2009年度 森泰吉郎記念研究振興基金 成果報告
研究課題「左右対称動物で保存されたmiRNA-標的遺伝子の解析」
慶應義塾大学大学院 政策メディア研究科 修士過程一年
高根香織
Computational prediction and experimental validation of evolutionarily conserved microRNA target genes
in bilaterian animals
Graduate School of Media and Governance, Keio university, Master’s Program 1st-year
Kahori Takane
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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.
Research achievement
Progress Report (2009)
Journal publication (2009)
Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals
Takane K, Fujishima K, Watanabe Y, Sato A, Saito N, Tomita M, Kanai A.
Talks in academic conference (2009)
- 第8回新しいRNA/RNPを見つける会, 2009, Yokohama, Japan:
左右対称動物で進化的に保存されたmiRNA-標的遺伝子の予測と検証
高根 香織
- 第32回日本分子生物学会年会, 2009, Yokohama, Japan:
Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals
Kahori Takane, Kosuke Fujishima, Yuka Watanabe, Asako Sato, Nobuto Saito, Masaru Tomita, Akio Kanai
Poster sessions in academic conference (2009)
- RNA conference 2009 (Fourteenth Annual Meeting of the RNA Society), 2009, Madison, USA:
Prediction and validation of evolutionary conserved microRNA target genes in bilateria
Kahori Takane, Kosuke Fujishima, Yuka Watanabe, Asako Sato, Nobuto Saito, Masaru Tomita, Akio Kanai
- 第32回日本分子生物学会年会, 2009, Yokohama, Japan:
Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals
Kahori Takane, Kosuke Fujishima, Yuka Watanabe, Asako Sato, Nobuto Saito, Masaru Tomita, Akio Kanai
©Kahori Takane All Rights Reserved