Uncovering the role and regulation of 3D DNA-RNA nuclear dynamics in controlling cell fate decisions

Introduction

At the onset of mammalian life, the first lineage specification decision is made where embryonic cells opt to become either part of the placenta or the future body. Proper regulation of this choice is crucial for subsequent development.

Research Gap

However, we don’t know how the transcription program and 3D genome architecture arise, interconnect, and are controlled to determine the fate of each cell in a developing embryo. Recent studies, including my work, suggest that in addition to canonical mRNA-coding genes, RNAs from the “dark” parts of the genome (e.g., transposons, repeats, long non-coding RNAs) play a significant role during these events. Yet, how specific classes of RNA regulate gene expression and nuclear architecture post-fertilization remains elusive.

Research Aim

The main aim of my proposal is to understand the interrelationship between 3D genome organization and the transcriptome across early development and to identify novel factors that lead to the first cell-fate decision and concomitant decrease in cell potency.

Methodology

Recent technical advances, which I co-developed, enabled simultaneous measurement of 3D genome organization and the transcriptome, and facilitated large-scale functional screens in early mammalian embryos.

Objectives

Thus, I now propose to generate spatiotemporal maps of 3D DNA and RNA organization from early mouse embryos at single-cell resolution (Obj.1) to build a complete picture of the relationships between nuclear architecture and emerging cell-type specific transcriptome that drive early cell fate choices.

1. Combine these data with large-scale in vivo perturbations targeting protein coding genes (Obj.2).
2. Investigate dark genome RNAs (Obj.3) to identify key inducers/regulators of lineage specification.
3. Determine molecular mechanisms governing cell-state transitions.

Implications

The proposed research will help us to control, correct, and eventually employ early stages of embryonic development and their high cell potency in vitro in reproductive medicine and stem cell research.