ArticleNucleic acids research2022
PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors.Nature methods · 2026Article
- A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function.Nature biotechnology · 2026Article
- Bridging sequence-structure motifs and genetic variants for genome-wide dynamic RNA-protein interaction profiling.Nature communications · 2026Article
- Review
- RNA functional modulation by Mitoxantrone via RNA structural ensemble repartitioning.Nature communications · 2026Article
- PRIME-BSPre: a genome-wide protein-RNA binding sites prediction method based on templates.BMC genomics · 2026Article
- CisBP-RNA: a web resource for eukaryotic RNA-binding proteins and their motifs.Nucleic acids research · 2026Article
- Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.Communications biology · 2025Article
- TRAFICA: an open chromatin language model to improve transcription factor binding affinity prediction.Bioinformatics (Oxford, England) · 2025Article
- PaRPI predicts RNA-Protein interactions from cross-protocol and cross-batch RNA-binding protein datasets.Communications biology · 2025Article
- Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.RNA (New York, N.Y.) · 2025Article
- LncRNA-Protein Interactions: A Key to Deciphering LncRNA Mechanisms.Biomolecules · 2025Review
- DeepFusion: A deep bimodal information fusion network for unraveling protein-RNA interactions using in vivo RNA structures.Computational and structural biotechnology journal · 2024Article
- Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.bioRxiv : the preprint server for biology · 2024Article
- ePRINT: exonuclease assisted mapping of protein-RNA interactions.Genome biology · 2024Article
- Review
- Dynamic characterization and interpretation for protein-RNA interactions across diverse cellular conditions using HDRNet.Nature communications · 2023Article
- RNA-binding proteins that lack canonical RNA-binding domains are rarely sequence-specific.Scientific reports · 2023Article
- Stacking-ac4C: an ensemble model using mixed features for identifying n4-acetylcytidine in mRNA.Frontiers in immunology · 2023Article
- qNABpredict: Quick, accurate, and taxonomy-aware sequence-based prediction of content of nucleic acid binding amino acids.Protein science : a publication of the Protein Society · 2023Article
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7 authors.
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Abstract
Modelling both primary sequence and secondary structure preferences for RNA binding proteins (RBPs) remains an ongoing challenge. Current models use varied RNA structure representations and can be difficult to interpret and evaluate. To address these issues, we present a universal RNA motif-finding/scanning strategy, termed PRIESSTESS (Predictive RBP-RNA InterpretablE Sequence-Structure moTif regrESSion), that can be applied to diverse RNA binding datasets. PRIESSTESS identifies dozens of enriched RNA sequence and/or structure motifs that are subsequently reduced to a set of core motifs by logistic regression with LASSO regularization. Importantly, these core motifs are easily visualized and interpreted, and provide a measure of RBP secondary structure specificity. We used PRIESSTESS to interrogate new HTR-SELEX data for 23 RBPs with diverse RNA binding modes and captured known primary sequence and secondary structure preferences for each. Moreover, when applying PRIESSTESS to 144 RBPs across 202 RNA binding datasets, 75% showed an RNA secondary structure preference but only 10% had a preference besides unpaired bases, suggesting that most RBPs simply recognize the accessibility of primary sequences.
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