# Role of nucleosome architecture in cellular reprogramming

> **NIH NIH R01** · UNIVERSITY OF NORTH DAKOTA · 2024 · $296,100

## Abstract

PROJECT SUMMARY
Enhancer formation at precise chromatin loci by transcription factors enables appropriate gene activation
to biological demand. This essential process is challenged by the millions of matches to transcription
factor binding motifs present in the human genome. Chromatin structure is also known to act as a
physical barrier for many transcription factors. How do transcription factors overcome chromatin barriers
and selectively activate appropriate genomic loci while they are competing against chromatin barriers?
The answer to this fundamental question is still largely unknown. Recently, a subset of transcription
factors, so-called pioneer factors, have been identified as essential proteins required to modify chromatin
accessibility during cellular reprogramming. Unlike other transcription factors, pioneer factors are capable
of binding to nucleosomes at closed (inactive) chromatin sites and inducing chromatin opening. Since
nucleosome formation was thought to act as a physical barrier, identification of pioneer factors’ action on
chromatin is fundamental to understanding the cellular reprogramming processes. Misregulation of
pioneer factors is associated with various human diseases including cancer. Therefore, there is a critical
need to identify the molecular mechanisms underlying pioneer factor-induced cellular reprogramming.
Our long-term goal is to elucidate the molecular mechanisms of transcription factor-induced cellular
reprogramming. We previously demonstrated that GATA3 acts as a pioneer factor that can directly bind
closed chromatin and activate epithelial marker genes during the mesenchymal-to-epithelial transition
(MET) in triple-negative breast cancer cells. Using this cellular reprogramming model system, we further
identified the unique nucleosome positioning enriched at GATA3 target loci. Our Cryo-EM structure
analysis of the GATA3-nucleosome complex revealed that the motif recognition by GATA3 on the
nucleosome differs from histone-free DNAs. Chromatin structural analysis during MET also identified that
chromatin opening and de novo enhancer formation by GATA3 is site-specific and only observed at a
subset of GATA3 binding sites. Based on this evidence, we hypothesize that nucleosome positioning and
structure at the pioneer factor GATA3 binding site dictate the readout (chromatin opening and gene
activation) of GATA3 binding and is directly involved in MET. The primary goals of this application are to:
(1) identify specific nucleosome positioning and conformation that are essential for successful GATA3-
induced cellular reprogramming; (2) identify the roles of chromatin remodeling enzymes during GATA3-
induced MET, and; (3) discover minimum chromatin components for GATA3-induced enhancer
formation. We will use several novel approaches including high-resolution mapping methods for
nucleosome positioning and transcription factors’ footprint. These results will provide a basis for
understanding cellular reprogramming pro...

## Key facts

- **NIH application ID:** 10907409
- **Project number:** 5R01GM148729-02
- **Recipient organization:** UNIVERSITY OF NORTH DAKOTA
- **Principal Investigator:** Motoki Takaku
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $296,100
- **Award type:** 5
- **Project period:** 2023-09-01 → 2028-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10907409

## Citation

> US National Institutes of Health, RePORTER application 10907409, Role of nucleosome architecture in cellular reprogramming (5R01GM148729-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10907409. Licensed CC0.

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