# Function of Chromatin Features in Cellular Programming

> **NIH NIH R35** · UNIVERSITY OF ROCHESTER · 2022 · $385,000

## Abstract

PROJECT SUMMARY / ABSTRACT
Maintaining stable gene transcription patterns is critical for cellular programming. Likewise, orderly switching
from one transcription pattern to another, termed reprogramming, is necessary for development, as well as for
numerous other biological processes. Dysregulated reprogramming can have catastrophic consequences, with
outcomes ranging from developmental disease to cancer. Notably, epigenetic abnormalities, failure to
differentiate, and inappropriate cellular programming are intricately linked to carcinogenesis. Our objective is to
define the function of H2A.Z (a variant form of histone H2A) in regulating cellular programming in vivo. We will
utilize the zebrafish model for early embryonic development, combined with a series of next-generation genome-
wide sequencing approaches, to functionally test how H2A.Z patterns regulate several aspects of cellular
reprogramming, including transcriptional activation. Regulation of gene transcription occurs through two primary
components: enhancers, the major cis-regulatory DNA sequence component, and transcription factors, the major
trans-regulatory DNA-binding protein component. However, due to technical challenges associated with in vivo
studies, several critical unknowns limit our understanding of how these elements function. For example, what
regulates activation of cell-type-specific enhancers among the many thousands of enhancers in the genome?
Likewise, among millions of small DNA-binding motifs, how are transcription factors able to selectively bind at a
discrete subset of locations? One interesting possibility is that interplay between transcription factors,
polymerase machinery, and epigenetic marks, regulates the binding of transcription factors, and the activity of
enhancers. We recently defined the function of specialized ‘Placeholder’ nucleosomes in developmental
reprogramming of gametes to stems cells in zebrafish. Placeholder nucleosomes enable proper genome-wide
pattering of epigenetic marks and facilitate activation of the zygotic genome. We determined that the major
functional unit of Placeholder nucleosomes, the histone variant H2A.Z, becomes localized to enhancer regions
during the subsequent stages of zebrafish development, when differentiation and cell-type specification occurs.
This led us to hypothesize that reorganization of H2A.Z patterns is a major factor in controlling developmental
cell-type specification. To test this hypothesis, we will genetically manipulate the regulators of H2A.Z localization
in zebrafish embryos, and then assess genome-wide impacts on enhancer activity, and cell-type-specific
transcription factor binding. Successful completion of this project will define the role of H2A.Z in controlling gene
expression patterns and in cellular programming. We propose that this broader concept, where changes in
epigenetic marks underlie cellular reprogramming, might be a general principle in biology, with relevance to
developmental biology...

## Key facts

- **NIH application ID:** 10383776
- **Project number:** 5R35GM137833-03
- **Recipient organization:** UNIVERSITY OF ROCHESTER
- **Principal Investigator:** Patrick J. Murphy
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $385,000
- **Award type:** 5
- **Project period:** 2020-07-01 → 2025-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10383776

## Citation

> US National Institutes of Health, RePORTER application 10383776, Function of Chromatin Features in Cellular Programming (5R35GM137833-03). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10383776. Licensed CC0.

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