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Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins.
Weirick, Tyler; Militello, Giuseppe; Hosen, Mohammed Rabiul; John, David; Moore Iv, Joseph B; Uchida, Shizuka.
Afiliación
  • Weirick T; Cardiovascular Innovation Institute, University of Louisville, Louisville, KY 40202, USA.
  • Militello G; RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
  • Hosen MR; Cardiovascular Innovation Institute, University of Louisville, Louisville, KY 40202, USA.
  • John D; Department of Molecular Cellular and Developmental Biology, Yale University, Yale Science Building - 260 Whitney Avenue, New Haven, CT 06511, USA.
  • Moore Iv JB; Department of Internal Medicine-II, Molecular Cardiology, Biomedical Center (BMZ), University of Bonn, Sigmund-Freud-Str. 25, Bonn 53127, Germany.
  • Uchida S; Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, Frankfurt am Main 60590, Germany.
High Throughput ; 8(4)2019 Nov 29.
Article en En | MEDLINE | ID: mdl-31795425
Studies in epitranscriptomics indicate that RNA is modified by a variety of enzymes. Among these RNA modifications, adenosine to inosine (A-to-I) RNA editing occurs frequently in the mammalian transcriptome. These RNA editing sites can be detected directly from RNA sequencing (RNA-seq) data by examining nucleotide changes from adenosine (A) to guanine (G), which substitutes for inosine (I). However, a careful investigation of such nucleotide changes must be conducted to distinguish sequencing errors and genomic mutations from the genuine editing sites. Building upon our recent introduction of an easy-to-use bioinformatics tool, RNA Editor, to detect RNA editing events from RNA-seq data, we examined the extent by which RNA editing events affect the binding of RNA-binding proteins (RBP). Through employing bioinformatic techniques, we uncovered that RNA editing sites occur frequently in RBP-bound regions. Moreover, the presence of RNA editing sites are more frequent when RNA editing islands were examined, which are regions in which RNA editing sites are present in clusters. When the binding of one RBP, human antigen R [HuR; encoded by ELAV-like protein 1 (ELAV1)], was quantified experimentally, its binding was reduced upon silencing of the RNA editing enzyme adenosine deaminases acting on RNA (ADAR) compared to the control-suggesting that the presence of RNA editing islands influence HuR binding to its target regions. These data indicate RNA editing as an important mediator of RBP-RNA interactions-a mechanism which likely constitutes an additional mode of post-transcription gene regulation in biological systems.
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Texto completo: 1 Banco de datos: MEDLINE Idioma: En Revista: High Throughput Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos

Texto completo: 1 Banco de datos: MEDLINE Idioma: En Revista: High Throughput Año: 2019 Tipo del documento: Article País de afiliación: Estados Unidos