ArticleProceedings of the National Academy of Sciences of the United States of America2008
Computational prediction of RNA structural motifs involved in posttranscriptional regulatory processes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed, 124 citations in OpenAlex.
- An intrinsically disordered region mediates RNA-binding selectivity and cellular activities of LARP6.Nature communications · 2026Article
- RNA Structure and Its Function.Methods in molecular biology (Clifton, N.J.) · 2026Article
- RNAelem: an algorithm for discovering sequence-structure motifs in RNA bound by RNA-binding proteins.Bioinformatics advances · 2024Article
- RNANetMotif: Identifying sequence-structure RNA network motifs in RNA-protein binding sites.PLoS computational biology · 2022Article
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The RNA structurome in the asexual blood stages of malaria pathogenRNA biology · 2021Article
- Spatio-temporal mRNA tracking in the early zebrafish embryo.Nature communications · 2021Article
- High-Temperature-Responsive Poplar lncRNAs Modulate Target Gene Expression via RNA Interference and Act as RNA Scaffolds to Enhance Heat Tolerance.International journal of molecular sciences · 2020Article
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- Activity of MCPIP1 RNase in tumor associated processes.Journal of experimental & clinical cancer research : CR · 2019Review
- POSTAR2: deciphering the post-transcriptional regulatory logics.Nucleic acids research · 2019Article
- Osmotic stress-responsive promoter upstream transcripts (PROMPTs) act as carriers of MYB transcription factors to induce the expression of target genes in Populus simonii.Plant biotechnology journal · 2019Article
- DistinctDevelopment (Cambridge, England) · 2018Article
- Feature-Based and String-Based Models for Predicting RNA-Protein Interaction.Molecules (Basel, Switzerland) · 2018Article
- A Massively Parallel Reporter Assay of 3' UTR Sequences Identifies In Vivo Rules for mRNA Degradation.Molecular cell · 2017Article
- Article
- RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing.Genomics, proteomics & bioinformatics · 2017Review
- Distinct cis elements in the 3' UTR of the C. elegans cebp-1 mRNA mediate its regulation in neuronal development.Developmental biology · 2017Article
- Associating transcription factors and conserved RNA structures with gene regulation in the human brain.Scientific reports · 2017Article
- RNA toxicity and foci formation in microsatellite expansion diseases.Current opinion in genetics & development · 2017Review
3 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Messenger RNA molecules are tightly regulated, mostly through interactions with proteins and other RNAs, but the mechanisms that confer the specificity of such interactions are poorly understood. It is clear, however, that this specificity is determined by both the nucleotide sequence and secondary structure of the mRNA. Here, we develop RNApromo, an efficient computational tool for identifying structural elements within mRNAs that are involved in specifying posttranscriptional regulations. By analyzing experimental data on mRNA decay rates, we identify common structural elements in fast-decaying and slow-decaying mRNAs and link them with binding preferences of several RNA binding proteins. We also predict structural elements in sets of mRNAs with common subcellular localization in mouse neurons and fly embryos. Finally, by analyzing pre-microRNA stem-loops, we identify structural differences between pre-microRNAs of animals and plants, which provide insights into the mechanism of microRNA biogenesis. Together, our results reveal unexplored layers of posttranscriptional regulations in groups of RNAs and are therefore an important step toward a better understanding of the regulatory information conveyed within RNA molecules. Our new RNA motif discovery tool is available online.
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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.