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Unveiling Chloroplast RNA Editing Events Using Next Generation Small RNA Sequencing Data

Organellar RNA editing involves the modification of nucleotide sequences to maintain conserved protein functions, mainly by reverting non-neutral codon mutations. The loss of plastid editing events, resulting from mutations in RNA editing factors or through stress interference, leads to developmenta...

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Autores principales: Rodrigues, Nureyev F., Christoff, Ana P., da Fonseca, Guilherme C., Kulcheski, Franceli R., Margis, Rogerio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5626879/
https://www.ncbi.nlm.nih.gov/pubmed/29033962
http://dx.doi.org/10.3389/fpls.2017.01686
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author Rodrigues, Nureyev F.
Christoff, Ana P.
da Fonseca, Guilherme C.
Kulcheski, Franceli R.
Margis, Rogerio
author_facet Rodrigues, Nureyev F.
Christoff, Ana P.
da Fonseca, Guilherme C.
Kulcheski, Franceli R.
Margis, Rogerio
author_sort Rodrigues, Nureyev F.
collection PubMed
description Organellar RNA editing involves the modification of nucleotide sequences to maintain conserved protein functions, mainly by reverting non-neutral codon mutations. The loss of plastid editing events, resulting from mutations in RNA editing factors or through stress interference, leads to developmental, physiological and photosynthetic alterations. Recently, next generation sequencing technology has generated the massive discovery of sRNA sequences and expanded the number of sRNA data. Here, we present a method to screen chloroplast RNA editing using public sRNA libraries from Arabidopsis, soybean and rice. We mapped the sRNAs against the nuclear, mitochondrial and plastid genomes to confirm predicted cytosine to uracil (C-to-U) editing events and identify new editing sites in plastids. Among the predicted editing sites, 40.57, 34.78, and 25.31% were confirmed using sRNAs from Arabidopsis, soybean and rice, respectively. SNP analysis revealed 58.2, 43.9, and 37.5% new C-to-U changes in the respective species and identified known and new putative adenosine to inosine (A-to-I) RNA editing in tRNAs. The present method and data reveal the potential of sRNA as a reliable source to identify new and confirm known editing sites.
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spelling pubmed-56268792017-10-13 Unveiling Chloroplast RNA Editing Events Using Next Generation Small RNA Sequencing Data Rodrigues, Nureyev F. Christoff, Ana P. da Fonseca, Guilherme C. Kulcheski, Franceli R. Margis, Rogerio Front Plant Sci Plant Science Organellar RNA editing involves the modification of nucleotide sequences to maintain conserved protein functions, mainly by reverting non-neutral codon mutations. The loss of plastid editing events, resulting from mutations in RNA editing factors or through stress interference, leads to developmental, physiological and photosynthetic alterations. Recently, next generation sequencing technology has generated the massive discovery of sRNA sequences and expanded the number of sRNA data. Here, we present a method to screen chloroplast RNA editing using public sRNA libraries from Arabidopsis, soybean and rice. We mapped the sRNAs against the nuclear, mitochondrial and plastid genomes to confirm predicted cytosine to uracil (C-to-U) editing events and identify new editing sites in plastids. Among the predicted editing sites, 40.57, 34.78, and 25.31% were confirmed using sRNAs from Arabidopsis, soybean and rice, respectively. SNP analysis revealed 58.2, 43.9, and 37.5% new C-to-U changes in the respective species and identified known and new putative adenosine to inosine (A-to-I) RNA editing in tRNAs. The present method and data reveal the potential of sRNA as a reliable source to identify new and confirm known editing sites. Frontiers Media S.A. 2017-09-29 /pmc/articles/PMC5626879/ /pubmed/29033962 http://dx.doi.org/10.3389/fpls.2017.01686 Text en Copyright © 2017 Rodrigues, Christoff, da Fonseca, Kulcheski and Margis. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Rodrigues, Nureyev F.
Christoff, Ana P.
da Fonseca, Guilherme C.
Kulcheski, Franceli R.
Margis, Rogerio
Unveiling Chloroplast RNA Editing Events Using Next Generation Small RNA Sequencing Data
title Unveiling Chloroplast RNA Editing Events Using Next Generation Small RNA Sequencing Data
title_full Unveiling Chloroplast RNA Editing Events Using Next Generation Small RNA Sequencing Data
title_fullStr Unveiling Chloroplast RNA Editing Events Using Next Generation Small RNA Sequencing Data
title_full_unstemmed Unveiling Chloroplast RNA Editing Events Using Next Generation Small RNA Sequencing Data
title_short Unveiling Chloroplast RNA Editing Events Using Next Generation Small RNA Sequencing Data
title_sort unveiling chloroplast rna editing events using next generation small rna sequencing data
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5626879/
https://www.ncbi.nlm.nih.gov/pubmed/29033962
http://dx.doi.org/10.3389/fpls.2017.01686
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