# Enhancer Connectomes in Regulation of Gene Expression

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2023 · $462,597

## Abstract

ABSTRACT
Mammalian cells exhibit a precise gene regulation process, during which enhancers mediate rapid gene
activation programs in response to different signals and ligands. While many principles of chromosomal
mechanisms underlying enhancer functions have been deduced in the 39 years since their initial discovery,
striking gaps in our knowledge remain. These include actions of a series of previously unknown, but required,
enhancer-recruited complexes; contributions of physicochemical properties of enhancer condensates formed on
the estrogen receptor  (ER) in signaling-dependent regulation; and the potentially important roles of
interactions with subnuclear architectural structures. Further, because global genomic methods determine
epigenomic events at only a single point in time, another striking gap in our knowledge is understanding the
temporal principles underlying regulation of regulated transcriptional programs. Under physiological conditions,
many signals present as a continuum from acute to chronic stimulation; however, the mechanistic and functional
distinctions between acute and chronic enhancer activation remain poorly understood. Here, we take advantage
of our knowledge of gene transcriptional control by nuclear receptors, exemplified by estrogen 17β-estradiol (E2)-
dependent activation of transcriptional programs to address these basic questions. The central challenge in this
competitive renewal is to provide a unified molecular logic that mechanistically links a series of required, but
overlooked, components of signal-dependent enhancer activation strategies that underlie acute and chronic
regulated gene expression programs. We will initiate a comprehensive investigation of new dynamic enhancer
complexes and their interactions with the subnuclear architectural structures critically regulating transcription.
These include the function of promoter antisense transcripts in promoter pause-release regulation; investigation
of required contributions of Ku70 homodimers reading the TopoisomerseI:DNA covalent intermediate to
assemble a new complex required for promoter pausing and enhancer activation events. We will investigate
whether short sequences and specific amino acids in the ERN-terminal IDR mediate assembly of key RNP
condensate components required for robust activation, including an unexpected role of KAP1 in these activation
events. We will establish real time, multicolor imaging to uncover the dynamics of activated enhancer
interactions, enhancer bursting events and relationship of activation to interactions with subnuclear architectural
structures. We will explore the hypothesis that the most robust eRNA:protein enhancer condensates form a
homotypic enhancer network resulting in cooperative activation of a subset of similarly activated homotypic
enhancers separated by multiple TADs or even located on other chromosomes, properties are lost following
chronic signal/ligand activation. These approaches will be complemented by a...

## Key facts

- **NIH application ID:** 10543856
- **Project number:** 5R01DK018477-47
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** MICHAEL G ROSENFELD
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $462,597
- **Award type:** 5
- **Project period:** 1998-10-01 → 2025-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10543856

## Citation

> US National Institutes of Health, RePORTER application 10543856, Enhancer Connectomes in Regulation of Gene Expression (5R01DK018477-47). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10543856. Licensed CC0.

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