ArticleGenome research2010
Signatures of RNA binding proteins globally coupled to effective microRNA target sites.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 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
72 citing papers in PubMed, 111 citations in OpenAlex.
- Seedless 3' pairing enables miR-17 family miRNAs to seize let-7 target sites.Nucleic acids research · 2026Article
- Bridging sequence-structure motifs and genetic variants for genome-wide dynamic RNA-protein interaction profiling.Nature communications · 2026Article
- Article
- bayesReact: expression-coupled regulatory motif analysis detects microRNA activity across cancers, tissues, and at the single-cell level.Nucleic acids research · 2026Article
- Systematic transcriptomic analysis and temporal modelling of human fibroblast senescence.Frontiers in aging · 2024Article
- Noncoding RNAs: Novel Targets for Opioid Tolerance.Current neuropharmacology · 2023Review
- A regulatory network of microRNAs confers lineage commitment during early developmental trajectories of B and T lymphocytes.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- CELF Family Proteins in Cancer: Highlights on the RNA-Binding Protein/Noncoding RNA Regulatory Axis.International journal of molecular sciences · 2021Review
- BOPC1 Enantiomers Preparation and HuR Interaction Study. From Molecular Modeling to a Curious DEEP-STD NMR Application.ACS medicinal chemistry letters · 2020Article
- Quantification and discovery of sequence determinants of protein-per-mRNA amount in 29 human tissues.Molecular systems biology · 2019Article
- Cryptic sequence features in the active postmortem transcriptome.BMC genomics · 2018Article
- TGF-β induces miR-100 and miR-125b but blocks let-7a through LIN28B controlling PDAC progression.Nature communications · 2018Article
- Regmex: a statistical tool for exploring motifs in ranked sequence lists from genomics experiments.Algorithms for molecular biology : AMB · 2018Article
- Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors.PLoS computational biology · 2017Article
- AUF1 regulation of coding and noncoding RNA.Wiley interdisciplinary reviews. RNA · 2017Review
- The microRNA network is altered in anterior cingulate cortex of patients with unipolar and bipolar depression.Journal of psychiatric research · 2016Article
- SNHG16 is regulated by the Wnt pathway in colorectal cancer and affects genes involved in lipid metabolism.Molecular oncology · 2016Article
- Identifying functional cancer-specific miRNA-mRNA interactions in testicular germ cell tumor.Journal of theoretical biology · 2016Article
- IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction.BMC genomics · 2016Article
- MicroRNAs Are Involved in the Development of Morphine-Induced Analgesic Tolerance and Regulate Functionally Relevant Changes in Serpini1.Frontiers in molecular neuroscience · 2016Article
12 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MicroRNAs (miRNAs) and small interfering RNAs (siRNAs), bound to Argonaute proteins (RISC), destabilize mRNAs through base-pairing with the mRNA. However, the gene expression changes after perturbations of these small RNAs are only partially explained by predicted miRNA/siRNA targeting. Targeting may be modulated by other mRNA sequence elements such as binding sites for the hundreds of RNA binding proteins (RNA-BPs) expressed in any cell, and this aspect has not been systematically explored. Across a panel of published experiments, we systematically investigated to what extent sequence motifs in 3' untranslated regions (UTRs) correlate with expression changes following transfection of small RNAs. The most significantly overrepresented motifs in down-regulated mRNAs are two novel U-rich motifs (URMs), UUUUAAA and UUUGUUU, recently discovered as binding sites for the ELAVL4 (also known as HuD) RNA-BP. Surprisingly, the most significantly overrepresented motif in up-regulated mRNAs is the heptanucleotide AU-rich element (ARE), UAUUUAU, which is known to affect mRNA stability via at least 20 different RNA-BPs. We show that destabilization mediated by the transfected miRNA is generally attenuated by ARE motifs and augmented by URM motifs. These ARE and URM signatures were confirmed in different types of published experiments covering eight different cell lines. Finally, we show that both ARE and URM motifs couple to presumed endogenous miRNA binding sites in mRNAs bound by Argonaute proteins. This is the first systematic investigation of 3' UTR motifs that globally couple to regulation by miRNAs and may potentially antagonize or cooperate with miRNA/siRNA regulation. Our results suggest that binding sites of miRNAs and RNA-BPs should be considered in combination when interpreting and predicting miRNA regulation in vivo.
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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.