ArticleMolecular cell2021
Revealing protein-protein interactions at the transcriptome scale by sequencing.
Article in Molecular cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 57 citations in OpenAlex.
- SoPPIs: a highly parallelized protein-protein-interaction screening method in prokaryotic and eukaryotic hosts.Nucleic acids research · 2026Article
- Genome-wide mapping of RNA-protein associations through sequencing.Nature biotechnology · 2026Article
- RNA-binding activity of PHGDH drives amyloid-beta production in a human brain organoid model of sporadic Alzheimer's disease.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq.bioRxiv : the preprint server for biology · 2026Article
- Click-linking: a cell-compatible protein crosslinking method based on click chemistry.Nature communications · 2025Article
- Large-scale protein interactome reveals lineage-specific genes driving plant-parasitic nematode adaptive innovations.Science advances · 2025Article
- Spatially resolved subcellular protein-protein interactomics in drug-perturbed lung-cancer cultures and tissues.Nature biomedical engineering · 2025Article
- NetREm: Network Regression Embeddings reveal cell-type transcription factor coordination for gene regulation.Bioinformatics advances · 2025Article
- Long Non-Coding RNAs, Nuclear Receptors and Their Cross-Talks in Cancer-Implications and Perspectives.Cancers · 2024Review
- NUP43 promotes PD-L1/nPD-L1/PD-L1 feedback loop via TM4SF1/JAK/STAT3 pathway in colorectal cancer progression and metastatsis.Cell death discovery · 2024Article
- From beer to breadboards: yeast as a force for biological innovation.Genome biology · 2024Review
- SaLT&PepPr is an interface-predicting language model for designing peptide-guided protein degraders.Communications biology · 2023Article
- Mapping the protein-protein interactome in the tumor immune microenvironment.Antibody therapeutics · 2023Review
- ActivePPI: quantifying protein-protein interaction network activity with Markov random fields.Bioinformatics (Oxford, England) · 2023Article
- A novel approach for the analysis of single-cell RNA sequencing identifies TMEM14B as a novel poor prognostic marker in hepatocellular carcinoma.Scientific reports · 2023Article
- Comorbidity genetic risk and pathways impact SARS-CoV-2 infection outcomes.Scientific reports · 2023Article
- Article
- Contrast subgraphs allow comparing homogeneous and heterogeneous networks derived from omics data.GigaScience · 2022Article
- Native holdup (nHU) to measure binding affinities from cell extracts.Science advances · 2022Article
- Deciphering Spatial Protein-Protein Interactions in Brain Using Proximity Labeling.Molecular & cellular proteomics : MCP · 2022Review
Corrections and comments
- Erratum issued
Authors and funding
12 authors at 3 institutions in 1 country.
Funding
Abstract
We describe PROPER-seq (protein-protein interaction sequencing) to map protein-protein interactions (PPIs) en masse. PROPER-seq first converts transcriptomes of input cells into RNA-barcoded protein libraries, in which all interacting protein pairs are captured through nucleotide barcode ligation, recorded as chimeric DNA sequences, and decoded at once by sequencing and mapping. We applied PROPER-seq to human embryonic kidney cells, T lymphocytes, and endothelial cells and identified 210,518 human PPIs (collected in the PROPER v.1.0 database). Among these, 1,365 and 2,480 PPIs are supported by published co-immunoprecipitation (coIP) and affinity purification-mass spectrometry (AP-MS) data, 17,638 PPIs are predicted by the prePPI algorithm without previous experimental validation, and 100 PPIs overlap human synthetic lethal gene pairs. In addition, four previously uncharacterized interaction partners with poly(ADP-ribose) polymerase 1 (PARP1) (a critical protein in DNA repair) known as XPO1, MATR3, IPO5, and LEO1 are validated in vivo. PROPER-seq presents a time-effective technology to map PPIs at the transcriptome scale, and PROPER v.1.0 provides a rich resource for studying PPIs.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.