ArticleNucleic acids research2019
Deciphering human ribonucleoprotein regulatory networks.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
41 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The genetic and biochemical determinants of mRNA degradation rates in mammals.Genome biology · 2022Pooled it
- The Interactions of Tau, RNA, and Stress Granules in Neurodegenerative Disease: A Comprehensive Review.Cells · 2026Review
- Post-transcriptional regulatory networks: The dynamic interplay of RNA-binding proteins.The FEBS journal · 2026Review
- PCLIPtools: a robust framework for identifying RNA-protein interaction sites from PAR-CLIP experiments.Nucleic acids research · 2026Article
- Systematic evaluation of tools used for single-cell mCommunications biology · 2025Article
- PCLIPtools: A Robust Framework for Identifying RNA-Protein Interaction Sites from PAR-CLIP experiments.bioRxiv : the preprint server for biology · 2025Article
- Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.RNA (New York, N.Y.) · 2025Article
- RNA binding proteins (RBPs) on genetic stability and diseases.Global medical genetics · 2025Review
- Predicting functional UTR variants by integrating region-specific features.Briefings in bioinformatics · 2024Article
- Review
- Improved discovery of RNA-binding protein binding sites in eCLIP data using DEWSeq.Nucleic acids research · 2024Article
- PAR-dCLIP: Enabling detection of RNA binding protein target transcripts bound at 5' termini through the incorporation of a decapping step.Methods in enzymology · 2024Article
- A systematic benchmark of machine learning methods for protein-RNA interaction prediction.Briefings in bioinformatics · 2023Article
- Article
- A computational map of the human-SARS-CoV-2 protein-RNA interactome predicted at single-nucleotide resolution.NAR genomics and bioinformatics · 2023Article
- RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins.Nucleic acids research · 2023Article
- Identifying interpretable gene-biomarker associations with functionally informed kernel-based tests in 190,000 exomes.Nature communications · 2022Article
- RiPCA: An Assay for the Detection of RNA-Protein Interactions in Live Cells.Current protocols · 2022Article
- Targeted RNA editing: novel tools to study post-transcriptional regulation.Molecular cell · 2022Review
- A global analysis on the differential regulation of RNA binding proteins (RBPs) by TNF-α as potential modulators of metabolic syndromes.BBA advances · 2022Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
RNA-binding proteins (RBPs) control and coordinate each stage in the life cycle of RNAs. Although in vivo binding sites of RBPs can now be determined genome-wide, most studies typically focused on individual RBPs. Here, we examined a large compendium of 114 high-quality transcriptome-wide in vivo RBP-RNA cross-linking interaction datasets generated by the same protocol in the same cell line and representing 64 distinct RBPs. Comparative analysis of categories of target RNA binding preference, sequence preference, and transcript region specificity was performed, and identified potential posttranscriptional regulatory modules, i.e. specific combinations of RBPs that bind to specific sets of RNAs and targeted regions. These regulatory modules represented functionally related proteins and exhibited distinct differences in RNA metabolism, expression variance, as well as subcellular localization. This integrative investigation of experimental RBP-RNA interaction evidence and RBP regulatory function in a human cell line will be a valuable resource for understanding the complexity of post-transcriptional regulation.
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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.