ReviewWiley interdisciplinary reviews. RNA
Finding the target sites of RNA-binding proteins.
Review in Wiley interdisciplinary reviews. RNA. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
What it found
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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.
The trial behind it
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
63 citing papers in PubMed.
- ProRB: a structure-free unified framework for joint prediction and design of protein-RNA interactions.Nucleic acids research · 2026Article
- Enhancement of Therapeutic mRNA Translation in Cellular Stress Conditions.International journal of molecular sciences · 2026Review
- Holistic overview of regulatory networks governing seed dormancy and germination in plants.Science China. Life sciences · 2026Review
- UTR-DynaPro: a CNN-transformer multimodal language model for decoding 5'UTR regulatory mechanisms.Scientific reports · 2026Article
- Deep generative model of RNAs based on variational autoencoder with context-free grammar.Bioinformatics (Oxford, England) · 2025Article
- EDCLoc: a prediction model for mRNA subcellular localization using improved focal loss to address multi-label class imbalance.BMC genomics · 2024Article
- A commitment for life: Decades of unraveling the molecular mechanisms behind seed dormancy and germination.The Plant cell · 2024Review
- A 5' UTR Language Model for Decoding Untranslated Regions of mRNA and Function Predictions.Nature machine intelligence · 2024Article
- Article
- Transfer Learning Allows Accurate RBP Target Site Prediction with Limited Sample Sizes.Biology · 2023Article
- COVIDanno, COVID-19 annotation in human.Frontiers in microbiology · 2023Article
- The SWI/SNF subunit BRG1 affects alternative splicing by changing RNA binding factor interactions with nascent RNA.Molecular genetics and genomics : MGG · 2022Article
- Protein-Specific Prediction of RNA-Binding Sites Based on Information Entropy.Computational intelligence and neuroscience · 2022Article
- Article
- Dynamic Variations of 3'UTR Length Reprogram the mRNA Regulatory Landscape.Biomedicines · 2021Review
- Spatial correlation statistics enable transcriptome-wide characterization of RNA structure binding.Cell reports methods · 2021Article
- Destruction of DNA-Binding Proteins by Programmable Oligonucleotide PROTAC (O'PROTAC): Effective Targeting of LEF1 and ERG.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Article
- Ribosome as a Translocase and Helicase.Biochemistry. Biokhimiia · 2021Review
- Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins.Bioinformatics (Oxford, England) · 2021Article
- Interpretation of deep learning in genomics and epigenomics.Briefings in bioinformatics · 2021Review
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
RNA-protein interactions differ from DNA-protein interactions because of the central role of RNA secondary structure. Some RNA-binding domains (RBDs) recognize their target sites mainly by their shape and geometry and others are sequence-specific but are sensitive to secondary structure context. A number of small- and large-scale experimental approaches have been developed to measure RNAs associated in vitro and in vivo with RNA-binding proteins (RBPs). Generalizing outside of the experimental conditions tested by these assays requires computational motif finding. Often RBP motif finding is done by adapting DNA motif finding methods; but modeling secondary structure context leads to better recovery of RBP-binding preferences. Genome-wide assessment of mRNA secondary structure has recently become possible, but these data must be combined with computational predictions of secondary structure before they add value in predicting in vivo binding. There are two main approaches to incorporating structural information into motif models: supplementing primary sequence motif models with preferred secondary structure contexts (e.g., MEMERIS and RNAcontext) and directly modeling secondary structure recognized by the RBP using stochastic context-free grammars (e.g., CMfinder and RNApromo). The former better reconstruct known binding preferences for sequence-specific RBPs but are not suitable for modeling RBPs that recognize shape and geometry of RNAs. Future work in RBP motif finding should incorporate interactions between multiple RBDs and multiple RBPs in binding to RNA.
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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.