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Cited by 1,791MicroRNA in disease regulationRNA Research and SplicingPlant Molecular Biology Research

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

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Chi, Sung Wook, Zang, Julie B., Mele, Aldo, Darnell, Robert B.·2009·Nature
DOI 10.1038/nature08170PMC PMC2733940
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Abstract

MicroRNAs (miRNAs) have critical roles in the regulation of gene expression; however, as miRNA activity requires base pairing with only 6-8 nucleotides of messenger RNA, predicting target mRNAs is a major challenge. Recently, high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) has identified functional protein-RNA interaction sites. Here we use HITS-CLIP to covalently crosslink native argonaute (Ago, also called Eif2c) protein-RNA complexes in mouse brain. This produced two simultaneous data sets-Ago-miRNA and Ago-mRNA binding sites-that were combined with bioinformatic analysis to identify interaction sites between miRNA and target mRNA. We validated genome-wide interaction maps for miR-124, and generated additional maps for the 20 most abundant miRNAs present in P13 mouse brain. Ago HITS-CLIP provides a general platform for exploring the specificity and range of miRNA action in vivo, and identifies precise sequences for targeting clinically relevant miRNA-mRNA interactions.

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  • Affinity purification via antibodies against Ago2 serves to isolate active miRNAs from tissue lysates.

    “affinity purification via antibodies against Ago2 serves to isolate active miRNAs from tissue lysates (Chi et al., 2009).”

    From MicroRNA Profiling Reveals Marker of Motor Neuron Disease in ALS Models (2017) · cites this paper as Chi et al., 2009

    The ‘Ago RNA targets in the mouse brain’ section (page unavailable) reports immunoprecipitating Ago from mouse neocortex and recovering Ago-bound miRNAs. The Methods summary names two monoclonal antibodies, but our copy does not identify them as Ago2-specific or establish that every recovered miRNA was active; the method also includes UV crosslinking and further purification. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • Early methods including RIP and CLIP of AGO proteins provided the first broad view of the miRNA interaction landscape.

    “Early methods including RNA Immunoprecipitation (RIP) and CrossLinking and ImmunoPrecipitation (CLIP) of AGO proteins provided the first broad view of the miRNA interaction landscape, revealing principles of miRNA regulation mechanisms as well as an overview of mRNAs regulated by miRNAs (Chi et al., 2009;Hafner et al., 2010).”

    From Scalable and deep profiling of mRNA targets for individual microRNAs with chimeric eCLIP (2022) · cites this paper as Chi et al., 2009

  • Ago HITS-CLIP has been used to profile miRNA-mRNA targets in the mouse brain.

    “Recently, Ago HITS-CLIP has been used to profile miRNA-mRNA targets in the mouse brain (Chi et al., 2009).”

    From Cell-Type-Based Analysis of MicroRNA Profiles in the Mouse Brain (2012) · cites this paper as Chi et al., 2009

  • miR-125b has a role in neuronal differentiation and cytoskeletal organization.

    “Recent studies using gene ontology analysis of putative miR-125b targets suggests a role for this miRNA in neuronal differentiation and cytoskeletal organization (Chi et al., 2009; Le et al., 2009).”

    From Regulation of Synaptic Structure and Function by FMRP-Associated MicroRNAs miR-125b and miR-132 (2010) · cites this paper as Chi et al., 2009

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References 52 · Cited by 1,791

Research works printed but not linked: 43

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Authors
Chi, S. W., Zang, J. B., Mele, A., & Darnell, R. B.
Affiliations
Howard Hughes Medical Institute (US)
Corresponding author
Darnell, Robert B.
ORCID
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2009-06-17
Volume
460
Issue
7254
Pages
479-486
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
DOI
10.1038/nature08170
PMC
PMC2733940
OpenAlex
W2104806799
Cited by
1,791
References
52
Citations by year
2026: 26 · 2025: 40 · 2024: 54 · 2023: 81 · 2022: 55 · 2021: 80 · 2020: 92 · 2019: 102 · 2018: 97 · 2017: 107 · 2016: 102 · 2015: 153 · 2014: 163 · 2013: 175 · 2012: 183
FWCI
51.91
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
Funders
  • Howard Hughes Medical Institute
  • National Institute of Neurological Disorders and Stroke (R01NS034389)
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, Argonaute proteins, HITS-CLIP, RNA-induced silencing complex, miRNA target prediction, miR-124, mouse brain, gene expression regulation, RNA interference therapy, protein-RNA binding sites
MeSH terms
Animals, Cross-Linking Reagents, Gene Expression Regulation, HeLa Cells, Humans, Reproducibility of Results, Protein Interaction Mapping, MicroRNAs, Immunoprecipitation, Mice

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