# Epigenetic control of the stem cell gene regulatory network

> **NIH NIH R01** · UNIV OF MASSACHUSETTS MED SCH WORCESTER · 2020 · $382,320

## Abstract

Embryonic stem cells (ESCs) derived from the inner cell mass of blastocyst stage embryos are a powerful in
vitro model for cellular differentiation and a potential source of cells for regenerative therapies. A better
understanding of the factors controlling differentiation is necessary to robustly direct ESCs to produce mature
cell types for therapeutic purposes. In addition, perturbations in differentiation in vivo lead to defects in early
embryos and failed pregnancies. We are focusing on elucidating the components and wiring of the ESC gene
regulatory network, in order to better control ESC differentiation and gain a more complete understanding of
early development. Although three classes of regulatory factors comprise the ESC GRN—transcription factors,
epigenetic regulators, and RNAs—the functions of only the first two classes are understood to a degree. We
recently uncovered a key role for a structural feature of the ESC epigenome, RNA/DNA hybrids (RDHs), in cell
fate. We found that RDHs are necessary to maintain the differentiation potential of ESCs—cells with reduced
RDHs showed poor differentiation fidelity and a skewed differentiation profile. We recently found that RDHs
play a key role in the ESC GRN, which likely accounts for these phenotypes. Depletion of RDHs leads to
misregulation of thousands of genes. Interestingly, for a small fraction of these genes, we found that RDHs
regulate the binding of two key epigenetic regulatory factors, PRC2 and Tip60-p400. However, most genes
regulated by RDHs are neither direct nor indirect targets of these factors, raising the question of what other
components of the GRN are modulated by RDHs. Here we propose to use epigenomic profiling and systems
level approaches to comprehensively elucidate the roles of RDHs in the GRN. In addition, we will utilize a novel
method for identification of new RDH-binding factors. Finally, we will use single cell profiling techniques to
elucidate how RDHs regulate cell fate on a cell-by-cell basis. These studies will provide multiple new insights
into how RNAs function within the ESC GRN. In addition, these studies will enhance our understanding of how
cells acquire specific fates during ESC differentiation.

## Key facts

- **NIH application ID:** 9932461
- **Project number:** 5R01HD072122-09
- **Recipient organization:** UNIV OF MASSACHUSETTS MED SCH WORCESTER
- **Principal Investigator:** Thomas G Fazzio
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $382,320
- **Award type:** 5
- **Project period:** 2012-08-15 → 2023-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9932461

## Citation

> US National Institutes of Health, RePORTER application 9932461, Epigenetic control of the stem cell gene regulatory network (5R01HD072122-09). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9932461. Licensed CC0.

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