Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding

By A. Helwak, Grzegorz Kudla, Tatiana Dudnakova, David Tollervey. Cell, 2013

1,296 citations recorded by the source corpus.

Summary 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.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/dcd21b961469cc3473d57cc83bc610726e8c25d8

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Citations in the corpus

Global Mapping of Small RNA-Target Interactions in Bacteria (2016, methodology): “…the CLASH and iPAR-CLIP methodologies that were applied to detect protein-mediated miRNA-target interactions in eukaryotes (Grosswendt et al., 2014; Helwak et al., 2013), we developed RIL-seq (RNA interaction by ligation and sequencing), an experimental-compu-tational methodology for detecting…”
miRDB: an online resource for microRNA target prediction and functional annotations (2014, methodology): “In some cases, a second mature miRNA was selected from the same precursor if its expression level was no less than 10% of that of the dominant mature miRNA and its read count was no less than 5 reads per million reads as determined by RNA-seq experiments.”
PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways (2013, methodology): “Recently, a large number of miRNA target sites have been identified by the CLASH experiments (26), which is the first highthroughput technology that allows direct observation of miRNA–target pairs without the assistance of computational target prediction or scanning.”
Metazoan MicroRNAs (2018, background): “High-throughput analyses of mRNA segments that crosslink to Argonaute show that in cells miRNA silencing complexes bind to many sites that lack contiguous 6- nt matches to the seed region, such that in aggregate these noncanonical sites account for approximately half of the intracellular crosslinks ”
miRDB: an online database for prediction of functional microRNA targets (2019, methodology): “On the other hand, we also analyzed public CLIP-ligation data (10,11) to identify paired miRNA / target transcripts that reside in the same miRISC complex.”
miRTarBase 2020: updates to the experimentally validated microRNA–target interaction database (2019, background): “Given the surge of high-throughput sequencing technologies (15), the sequencing data obtained from CLIP (16), PAR-CLIP (17) and CLASH (18) can be used to explore miRNAs and their targets with expression evidence.”
miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database (2015, methodology): “Large-scale MTIs have been recently identified using the CLIP-seq approach including HITS-CLIP, PAR-CLIP and CLASH.”
miRNAs as Biomarkers in Disease: Latest Findings Regarding Their Role in Diagnosis and Prognosis (2020, background): “However, in human cells, about 60% of the interactions between the miRISC complex and mRNA are non-canonical [27], which means that their chains are not always entirely complementary [28].”
Recent advances in RNA structurome (2022, background): “elegans (Helwak et al., 2013; Kudla et al., 2011; Shen et al., 2018) Pros: Genome-wide in vivo RBP-RNA and RNA-RNA interaction Cons: Profile a defined RBP-organized RNA duplexes only, require radioisotopes during library construction, ligation is performed in dilute solution, relies on overexpressed”
Revealing protein–lncRNA interaction (2015, background): “It was applied up to now for the high-throughput depiction of the miRNA–target RNA interaction mediated by the AGO protein, but it can in principle be extended to other RNA–RNA interactions involving other proteins [134].”
An overview of microRNAs (2015, neutral): “matched targets have been identified[71-74].”
DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions (2017, methodology): “0 Database Total entries >1 080 000 Entries from low-yield methods 10 339 Entries from high-throughput methods ∼1 069 000 Cell types 516 Tissues 85 Publications 1208 Support from direct experiments miRNA–gene entries ∼790 300 miRNAs 1761 Targeted genes 27 613 Publications 968 Analyzed high-throughpu”