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  1. Article ; Online: Vertebrate virus-encoded microRNAs and their sequence conservation.

    Takane, Kahori / Kanai, Akio

    Japanese journal of infectious diseases

    2011  Volume 64, Issue 5, Page(s) 357–366

    Abstract: An increasing number of studies have reported that approximately 400 microRNAs (miRNAs), encoded by vertebrate viruses, regulate the expression of both host and viral genes. Many studies have used computational and/or experimental analyses to identify ... ...

    Abstract An increasing number of studies have reported that approximately 400 microRNAs (miRNAs), encoded by vertebrate viruses, regulate the expression of both host and viral genes. Many studies have used computational and/or experimental analyses to identify the target genes of miRNAs, thereby enabling us to understand miRNA functions. Here, we suggest that important aspects become apparent when we focus on conserved viral miRNAs, although these miRNA sequences generally show little similarity among viral species. Reliable viral miRNA-target gene pairs can be efficiently identified using evolutionary information. In this review, we summarize information on (i) the nucleotide sequence conservation among viral miRNAs and (ii) the RNAs targeted by viral miRNAs. Recent advances in these topics are discussed.
    MeSH term(s) Animals ; Conserved Sequence ; Gene Expression Regulation, Viral ; Host-Pathogen Interactions ; Humans ; MicroRNAs/genetics ; Viruses/genetics ; Viruses/pathogenicity
    Chemical Substances MicroRNAs
    Language English
    Publishing date 2011
    Publishing country Japan
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1478383-6
    ISSN 1884-2836 ; 1344-6304
    ISSN (online) 1884-2836
    ISSN 1344-6304
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals.

    Takane, Kahori / Fujishima, Kosuke / Watanabe, Yuka / Sato, Asako / Saito, Nobuto / Tomita, Masaru / Kanai, Akio

    BMC genomics

    2010  Volume 11, Page(s) 101

    Abstract: Background: In many eukaryotes, microRNAs (miRNAs) bind to complementary sites in the 3'-untranslated regions (3'-UTRs) of target messenger RNAs (mRNAs) and regulate their expression at the stage of translation. Recent studies have revealed that many ... ...

    Abstract Background: In many eukaryotes, microRNAs (miRNAs) bind to complementary sites in the 3'-untranslated regions (3'-UTRs) of target messenger RNAs (mRNAs) and regulate their expression at the stage of translation. Recent studies have revealed that many miRNAs are evolutionarily conserved; however, the evolution of their target genes has yet to be systematically characterized. We sought to elucidate a set of conserved miRNA/target-gene pairs and to analyse the mechanism underlying miRNA-mediated gene regulation in the early stage of bilaterian evolution.
    Results: Initially, we extracted five evolutionarily conserved miRNAs (let-7, miR-1, miR-124, miR-125/lin-4, and miR-34) among five diverse bilaterian animals. Subsequently, we designed a procedure to predict evolutionarily conserved miRNA/target-gene pairs by introducing orthologous gene information. As a result, we extracted 31 orthologous miRNA/target-gene pairs that were conserved among at least four diverse bilaterian animals; the prediction set showed prominent enrichment of orthologous miRNA/target-gene pairs that were verified experimentally. Approximately 84% of the target genes were regulated by three miRNAs (let-7, miR-1, and miR-124) and their function was classified mainly into the following categories: development, muscle formation, cell adhesion, and gene regulation. We used a reporter gene assay to experimentally verify the downregulation of six candidate pairs (out of six tested pairs) in HeLa cells.
    Conclusions: The application of our new method enables the identification of 31 miRNA/target-gene pairs that were expected to have been regulated from the era of the common bilaterian ancestor. The downregulation of all six candidate pairs suggests that orthologous information contributed to the elucidation of the primordial set of genes that has been regulated by miRNAs; it was also an efficient tool for the elimination of false positives from the predicted candidates. In conclusion, our study identified potentially important miRNA-target pairs that were evolutionarily conserved throughout diverse bilaterian animals and that may provide new insights into early-stage miRNA functions.
    MeSH term(s) 3' Untranslated Regions ; Animals ; Computational Biology ; Conserved Sequence/genetics ; Down-Regulation ; Evolution, Molecular ; Gene Expression Regulation ; HeLa Cells ; Humans ; MicroRNAs/genetics ; Sequence Alignment ; Sequence Analysis, RNA
    Chemical Substances 3' Untranslated Regions ; MIRN1 microRNA, human ; MIRN124 microRNA, human ; MicroRNAs ; mirnlet7 microRNA, human
    Language English
    Publishing date 2010-02-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1471-2164
    ISSN (online) 1471-2164
    DOI 10.1186/1471-2164-11-101
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals

    Watanabe Yuka / Fujishima Kosuke / Takane Kahori / Sato Asako / Saito Nobuto / Tomita Masaru / Kanai Akio

    BMC Genomics, Vol 11, Iss 1, p

    2010  Volume 101

    Abstract: Abstract Background In many eukaryotes, microRNAs (miRNAs) bind to complementary sites in the 3'-untranslated regions (3'-UTRs) of target messenger RNAs (mRNAs) and regulate their expression at the stage of translation. Recent studies have revealed that ... ...

    Abstract Abstract Background In many eukaryotes, microRNAs (miRNAs) bind to complementary sites in the 3'-untranslated regions (3'-UTRs) of target messenger RNAs (mRNAs) and regulate their expression at the stage of translation. Recent studies have revealed that many miRNAs are evolutionarily conserved; however, the evolution of their target genes has yet to be systematically characterized. We sought to elucidate a set of conserved miRNA/target-gene pairs and to analyse the mechanism underlying miRNA-mediated gene regulation in the early stage of bilaterian evolution. Results Initially, we extracted five evolutionarily conserved miRNAs ( let-7 , miR-1 , miR-124 , miR-125/lin-4 , and miR-34 ) among five diverse bilaterian animals. Subsequently, we designed a procedure to predict evolutionarily conserved miRNA/target-gene pairs by introducing orthologous gene information. As a result, we extracted 31 orthologous miRNA/target-gene pairs that were conserved among at least four diverse bilaterian animals; the prediction set showed prominent enrichment of orthologous miRNA/target-gene pairs that were verified experimentally. Approximately 84% of the target genes were regulated by three miRNAs ( let-7, miR-1 , and miR-124 ) and their function was classified mainly into the following categories: development, muscle formation, cell adhesion, and gene regulation. We used a reporter gene assay to experimentally verify the downregulation of six candidate pairs (out of six tested pairs) in HeLa cells. Conclusions The application of our new method enables the identification of 31 miRNA/target-gene pairs that were expected to have been regulated from the era of the common bilaterian ancestor. The downregulation of all six candidate pairs suggests that orthologous information contributed to the elucidation of the primordial set of genes that has been regulated by miRNAs; it was also an efficient tool for the elimination of false positives from the predicted candidates. In conclusion, our study identified potentially important miRNA-target pairs that were evolutionarily conserved throughout diverse bilaterian animals and that may provide new insights into early-stage miRNA functions.
    Keywords Genetics ; QH426-470 ; Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Genetics ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Biotechnology ; TP248.13-248.65
    Subject code 500
    Language English
    Publishing date 2010-02-01T00:00:00Z
    Publisher BioMed Central
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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