Elucidating the interplay between nuclear compartments and transcriptional dynamics during differentiation

Introduction

Development is driven by transcriptional programs where specific gene regulatory networks (GRN) control genes on several time scales. However, the extent to which transcriptional dynamics are coordinated for different genes and how the differential downregulation of the progenitor GRN determines cell fate remains poorly understood.

Challenges in Measurement

This is in part due to the difficulty of measuring genome-wide transcription with temporal resolution in complex developmental systems. Additionally, transcription occurs in the nuclear context, where the nucleoplasm is compartmentalized into a variety of highly dynamic condensates known as membraneless organelles (MLOs). These include:

• Nucleoli
• PML (promyelocytic leukaemia) nuclear bodies (PML-NBs)
• Nuclear speckles (NSs)

Impact of MLOs on Differentiation

The homeostasis of these MLOs changes during differentiation, but their impact on transcription and lineage commitment remains elusive.

Research Objectives

In DynaDiff, I aim to investigate the link between PML-NBs and NSs and transcriptional regulation during mammalian differentiation by:

1. Developing single-cell RNA sequencing (scRNA-seq) methods to characterize transcriptional dynamics in mouse and human embryonic stem cells (m/hESCs) during the exit from pluripotency.
2. Determining the role of PML-NBs and NSs on transcriptional dynamics during differentiation.
3. Assessing the role of PML-NBs and NSs in organizing chromatin conformation and its link to active transcription.

Technological Breakthrough

I recently made a significant technological breakthrough, finally bringing long-awaited temporal resolution to scRNA-seq. This expertise, in combination with my background in high-throughput microscopy and computational analysis, allows me to lead and conduct DynaDiff successfully.

Importance of hESCs

Finally, hESCs have the potential to form cell types from the three primary germ layers. Our knowledge of this system is paramount to understanding human early embryonic development for the treatment of developmental disorders and for the development of regenerative medicine.