論文

査読有り 国際誌
2020年7月24日

Multilateral Bioinformatics Analyses Reveal the Function-Oriented Target Specificities and Recognition of the RNA-Binding Protein SFPQ.

iScience
  • Kei Iida
  • ,
  • Masatoshi Hagiwara
  • ,
  • Akihide Takeuchi

23
7
開始ページ
101325
終了ページ
101325
記述言語
英語
掲載種別
研究論文(学術雑誌)
DOI
10.1016/j.isci.2020.101325
出版者・発行元
Elsevier BV

RNA-binding proteins (RBPs) recognize consensus sequences and regulate specific target mRNAs. However, large-scale CLIP-seq revealed loose and broad binding of RBPs to larger proportion of expressed mRNAs: e.g. SFPQ binds to >10,000 pre-mRNAs but distinctly regulates <200 target genes during neuronal development. Identification of crucial binding for regulation and rules of target recognition is highly anticipated for systemic understanding of RBP regulations. For a breakthrough solution, we developed a bioinformatical method for CLIP-seq and transcriptome data by adopting iterative hypothesis testing. Essential binding was successfully identified in C-rich sequences close to the 5' splice sites of long introns, which further proposed target recognition mechanism via association between SFPQ and splicing factors during spliceosome assembly. The identified features of functional binding enabled us to predict regulons and also target genes in different species. This multilateral bioinformatics approach facilitates the elucidation of functionality, regulatory mechanism, and regulatory networks of RBPs.

リンク情報
DOI
https://doi.org/10.1016/j.isci.2020.101325
PubMed
https://www.ncbi.nlm.nih.gov/pubmed/32659723
PubMed Central
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7358709

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