# CASCADE: A high-throughput assay to characterize gene-regulatory complexes affected by single-nucleotide polymorphisms

> **NIH NIH R21** · BOSTON UNIVERSITY (CHARLES RIVER CAMPUS) · 2020 · $453,750

## Abstract

Project Summary
Studies have identified thousands of single-nucleotide polymorphisms (SNPs) associated with a range of
diseases, but the causal nucleotide changes and mechanisms remain largely unknown. A current
bottleneck in the field is that characterization of SNP mechanism greatly lags SNP identification. Analyses
suggest that causal variants underlying disease risk are often non-coding SNP (ncSNPs) that function
through their effects on gene expression. The primary means by which ncSNPs affect gene expression is
by altering binding sites for transcription factor-cofactor (TF-CoF) complexes. Therefore, a major
challenge in understanding disease susceptibility and etiology is to characterize the mechanisms by which
the thousands of ncSNPs disrupt the binding of TF-CoF complexes to alter gene expression.
 To address this challenge, we have recently developed CASCADE – a high-throughput microarray-
based method to screen the impact of ncSNPs on the DNA-binding of TF-CoF complexes. In this
proposal, we will use our CASCADE approach to study TF-CoF complexes in diverse immune cell states,
and study their disruption by disease-associated ncSNPs. To determine the cell state-dependence of our
ncSNP annotations and TF-CoF complexes, we will examine results using cell lines as well as primary
human cells. To assess CoF specificity for TF classes, and which CoFs are affected by the largest
number of ncSNPs (i.e., assay coverage), we will study TF-CoF complexes comprising diverse CoFs and
CoF subcomponents. Our goal is to develop CASCADE as a general high-throughput platform to
biophysically characterize the regulatory complexes affected by ncSNPs.

## Key facts

- **NIH application ID:** 10042422
- **Project number:** 1R21HG011289-01
- **Recipient organization:** BOSTON UNIVERSITY (CHARLES RIVER CAMPUS)
- **Principal Investigator:** Trevor Siggers
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $453,750
- **Award type:** 1
- **Project period:** 2020-08-15 → 2024-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10042422

## Citation

> US National Institutes of Health, RePORTER application 10042422, CASCADE: A high-throughput assay to characterize gene-regulatory complexes affected by single-nucleotide polymorphisms (1R21HG011289-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10042422. Licensed CC0.

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