Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions
Abstract
We use Caenorhabditis elegans to test proposed general rules for microRNA (miRNA)-target interactions. We show that G.U base pairing is tolerated in the 'seed' region of the lsy-6 miRNA interaction with its in vivo target cog-1, and that 6- to 8-base-pair perfect seed pairing is not a generally reliable predictor for an interaction of lsy-6 with a 3' untranslated region (UTR). Rather, lsy-6 can functionally interact with its target site only in specific 3' UTR contexts. Our findings illustrate the difficulty of establishing generalizable rules of miRNA-target interactions.
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Current target prediction algorithms often identify many false positive target genes and there is no strong overlap in predicted target gene list among prediction algorithms.
“current target prediction algorithms often identify many false positive target genes and there is no strong overlap in the predicted target gene list among prediction algorithms [138-141].”
From MicroRNAs in brain cholesterol metabolism and their implications for Alzheimer's disease (2016) · cites this paper as [138]
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References 22 · Cited by 435
- Authors
- Didiano, D., & Hobert, O.
- Affiliations
- Howard Hughes Medical Institute (US)
- Corresponding author
- Hobert, Oliver
- ORCID
- Hobert, Oliver
- Venue
- Nature Structural & Molecular Biology
- Published
- 2006-08-20
- Volume
- 13
- Issue
- 9
- Pages
- 849-851
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- OpenAlex
- W2030093783
- Cited by
- 435
- References
- 22
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 4 · 2023: 2 · 2022: 5 · 2021: 16 · 2020: 11 · 2019: 9 · 2018: 17 · 2017: 15 · 2016: 16 · 2015: 17 · 2014: 34 · 2013: 35 · 2012: 41
- FWCI
- 17.76
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (5r03hd050334-02)
- National Institute of Neurological Disorders and Stroke (R01NS050266, R01NS039996)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (1R03HD050334-01)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Keywords
- miRNA-target interactions, 3' untranslated region, Caenorhabditis elegans, RNA secondary structure
- MeSH terms
- Animals, Base Sequence, Molecular Sequence Data, Caenorhabditis elegans, Base Pairing, 3' Untranslated Regions, MicroRNAs
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