# Analyzing pioneer factor dynamics and function during differentiation and reprogramming

> **NIH NIH F32** · FRED HUTCHINSON CANCER RESEARCH CENTER · 2020 · $65,310

## Abstract

Project Summary/Abstract
 The long-term objectives of this proposal include the following: 1) to
determine the frequency and necessity of pioneer factor-nucleosome interactions
genome wide during cell differentiation, and 2) to characterize the individual
and cooperative pioneer factor-nucleosome interactions that occur during
induced pluripotency. Cell fate decisions require exquisite spatiotemporal
regulation of transcription factor (TF) binding to enhancers to mediate gene
regulation, which is frequently co-opted in a variety of diseases. It is well
established that active enhancers are locally depleted of nucleosomes, and that
TF binding is coincident with, and often required for, local chromatin
accessibility. However, it remains unclear how TFs might play an active role in
displacing nucleosomes at enhancers. One hypothesis is that “pioneer” TFs, so
called because they are expressed early in cell differentiation and bind to their
enhancer targets before they are rendered strongly accessible, directly bind and
displace nucleosomes to facilitate accessibility. However, such a mechanism has
never been validated on individual templates in vivo, chiefly due to the difficulty
in testing for the presence of the putative intermediate TF-nucleosome particle.
Lacking a direct test for in vivo pioneer activity, putative mechanisms for
nucleosome eviction by pioneer TFs remain untested, and the locus specificity of
pioneer activity is largely unknown. Moreover, the frequency and importance of
TF pioneer activity in either natural differentiation systems or TF overexpression
contexts during cellular reprogramming remain uncharacterized. To directly test
the pioneer TF model, I will leverage an in situ, micrococcal nuclease (MNase)
digestion-based alternative to ChIP-seq known as CUT&RUN, in which DNA
fragment size is directly informative of the minimal protein-protected sequence,
and therefore can distinguish direct TF binding from binding through a
nucleosomal intermediate. I will use this information to determine the genome-
wide landscape of pioneer factor-nucleosome interactions in embryonic stem cell
differentiation and during induced pluripotency, and test the necessity of such
interactions using functional genetic experiments. These insights will help us to
understand how pioneer factors function to activate pathogenic gene expression
in diseases such as cancer. I feel that my proposed project fits the mission of
NIGMS to fund research in fundamental biology that uncovers new insights that
could positively impact human health.
!

## Key facts

- **NIH application ID:** 9911897
- **Project number:** 1F32GM129954-01A1
- **Recipient organization:** FRED HUTCHINSON CANCER RESEARCH CENTER
- **Principal Investigator:** Michael P Meers
- **Activity code:** F32 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $65,310
- **Award type:** 1
- **Project period:** 2020-03-01 → 2021-02-28

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9911897

## Citation

> US National Institutes of Health, RePORTER application 9911897, Analyzing pioneer factor dynamics and function during differentiation and reprogramming (1F32GM129954-01A1). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/9911897. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*