Revealing protein-protein interactions at the transcriptome scale by sequencing

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.