# High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes

> **NIH NIH UM1** · DUKE UNIVERSITY · 2021 · $956,415

## Abstract

ABSTRACT
Large scale genome annotation consortia such as ENCODE, Epigenomics Roadmap, and
others have identified millions of putative regulatory elements. We now need to focus efforts on
comprehensively characterizing and quantifying the function of those elements, and noncoding
variants that map within these regions, on gene expression and cell phenotypes. Our long-term
goal is to assign function to every regulatory element and noncoding variant in the human
genome, understand how that function changes in different contexts, and use that information to
better understand cell fitness, disease mechanisms, cell lineage specification, and tissue
homeostasis. To accomplish this goal, we have developed multiple novel high-throughput
CRISPR-based technologies for characterizing the function of putative gene regulatory
elements by perturbing their activity in their endogenous, native context. We have coupled these
methods with single-cell RNA-seq to identify the target gene(s) for each regulatory element. We
have also developed dCas9 effector mice to characterize elements in their natural in vivo
context. In addition, we have developed population-based high-throughput reporter assays
(POP-STARR) to characterize the impact of noncoding genetic variation across the entire
genome. The objective of this proposal is to apply and share our compendium of
complementary, robust, scaleable, and well-characterized methods by working collaboratively to
support the IGVF Consortium goals of understanding how genomes and genomic variation
function and orchestrate complex phenotypes. Our track record in developing, applying, and
sharing these high-throughput characterization methods, as well as providing access to all data,
supports that we will be successful in accomplishing our objective via the following specific
aims: Aim 1. Characterize all gene regulatory elements essential for cell survival. Aim 2.
Characterize all gene regulatory elements essential to cell lineage specification. Aim 3.
Characterize all gene regulatory elements in select eQTL regions. Aim 4. Characterize all non-
coding elements essential to tissue homeostasis in a mouse model. We will make all data
immediately available, as well as share comprehensive protocols, reagents, and analysis tools
to the scientific community. Together, the diverse approaches of this Characterization Center will
lead to transformative progress in understanding the role of regulatory elements and noncoding
variants across many diverse phenotypes.

## Key facts

- **NIH application ID:** 10297406
- **Project number:** 1UM1HG012053-01
- **Recipient organization:** DUKE UNIVERSITY
- **Principal Investigator:** GREGORY E CRAWFORD
- **Activity code:** UM1 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $956,415
- **Award type:** 1
- **Project period:** 2021-09-01 → 2026-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10297406

## Citation

> US National Institutes of Health, RePORTER application 10297406, High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes (1UM1HG012053-01). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10297406. Licensed CC0.

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