# PRODIGE: A high-throughput tool for joint profiling of protein-DNA interactions and gene expression in single cells

> **NIH NIH R21** · INSTITUTE FOR SYSTEMS BIOLOGY · 2022 · $228,750

## Abstract

PROJECT SUMMARY/ABSTRACT
Protein-DNA interactions control access to genes in chromatins and regulate the spatial- and temporal-specific
gene expression. These interactions are crucial for cell differentiation and the maintenance of cellular diversity.
Dysregulated patterns of protein-DNA interactions are often associated with disease states. Applications of next-
generation epigenomic sequencing techniques have enabled deconvolution of protein-DNA interactions at
single-cell level. However, it remains challenging to define how cell-to-cell heterogeneity in protein-DNA
interactions impacts gene expression variability. Currently available methods for joint profiling protein-DNA
interactions and gene expression from single cells require laborious genetic manipulation, suffer relatively low
throughput, and are impossible to specifically map proteins with post-translational modifications, such as histone
marks. To address these unmet needs, we propose to develop PRODIGE – a high-throughput tool for joint
profiling of protein-DNA interactions and gene expression in the same single cells without the need of genetic
manipulations. It is enabled by a strategic integration of reversible cell fixation, antibody-guided chromatin
tagmentation, novel deformable and degradable barcoded hydrogel beads, droplet microfluidics, and next-
generation sequencing technology. In Aim 1, we will develop technical components and analytical pipelines of
PRODIGE. We will prepare protein A-Tn5 transposome for antibody-guided Tn5 tagmentation, fabricate
microfluidic devices for single-cell PRODIGE assay, and synthesize a barcoded library of deformable and
degradable barcoded hydrogel beads for single-cell barcoding. In Aim 2, we will optimize the method in bulk and
single-cell levels, and assess the performance of PRODIGE (joint analysis) in comparison to other stand-alone
counterparts. In Aim 3, we will benchmark PRODIGE to established tools for joint single-cell profiling of protein-
DNA interactions and transcriptome. Successful implementation of the proposed program will deliver a high-
throughput tool to quantify how cell-to-cell heterogeneity in protein-DNA binding influences gene expression
variability, decipher cell-type-specific patterns of upstream protein-DNA interactions and their transcriptional
outputs, and identify protein-mediated mechanisms that regulate cell-type-associated transcriptional programs
in heterogeneous cell populations and under different developmental and/or disease conditions.

## Key facts

- **NIH application ID:** 10492769
- **Project number:** 5R21GM140391-02
- **Recipient organization:** INSTITUTE FOR SYSTEMS BIOLOGY
- **Principal Investigator:** Wei Wei
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $228,750
- **Award type:** 5
- **Project period:** 2021-09-30 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10492769

## Citation

> US National Institutes of Health, RePORTER application 10492769, PRODIGE: A high-throughput tool for joint profiling of protein-DNA interactions and gene expression in single cells (5R21GM140391-02). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10492769. Licensed CC0.

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