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.
Highlights
IntroductionMicroRNAs (miRNAs) are a class of endogenous non-coding RNA in length of 22 nucleotides (nt) on average
MicroRNAs are a class of endogenous non-coding RNA in length of 22 nucleotides on average
Deep sequencing of small RNA transcriptome A total of 8,053,300 raw reads were generated by sequencing the small RNA transcriptome of the tube foot using HiSeq 2000 platform
Summary
MicroRNAs (miRNAs) are a class of endogenous non-coding RNA in length of 22 nucleotides (nt) on average. The miRNAs could post-transcriptionally regulate gene expression of growth, development, differentiation and many other biological processes [1]. A primary miRNA (pri-miRNA) is first transcribed from a miRNA gene by the RNA polymerase II or III enzyme in the nucleus. After being cleaved by a complex composed of RNase III enzyme Drosha, the pri-miRNA is transformed into precursor miRNA (pre-miRNA), a short stemloop structure (,60–70 nt) [4,5]. The pre-miRNA is transported across the nuclear membrane and processed by another RNase enzyme, Dicer, to produce the mature miRNA (,18– 25 nt) in the cytoplasm [6,7]. The mature miRNA functions by being incorporated into an RNA-induced silencing complex (RISC) to regulate the gene expression post-transcriptionally
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