# Functional characterization of an enhancer RNA in cerebral ischemia

> **NIH NIH R01** · UNIVERSITY OF SOUTH FLORIDA · 2024 · $362,537

## Abstract

Recent studies have reported widespread transcription of mammalian enhancers into noncoding RNA
transcripts in a stimulus-dependent manner. Growing evidence shows that these enhancer RNAs (eRNAs)
have essential roles in orchestrating higher-order chromatin interactions to facilitate gene expression and
phenotypic outcomes during development and disease. As a result, eRNAs are emerging as an important
component of the gene regulatory machinery. Due to their very recent discovery, the expression and roles of
eRNAs in stroke is virtually unknown. Recently, we applied a combination of genome-wide RNA-seq and
genome-wide enhancer mapping using ChIP-seq to identify a number of stroke-induced eRNAs at multiple
time-points of reperfusion in the mouse cerebral cortex. Our preliminary data confirmed enhancer activity of the
genomic loci encoding the eRNAs, showed that the eRNAs are localized to the chromatin, and revealed an
important role for one such eRNA in modulating post-stroke brain damage and gene expression. The
molecular interactions, functional mechanisms and sex-dependent effects of eRNAs on the post-stroke
pathophysiology are unexplored. In the current project, we build upon our preliminary data to evaluate eRNA
functionality in-depth during stroke in the adult mouse cortex. Specific Aim 1 will use a combination of
crosslinking-immunoprecipitation, fluorescence in situ hybridization and transcriptional-state analysis to
determine the molecular targets of the eRNAs as a function of post-stroke reperfusion time in the mouse
cortex. Specific Aim 2 will employ eRNA loss-of-function in vivo followed by cellular, physiological, pathological
and neurological analyses to evaluate the role of the eRNA in propagating the post-stroke pathophysiology.
Specific Aim 3 will evaluate the molecular targets and pathophysiological effects of the eRNA in the female
mouse cortex. Together, this work will illuminate the significance of eRNAs in the cerebral cortex and may
reveal novel gene regulatory relationships in stroke. This work will pave the way for future studies exploring the
therapeutic manipulation of eRNAs to improve post-stroke outcomes.

## Key facts

- **NIH application ID:** 10928748
- **Project number:** 5R01NS115835-05
- **Recipient organization:** UNIVERSITY OF SOUTH FLORIDA
- **Principal Investigator:** Ashutosh Dharap
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $362,537
- **Award type:** 5
- **Project period:** 2021-09-25 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10928748

## Citation

> US National Institutes of Health, RePORTER application 10928748, Functional characterization of an enhancer RNA in cerebral ischemia (5R01NS115835-05). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10928748. Licensed CC0.

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