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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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GO terms for predicted target genes.
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pone-0111820-g005: GO terms for predicted target genes.

Mentions: In total, 16,331 and 15,758 reads were extracted from 3′-UTR and 5′-UTR regions [29]. With these sequences, the putative target genes of identified miRNAs were predicted using the program miRanda-3.3 [30]. The sequences of predicted target genes were listed in Table S2. To understand the functional networks of the target genes, GO analysis was performed. GO analysis showed that these target genes were involved in a large number of physiological processes at the levels of molecular function, cellular component and biological processes. The GO terms were relatively even-distributed in different categories of GO terms with the exception of molecular function where the binding and protein binding terms were dominant (Figure 5).


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)

GO terms for predicted target genes.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111820-g005: GO terms for predicted target genes.
Mentions: In total, 16,331 and 15,758 reads were extracted from 3′-UTR and 5′-UTR regions [29]. With these sequences, the putative target genes of identified miRNAs were predicted using the program miRanda-3.3 [30]. The sequences of predicted target genes were listed in Table S2. To understand the functional networks of the target genes, GO analysis was performed. GO analysis showed that these target genes were involved in a large number of physiological processes at the levels of molecular function, cellular component and biological processes. The GO terms were relatively even-distributed in different categories of GO terms with the exception of molecular function where the binding and protein binding terms were dominant (Figure 5).

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