ArticleNature methods2015
Mutational interference mapping experiment (MIME) for studying RNA structure and function.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Systematic analysis of cotranscriptional RNA folding using transcription elongation complex display.Nature communications · 2025Article
- MMTV RNA packaging requires an extended long-range interaction for productive Gag binding to packaging signals.PLoS biology · 2024Article
- Role of RNA structural plasticity in modulating HIV-1 genome packaging and translation.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Isoform-specific RNA structure determination using Nano-DMS-MaP.Nature protocols · 2024Review
- HIV-1 RNA genome packaging: it's G-rated.mBio · 2024Review
- Identification of a putative Gag binding site critical for feline immunodeficiency virus genomic RNA packaging.RNA (New York, N.Y.) · 2023Article
- Nano-DMS-MaP allows isoform-specific RNA structure determination.Nature methods · 2023Article
- Article
- Human Retrovirus Genomic RNA Packaging.Viruses · 2022Review
- Short- and long-range interactions in the HIV-1 5' UTR regulate genome dimerization and packaging.Nature structural & molecular biology · 2022Article
- Advances in HIV-1 Assembly.Viruses · 2022Review
- Review
- Structural maturation of the HIV-1 RNA 5' untranslated region by Pr55RNA biology · 2022Article
- HIV-1 Packaging Visualised by In-Gel SHAPE.Viruses · 2021Article
- HIV-1 integrase binding to genomic RNA 5'-UTR induces local structural changes in vitro and in virio.Retrovirology · 2021Article
- Review
- A purine loop and the primer binding site are critical for the selective encapsidation of mouse mammary tumor virus genomic RNA by Pr77Gag.Nucleic acids research · 2021Article
- ITN-VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics.Viruses · 2021Article
- Post-Translational Modifications of Retroviral HIV-1 Gag Precursors: An Overview of Their Biological Role.International journal of molecular sciences · 2021Review
- Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA regulates many biological processes; however, identifying functional RNA sequences and structures is complex and time-consuming. We introduce a method, mutational interference mapping experiment (MIME), to identify, at single-nucleotide resolution, the primary sequence and secondary structures of an RNA molecule that are crucial for its function. MIME is based on random mutagenesis of the RNA target followed by functional selection and next-generation sequencing. Our analytical approach allows the recovery of quantitative binding parameters and permits the identification of base-pairing partners directly from the sequencing data. We used this method to map the binding site of the human immunodeficiency virus-1 (HIV-1) Pr55(Gag) protein on the viral genomic RNA in vitro, and showed that, by analyzing permitted base-pairing patterns, we could model RNA structure motifs that are crucial for protein binding.
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