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Int J Biol Sci
2011 Feb 16;72:180-92. doi: 10.7150/ijbs.7.180.
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Novel and conserved micrornas in Dalian purple urchin (Strongylocentrotus nudus) identified by next generation sequencing.
Wei Z
,
Liu X
,
Feng T
,
Chang Y
.
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MicroRNAs are regulators in regulation of broad range of phenotypes. The purple urchin, Strongylocentrotus nudus, is one of the most important marine economic animals that widely distributed in the cold seas along the coasts of eastern pacific area. To date, only 45 microRNAs have been identified in a related species, Strongylocentrotus purpurtus, and there is no report on S. nudus microRNAs. Herein, solexa sequencing technology was used to high throughput sequencing analysis of microRNAs in small RNA library isolated from five tissues of S. nudus. Totally, 8,966,865 reads were yielded, 131,015 of which were related to 415 unique microRNAs including 345 deuterostoma conserved and 70 urchin specific microRNAs, as well as 5 microRNA* sequences. The miRNA features including length distribution, end variations and genomic locations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways that regulated by urchin miRNAs, of which signal transduction mechanisms was the subgroup containing the maximum targets. In addition, the expression of 100 miRNAs in female gonad was confirmed using microRNA microarray analysis. This study provides a first large scale cloning and characterization of S.nudus miRNAs and their potential targets, providing the foundation for further characterization for their role in the regulation of diversity of physiological processes.
Figure 1. Length distribution of raw reads and mapped reads. A: distribution of mature sequences of unique miRNAs identified in this research; B: distribution of sequenced reads related to miRNAs.
Figure 2. Targets and characters of identified S.nudus miRNAs. A: KOG classes of predicted targets; B: conservation profile of identified miRNAs, values on Y axis indicate the number of conserved miRNA between S.nudus and queried specie; C: Top 25 miRNAs with maximum signal detected in female gonad, spu-mir-71, -22 and -31 refer to known S.purpuratus miRNAs which added in to probes.
Figure 3. Clustered profile of S. nudus microRNAs in 3 selected scaffolds. A: miRNA gene clusters in urchin. The location of microRNAs in 3 scaffolds were showed. Rightward arrow indicate the locatzation o f mature sequences at the positive strand, while leftward arrow indicate at minus strand. Double arrow represented miRNA and their miRNA* were located in the same pre-miRNA sequences at 5' and 3' termini respectively. B: Sequences alignment of 21 miRNAs clustered in scaffold78427, no significant sequences similiarity was found in these miRNAs. C: Three microRNAs and their microRNA*s, upper-case letters refer to mature sequences, while underlined leters refer to miRNA* sequences.
Figure 4. Sequences alignment of Snu-mir-375 and its homologous miRNAs
Figure 5. Distribution of predicted targets of miRNAs clustered scaffold78427. ACTM: Amino acid transport and metabolism; CTM: Carbohydrate transport and metabolism; CWMEB: Cell wall/ membrane/ envelope biogenesis; PMPTC: Post-translational modification, protein turnover, chaperones; CSD: Chromatin structure and dynamics; IITM: Inorganic ion transport and metabolism; ITSVT: Intracellular trafficking, secretion and vesicular transport; LTM: Lipid transport and metabolism; NTM: Nucleotide transport and metabolism; RRR: Replication, recombination and repair; RSB: ribosomal structure and biogenesis; RPM: RNA processing and modification; SMBTC: Secondary metabolites biosynthesis, transport and catabolism; STM: Signal transduction mechanisms.
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