# Organizational principles and functional role of 3D enhancer hubs in cell fate decisions

> **NIH NIH R01** · WEILL MEDICAL COLL OF CORNELL UNIV · 2021 · $440,353

## Abstract

Project Summary
Embryonic development and tissue homeostasis rely on the tight regulation of cell-type specific transcriptional
programs by particular transcription factors (TFs) and their target enhancers. The emergence of three-
dimensional (3D) genome organization as an important layer of transcriptional control, stresses the fact that
understanding how enhancers communicate with target genes to coordinate transcriptional activity requires
knowledge of the 3D nuclear topology. In a recent study, we captured a drastic rewiring of three-dimensional
regulatory contacts between somatic cells and embryonic stem cells (ESCs) by H3K27ac HiChIP and identified
complex 3D “enhancer hubs”, where enhancers are spatially clustered with multiple highly-expressed genes
with known or predicted functions in regulation of stemness. Genetic or epigenetic modulation of such
enhancers in ESCs resulted in downregulation of all hub-connected genes and partial differentiation, which
supports a vital role for these architectural nodes in gene coregulation and cell identity. In addition, we
provided proteomics and genetic evidence that KLF family TFs play an important role in the organization and
regulation of 3D enhancer hubs in ESCs and identified candidate cofactors. Based on these results, we
hypothesize that 3D enhancer hubs function as architectural “headquarters” of cell identity, where cell
type-specific genes are sequestered by specific transcriptional regulators to facilitate coordinated
gene expression. Here, we will test this hypothesis both in the contexts of mouse ESCs, and of early
developmental cell fate decisions using in vitro and in vivo approaches. Specifically, we aim to (1) target
systematically enhancers and genes within hubs to determine the functional consequences on the pluripotent
transcriptional network and the stability of ESC identity, (2) determine the critical protein factors and activities
that control enhancer hub formation and functionality and (3) identify and characterize 3D enhancer hubs that
are critical for acquisition and maintenance of each of the early developmental fates. Successful completion of
our aims will offer mechanistic insights into the organization and regulation of 3D enhancer hubs, determine
their role in cell fate control and reveal novel ways for engineering cell identity by targeting critical architectural
nodes and factors.

## Key facts

- **NIH application ID:** 10239060
- **Project number:** 5R01GM138635-02
- **Recipient organization:** WEILL MEDICAL COLL OF CORNELL UNIV
- **Principal Investigator:** Effie Apostolou
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $440,353
- **Award type:** 5
- **Project period:** 2020-08-15 → 2024-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10239060

## Citation

> US National Institutes of Health, RePORTER application 10239060, Organizational principles and functional role of 3D enhancer hubs in cell fate decisions (5R01GM138635-02). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10239060. Licensed CC0.

---

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