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High-Throughput Sequencing of RNA Silencing-Associated Small RNAs in Olive (Olea europaea L.)

Small RNAs (sRNAs) of 20 to 25 nucleotides (nt) in length maintain genome integrity and control gene expression in a multitude of developmental and physiological processes. Despite RNA silencing has been primarily studied in model plants, the advent of high-throughput sequencing technologies has ena...

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Autores principales: Donaire, Livia, Pedrola, Laia, de la Rosa, Raúl, Llave, César
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225373/
https://www.ncbi.nlm.nih.gov/pubmed/22140484
http://dx.doi.org/10.1371/journal.pone.0027916
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author Donaire, Livia
Pedrola, Laia
de la Rosa, Raúl
Llave, César
author_facet Donaire, Livia
Pedrola, Laia
de la Rosa, Raúl
Llave, César
author_sort Donaire, Livia
collection PubMed
description Small RNAs (sRNAs) of 20 to 25 nucleotides (nt) in length maintain genome integrity and control gene expression in a multitude of developmental and physiological processes. Despite RNA silencing has been primarily studied in model plants, the advent of high-throughput sequencing technologies has enabled profiling of the sRNA component of more than 40 plant species. Here, we used deep sequencing and molecular methods to report the first inventory of sRNAs in olive (Olea europaea L.). sRNA libraries prepared from juvenile and adult shoots revealed that the 24-nt class dominates the sRNA transcriptome and atypically accumulates to levels never seen in other plant species, suggesting an active role of heterochromatin silencing in the maintenance and integrity of its large genome. A total of 18 known miRNA families were identified in the libraries. Also, 5 other sRNAs derived from potential hairpin-like precursors remain as plausible miRNA candidates. RNA blots confirmed miRNA expression and suggested tissue- and/or developmental-specific expression patterns. Target mRNAs of conserved miRNAs were computationally predicted among the olive cDNA collection and experimentally validated through endonucleolytic cleavage assays. Finally, we use expression data to uncover genetic components of the miR156, miR172 and miR390/TAS3-derived trans-acting small interfering RNA (tasiRNA) regulatory nodes, suggesting that these interactive networks controlling developmental transitions are fully operational in olive.
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spelling pubmed-32253732011-12-02 High-Throughput Sequencing of RNA Silencing-Associated Small RNAs in Olive (Olea europaea L.) Donaire, Livia Pedrola, Laia de la Rosa, Raúl Llave, César PLoS One Research Article Small RNAs (sRNAs) of 20 to 25 nucleotides (nt) in length maintain genome integrity and control gene expression in a multitude of developmental and physiological processes. Despite RNA silencing has been primarily studied in model plants, the advent of high-throughput sequencing technologies has enabled profiling of the sRNA component of more than 40 plant species. Here, we used deep sequencing and molecular methods to report the first inventory of sRNAs in olive (Olea europaea L.). sRNA libraries prepared from juvenile and adult shoots revealed that the 24-nt class dominates the sRNA transcriptome and atypically accumulates to levels never seen in other plant species, suggesting an active role of heterochromatin silencing in the maintenance and integrity of its large genome. A total of 18 known miRNA families were identified in the libraries. Also, 5 other sRNAs derived from potential hairpin-like precursors remain as plausible miRNA candidates. RNA blots confirmed miRNA expression and suggested tissue- and/or developmental-specific expression patterns. Target mRNAs of conserved miRNAs were computationally predicted among the olive cDNA collection and experimentally validated through endonucleolytic cleavage assays. Finally, we use expression data to uncover genetic components of the miR156, miR172 and miR390/TAS3-derived trans-acting small interfering RNA (tasiRNA) regulatory nodes, suggesting that these interactive networks controlling developmental transitions are fully operational in olive. Public Library of Science 2011-11-28 /pmc/articles/PMC3225373/ /pubmed/22140484 http://dx.doi.org/10.1371/journal.pone.0027916 Text en Donaire et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Donaire, Livia
Pedrola, Laia
de la Rosa, Raúl
Llave, César
High-Throughput Sequencing of RNA Silencing-Associated Small RNAs in Olive (Olea europaea L.)
title High-Throughput Sequencing of RNA Silencing-Associated Small RNAs in Olive (Olea europaea L.)
title_full High-Throughput Sequencing of RNA Silencing-Associated Small RNAs in Olive (Olea europaea L.)
title_fullStr High-Throughput Sequencing of RNA Silencing-Associated Small RNAs in Olive (Olea europaea L.)
title_full_unstemmed High-Throughput Sequencing of RNA Silencing-Associated Small RNAs in Olive (Olea europaea L.)
title_short High-Throughput Sequencing of RNA Silencing-Associated Small RNAs in Olive (Olea europaea L.)
title_sort high-throughput sequencing of rna silencing-associated small rnas in olive (olea europaea l.)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225373/
https://www.ncbi.nlm.nih.gov/pubmed/22140484
http://dx.doi.org/10.1371/journal.pone.0027916
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