# High resolution characterization of epigenetic dynamics in gastrointestinal cell plasticity

> **NIH NIH R03** · UNIVERSITY OF SOUTHERN CALIFORNIA · 2023 · $123,750

## Abstract

Project Summary
Continuous differentiation of intestinal stem cells (ISCs) maintains the integrity of intestinal epithelium while
producing diverse functional cells at rapid pace. This epithelium also displays remarkable cell plasticity,
including the ability of mature cells to dedifferentiate into stem cells upon loss of ISCs. As many genetic and
signaling drivers of this cell fate reversion are being discovered, cell intrinsic epigenetic controls that must be
rewired for cell plasticity, remain largely unknown. Using state-of-the-art single-cell sc-Multiome assays that
reveal chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) in parallel, we have recently
produced high-quality data comparing native epithelial cells and cells undergoing regeneration upon ISC
ablation. Using these data and innovative computational methods, we will chart the chromatin and gene
expression dynamic underlying cell fate changes in intestinal regeneration, and identify key epigenetic
modulators and transcription factor controllers of this process. In conjunction with these analyses, we propose
to delineate promoter and enhancer relevant epigenetic controls (histone modifications) through the time
course of regeneration.
Aberrant chromatin structure can cause gene dysregulation and contribute to tumorigenesis, including
colorectal cancer. DNA methylation is the most frequently modulated epigenetic modality in colorectal as well
as many other cancers. However, determinants of the reciprocal interactions between DNA methylation and
mutational changes or other epigenetic layers have not been studied critically. Also missing is the knowledge
of how early in tumorigenesis does the DNA methylation change occur and how uniform are the changes in
DNA methylation across cells. Technological limitations have been the most significant barrier for such
analyses, as current methods to characterize DNA methylation at single-cell level suffer from low CpG
coverage limited to gene promoters and GpG islands, which precludes understanding of the true breadth of
DNA methylation change, particularly at gene regulatory enhancers. We propose to override these limitations
through development of a novel assay for characterizing DNA methylation as well as RNA expression at
single-cell level. We combine chemical methods geared to preserve DNA integrity and gentler nuclei handling
based on magnetic bead capture in our method called scTaMT-seq, which will provide a robust protocol for
analyzing DNA methylation in unprecedented detail at highest possible resolution. This technology will propel
the understanding of epigenomic impact on various biological processes, particularly cancer.

## Key facts

- **NIH application ID:** 10576232
- **Project number:** 1R03DK134799-01
- **Recipient organization:** UNIVERSITY OF SOUTHERN CALIFORNIA
- **Principal Investigator:** Unmesh Jadhav
- **Activity code:** R03 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $123,750
- **Award type:** 1
- **Project period:** 2023-02-01 → 2025-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10576232

## Citation

> US National Institutes of Health, RePORTER application 10576232, High resolution characterization of epigenetic dynamics in gastrointestinal cell plasticity (1R03DK134799-01). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10576232. Licensed CC0.

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