# How phase-separation in the nucleus organizes 3D spatial assembly and gene regulation

> **NIH NIH R01** · CALIFORNIA INSTITUTE OF TECHNOLOGY · 2020 · $1,070,775

## Abstract

Project Summary
Gene regulation is a highly complex process that involves the recruitment of numerous regulatory factors as well
as dynamic 3-dimensional spatial rearrangements of DNA, RNA, and protein molecules that are important for
quantitatively controlling the rate of gene regulation. Yet, how these various components interact simultaneously
and what their quantitative contributions are to gene regulation remains unresolved largely because of the lack
of methods that can integrate combinatorial molecular binding, spatial information, and quantitative
measurements of various aspects of gene regulation within the same individual cell. Here we will develop highly
innovative methods that will allow us to generate dynamic molecular movies that monitor the movement of DNA,
RNA. and protein molecules at high resolution in a manner that provides information about the spatial
arrangement of molecules along with simultaneous information about transcription rates and mRNA splicing
rates within single cells. To achieve this, we will develop pioneering new genomic methods for measuring the
spatial interactions of RNA, DNA, and protein with single cell capabilities and build novel quantitative and
computational modeling approaches to generate high resolution temporal “movies” from snapshots derived from
tens of thousands of synchronized single cells. We will use these approaches to quantitatively understand the
dynamic assembly of RNA-protein complexes, localization to DNA, and structural dynamics of genomic DNA
and how these integrated components impact gene regulation across time. Specifically, we will dissect the
dynamics of three RNA-mediated processes that link dynamic 3D nuclear structure and gene regulation in unique
regulatory paradigms in biology and disease: (i) chromosome-wide transcriptional silencing, (ii) kinetic coupling
of mRNA transcription and splicing, and (iii) RNA-induced aggregation and cellular toxicity in neurodegenerative
disorders. Together, the results of this proposal will generate highly innovative new approaches for quantitatively
measuring molecular and spatial dynamics of various regulators and their role in gene regulation.

## Key facts

- **NIH application ID:** 10022072
- **Project number:** 1R01DA053178-01
- **Recipient organization:** CALIFORNIA INSTITUTE OF TECHNOLOGY
- **Principal Investigator:** Mitchell Guttman
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $1,070,775
- **Award type:** 1
- **Project period:** 2020-09-01 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10022072

## Citation

> US National Institutes of Health, RePORTER application 10022072, How phase-separation in the nucleus organizes 3D spatial assembly and gene regulation (1R01DA053178-01). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10022072. Licensed CC0.

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