Limits...
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.

Show MeSH
Analyses of the nucleotide bias at the first position of miRNAs and each position of miRNAs with length of 22 nucleotides.A: The nucleotide bias at the first position of miRNAs. B: The nucleotide bias at each position of miRNAs with length of 22 nucleotides.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4221132&req=5

pone-0111820-g003: Analyses of the nucleotide bias at the first position of miRNAs and each position of miRNAs with length of 22 nucleotides.A: The nucleotide bias at the first position of miRNAs. B: The nucleotide bias at each position of miRNAs with length of 22 nucleotides.

Mentions: The nucleotide bias at the first position of the identified miRNAs was analyzed (Figure 3A). The miRNAs showed a significant bias to uracil (U) at the first nucleotide, which is especially true for the miRNAs with lengths of 18 nt to 23 nt. The percentages of the four nucleotides appearing at each position were also analyzed for the miRNAs with the length of 22 nucleotides. As shown in Figure 3B, it's clear that the 2nd, 3rd, 7th nucleotides are biased to G+C, and the 4th, 5th, 9th, 10th and 11th are significantly biased to A+U.


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)

Analyses of the nucleotide bias at the first position of miRNAs and each position of miRNAs with length of 22 nucleotides.A: The nucleotide bias at the first position of miRNAs. B: The nucleotide bias at each position of miRNAs with length of 22 nucleotides.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0111820-g003: Analyses of the nucleotide bias at the first position of miRNAs and each position of miRNAs with length of 22 nucleotides.A: The nucleotide bias at the first position of miRNAs. B: The nucleotide bias at each position of miRNAs with length of 22 nucleotides.
Mentions: The nucleotide bias at the first position of the identified miRNAs was analyzed (Figure 3A). The miRNAs showed a significant bias to uracil (U) at the first nucleotide, which is especially true for the miRNAs with lengths of 18 nt to 23 nt. The percentages of the four nucleotides appearing at each position were also analyzed for the miRNAs with the length of 22 nucleotides. As shown in Figure 3B, it's clear that the 2nd, 3rd, 7th nucleotides are biased to G+C, and the 4th, 5th, 9th, 10th and 11th are significantly biased to A+U.

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