Work

Protocol for massively parallel RNA assay combined with immunoprecipitation for high-throughput analysis of RNA-protein interactions in cells

Year: 2026

Type: article

Abstract: RNA functions are largely mediated through interactions with RNA-binding proteins (RBPs), and defining the molecular principles underlying these interactions is essential for understanding RNA biology. Here, we present a massively parallel RNA assay combined with immunoprecipitation (MPRNA-IP) that enables high-throughput analysis of RNA-protein interactions in cells. We describe detailed steps for oligonucleotide design, cloning, transfection, sequencing, and computational analysis. Together, these procedures allow high-throughput interrogation of RNA sequences to identify sequence and structural elements that contribute to protein binding. For complete details on the use and execution of this protocol, please refer to Lee et al. 1

Source: STAR Protocols

DOI: 10.1016/j.xpro.2026.104624

Authors: Yu Hsuan Lee, John L. Rinn, Taeyoung Hwang

Institutions: Lieber Institute for Brain Development, University of Colorado Boulder, Johns Hopkins University, Johns Hopkins Medicine

Language: English

Topic: RNA Research and Splicing

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $1,550

Funders: National Institutes of Health, National Institute of General Medical Sciences