# Charting the 3D epigenome in human brain development and diseases

> **NIH NIH U01** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2020 · $636,375

## Abstract

Project Summary
Cis-regulatory elements control Cell-type-specific gene regulation via looping with their targeting genes.
Therefore, mapping the 3D chromatin interactions between promoters and cis-regulatory elements will be pivotal
to understand the functions of regulatory regions. Besides, many genetic variants associated with
neuropsychiatric diseases reside in the putative cis-regulatory elements. They may contribute to disease by
affecting regulatory sequences function, but the exact mechanisms of how they contribute to diseases via gene
regulation remain unknown. Here, we aim to make substantial advances in understanding how the 3D
epigenome contributes to brain development and diseases by mapping and analyzing the dynamic changes
during the human prefrontal cortex development. We will first map transcriptome, chromatin accessibility, and
3D chromatin loops in six distinct cell types from the developing prefrontal cortex and perform an integrative
analysis to interrogate how chromatin interaction control gene expression and development. Second, we will
integrate the 3D epigenomic datasets with medical genetics resources to gain insights into cell types, genomic
loci, and biological pathways that are causal to diseases, link GWAS SNPs with their target genes. Third, to
establish cell-type-specific functional links between chromatin loops and target gene expression, we will test the
biological consequences of distal regulatory regions interacting with promoters in iPSC models and primary cells.
Our project will reveal new insight into the biological functions of the 3D epigenome in brain development and
diseases.

## Key facts

- **NIH application ID:** 10116735
- **Project number:** 1U01DA052713-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** ARNOLD KRIEGSTEIN
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $636,375
- **Award type:** 1
- **Project period:** 2020-09-30 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10116735

## Citation

> US National Institutes of Health, RePORTER application 10116735, Charting the 3D epigenome in human brain development and diseases (1U01DA052713-01). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/10116735. Licensed CC0.

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