# Mapping regulatory elements and chromatin structures in prostate tumor subtypes at single nucleosome resolution

> **NIH NIH R21** · UNIVERSITY OF SOUTHERN CALIFORNIA · 2022 · $226,784

## Abstract

Project Summary/Abstract
The clinical behavior and progression of prostate tumors vary case by case. To develop improved clinical
intervention, we need to better understand the molecular mechanisms leading to different prostate tumor
subtypes. The activities of distal regulatory elements called enhancers, which are bound by cell-type specific
transcription factors (TFs), are critical in regulating cell fate decisions. Active enhancers regulate genes located
at great genomic distances by forming chromatin loops. To identify enhancers active in prostate tumor
subtypes, we and others performed chromatin immunoprecipitation with sequencing (ChIP-seq) using the
H3K27ac histone mark antibody and identified >12,000 peaks differentially enriched among prostate tumor
subtypes. However, the size of H3K27ac ChIP-seq peaks (>1kb) is too large to determine enhancer regions
where TFs bind. To identify target genes of prostate cancer enhancers, genome-wide chromosome
conformation capture assay (Hi-C) was performed, revealing chromatin loops near enhancers. However, we
could not identify target genes of all enhancers active in a given cell due to the limited resolution of Hi-C data.
To elucidate molecular mechanisms linked to prostate tumor subtypes, better strategies to identify prostate
tumor subtype-specific enhancers and their target genes are crucially needed. Herein, we propose to develop
cost-effective methods that can measure the activities of 1) enhancers and 2) involved chromatin loops in
prostate tumor subtypes at single nucleosome resolution. In Aim 1, we will develop a method to identify active
enhancers in prostate tumor subtypes at single nucleosome resolution. In preliminary studies, we showed that
Nucleosome Occupancy and Methylome sequencing (NOMe-seq) can define TF-bound nucleosome-depleted
regions (<200bp) in enhancers at single molecule resolution. To identify prostate tumor subtype-specific
enhancers and TFs that bind to these regions, we will first integrate ChIP-seq and open chromatin datasets
and identify all enhancers active in prostate tumor subtypes. Next, using probes designed to measure the
activities of identified enhancers, we will perform targeted NOMe-seq in prostate cancer cells to identify
enhancers and TFs linked to prostate tumor subtypes. In Aim 2, we will develop a method to identify target
genes of enhancers active in prostate tumor subtypes at single nucleosome resolution. Recently, Micro-C is
reported to map chromatin loops between enhancers and promoters at single nucleosome resolution. We will
first identify genes that are differentially expressed among prostate tumor subtypes using matched DNA-seq
and RNA-seq datasets generated by TCGA and ORIEN consortia. We will next design probes that can
measure the chromatin looping between promoters of the identified genes and enhancers active in prostate
tumor subtypes and perform targeted Micro-C in prostate cancer cells. Our integrative multi-omic analyses and
focused deep s...

## Key facts

- **NIH application ID:** 10437895
- **Project number:** 5R21CA264637-02
- **Recipient organization:** UNIVERSITY OF SOUTHERN CALIFORNIA
- **Principal Investigator:** Suhn Kyong Rhie
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $226,784
- **Award type:** 5
- **Project period:** 2021-09-01 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10437895

## Citation

> US National Institutes of Health, RePORTER application 10437895, Mapping regulatory elements and chromatin structures in prostate tumor subtypes at single nucleosome resolution (5R21CA264637-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10437895. Licensed CC0.

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