# Non-Coding Genetic Vulnerabilities in Human Photoreceptor Function and Disease

> **NIH NIH R01** · SEATTLE CHILDREN'S HOSPITAL · 2020 · $470,750

## Abstract

PROJECT SUMMARY/ABSTRACT
Cis-regulatory elements (CREs) are critical sites of transcription factor (TF) binding to the genome that
orchestrate the expression of genes necessary for normal cellular function. Mutations within CREs can disrupt
TF binding and cause inherited human diseases including disorders of vision. The genomic location and
function of CREs that are necessary for human vision is largely unknown. This gap in knowledge is a
significant obstacle toward understanding the genetic regulation of normal human vision and to identifying
disease-causing mutations with CREs. The long-term goal for our research is to understand how genetic
variation within CREs shapes the structure and function of the retina and contributes to human vision. The
focused objective of this proposal is to determine the mechanisms by which CREs regulate essential gene
expression in photoreceptor cells and to determine how genetic mutations within CREs lead to retinal
disease. The central hypothesis driving this work is that discrete DNA sequences within CREs are required to
regulate essential photoreceptor gene expression and that CRE mutations that disrupt evolutionarily conserved
TF binding sites contribute to inherited visual disorders. To test this hypothesis we are pursuing the following
specific aims: 1) Determine the activity of human photoreceptor CREs in human retinal organoids using ATAC-
Seq, ChIP-Seq and RNA-Seq to compare them to CREs we have previously identified from adult and
developing human retinas. This will demonstrate the utility of organoids for studying photoreceptor CREs in
their native cellular-genomic context. 2) Test the function of patient-derived variants in human photoreceptor
CREs. Using high-throughput AAV-based reporter assays we will determine which CREs sequences are
sufficient to drive cell-type-specific expression in the mouse retina and human retinal organoids and determine
the consequence of sequence variants on CRE activity. 3) Determine the mechanisms by which multiple CREs
regulate the expression of a critical photoreceptor transcription factor, NRL. CRISPR/Cas9-based approaches
will target specific CREs at the NRL locus to reveal the contribution of each CRE to the expression of this
essential gene and to serve as a case study for the regulation of other essential genes. The contribution of this
research will be to elucidate the mechanisms by which CREs regulate genes that are necessary for human
photoreceptor function and survival. This work will enable the systematic identification and interpretation of
genetic variants within CREs and therefore improve genetic diagnostics for unexplained retinal disease. By
opening up the non-coding genome to functional analyses it will be possible for the first time to determine the
mechanisms by which individual CREs regulate specific genes that are critical for photoreceptor cell function in
a high-throughput and comprehensive manner. This will enable discovery of genetic contributi...

## Key facts

- **NIH application ID:** 9902484
- **Project number:** 5R01EY028584-02
- **Recipient organization:** SEATTLE CHILDREN'S HOSPITAL
- **Principal Investigator:** TIMOTHY JOEL CHERRY
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $470,750
- **Award type:** 5
- **Project period:** 2019-04-01 → 2024-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9902484

## Citation

> US National Institutes of Health, RePORTER application 9902484, Non-Coding Genetic Vulnerabilities in Human Photoreceptor Function and Disease (5R01EY028584-02). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/9902484. Licensed CC0.

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