An alternative mode of microRNA target recognition View Full Text


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Article Info

DATE

2012-03

AUTHORS

Sung Wook Chi, Gregory J Hannon, Robert B Darnell

ABSTRACT

MicroRNAs (miRNAs) regulate mRNA targets through perfect pairing with their seed region (positions 2-7). Recently, a precise genome-wide map of miRNA interaction sites in mouse brain was generated by high-throughput sequencing and analysis of clusters of ~50-nucleotide mRNA tags cross-linked to Argonaute (Ago HITS-CLIP). By analyzing Ago HITS-CLIP 'orphan clusters'-Ago binding regions from HITS-CLIP that cannot be explained by canonical seed matches-we have now identified an alternative binding mode used by miRNAs. Specifically, G-bulge sites (positions 5-6) are often bound and regulated by miR-124 in brain. More generally, bulged sites comprise ≥15% of all Ago-miRNA interactions in mouse brain and are evolutionarily conserved. We call position 6 the 'pivot' nucleotide and suggest a model in which a transitional 'nucleation bulge' leads to functional bulge mRNA-miRNA interactions, expanding the number of potential miRNA regulatory sites. More... »

PAGES

321

References to SciGraph publications

  • 2011-02. Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2008-09. The impact of microRNAs on protein output in NATURE
  • 2005-02. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs in NATURE
  • 2009-10-08. Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes in NATURE
  • 2009-07. Corrigendum: Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs in NATURE BIOTECHNOLOGY
  • 2008-10-23. MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation in NATURE
  • 2009-06. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs in NATURE BIOTECHNOLOGY
  • 2009-07. Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps in NATURE
  • 2008-11. Structure of the guide-strand-containing argonaute silencing complex in NATURE
  • 2008-11. HITS-CLIP yields genome-wide insights into brain alternative RNA processing in NATURE
  • 2008-12-18. Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex in NATURE
  • 2004-09. The functions of animal microRNAs in NATURE
  • 2007-04. Potent effect of target structure on microRNA function in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2010-01. RNA processing and its regulation: global insights into biological networks in NATURE REVIEWS GENETICS
  • 2010-07. Pathogenic LRRK2 negatively regulates microRNA-mediated translational repression in NATURE
  • 2008-09. Small RNAs: The seeds of silence in NATURE
  • 2004-07. MicroRNAs: small RNAs with a big role in gene regulation in NATURE REVIEWS GENETICS
  • 2007-06-28. A microRNA component of the p53 tumour suppressor network in NATURE
  • 2010-02. Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2006-09. Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions in NATURE STRUCTURAL & MOLECULAR BIOLOGY
  • 2008-09. Widespread changes in protein synthesis induced by microRNAs in NATURE
  • 2008-09. mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein–enriched transcripts in NATURE METHODS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nsmb.2230

    DOI

    http://dx.doi.org/10.1038/nsmb.2230

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/22343717


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    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1038/nsmb.2230'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/nsmb.2230'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/nsmb.2230'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/nsmb.2230'


     

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