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Characterization and Expression Analysis of MicroRNAs in the Tube Foot of Sea Cucumber Apostichopus japonicus

MicroRNAs (miRNAs) are a class of endogenous non-coding small RNA with average length of 22 nucleotides, participating in the post-transcriptional regulation of gene expression. In this study, we report the identification and characterization of miRNAs in the tube foot of sea cucumber (Apostichopus...

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Autores principales: Wang, Hongdi, Liu, Shikai, Cui, Jun, Li, Chengze, Qiu, Xuemei, Chang, Yaqing, Liu, Zhanjiang, Wang, Xiuli
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4221132/
https://www.ncbi.nlm.nih.gov/pubmed/25372871
http://dx.doi.org/10.1371/journal.pone.0111820
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author Wang, Hongdi
Liu, Shikai
Cui, Jun
Li, Chengze
Qiu, Xuemei
Chang, Yaqing
Liu, Zhanjiang
Wang, Xiuli
author_facet Wang, Hongdi
Liu, Shikai
Cui, Jun
Li, Chengze
Qiu, Xuemei
Chang, Yaqing
Liu, Zhanjiang
Wang, Xiuli
author_sort Wang, Hongdi
collection PubMed
description MicroRNAs (miRNAs) are a class of endogenous non-coding small RNA with average length of 22 nucleotides, participating in the post-transcriptional regulation of gene expression. In this study, we report the identification and characterization of miRNAs in the tube foot of sea cucumber (Apostichopus japonicus) by next generation sequencing with Illumina HiSeq 2000 platform. Through the bioinformatic analysis, we identified 260 conserved miRNAs and six novel miRNAs from the tube foot small RNA transcriptome. Quantitative realtime PCR (qRT-PCR) was performed to characterize the specific expression in the tube foot. The results indicated that four miRNAs, including miR-29a, miR-29b, miR-2005 and miR-278-3p, were significantly up-regulated in the tube foot. The target genes of the four specifically expressed miRNAs were predicted in silico and validated by performing qRT-PCR. Gene ontology (GO) and KEGG pathway analyses with the target genes of these four miRNAs were conducted to further understand the regulatory function in the tube foot. This is the first study to profile the miRNA transcriptome of the tube foot in sea cucumber. This work will provide valuable genomic resources to understand the mechanisms of gene regulation in the tube foot, and will be useful to assist the molecular breeding in sea cucumber.
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spelling pubmed-42211322014-11-12 Characterization and Expression Analysis of MicroRNAs in the Tube Foot of Sea Cucumber Apostichopus japonicus Wang, Hongdi Liu, Shikai Cui, Jun Li, Chengze Qiu, Xuemei Chang, Yaqing Liu, Zhanjiang Wang, Xiuli PLoS One Research Article MicroRNAs (miRNAs) are a class of endogenous non-coding small RNA with average length of 22 nucleotides, participating in the post-transcriptional regulation of gene expression. In this study, we report the identification and characterization of miRNAs in the tube foot of sea cucumber (Apostichopus japonicus) by next generation sequencing with Illumina HiSeq 2000 platform. Through the bioinformatic analysis, we identified 260 conserved miRNAs and six novel miRNAs from the tube foot small RNA transcriptome. Quantitative realtime PCR (qRT-PCR) was performed to characterize the specific expression in the tube foot. The results indicated that four miRNAs, including miR-29a, miR-29b, miR-2005 and miR-278-3p, were significantly up-regulated in the tube foot. The target genes of the four specifically expressed miRNAs were predicted in silico and validated by performing qRT-PCR. Gene ontology (GO) and KEGG pathway analyses with the target genes of these four miRNAs were conducted to further understand the regulatory function in the tube foot. This is the first study to profile the miRNA transcriptome of the tube foot in sea cucumber. This work will provide valuable genomic resources to understand the mechanisms of gene regulation in the tube foot, and will be useful to assist the molecular breeding in sea cucumber. Public Library of Science 2014-11-05 /pmc/articles/PMC4221132/ /pubmed/25372871 http://dx.doi.org/10.1371/journal.pone.0111820 Text en © 2014 Wang 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
Wang, Hongdi
Liu, Shikai
Cui, Jun
Li, Chengze
Qiu, Xuemei
Chang, Yaqing
Liu, Zhanjiang
Wang, Xiuli
Characterization and Expression Analysis of MicroRNAs in the Tube Foot of Sea Cucumber Apostichopus japonicus
title Characterization and Expression Analysis of MicroRNAs in the Tube Foot of Sea Cucumber Apostichopus japonicus
title_full Characterization and Expression Analysis of MicroRNAs in the Tube Foot of Sea Cucumber Apostichopus japonicus
title_fullStr Characterization and Expression Analysis of MicroRNAs in the Tube Foot of Sea Cucumber Apostichopus japonicus
title_full_unstemmed Characterization and Expression Analysis of MicroRNAs in the Tube Foot of Sea Cucumber Apostichopus japonicus
title_short Characterization and Expression Analysis of MicroRNAs in the Tube Foot of Sea Cucumber Apostichopus japonicus
title_sort characterization and expression analysis of micrornas in the tube foot of sea cucumber apostichopus japonicus
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4221132/
https://www.ncbi.nlm.nih.gov/pubmed/25372871
http://dx.doi.org/10.1371/journal.pone.0111820
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