ArticleMethods (San Diego, Calif.)2017
RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins.
Article in Methods (San Diego, Calif.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
40 citing papers in PubMed, 72 citations in OpenAlex.
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- A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function.Nature biotechnology · 2026Article
- Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.Nucleic acids research · 2026Article
- Splicing of ultraconserved poison exons controls mitotic fidelity and stem cell viability.bioRxiv : the preprint server for biology · 2026Article
- PTBP1 controls miRNA loading on target RNAs: lessons from the CyCoNP lncRNA.RNA (New York, N.Y.) · 2026Article
- RNA binding of GAPDH controls transcript stability and protein translation in acute myeloid leukemia.RNA biology · 2025Article
- Nano-Mod-Amp reveals RNA sequence, structural and cell type specific features of pseudouridylation by PUS7.bioRxiv : the preprint server for biology · 2025Article
- At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways.The New phytologist · 2025Article
- The dual role of RNA-binding proteins: promotion of tumorigenesis, drug resistance, and emerging therapeutic targets.Acta biochimica et biophysica Sinica · 2025Article
- RNA binding proteins (RBPs) on genetic stability and diseases.Global medical genetics · 2025Review
- Definition of the binding specificity of the T7 bacteriophage primase by analysis of a protein binding microarray using a thermodynamic model.Nucleic acids research · 2024Article
- Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human.Nature genetics · 2024Article
- Sensing nucleotide composition in virus RNA.Bioscience reports · 2023Review
- Uncovering a mammalian neural-specific poly(A) binding protein with unique properties.Genes & development · 2023Article
- RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific.Scientific reports · 2023Article
- PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins.Nucleic acids research · 2022Article
- A massively parallel reporter assay reveals focused and broadly encoded RNA localization signals in neurons.Nucleic acids research · 2022Article
- Widespread autogenous mRNA-protein interactions detected by CLIP-seq.Nucleic acids research · 2022Article
- Single-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation.Nature communications · 2022Article
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Authors and funding
6 authors at 1 institution in 1 country.
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Abstract
RNA-binding proteins (RBPs) participate in diverse cellular processes and have important roles in human development and disease. The human genome, and that of many other eukaryotes, encodes hundreds of RBPs that contain canonical sequence-specific RNA-binding domains (RBDs) as well as numerous other unconventional RNA binding proteins (ucRBPs). ucRBPs physically associate with RNA but lack common RBDs. The degree to which these proteins bind RNA, in a sequence specific manner, is unknown. Here, we provide a detailed description of both the laboratory and data processing methods for RNAcompete, a method we have previously used to analyze the RNA binding preferences of hundreds of RBD-containing RBPs, from diverse eukaryotes. We also determine the RNA-binding preferences for two human ucRBPs, NUDT21 and CNBP, and use this analysis to exemplify the RNAcompete pipeline. The results of our RNAcompete experiments are consistent with independent RNA-binding data for these proteins and demonstrate the utility of RNAcompete for analyzing the growing repertoire of ucRBPs.
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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.