Towards Realistic Modelling of Nucleosome Organization Inside Functional Chromatin Domains

Project Information

InsideChromatin

Grant agreement ID: 803326

DOI

10.3030/803326

Project closed

EC signature date 17 October 2018

Start date 1 April 2019

End date 31 March 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 490 380,00

EU contribution

€ 1 490 380,00

Coordinated by

THE CHANCELLOR MASTERS AND SCHOLARS OF THE UNIVERSITY OF CAMBRIDGE
United Kingdom

Periodic Reporting for period 4 - InsideChromatin (Towards Realistic Modelling of Nucleosome Organization Inside Functional Chromatin Domains)

Reporting period: 2023-10-01 to 2025-03-31

Summary of the context and overall objectives of the project

A fundamental open challenge in molecular and cellular biology is to understand how the genome is organised in three-dimensional space and how this organisation influences gene function. Chromatin is a dynamic and heterogeneous material whose structure arises from the interplay of nucleosome breathing, histone modifications, DNA mechanics, architectural proteins, and phase separation. Despite decades of research, we lack mechanistic, high-resolution models that can integrate these factors and connect local biochemical regulation to chromatin folding across kilobase to megabase scales.

Understanding chromatin structure mechanistically is important for society because it underpins essential biological processes such as development, cellular identity, and genome maintenance. Its dysregulation is implicated in cancer, ageing, neurodegenerative disorders, and numerous epigenetic diseases. Developing realistic models of chromatin organisation is therefore critical for improving our understanding of gene regulation, for interpreting large-scale genomic and epigenomic data, and for informing future therapeutic strategies that target genome structure and function.

The overarching objective of this roject was to develop a new generation of multiscale computational models that achieve realistic, mechanistic descriptions of chromatin structure and biomolecular phase separation. Specifically, the project aimed to:
1. Develop a high-resolution coarse-grained model of chromatin.
2. Extend this model to describe functional chromatin domains.
3. Create approaches to predict chromatin structure at megabase scales.
4. Integrate chromatin and protein models to determine the role of liquid–liquid phase separation in genome and cellular organisation.

All these objectives were achieved. The project has delivered multiple multiscale simulation frameworks that combine molecular accuracy with large-scale predictive power, enabling the first realistic simulations of chromatin and biomolecular condensates across multiple levels of resolution. These models provide a mechanistic understanding of how nucleosome dynamics, DNA mechanics, histone variants and protein phase behaviour collectively regulate genome organisation. The resulting computational platform forms a robust foundation for future predictive studies linking molecular interactions to emergent behaviours of chromatin.

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

From the start of the project to the end of the reporting period, the team advanced the state of the art in computational modelling of biomolecular organisation and applied these novel frameworks to key questions in chromatin biology and phase separation. During the final period, this work resulted in 28 peer-reviewed publications, contributing to a total of 40 publications during the grant. The project fully met its four primary objectives:

O1. Develop a high-resolution coarse-grained chromatin model.
We created a new model that captures nucleosome breathing, epigenetic variation, post-translational modifications and linker DNA mechanics (Farr et al. Nat Commun 2021; Chen et al. Nat Commun 2025). This enables realistic predictions of chromatin dynamics and phase behaviour.

O2. Extend the model to functional chromatin domains.
Our simulations reproduced heterogeneity in in vivo chromatin organisation and explained why regular 30-nm fibres are rarely observed experimentally (Sridhar et al. PNAS 2020; Sridhar et al. NAR 2020). We discovered that nucleosome breathing and H1 binding generate disordered, liquid-like chromatin states.

O3. Develop methods to predict chromatin structure at the megabase scale.
We produced the first framework capable of modelling megabase-sized chromatin with molecularly informed interactions (Brown et al. Cell Reports 2023; Chen et al. Nat Commun 2025). These models integrate experimental genomic data and reproduce key structural features of chromatin domains.

O4. Extend the models to study biomolecular phase separation.
We developed and benchmarked five simulation frameworks describing the phase behaviour of proteins and protein–RNA systems (Joseph et al. Nat Comput Sci 2021; Tejedor et al. ACS Cent Sci 2025; Garaizar et al. PNAS 2022; Tejedor et al. Nat Commun 2023). These models outperform existing approaches and provide accurate predictions of condensate stability, ageing, material properties and multiphase organisation.

Representative scientific advances.
– Nucleosome breathing promotes a disordered, phase-separated chromatin state (Farr et al 2021).
– Linker DNA length finely tunes chromatin condensate stability at single-base-pair resolution (Chen et al. 2025).
– Protein disorder-to-order transitions determine condensate ageing and morphology (Garaizar et al. 2022).
– New models (Mpipi, Mpipi-Recharged) accurately capture π–π, cation–π and electrostatic interactions in condensates (Joseph et al 2021; Tejedor et al 2025).

Exploitation and dissemination.
All methods have been released as open-source software, enabling widespread reuse by the chromatin and phase separation communities. Results have been disseminated through high-impact publications, conference presentations, invited talks, and collaborative experimental studies. The modelling frameworks are already being used by external groups to interpret experimental data and design new experiments.

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 project has advanced the field beyond the state of the art in several ways:

1. Multiscale modelling of chromatin.
We developed the first multiscale framework capable of resolving individual nucleosomes within gene-sized domains while incorporating biochemical complexity, nucleosome deformation, linker DNA flexibility and epigenetic heterogeneity (Farr et al. 2021; Chen et al. 2025). No previous model achieved this combination of resolution and scale.

2. New predictive models for biomolecular phase separation.
The Mpipi and Mpipi-Recharged models (Joseph et al 2021; Tejedor et al 2025) set new benchmarks for accuracy in predicting protein condensate behaviour, including composition dependence, protein–RNA interactions and condensate ageing. These have reshaped methodological standards in the field.

3. Conceptual advances in chromatin biology.
Our work provides mechanistic explanations for why regular chromatin fibres are rarely seen in vivo, how nucleosome breathing drives liquid-like heterogeneity, and how DNA mechanics and histone variants modulate condensate stability. These insights connect molecular-scale processes to emergent genome-scale organisation.

4. Integration with experiment at unprecedented resolution.
Our models achieve quantitative agreement with FRET, biochemical assays, and other experimental observables, enabling predictive exploration of chromatin structure and material properties.

All major results have already been delivered. We expect the modelling frameworks will continue to generate new insights as they are applied by the community. The project leaves behind a powerful, sustainable computational platform for future research in chromatin organisation and phase separation.

This is an illustration of the multiscale method of InsideChromatin