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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
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Proteomics01:33

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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Related Experiment Video

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iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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Genome-wide mapping of RNA-protein associations through sequencing.

Zhijie Qi1, Shuanghong Xue1, Junchen Chen2

  • 1Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, USA.

Nature Biotechnology
|September 9, 2025
PubMed
Summary

We developed PRIM-seq, a novel sequencing method to identify RNA-binding proteins and their associated RNAs. This approach maps thousands of RNA-protein interactions, revealing new insights into gene regulation.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • RNA-protein interactions are crucial for gene expression and cellular functions.
  • Comprehensive mapping of these interactions is difficult due to RNA and protein structural diversity.
  • Existing methods often require gene- or protein-specific reagents, limiting broad application.

Purpose of the Study:

  • To introduce a novel method, PRIM-seq (protein-RNA interaction mapping by sequencing), for concurrent identification of RNA-binding proteins and their associated RNAs.
  • To construct a comprehensive human RNA-protein association network (HuRPA) without the need for specific reagents.
  • To enable systematic discovery and prioritization of RNA-binding proteins and their targets.

Main Methods:

  • PRIM-seq utilizes proximity ligation to generate unique chimeric DNA sequences from RNAs and protein-linked DNA barcodes.
  • These chimeric sequences are decoded through high-throughput sequencing.
  • The method was applied to two human cell lines to build the HuRPA network.

Main Results:

  • The human RNA-protein association network (HuRPA) was constructed, detailing over 350,000 associations between approximately 7,000 RNAs and 11,000 proteins.
  • Identified 2,610 proteins interacting with at least 10 distinct RNAs.
  • Experimentally validated the tumorigenesis-associated lincRNA LINC00339 and RNA-associating abilities of chromatin regulators (SMC1A, SMC3, RAD21) and metabolic enzyme PHGDH.

Conclusions:

  • PRIM-seq is an effective method for de novo identification of RNA-binding proteins and their RNA targets.
  • The developed HuRPA network provides a valuable resource for understanding RNA-protein interactions in humans.
  • PRIM-seq facilitates systematic discovery and prioritization of RNA-binding proteins and targets without prior knowledge or specific reagents.