Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding
Open accessAbstract
MicroRNAs (miRNAs) play key roles in gene regulation, but reliable bioinformatic or experimental identification of their targets remains difficult. To provide an unbiased view of human miRNA targets, we developed a technique for ligation and sequencing of miRNA-target RNA duplexes associated with human AGO1. Here, we report data sets of more than 18,000 high-confidence miRNA-mRNA interactions. The binding of most miRNAs includes the 5' seed region, but around 60% of seed interactions are noncanonical, containing bulged or mismatched nucleotides. Moreover, seed interactions are generally accompanied by specific, nonseed base pairing. 18% of miRNA-mRNA interactions involve the miRNA 3' end, with little evidence for 5' contacts, and some of these were functionally validated. Analyses of miRNA:mRNA base pairing showed that miRNA species systematically differ in their target RNA interactions, and strongly overrepresented motifs were found in the interaction sites of several miRNAs. We speculate that these affect the response of RISC to miRNA-target binding.
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A suite of chimeric CLIP methods including CLASH, modified iPAR-CLIP, and CLEAR-CLIP were developed to enable direct experimental mapping of microRNA:target interactions.
“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 Helwak et al., 2013
Prior chimeric CLIP experiments using spike-in of E. coli, Drosophila, or yeast lysate suggested a low (1-5%) rate of interactions formed in vitro after cell lysis.
“Prior chimeric CLIP experiments using spike-in of E. coli, Drosophila, or yeast lysate (Helwak et al., 2013;Moore et al., 2015) suggested a low (1-5%) rate of interactions formed in vitro after cell lysis”
From Scalable and deep profiling of mRNA targets for individual microRNAs with chimeric eCLIP (2022) · cites this paper as Helwak et al., 2013
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- Authors
- Helwak, A., Kudla, G., Dudnakova, T., & Tollervey, D.
- Affiliations
- Wellcome Centre for Cell Biology (GB)
- Corresponding author
- Tollervey, David
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2013-04
- Volume
- 153
- Issue
- 3
- Pages
- 654-665
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3650559
- OpenAlex
- W2150395782
- Cited by
- 1,269
- References
- 7
- Citations by year
- 2026: 40 · 2025: 60 · 2024: 70 · 2023: 84 · 2022: 99 · 2021: 103 · 2020: 109 · 2019: 101 · 2018: 124 · 2017: 113 · 2016: 101 · 2015: 116 · 2014: 125 · 2013: 24
- FWCI
- 43.04
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, other-oa)
- Funders
- Wellcome Trust (092076, 097383, 077248)
- 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
- microRNA, miRNA-mRNA interactions, CLASH, AGO1, RNA-induced silencing complex, seed region, miRNA target identification
- MeSH terms
- Genetic Techniques, Humans, RNA, Messenger, Gene Expression Profiling, RNA, Untranslated, RNA-Induced Silencing Complex, MicroRNAs, Eukaryotic Initiation Factors, HEK293 Cells, High-Throughput Nucleotide Sequencing, Nucleotide Motifs, Argonaute Proteins
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