CORDIS - EU research results

Elucidating the interplay between nuclear compartments and transcriptional dynamics during differentiation

Project description

Exploring mammalian development with stem cells

Mammalian development is an incredibly complex and poorly understood process, governed largely by genes and gene regulatory networks. The ERC-funded DynaDiff project seeks to unravel the complexities of this process by investigating the role of nucleoplasmic membrane-less organelles in transcriptional dynamics during mammalian stem-cell differentiation. The project will also characterise the transcriptional dynamics of mouse and human stem cells utilising single-cell RNA sequencing. The study will then explore the role of pro-myelocytic leukaemia nuclear bodies and nuclear speckles in the transcription dynamics of these pluripotent cells and the effect they have on the organisation of chromatin conformations. This research will provide vital clues to human development and may assist developmental and regenerative medical therapies.


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. This in part due to the difficulty of measuring genome-wide transcription with temporal resolution in complex developmental systems. Plus, transcription occurs in the nuclear context, where the nucleoplasm is compartmentalized into a variety of highly dynamic condensates known as membraneless organelles (MLOs), which include nucleoli, PML (promyelocytic leukaemia) nuclear bodies (PML-NBs), and nuclear speckles (NSs). The homeostasis of these MLOs changes during differentiation, but their impact on transcription and lineage commitment remains elusive. 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, and 3) assessing the role of PML-NBs and NSs in organizing chromatin conformation and its link to active transcription. 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. Finally, hESCs have the potential to form cell types from the three primary germ layers. Our knowledge of this system is paramount to understand human early embryonic development for the treatment of developmental disorders, and for the development of regenerative medicine.

Host institution

Net EU contribution
€ 1 498 372,00
85764 Neuherberg

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Bayern Oberbayern München, Landkreis
Activity type
Research Organisations
Total cost
€ 1 498 372,00

Beneficiaries (1)