Abstract：
:To exert regulatory function, miRNAs guide Argonaute (AGO) proteins to partially complementary sites on target RNAs. Crosslinking and immunoprecipitation (CLIP) assays are state-of-the-art to map AGO binding sites, but assigning the targeting miRNA to these sites relies on bioinformatics predictions and is therefore indirect. To directly and unambiguously identify miRNA:target site interactions, we modified our CLIP methodology in C. elegans to experimentally ligate miRNAs to their target sites. Unexpectedly, ligation reactions also occurred in the absence of the exogenous ligase. Our in vivo data set and reanalysis of published mammalian AGO-CLIP data for miRNA-chimeras yielded ∼17,000 miRNA:target site interactions. Analysis of interactions and extensive experimental validation of chimera-discovered targets of viral miRNAs suggest that our strategy identifies canonical, noncanonical, and nonconserved miRNA:targets. About 80% of miRNA interactions have perfect or partial seed complementarity. In summary, analysis of miRNA:target chimeras enables the systematic, context-specific, in vivo discovery of miRNA binding.
journal_name
Mol Celljournal_title
Molecular cellauthors
Grosswendt S,Filipchyk A,Manzano M,Klironomos F,Schilling M,Herzog M,Gottwein E,Rajewsky Ndoi
10.1016/j.molcel.2014.03.049subject
Has Abstractpub_date
2014-06-19 00:00:00pages
1042-1054issue
6eissn
1097-2765issn
1097-4164journal_volume
54pub_type
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