Proteins and RNAs are constantly interacting inside our cells, shaping how genes are expressed and how cellular processes are carried out. Mapping these interactions is difficult because of the wide variety of RNA-protein structures, but a new tool offers an innovative way forward.

Researchers from the University of California San Diego have developed PRIM-seq, short for protein-RNA interaction mapping by sequencing. This technique links RNA molecules to unique DNA barcodes that are attached to proteins, then uses RNA sequencing to decode these pairings. With PRIM-seq, the team created a human RNA-protein association network called HuRPA, which includes more than 350,000 connections between about 7,000 RNAs and 11,000 proteins.

PRIM-seq experimental pipeline

a, Step 1. SMART-display takes mRNA from input cells to produce a library of mRNA-barcoded proteins. The protein and its mRNA label are covalently linked through puromycin. b, Step 2. REILIS converts each RNA-protein pair to a chimeric DNA sequence, with a ‘protein-end’ read originating from the protein’s mRNA label (green) and an ‘RNA-end’ read originating from the associated RNA (purple). c, PRIM-seq read pairs with the protein-end aligned to the PHGDH gene and the RNA-end aligned to the ATF4 gene.

Some of the findings are especially noteworthy. The team confirmed that LINC00339, a long non-coding RNA previously linked to cancer, interacts with a large number of proteins. They also validated that chromatin regulators like SMC1A and SMC3, as well as the metabolic enzyme PHGDH, form important RNA connections.

PRIM-seq provides scientists with a way to study thousands of RNA-protein interactions at once. This method can help prioritize which proteins and RNAs to study in more detail, opening the door to discoveries in areas such as cancer biology, gene regulation, and cellular metabolism.

Availability – PRIMseqTools and its source code and complete documentation are available at GitHub (https://github.com/Zhong-Lab-UCSD/PRIMseqTools).