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Pairing beyond the Seed Supports MicroRNA Targeting Specificity
Open accessAbstract
To identify endogenous miRNA-target sites, we isolated AGO-bound RNAs from Caenorhabditis elegans by individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP), which fortuitously also produced miRNA-target chimeric reads. Through the analysis of thousands of reproducible chimeras, pairing to the miRNA seed emerged as the predominant motif associated with functional interactions. Unexpectedly, we discovered that additional pairing to 3' sequences is prevalent in the majority of target sites and leads to specific targeting by members of miRNA families. By editing an endogenous target site, we demonstrate that 3' pairing determines targeting by specific miRNA family members and that seed pairing is not always sufficient for functional target interactions. Finally, we present a simplified method, chimera PCR (ChimP), for the detection of specific miRNA-target interactions. Overall, our analysis revealed that sequences in the 5' as well as the 3' regions of a miRNA provide the information necessary for stable and specific miRNA-target interactions in vivo.
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“To enable this direct experimental mapping of microRNA:target interactions, a suite of chimeric CLIP methods including CrossLinking And Sequencing of Hybrids (CLASH), modified iPAR-CLIP, and CLEAR-CLIP (Broughton et al., 2016;Grosswendt et al., 2014;Helwak et al., 2013;Moore et al., 2015) were developed.”
From Scalable and deep profiling of mRNA targets for individual microRNAs with chimeric eCLIP (2022) · cites this paper as Broughton et al., 2016
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“However, interaction of miRNAs with other regions, including the 5′ UTR, coding sequence, and gene promoters, have also been reported.”
From Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation (2018) · cites this paper as [15]
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Metadata
- Authors
- Broughton, J. P., Lovci, M. T., Huang, J. L., Yeo, G. W., & Pasquinelli, A. E.
- Affiliations
- University of California San Diego (US)
- Corresponding author
- Pasquinelli, Amy E.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2016-10
- Volume
- 64
- Issue
- 2
- Pages
- 320-333
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC5074850
- OpenAlex
- W2528044351
- Cited by
- 487
- References
- 55
- Citations by year
- 2026: 31 · 2025: 55 · 2024: 62 · 2023: 59 · 2022: 58 · 2021: 89 · 2020: 54 · 2019: 39 · 2018: 24 · 2017: 13 · 2016: 2
- FWCI
- 10.82
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institutes of Health (P40OD010440)
- National Human Genome Research Institute (R01HG004659)
- National Institute of General Medical Sciences (R01GM071654)
- National Institute of Neurological Disorders and Stroke (R01NS075449)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
- Keywords
- microRNA binding sites, miRNA-target interactions, iCLIP, Caenorhabditis elegans, miRNA families
- MeSH terms
- Animals, Base Sequence, Binding Sites, Exons, Gene Expression Regulation, Introns, Protein Binding, RNA, Messenger, RNA-Binding Proteins, Caenorhabditis elegans, RNA, Helminth, Base Pairing, RNA, Small Nucleolar, Caenorhabditis elegans Proteins, MicroRNAs, Immunoprecipitation, RNA, Long Noncoding
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