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Characterization and expression analysis of microRNAs in the tube foot of sea cucumber Apostichopus japonicus.

Wang H, Liu S, Cui J, Li C, Qiu X, Chang Y, Liu Z, Wang X - PLoS ONE (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China.

ABSTRACT
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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Quantitative realtime PCR analysis of the expression of miR-29a, miR-29b, miR-2005 and miR-278-3p in different tissues of sea cucumber.The tissues are abbreviated as follows: TF, tube foot; I, intestine; RT, respiratory tree, and C, coelomocytes. A: qRT-PCR using β-actin as the reference gene. B: qRT-PCR using Cytb as the reference gene. Bars are shown as mean ± standard deviation. Bars with different superscripts indicate that they are significantly different from each other (p<0.05).
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pone-0111820-g006: Quantitative realtime PCR analysis of the expression of miR-29a, miR-29b, miR-2005 and miR-278-3p in different tissues of sea cucumber.The tissues are abbreviated as follows: TF, tube foot; I, intestine; RT, respiratory tree, and C, coelomocytes. A: qRT-PCR using β-actin as the reference gene. B: qRT-PCR using Cytb as the reference gene. Bars are shown as mean ± standard deviation. Bars with different superscripts indicate that they are significantly different from each other (p<0.05).

Mentions: To analyze the tissue-specific expression of the identified miRNAs, 19 miRNAs were selected to perform quantitative real-time PCR (qRT-PCR) analysis in four different tissues, including intestine, respiratory tree, hemocyte and tube feet. As shown in Figure 6, four of the 19 selected miRNAs, i.e. miR-29a, miR-29b, miR-2005 and miR-278-3p, were significantly up-regulated in the tube foot of A. japonicus. Therefore, these four miRNAs were considered as the candidates that were specifically expressed in the tube foot.


Characterization and expression analysis of microRNAs in the tube foot of sea cucumber Apostichopus japonicus.

Wang H, Liu S, Cui J, Li C, Qiu X, Chang Y, Liu Z, Wang X - PLoS ONE (2014)

Quantitative realtime PCR analysis of the expression of miR-29a, miR-29b, miR-2005 and miR-278-3p in different tissues of sea cucumber.The tissues are abbreviated as follows: TF, tube foot; I, intestine; RT, respiratory tree, and C, coelomocytes. A: qRT-PCR using β-actin as the reference gene. B: qRT-PCR using Cytb as the reference gene. Bars are shown as mean ± standard deviation. Bars with different superscripts indicate that they are significantly different from each other (p<0.05).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4221132&req=5

pone-0111820-g006: Quantitative realtime PCR analysis of the expression of miR-29a, miR-29b, miR-2005 and miR-278-3p in different tissues of sea cucumber.The tissues are abbreviated as follows: TF, tube foot; I, intestine; RT, respiratory tree, and C, coelomocytes. A: qRT-PCR using β-actin as the reference gene. B: qRT-PCR using Cytb as the reference gene. Bars are shown as mean ± standard deviation. Bars with different superscripts indicate that they are significantly different from each other (p<0.05).
Mentions: To analyze the tissue-specific expression of the identified miRNAs, 19 miRNAs were selected to perform quantitative real-time PCR (qRT-PCR) analysis in four different tissues, including intestine, respiratory tree, hemocyte and tube feet. As shown in Figure 6, four of the 19 selected miRNAs, i.e. miR-29a, miR-29b, miR-2005 and miR-278-3p, were significantly up-regulated in the tube foot of A. japonicus. Therefore, these four miRNAs were considered as the candidates that were specifically expressed in the tube foot.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China.

ABSTRACT
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.

Show MeSH