Computational prediction of lncRNA-mRNA interactionsby integrating tissue specificity in human transcriptome

Junichi Iwakiri*, Goro Terai, Michiaki Hamada


研究成果: Comment/debate査読

31 被引用数 (Scopus)


Long noncoding RNAs (lncRNAs) play a key role in normal tissue differentiation and cancer development through their tissue-specific expression in the human transcriptome. Recent investigations of macromolecular interactions have shown that tissue-specific lncRNAs form base-pairing interactions with various mRNAs associated with tissue-differentiation, suggesting that tissue specificity is an important factor controlling human lncRNA-mRNA interactions. Here, we report investigations of the tissue specificities of lncRNAs and mRNAs by using RNA-seq data across various human tissues as well as computational predictions of tissue-specific lncRNA-mRNA interactions inferred by integrating the tissue specificity of lncRNAs and mRNAs into our comprehensive prediction of human lncRNA-RNA interactions. Our predicted lncRNA-mRNA interactions were evaluated by comparisons with experimentally validated lncRNA-mRNA interactions (between the TINCR lncRNA and mRNAs), showing the improvement of prediction accuracy over previous prediction methods that did not account for tissue specificities of lncRNAs and mRNAs. In addition, our predictions suggest that the potential functions of TINCR lncRNA not only for epidermal differentiation but also for esophageal development through lncRNA-mRNA interactions. Reviewers: This article was reviewed by Dr. Weixiong Zhang and Dr. Bojan Zagrovic.

ジャーナルBiology Direct
出版ステータスPublished - 2017 6月 8

ASJC Scopus subject areas

  • 免疫学
  • 生態、進化、行動および分類学
  • モデリングとシミュレーション
  • 生化学、遺伝学、分子生物学(全般)
  • 農業および生物科学(全般)
  • 応用数学


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