# Revealing protein-protein interactions and RNA-protein interactions at genome-scale in two weeks

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2020 · $375,978

## Abstract

Revealing protein-protein interactions and RNA-protein interactions at genome-scale in two weeks
Abstract
Our ability to interpret the human genome is limited by our knowledge of the interaction networks of the products
of the genome sequence, including RNAs and proteins. If we had a complete reference map of all DNA-DNA,
protein-DNA, RNA-DNA, RNA-RNA, RNA-protein, and protein-protein interactions, we would have a completely
new approach to reading the book of the human genome. Recent technology breakthroughs, including those led
by NIH Common Fund programs, enabled genome-wide mapping of DNA-DNA, protein-DNA, RNA-DNA, and
RNA-RNA interactions en masse. However, genome-scale mapping of RNA-protein interactions (RPI) and
protein-protein interactions (PPI) remain laborious and resource-intensive. In this project, we propose two
extremely high-throughput genomic-based technologies for mapping human RPI and PPI networks at genome
scale. We will develop bioinformatics tools to analyze the data with statistical rigor. Specifically, we propose an
“all-vs-all” approach to map PPI and RPI networks. These genomics technologies and their coupled genomic
informatics tools will generate reference maps of human PPI and RPI networks. In the long term, such maps will
greatly facilitate the interpretation of the functions of the human genome. In Aim 1, we will develop an extremely
high-throughput technology called “PPI-seq” to map the PPI network at genome-scale. PPI-seq is expected to
be capable of generating a reference map of the human PPI network within a single lab in 2 weeks' time, with
an expected yield of ~50,000 high-confidence pairwise PPIs. In Aim 2, we will develop an extremely high-
throughput technology called “RPI-seq” to map the RPI network at genome-scale. RPI-seq is expected to be
capable of generating a reference map of the human RPI network within single lab in 2 weeks' time. RPI-seq will
simultaneous reveal RNA binding proteins (RBP) and the RNAs bound by each RBP.

## Key facts

- **NIH application ID:** 10032303
- **Project number:** 1R01GM138852-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Sheng Zhong
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $375,978
- **Award type:** 1
- **Project period:** 2020-09-18 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10032303

## Citation

> US National Institutes of Health, RePORTER application 10032303, Revealing protein-protein interactions and RNA-protein interactions at genome-scale in two weeks (1R01GM138852-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10032303. Licensed CC0.

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