Genome-wide mapping of RNA-protein associations through sequencing

Zhijie Qi; Shuanghong Xue; Junchen Chen; Wenxin Zhao; Kara Johnson; Xingzhao Wen; John Lalith Charles Richard; Pei Lin; Sheng Zhong

doi:10.1038/s41587-025-02780-z

Genome-wide mapping of RNA-protein associations through sequencing

Nat Biotechnol. 2025 Sep 9. doi: 10.1038/s41587-025-02780-z. Online ahead of print.

Authors

Zhijie Qi^#¹, Shuanghong Xue^#¹, Junchen Chen², Wenxin Zhao², Kara Johnson², Xingzhao Wen³, John Lalith Charles Richard², Pei Lin², Sheng Zhong^{4

5

6}

Affiliations

¹ Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA.
² Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
³ Program in Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA.
⁴ Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA. szhong@ucsd.edu.
⁵ Shu Chien-Gene Lay Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. szhong@ucsd.edu.
⁶ Program in Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA, USA. szhong@ucsd.edu.

^# Contributed equally.

PMID: 40925998
DOI: 10.1038/s41587-025-02780-z

Abstract

RNA-protein interactions critically regulate gene expression and cellular processes, yet their comprehensive mapping remains challenging due to their structural diversity. We introduce PRIM-seq (protein-RNA interaction mapping by sequencing), a method for concurrent de novo identification of RNA-binding proteins and their associated RNAs. PRIM-seq generates unique chimeric DNA sequences by proximity ligation of RNAs with protein-linked DNA barcodes, which are subsequently decoded through sequencing. We apply PRIM-seq to two human cell lines and construct a human RNA-protein association network (HuRPA), encompassing >350,000 associations involving ~7,000 RNAs and ~11,000 proteins, including 2,610 proteins that each interact with at least 10 distinct RNAs. We experimentally validate the tumorigenesis-associated lincRNA LINC00339, the RNA with the highest number of protein associations in HuRPA, as a protein-associated RNA. We further validate the RNA-associating abilities of chromatin-conformation regulators SMC1A, SMC3 and RAD21, as well as the metabolic enzyme PHGDH. PRIM-seq enables systematic discovery and prioritization of RNA-binding proteins and their targets without gene- or protein-specific reagents.

Abstract

Grants and funding