# Regulatory elements of replication timing and 3D genome organization

> **NIH NIH R35** · UNIVERSITY OF MINNESOTA · 2020 · $378,043

## Abstract

PROJECT SUMMARY
Increasing evidence indicates that three-dimensional (3D) genome organization is required to regulate
gene function and its alterations are associated with many diseases. The genome is organized into
compartments that align with the temporal order of DNA replication (replication timing – RT). However,
little is known about the mechanisms underlying 3D genome organization. Recently, we identified cis
elements of RT and 3D genome organization control (early replicating control elements – ERCEs) in
murine embryonic stem cells. ERCEs are enriched in enhancer epigenetic marks, form strong chromatin
interactions and are bound by pluripotency-specific transcription factors. Moreover, I developed an
integrative model of gene regulatory networks that predicts that co-occupancy of cell type-specific
transcription factors regulate RT. Here, we will study what are the regulatory elements of genome
organization in human differentiated cell types, investigate how trans-acting factors control these
elements, and define how 3D genome organization is remodeled during development and evolution.
Our central hypothesis is that co-occupancy of cell type-specific transcription factors at ERCEs
is required to regulate the 3D genome organization. To test this hypothesis, we will delete and insert
candidate ERCEs into the genome of human differentiated cell types and test their effect on RT, 3D
genome organization and gene expression. We will track ERCE activation using highly-synchronous
human embryonic stem cells differentiation systems. Finally, we will analyze 3D genome organization
evolution using primary cells derived from different species. My laboratory is uniquely positioned to
perform the proposed research with broad expertise in the experimental design and analysis of 3D
genome organization during human cell fate commitment. Moreover, numerous resources available at
the University of Minnesota will facilitate the success of this project, including state-of-the-art
technologies for genome editing (Genome Engineering Shared Resource), next-generation sequencing
(Genomics Center), stem cells (Stem Cell Institute), imaging (Imaging Center) and bioinformatic tools
(Minnesota Supercomputing Institute). We expect that our work will contribute significantly to understand
the fundamental principles of genome organization and its relationship to gene function. The proposed
research combines several innovative aspects such as integrative computational models to predict
regulatory elements of large-scale chromatin organization, genome engineering technologies and
optimized differentiation protocols of human embryonic stem cells to dissect the mechanisms that
control 3D genome organization during development and evolution.

## Key facts

- **NIH application ID:** 10027344
- **Project number:** 1R35GM137950-01
- **Recipient organization:** UNIVERSITY OF MINNESOTA
- **Principal Investigator:** Juan Carlos Rivera-Mulia
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $378,043
- **Award type:** 1
- **Project period:** 2020-07-01 → 2025-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10027344

## Citation

> US National Institutes of Health, RePORTER application 10027344, Regulatory elements of replication timing and 3D genome organization (1R35GM137950-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10027344. Licensed CC0.

---

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