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Title: Multilateral Bioinformatics Analyses Reveal the Function-Oriented Target Specificities and Recognition of the RNA-Binding Protein SFPQ
Authors: Iida, Kei  kyouindb  KAKEN_id  orcid (unconfirmed)
Hagiwara, Masatoshi  kyouindb  KAKEN_id
Takeuchi, Akihide  kyouindb  KAKEN_id
Author's alias: 飯田, 慶
萩原, 正敏
武内, 章英
Issue Date: 24-Jul-2020
Publisher: Elsevier BV
Journal title: iScience
Volume: 23
Issue: 7
Thesis number: 101325
Abstract: 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.
Description: RNA結合タンパク質の標的分子探索手法を開発 --複雑なRNA制御のメカニズム解明に期待--. 京都大学プレスリリース. 2020-07-07.
Rights: © 2020 The Author(s). This is an open access article under the CC BY-NC-ND license (
DOI(Published Version): 10.1016/j.isci.2020.101325
PubMed ID: 32659723
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