Elucidating the interplay between nuclear compartments and transcriptional dynamics during differentiation in human embryonic stem cells
| Title | Elucidating the interplay between nuclear compartments and transcriptional dynamics during differentiation in human embryonic stem cells |
|---|---|
| Acronym | DynaDiff |
| Website | https://www.pioneercampus.org/ |
| Start date | 2022-09-01 |
| End date | 2027-08-31 |
| Sponsor | European Research Council - Starting Grant (ERC-StG) |
| Institution | Helmholtz Zentrum München |
Associated cell lines
Project Description
Development is driven by specific regulatory networks that 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 gene regulatory networks determines cell fate remains poorly understood. This is in part due to the difficulty of measuring transcription with sufficient 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, promyelocytic leukaemia nuclear bodies (PML-NBs), and nuclear speckles (NSs). While we know that the homeostasis of these MLOs changes during differentiation, their impact on transcription, chromatin organization and lineage commitment remains elusive. In DynaDiff, I ask: What is the functional interplay between nuclear MLOs, chromatin organization and the dynamics of transcriptional networks during fate decisions? Specifically, I will focus on the exit form pluripotency and early differentiation of human embryonic stem cells (hESCs) by 1) developing single-cell RNA sequencing (scRNA-seq) methods to characterize transcriptional dynamics; 2) determining the role of PML-NBs and NSs on regulating transcription in hESC; and 3) assessing the role of nuclear MLOs in organizing chromatin conformation. As hESCs can form cell types from all three primary germ layers, our knowledge of this system is paramount to understand early embryonic development. As such, DynaDiff will lay the foundation for further developments in regenerative medicine.