# Control of the 4D chromatin landscape underlying gene activity during development

> **NIH NIH U01** · PRINCETON UNIVERSITY · 2022 · $646,200

## Abstract

Summary
 One of the grand challenges of modern biology is to understand how gene activity is controlled in space and
time, in the context of native chromosomes and in individual living cells. The goal of this proposal is to tackle
exactly this challenge: we will develop new approaches to measure and manipulate long-range chromosomal
interactions and quantify their effects on gene expression, in real-time and in living cells and tissues. By
quantitatively mapping the relationship between transcription factor assembly (e.g. formation of biomolecular
condensates), chromosome organization and transcription kinetics, our study will define how gene expression is
controlled at unprecedented resolution.
 Transcriptional regulation forms the basis of cellular differentiation during organismal development, and its
defects underlie a variety of disease states, from developmental disorders to cancer. Yet current methods are
limited: traditional live-imaging lacks the spatial resolution to accurately define chromosome organization at the
scale of individual genes, while bulk assays using fixed material are ill-suited for studying temporal dynamics. In
addition, membrane-less nuclear condensates, which form through liquid-liquid phase separation, are thought to
play key but as-yet-undefined roles in regulating transcription.
 To address these challenges, we will develop new imaging methods to measure chromosomal distances in
living cells and build optogenetic tools to assemble/disassemble chromosome loops and nuclear condensates.
We will deploy these tools to examine regulatory interactions at genomic scales characteristic of enhancer–
promoter interactions in flies and mammals (from tens to hundreds of kilobases), and study their implications in
the context of cell fate specification in the developing Drosophila embryo. The resulting technologies will be
applied to analogous transcriptional loci in mouse embryonic stem cells and organoids derived from these cells.
Together, the proposed studies will help reveal how robust mechanisms of cell type specification emerge from
stochastic processes such as transcriptional bursts, fluctuations in the size and stability of biomolecular
condensates, and dynamic instability of chromatin architecture. The overall goal of this project is to establish a
quantitative link between chromatin architecture and transcriptional activity, which will ultimately allow us to take
control of gene activity by re-engineering the transcriptional programs underlying developmental and disease
processes.

## Key facts

- **NIH application ID:** 10469417
- **Project number:** 5U01DK127429-03
- **Recipient organization:** PRINCETON UNIVERSITY
- **Principal Investigator:** Thomas Gregor
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $646,200
- **Award type:** 5
- **Project period:** 2020-09-17 → 2025-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10469417

## Citation

> US National Institutes of Health, RePORTER application 10469417, Control of the 4D chromatin landscape underlying gene activity during development (5U01DK127429-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10469417. Licensed CC0.

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