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Sci Rep
2015 Dec 04;5:17763. doi: 10.1038/srep17763.
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Identification and comparative analysis of complement C3-associated microRNAs in immune response of Apostichopus japonicus by high-throughput sequencing.
Zhong L
,
Zhang F
,
Zhai Y
,
Cao Y
,
Zhang S
,
Chang Y
.
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MicroRNAs (miRNAs) are important effectors in mediating host-pathogen interaction. In this report, coelomocytes miRNA libraries of three Japanese sea cucumbers Apostichopus japonicus were built by Illumina(®) Hiseq2000 from different time points after lipopolysaccharide challenge (at time 0 h, 6 h and 12 h). The clean data received from high throughput sequencing were used to sequences analysis. Referenced to the Strongylocentrotus purpuratus genome, 38 conserved miRNAs were found, and three miRNA candidates were predicted by software. According to the evidence resulting from the expression of AjC3, expressing levels of spu-miR-133, spu-miR-137 and spu-miR-2004 altered along with the expression of AjC3 changing at different time points after LPS injection. Thus, we speculated that the three miRNAs may have influence on A. japonicus complement C3. The spu-miR-137 and miR-137 gene family in miRBase were analyzed by bioinformatics. There is an obvious discrepancy between invertebrates and vertebrates. The first and ninth nucleotides in invertebrate miR-137 are offset compared vertebrate miR-137. Importantly, this is the first attempt to map the stage of immune response regulome in echinoderms, which might be considered as information for elucidating the intrinsic mechanism underlying the immune system in this species.
Figure 1. Size distribution of sequencing reads in three libraries.Different colors represent different libraries.
Figure 2. The predicted hairpin structures.The figures illustrate the predicted hairpin structures of novel-36 (a), novel-44 (b) and novel-45 (c), and the red parts reflect mature sequences.
Figure 3. Alignment of the mature miR-137.Asterisks (*) above the alignments indicate the positions of identity. Frames represent the different bases in vertebrate miR-137 at the first and ninth positions.
Figure 4. Phylogenetic relationships among members of the full-length sequences of miR-137 family hairpin.The tree was constructed using the Maximum Parsimony program from an alignment done with CLUSTAL W. Accession numbers for the sequence used in this alignment are given in Table 2.
Figure 6. Heat map of miRNAs related to the immune response.Heat map showing the differential expression of miRNAs in three libraries (log2 transformed relative expression values). miRNA with a higher expression level is mapped to the red part and miRNA with a lower expression level is mapped to the blue part.
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