High-Throughput Sequencing Reveals Differential Expression of miRNAs in Intestine from Sea Cucumber during Aestivation

Abstract

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.

Characterization and Expression Analysis of MicroRNAs in the Tube Foot of Sea Cucumber Apostichopus japonicus

“…This is consistent with the observation based on the systematic analysis of thousands of metazoan miRNAs [28]. In canonical cases, the 2 nd to the 8 th nucleotides of miRNAs, named as “seed region”, are perfectly complementary with their target sites.…”

“…One of the reasons is that total RNA in the tube foot is much less abundant than that in the haemocyte and intestine [28]. According to the length distribution of small RNAs, over 84.4% of the sequenced read had the length of 21–23 nt, which is the typical size range of miRNA.…”

Metabolomic responses of sea cucumber Apostichopus japonicus to thermal stresses

“…In order to elucidate its molecular mechanism, a comparative proteomic analysis of the global protein expression changes was also investigated after 7 days of exposure at 25°C in our previous work, and 8 proteins involved into material and energy metabolism showed significantly differential expression profiles during this process . Chen et al (2013) found that some microRNAs like miR-92, miR-2004, miR-2010 and miR-22 were also significantly over-expressed in aestivated sea cucumber, indicating that miRNAs were involved into this global transcriptional depression. But how these molecules affect sea cucumber metabolites and modulate metabolic pathways are still not well documented.…”

A potential antiapoptotic regulation: The interaction of heat shock protein 70 and apoptosis‐inducing factor mitochondrial 1 during heat stress and aestivation in sea cucumber

“…The sea cucumber, Apostichopus japonicus , is a commercially important marine organism that is raised in aquaculture along the coasts of China and has recently become a good model organism for studies of aestivation among marine invertebrates (Chen & Storey, ; Chen, Zhang, Liu, & Storey, ; Chen, Zhu, & Storey, ). This species naturally enters aestivation when ambient seawater temperature rises above 25°C during the summer months and can remain in dormancy for over 100 days (Yang et al., ).…”