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PLoS One
2013 Jan 01;810:e76120. doi: 10.1371/journal.pone.0076120.
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High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation.
Chen M
,
Zhang X
,
Liu J
,
Storey KB
.
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The regulatory role of miRNA in gene expression is an emerging hot new topic in the control of hypometabolism. Sea cucumber aestivation is a complicated physiological process that includes obvious hypometabolism as evidenced by a decrease in the rates of oxygen consumption and ammonia nitrogen excretion, as well as a serious degeneration of the intestine into a very tiny filament. To determine whether miRNAs play regulatory roles in this process, the present study analyzed profiles of miRNA expression in the intestine of the sea cucumber (Apostichopus japonicus), using Solexa deep sequencing technology. We identified 308 sea cucumber miRNAs, including 18 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA) after at least 15 days of continuous torpor, were compared with animals from a non-aestivation (NA) state (animals that had passed through aestivation and returned to the active state). We identified 42 differentially expressed miRNAs [RPM (reads per million) >10, |FC| (|fold change|) ≥ 1, FDR (false discovery rate) <0.01] during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-200-3p, miR-2004, miR-2010, miR-22, miR-252a, miR-252a-3p and miR-92 were significantly over-expressed during deep aestivation compared with non-aestivation animals. Preliminary analyses of their putative target genes and GO analysis suggest that these miRNAs could play important roles in global transcriptional depression and cell differentiation during aestivation. High-throughput sequencing data and microarray data have been submitted to GEO database.
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24143179
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Figure 1. Common and specific sequences summary of unique sRNAs between non-aestivation (NA) and DA (deep-aestivation) states.Three groups are shown: those specific to NA, those specific to DA, and those that are common to both. The percentage distribution of sequences between these three groups is shown along with the number of sRNA sequences in brackets.
Figure 2. Length distributions of clean reads in NA and DA.The x-axis indicates sequence sizes from 10 nt to 32 nt. The y-axis indicates the percentage of reads for every given size.
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