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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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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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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Related Experiment Video

Updated: Oct 25, 2025

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
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Revealing protein-protein interactions at the transcriptome scale by sequencing.

Kara L Johnson1, Zhijie Qi1, Zhangming Yan1

  • 1Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.

Molecular Cell
|August 4, 2021
PubMed
Summary

PROPER-seq is a new method to map protein-protein interactions (PPIs) efficiently. This technology identified over 210,000 human PPIs, including novel interactions with PARP1, providing a valuable resource for biological research.

Keywords:
Co-immunoprecipitationNetworkPARP1PROPER-seqProtein structureProtein-protein interactionProximity ligation assaySMART-displaySequencingSynthetic lethal

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • Protein-protein interactions (PPIs) are crucial for cellular functions.
  • Existing methods for mapping PPIs can be time-consuming and limited in scale.
  • A comprehensive understanding of the interactome is essential for deciphering complex biological processes.

Purpose of the Study:

  • To introduce PROPER-seq, a novel high-throughput technology for mapping protein-protein interactions.
  • To create a comprehensive database of human PPIs using PROPER-seq.
  • To identify novel interaction partners for key proteins like PARP1.

Main Methods:

  • PROPER-seq converts cellular transcriptomes into RNA-barcoded protein libraries.
  • Interacting protein pairs are captured via nucleotide barcode ligation, forming chimeric DNA sequences.
  • Sequencing and mapping decode the chimeric DNA to identify PPIs en masse.

Main Results:

  • PROPER-seq identified 210,518 human PPIs across kidney cells, T lymphocytes, and endothelial cells.
  • The PROPER v.1.0 database contains these identified PPIs, with validation against existing coIP and AP-MS data.
  • Four novel interaction partners for PARP1 (XPO1, MATR3, IPO5, LEO1) were identified and validated in vivo.

Conclusions:

  • PROPER-seq is a time-effective technology for large-scale PPI mapping at the transcriptome level.
  • The PROPER v.1.0 database offers a rich resource for studying PPIs and their biological significance.
  • PROPER-seq facilitates the discovery of novel protein interactions and functional insights.