# Uncovering fundamentals of gene regulation by enhancers

> **NIH NIH R35** · STANFORD UNIVERSITY · 2020 · $328,650

## Abstract

PROJECT SUMMARY/ABSTRACT
A class of cis-regulatory elements, called enhancers, play a central role in orchestrating spatiotemporally
precise gene expression programs during development. Perturbations in enhancer sequence or regulation can
lead to disease, including congenital malformations and cancer. Furthermore, enhancer sequence divergence
is emerging as an important mediator of human phenotypic variation. A key feature of enhancers is their ability
to activate transcription over long genomic distances of tens or even hundreds of kilobases away from their
target promoters. Discovery that, when active, enhancers are marked by unique chromatin signatures,
combined with genomic approaches such as ChIP-seq or Chromosomal Conformation Capture technologies
(3C and derivatives) facilitated enhancer annotation across cell types and species and provided key insights
into long-range regulation. Generally, however, in these population-level, fixed-cell assays, kinetic information
underlying enhancer activation at a single-cell level has been lost.
We recently developed a new imaging approach that allows us to label and track individual enhancer and
promoter elements in living cells, in their native chromosomal context and in different cellular and activity
states. Our proposed work further couples this technology with live-cell visualization of nascent transcripts to
capture the kinetic behavior of enhancers and promoters and its relationship with the discontinuous nature of
transcription. Using undifferentiated or differentiating stem cells as a cellular model, we will address major
open questions in enhancer biology, including the real-time frequency and dynamics of enhancer-promoter
contacts, their association with transcriptional bursts, and the role of chromatin topological organization in
enhancer function. We plan to introduce a series of perturbations to investigate how disruption of specific
events at enhancers, such as histone modification, variant incorporation or nucleosome remodeling, affects
dynamics of long-range chromosomal contacts and transcriptional activation at the single-cell level. In
complementary studies outlined in the second theme of the proposal, we are employing a diverse set of
genomic and genetic approaches to identify novel factors that are required for long-range gene regulation and
to define necessities and sufficiencies for enhancer activation within the native chromatin context. The two
main themes will allow us to revisit current models of enhancer function (e.g. enhancer looping, enhancer
delimitation by topologically associated domains, etc.) and will yield new concepts and mechanistic models of
long-range gene control in mammals, with broad future implications for understanding and treatment of human
disease.

## Key facts

- **NIH application ID:** 9929611
- **Project number:** 5R35GM131757-02
- **Recipient organization:** STANFORD UNIVERSITY
- **Principal Investigator:** Joanna Wysocka
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $328,650
- **Award type:** 5
- **Project period:** 2019-05-15 → 2024-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9929611

## Citation

> US National Institutes of Health, RePORTER application 9929611, Uncovering fundamentals of gene regulation by enhancers (5R35GM131757-02). Retrieved via AI Analytics 2026-06-11 from https://api.ai-analytics.org/grant/nih/9929611. Licensed CC0.

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