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Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins

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 exami...

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Autores principales: Weirick, Tyler, Militello, Giuseppe, Hosen, Mohammed Rabiul, John, David, Moore, Joseph B., Uchida, Shizuka
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6970233/
https://www.ncbi.nlm.nih.gov/pubmed/31795425
http://dx.doi.org/10.3390/ht8040019
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author Weirick, Tyler
Militello, Giuseppe
Hosen, Mohammed Rabiul
John, David
Moore, Joseph B.
Uchida, Shizuka
author_facet Weirick, Tyler
Militello, Giuseppe
Hosen, Mohammed Rabiul
John, David
Moore, Joseph B.
Uchida, Shizuka
author_sort Weirick, Tyler
collection PubMed
description 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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spelling pubmed-69702332020-02-04 Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins Weirick, Tyler Militello, Giuseppe Hosen, Mohammed Rabiul John, David Moore, Joseph B. Uchida, Shizuka High Throughput Article 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. MDPI 2019-11-29 /pmc/articles/PMC6970233/ /pubmed/31795425 http://dx.doi.org/10.3390/ht8040019 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Weirick, Tyler
Militello, Giuseppe
Hosen, Mohammed Rabiul
John, David
Moore, Joseph B.
Uchida, Shizuka
Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins
title Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins
title_full Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins
title_fullStr Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins
title_full_unstemmed Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins
title_short Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins
title_sort investigation of rna editing sites within bound regions of rna-binding proteins
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6970233/
https://www.ncbi.nlm.nih.gov/pubmed/31795425
http://dx.doi.org/10.3390/ht8040019
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