tumorigenic.

Recent discoveries have shown that the way DNA is folded in three-dimensional space inside the nucleus plays a crucial role in determining which genes are turned on or off. In particular, certain DNA elements known as “enhancers” can activate genes that are far away on the linear DNA sequence, brought close together by 3D folding. However, despite a growing number of observations linking genome architecture to gene regulation, the underlying mechanisms remain poorly understood.

The aim of the 4D-GenEx project was to uncover the physical principles that govern how the genome is spatially organized in the nucleus and how this organization influences gene expression. To achieve this, we developed innovative experimental and theoretical tools to visualize and manipulate the 3D genome in living cells, and to model the links between structure, dynamics, mechanics, and gene function.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Over the course of the project, we made several key advances:

• We showed how the local folding of DNA into structures known as topologically associating domains (TADs) enables cells to co-regulate multiple genes in a coordinated fashion. This was achieved by developing a microscopy approach to image the transcriptional activity of gene pairs at single-molecule resolution and developing a data analysis framework to quantify how transcription are coupled between gene pairs.
→ This work is presented in our eLife article.

• We developed a novel technique to physically manipulate a specific genomic region within the nucleus using magnetic nanoparticles. By applying controlled forces directly to the genome, we revealed the viscoelastic properties of chromatin and challenged the notion that it behaves like a gel, with direct implication for gene expression.
→ These findings appeared in our Science article.

• We constructed a unified theoretical framework to interpret the structure, dynamics, and mechanical behavior of chromosomes, based on principles of polymer physics. Our analysis demonstrated that existing models fail to reconcile all experimental observations and identified the physical conditions that a successful model must meet.
→ This work was published as a preprint and is currently under review.

• We synthesized and discussed emerging views on interphase chromatin mechanics and genome regulation in a review article in a widely read journal, laying out new conceptual directions for future research.
→ This appeared as a review in Current Opinion in Genetics & Development.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The 4D-GenEx project achieved several breakthroughs beyond the existing state of knowledge:
• We pioneered a method to actively perturb genome organization using live-cell magnetic micromanipulation — a first in the field.
• We developed new analytical frameworks for measuring and interpreting transcriptional co-regulation at the single-allele level.
• We introduced a novel physical theory connecting chromosome structure, dynamics, and mechanics, based on scaling laws and polymer models, opening new avenues for both experimental and theoretical work.

3levels.png