# DISCOVERY OF DNA DETERMINANTS OF TRANSCRIPTION FACTOR BINDING AND FUNCTION IN PHO

> **NIH NIH R01** · WASHINGTON UNIVERSITY · 2020 · $306,254

## Abstract

Project Summary
A major function of the non-protein-coding genome is to direct specific patterns of gene
expression by encoding binding sites for transcription factors. However, large genomes contain
millions of spurious copies of the short, degenerate sequence motifs that transcription factors
recognize. It is not understood how genuinely functional binding sites are distinguished from
non-functional motifs. This is a critical unsolved problem, because growing evidence indicates
that genetic variants that disrupt or create transcription factor binding sites play a widespread
role in disease, but we currently cannot accurately identify variants affect active binding sites.
To address this issue, our long term goal is to understand how active transcription factor binding
sites are specified by their DNA sequence features. Recent results suggest that functional
binding sites are distinguished from spurious motifs by critical local sequences that flank the
core motif. Using the mammalian retina as a physiologically relevant model system to address
this broad issue, we will investigate binding sites for the photoreceptor transcription factor CRX.
Our specific aims are: First, to understand how flanking DNA sequence features distinguish
transcriptionally active CRX binding sites from inactive genomic sequences with spurious CRX
motifs. Second, to quantify and model the effects of local flanking sequence features using a
tractable system of synthetic CRX binding sites. The major innovation of this proposal is to
measure both transcription factor binding and cis-regulatory activity on a large set of wild-type,
mutant, and synthetic sequences, and thereby directly quantify the relationship between flanking
DNA sequence, binding, and activity. Using recently developed high-throughput assays to
measure cis-regulatory activity and CRX binding affinity, we will directly test the functional role
of local flanking sequences by disrupting flanking sequence features of CRX binding sites. By
combining functional genomics and synthetic biology to investigate natural and synthetic CRX
binding sites, we will discover how different DNA sequence features combine to specify active
CRX sites in the genome. The result will improve our understanding of how sequence variants
outside core motifs affect transcription factor binding sites.

## Key facts

- **NIH application ID:** 9951058
- **Project number:** 5R01GM121755-04
- **Recipient organization:** WASHINGTON UNIVERSITY
- **Principal Investigator:** Michael Aaron White
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $306,254
- **Award type:** 5
- **Project period:** 2017-07-01 → 2022-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9951058

## Citation

> US National Institutes of Health, RePORTER application 9951058, DISCOVERY OF DNA DETERMINANTS OF TRANSCRIPTION FACTOR BINDING AND FUNCTION IN PHO (5R01GM121755-04). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/9951058. Licensed CC0.

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