Deciphering Small Noncoding RNAs during the Transition from Dormant Embryo to Germinated Embryo in Larches (Larix leptolepis)

Small RNAs (sRNAs), as a key component of molecular biology, play essential roles in plant development, hormone signaling, and stress response. However, little is known about the relationships among sRNAs, hormone signaling, and dormancy regulation in gymnosperm embryos. To investigate the roles of...

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Autores principales: Zhang, Junhong, Zhang, Shougong, Han, Suying, Li, Xinmin, Tong, Zaikang, Qi, Liwang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858266/
https://www.ncbi.nlm.nih.gov/pubmed/24339932
http://dx.doi.org/10.1371/journal.pone.0081452
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author Zhang, Junhong
Zhang, Shougong
Han, Suying
Li, Xinmin
Tong, Zaikang
Qi, Liwang
author_facet Zhang, Junhong
Zhang, Shougong
Han, Suying
Li, Xinmin
Tong, Zaikang
Qi, Liwang
author_sort Zhang, Junhong
collection PubMed
description Small RNAs (sRNAs), as a key component of molecular biology, play essential roles in plant development, hormone signaling, and stress response. However, little is known about the relationships among sRNAs, hormone signaling, and dormancy regulation in gymnosperm embryos. To investigate the roles of sRNAs in embryo dormancy maintenance and release in Larix leptolepis, we deciphered the endogenous “sRNAome” in dormant and germinated embryos. High-throughput sequencing of sRNA libraries showed that dormant embryos exhibited a length bias toward 24-nt while germinated embryos showed a bias toward 21-nt lengths. This might be associated with distinct levels of RNA-dependent RNA polymerase2 (RDR2) and/or RDR6, which is regulated by hormones. Proportions of miRNAs to nonredundant and redundant sRNAs were higher in germinated embryos than in dormant embryos, while the ratio of unknown sRNAs was higher in dormant embryos than in germinated embryos. We identified a total of 160 conserved miRNAs from 38 families, 3 novel miRNAs, and 16 plausible miRNA candidates, of which many were upregulated in germinated embryos relative to dormant embryos. These findings indicate that larches and possibly other gymnosperms have complex mechanisms of gene regulation involving miRNAs and other sRNAs operating transcriptionally and posttranscriptionally during embryo dormancy and germination. We propose that abscisic acid modulates embryo dormancy and germination at least in part through regulation of the expression level of sRNA-biogenesis genes, thus changing the sRNA components.
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spelling pubmed-38582662013-12-11 Deciphering Small Noncoding RNAs during the Transition from Dormant Embryo to Germinated Embryo in Larches (Larix leptolepis) Zhang, Junhong Zhang, Shougong Han, Suying Li, Xinmin Tong, Zaikang Qi, Liwang PLoS One Research Article Small RNAs (sRNAs), as a key component of molecular biology, play essential roles in plant development, hormone signaling, and stress response. However, little is known about the relationships among sRNAs, hormone signaling, and dormancy regulation in gymnosperm embryos. To investigate the roles of sRNAs in embryo dormancy maintenance and release in Larix leptolepis, we deciphered the endogenous “sRNAome” in dormant and germinated embryos. High-throughput sequencing of sRNA libraries showed that dormant embryos exhibited a length bias toward 24-nt while germinated embryos showed a bias toward 21-nt lengths. This might be associated with distinct levels of RNA-dependent RNA polymerase2 (RDR2) and/or RDR6, which is regulated by hormones. Proportions of miRNAs to nonredundant and redundant sRNAs were higher in germinated embryos than in dormant embryos, while the ratio of unknown sRNAs was higher in dormant embryos than in germinated embryos. We identified a total of 160 conserved miRNAs from 38 families, 3 novel miRNAs, and 16 plausible miRNA candidates, of which many were upregulated in germinated embryos relative to dormant embryos. These findings indicate that larches and possibly other gymnosperms have complex mechanisms of gene regulation involving miRNAs and other sRNAs operating transcriptionally and posttranscriptionally during embryo dormancy and germination. We propose that abscisic acid modulates embryo dormancy and germination at least in part through regulation of the expression level of sRNA-biogenesis genes, thus changing the sRNA components. Public Library of Science 2013-12-10 /pmc/articles/PMC3858266/ /pubmed/24339932 http://dx.doi.org/10.1371/journal.pone.0081452 Text en © 2013 Zhang 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
Zhang, Junhong
Zhang, Shougong
Han, Suying
Li, Xinmin
Tong, Zaikang
Qi, Liwang
Deciphering Small Noncoding RNAs during the Transition from Dormant Embryo to Germinated Embryo in Larches (Larix leptolepis)
title Deciphering Small Noncoding RNAs during the Transition from Dormant Embryo to Germinated Embryo in Larches (Larix leptolepis)
title_full Deciphering Small Noncoding RNAs during the Transition from Dormant Embryo to Germinated Embryo in Larches (Larix leptolepis)
title_fullStr Deciphering Small Noncoding RNAs during the Transition from Dormant Embryo to Germinated Embryo in Larches (Larix leptolepis)
title_full_unstemmed Deciphering Small Noncoding RNAs during the Transition from Dormant Embryo to Germinated Embryo in Larches (Larix leptolepis)
title_short Deciphering Small Noncoding RNAs during the Transition from Dormant Embryo to Germinated Embryo in Larches (Larix leptolepis)
title_sort deciphering small noncoding rnas during the transition from dormant embryo to germinated embryo in larches (larix leptolepis)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858266/
https://www.ncbi.nlm.nih.gov/pubmed/24339932
http://dx.doi.org/10.1371/journal.pone.0081452
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