Reshaping the nucleome to reveal its gene- and mechano-regulatory function

Introduction

The content of the cell nucleus is highly organized at different levels. Chromatin is partitioned into domains that carry different post-translational histone modifications, and it exhibits a multiscale structural organization from small loops to large compartments.

Chromatin-Associated Complexes

Nuclear RNAs and proteins recognize cues on chromatin, forming different types of chromatin-associated complexes and condensates. The nucleus as a whole is the largest and stiffest organelle of the cell and modulates its mechanical properties.

Dysregulation and Disease

Dysregulation of the nucleome at any level goes along with altered gene- and mechano-regulation in diseases such as metastatic cancers. Currently, the functions of the different organizational levels of chromatin, their mutual relationships, and the impact on cellular phenotypes are poorly defined.

Technical Limitations

Progress in this field has been hindered by several technical limitations:

1. The inability to study chromatin folding in single living cells, which would allow for interrogation of its dynamics, assessment of its response to perturbations in real-time, and relation to the mechanical properties of the same cell.
2. The lack of tools to selectively reengineer different levels of the nuclear organization to test their function.

RENOME Project Proposal

With the RENOME project, I propose to overcome these limitations by developing systems to study chromatin compartments in real-time and to reshape different organizational levels of the nucleome in a tunable manner.

Impact of RENOME

These tools will make it for the first time possible to define the functional impact of nuclear organization across scales, from single molecules to mammalian cultured cells and 3D organoids. RENOME links chromatin regulation, phase separation, and nuclear mechanobiology, with the goal to connect molecular mechanisms to cellular behavior.

Future Directions

By providing a multi-scale predictive model for the organization of the nucleome and a toolbox for its reengineering, it will lay the groundwork for future epigenetic therapies.