# Iteratively redefining developmental potential through poised enhancers

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2020 · $370,068

## Abstract

PROJECT SUMMARY/ABSTRACT:
There is a fundamental need to understand how transcription factors function together with their co-regulators
to redefine a cell’s developmental potential through cell fate transitions. Our current understanding is limited to
a small number of examples often based on simple linear pathways with a transcription factor upstream of its
co-regulators either activating or repressing an enhancer, which in turn regulates its cognate gene in time and
space. However, without a better understanding of the mutual dependencies between transcription factors and
their co-regulators including epigenetic enzymes and collaborative DNA binding factors, it will be impossible to
predict how manipulation of either will influence cell fate and developmental potential. The long-term goal of
the lab is to understand all levels of molecular control of cell fate transitions in order to efficiently reprogram
cells to desired phenotypes. The objective here is to focus on a transcription factor, Foxd3, which is essential
to maintain the developmental potential of various stem cells. The central hypothesis is that Foxd3 is used
iteratively in stem cells to redefine the cell’s development potential by establishing poised enhancers in
association with its co-regulators and collaborative cell specific transcription factors. This hypothesis derives
from preliminary data establishing a dual functional role for Foxd3 as a simultaneous activator and repressor
through its interaction with and regulation of multiple epigenetic factors. As such it poises genes and redefines
the developmental potential of different stem cell populations by moving to new enhancer sites. The following
specific aims are proposed: 1) Determine the epistatic relationship between Foxd3, H3K4 methylation,
nucleosome depletion, and H3K27 acetylation, 2) Uncover the mechanistic basis for Foxd3 movements during
the embryonic stem to epiblast cell transition, 3) Identify role of Foxd3 in cohesin recruitment and enhancer-
promoter looping during developmental gene activation. In aim 1, epistasis and structure-function analyses will
be performed using mutants of the Foxd3 and its coregulators to determine the interdependencies between the
factors in establishing a dual-functional complex at bound sites. In aim 2, post-translational modifications and
collaboration with other transcription factors will be evaluated to dissect the mechanistic basis of Foxd3
movements. In aim 3, Foxd3’s role in cohesin recruitment and enhancer-promoter looping will be evaluated
using time-course and epistasis experiments. The proposal is highly significant as it will provide novel
paradigms of gene control central to a cell’s developmental potential. These paradigms are unlikely to be
specific to Foxd3, but rather reflect general strategies used by stemness transcription factors to retain or
induce a stem cell’s full potential. Such knowledge will allow for better-designed strategies for cell manipulation
and ...

## Key facts

- **NIH application ID:** 9984440
- **Project number:** 5R01GM125089-04
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Robert Blelloch
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $370,068
- **Award type:** 5
- **Project period:** 2017-09-07 → 2022-07-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9984440

## Citation

> US National Institutes of Health, RePORTER application 9984440, Iteratively redefining developmental potential through poised enhancers (5R01GM125089-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9984440. Licensed CC0.

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