ArticleMethods (San Diego, Calif.)2012
MS2-TRAP (MS2-tagged RNA affinity purification): tagging RNA to identify associated miRNAs.
Article in Methods (San Diego, Calif.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 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.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
88 citing papers in PubMed, 137 citations in OpenAlex.
- Review
- A multivalent RNA affinity tag enables selective purification of tagged RNAs and bound proteins.Nucleic acids research · 2026Article
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- Modular engineering of thermoresponsive allosteric proteins.Nature chemical biology · 2026Article
- Tiam1 up-regulation by long non-coding RNA ABHD11-AS1 sponging of miR-182-5p causes β-catenin pathway activation to promote hexavalent chromium lung carcinogenesis.Journal of hazardous materials · 2026Article
- A molecular cartographer's toolkit for mapping RNA's uncharted realms.Cell reports · 2025Review
- Muscle-specific isoforms of FXR1 are necessary for miR-1-mediated repression of connexin 43 and are downregulated in pediatric dilated cardiomyopathy.American journal of physiology. Heart and circulatory physiology · 2025Article
- Engineering covalent small molecule-RNA complexes in living cells.Nature chemical biology · 2025Article
- Long non-coding RNA CAR10 promotes angiogenesis of lung adenocarcinoma by mediating nuclear LDHA to epigenetically regulate VEGFA/C.Communications biology · 2025Article
- Emerging RNA-centric technologies to probe RNA-protein interactions: importance in decoding the life cycle of positive sense single strand RNA viruses and antiviral discovery.Frontiers in cellular and infection microbiology · 2025Review
- A novel long non-coding RNA MIR4500HG003 promotes tumor metastasis through miR-483-3p-MMP9 axis in triple-negative breast cancer.Cell death & disease · 2024Article
- MicroRNA-22-3p displaces critical host factors from the 5' UTR and inhibits the translation of Coxsackievirus B3 RNA.Journal of virology · 2024Article
- Purification of In Vivo or In Vitro-Assembled RNA-Protein Complexes by RNA Centric Methods.Advances in experimental medicine and biology · 2024Article
- LncRNA MIR200CHG inhibits EMT in gastric cancer by stabilizing miR-200c from target-directed miRNA degradation.Nature communications · 2023Article
- Long Noncoding RNA AROD Inhibits Host Antiviral Innate Immunity via the miR-324-5p-CUEDC2 Axis.Microbiology spectrum · 2023Article
- General Strategies for RNA X-ray Crystallography.Molecules (Basel, Switzerland) · 2023Review
- LSM1-mediated Major Satellite RNA decay is required for nonequilibrium histone H3.3 incorporation into parental pronuclei.Nature communications · 2023Article
- A Novel Method to Isolate RNase MRP Using RNA Streptavidin Aptamer Tags.Bio-protocol · 2023Article
- The "LINC" between Δ40p53-miRNA Axis in the Regulation of Cellular Homeostasis.Molecular and cellular biology · 2023Article
- MS2-MBP-Based Affinity Purification of Nucleus- or Cytoplasm-Localized lncRNA-Protein Complexes Formed In Vivo.Methods in molecular biology (Clifton, N.J.) · 2023Article
28 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
Abstract
Cellular transcripts of all types, including coding messenger (m)RNAs and noncoding (nc)RNAs, are subject to extensive post-transcriptional regulation. Among the factors that elicit post-transcriptional control, microRNAs (miRNAs) have emerged as a major class of small regulatory RNAs. Since RNA-RNA interactions can be modeled computationally, several excellent programs have been developed to predict the interaction of miRNAs with target transcripts. However, many such predictions are not realized for different reasons, including absent or low-abundance expression of the miRNA in the cell, the existence of competing factors or conformational changes masking the microRNA site, and the possibility that target transcripts are not present in the prediction databases, as is the case for long ncRNAs. Here, we provide a systematic approach termed MS2-TRAP (tagged RNA affinity purification) for identifying miRNAs associated with a target transcript in the cellular context. We illustrate the use of this methodology by identifying microRNAs that associate with a long intergenic (li)ncRNA, based on the expression of the lincRNA tagged with MS2 RNA hairpins (lincRNA-p21-MS2) and the concomitant expression of a fusion protein recognizing the MS2 RNA hairpins, MS2-GST. After affinity pulldown of the ribonucleoprotein (RNP) complex comprising [MS2-GST/lincRNA-p21-MS2], the RNA in the pulldown material was isolated and reverse transcribed (RT). Subsequent assessment of the microRNAs present in the pulldown complex by using real-time quantitative (q)PCR analysis led to the identification of bona fide miRNAs that interact with and control the abundance of lincRNA-p21. We describe alternative designs and applications of this approach, and discuss its implications in deciphering post-transcriptional gene regulatory schemes.
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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.