# Retinoic acid target genes and transcriptional mechanisms during eye development

> **NIH NIH R01** · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · 2021 · $390,000

## Abstract

PROJECT SUMMARY
One of the most critical functions of the vitamin A (retinol) metabolite retinoic acid (RA) is control of
eye development. In mouse, RA synthesis occurs early in the optic field with expression of retinol
dehydrogenase-10 (RDH10) and all three retinaldehyde dehydrogenases (ALDH1A1, ALDH1A2,
ALDH1A3) that convert retinol to RA. RA diffuses to tissues throughout the optic placode, optic
vesicle, and adjacent mesenchyme to stimulate folding of the optic vesicle to form the optic cup by
E10.5. At E12.5-E14.5, RA is needed for further morphogenesis of the optic cup and surrounding
perioptic mesenchyme; loss of RA leads to microphthalmia. RA functions by binding to nuclear RA
receptors at RA response elements (RAREs) that either activate or repress transcription of key
genes. Binding of RA to RA receptors regulates recruitment of transcriptional coregulators such as
nuclear receptor coactivator (NCOA) and nuclear receptor corepressor (NCOR), which in turn
control binding of the generic coactivator p300 and the generic corepressor PRC2. However, a
major unsolved problem is what are the key genes controlled by RA during development of the eye;
only two candidate direct RA target genes are known (Pitx2 and Foxc1). As loss or gain of RA
activity alters expression of thousands of genes (perhaps many due to post-transcriptional effects),
it remains difficult to identify genes that are direct transcriptional targets of RA. In our Preliminary
Studies we addressed this question by comparing ChIP-seq and RNA-seq for tissues from
Aldh1a2-/- embryos lacking RA synthesis, thus identifying genes with altered expression when RA
is missing that also have nearby RA-regulated deposition of H3K27ac (gene activation mark) or
H3K27me3 (gene repression mark) associated with RAREs. Such RARE enhancers/silencers were
identified near genes already known to be required for embryonic development, thus validating our
approach. CRISPR knockouts for several predicted new direct RA target genes verified their
requirements for development. Here, we plan to use this approach to identify RA target genes and
PITX2 target genes during eye development by comparing ChIP-seq (H3K27ac & H3K27me3) and
RNA-seq for wild-type vs RA-deficient optic vesicle and eye, and wild-type vs Pitx2 knockout eye.
We will also identify RA-regulated enhancers and silencers in the eye to uncover the mechanisms
through which RA regulates Pitx2, Foxc1, or other genes. Our studies will provide vital information
on the mechanisms utilized by RA and PITX2 to control transcription in the eye and will identify
gene regulatory networks during eye formation. This knowledge will help determine how eye
defects occur, identify new genes or enhancers/silencers that may be mutational targets causing
human eye defects, and improve strategies to treat eye defects.

## Key facts

- **NIH application ID:** 10201360
- **Project number:** 1R01EY031745-01A1
- **Recipient organization:** SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE
- **Principal Investigator:** GREGG L DUESTER
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $390,000
- **Award type:** 1
- **Project period:** 2021-06-01 → 2025-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10201360

## Citation

> US National Institutes of Health, RePORTER application 10201360, Retinoic acid target genes and transcriptional mechanisms during eye development (1R01EY031745-01A1). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10201360. Licensed CC0.

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