# Leveraging genetic variation to dissect gene regulatory networks of reprogramming to pluripotency

> **NIH NIH U01** · UNIVERSITY OF CALIFORNIA LOS ANGELES · 2024 · $100,183

## Abstract

PROJECT SUMMARY
The reprogramming of somatic human cells to induced pluripotent stem cells (iPSCs) by only four transcription
factors (TFs) Oct4, Sox2, Klf4, and cMyc (OSKM) is one of the most striking remodelings of gene regulatory
networks. The remarkable ability of OSKM to reprogram diverse somatic cell types into iPSCs that are
functionally indistinguishable from embryonic stem cells indicates that OSKM leverages a fundamental
mechanism for network remodeling that may be generally applicable to all cell fate transitions. Previous studies
of reprogramming have identified the crucial role of cooperative TF binding in repressing somatic programs and
activating pluripotent ones. However, associating TF binding dynamics and epigenomic remodeling with key
bifurcation events during reprogramming is confounded by the highly heterogeneous nature of the
reprogramming process and the lack of knowledge regarding how the transition from somatic to pluripotent
regulatory programs occurs in individual cells. In this project, we aim to model the regulatory network underlying
the cell fate change of reprogramming using three types of single-cell multi-omic profiles generated from critical
time points during reprogramming. We will interrogate the network leveraging natural perturbation of
reprogramming and pluripotency by genetic variants. Genetic variation is well known to modulate the regulatory
network of pluripotency and contributes to the variability of cellular phenotypes and differentiation capacity of
iPSC lines. We will generate population-scale single-cell joint profiling of RNA and DNA methylation (snmCT-
seq), joint profiling of RNA and chromatin accessibility (scRNA + ATAC-seq) and single-nucleus joint profiling of
chromatin conformation and DNA methylation (sn-m3C-seq), allowing the cell-type-specific determination of
transcriptome, chromatin accessibility and methylation states at regulatory elements, as well as enhancer-gene
looping to connect non-coding variants to their regulatory target. To integrate OSKM binding with the single-cell
transcriptomic and epigenomic dynamics, we will determine the allele-specific binding of TFs and histone
modifications using a pooled-alleles ChIP-seq strategy. We will use Dynamic Regulatory Events Miner (DREM)
to construct predictive models by integrating transcription factor-gene interaction information with time- and
pseudotime-series genomics data. To determine the genetic regulation of the reprogramming network, we will
apply the novel statistical method FastGxE to distinguish cell-type-specific from the shared genetic component
of gene expression regulation, to enhance the sensitivity for identifying cell-type-specific quantitative trait loci
(QTLs). To test the regulatory network, we will experimentally determine the function of network hub genes and
non-coding variants using high-throughput CRISPR interference and precise variant replacement experiments.
Our proposed project integrates diverse approache...

## Key facts

- **NIH application ID:** 11089964
- **Project number:** 3U01HG012079-04S1
- **Recipient organization:** UNIVERSITY OF CALIFORNIA LOS ANGELES
- **Principal Investigator:** Chongyuan Luo
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $100,183
- **Award type:** 3
- **Project period:** 2021-09-01 → 2026-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/11089964

## Citation

> US National Institutes of Health, RePORTER application 11089964, Leveraging genetic variation to dissect gene regulatory networks of reprogramming to pluripotency (3U01HG012079-04S1). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/11089964. Licensed CC0.

---

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