High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation

PLoS One. 2013 Oct 15;8(10):e76120. doi: 10.1371/journal.pone.0076120. eCollection 2013.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Conserved Sequence
  • Estivation / genetics*
  • Gene Expression Profiling*
  • Gene Ontology
  • High-Throughput Nucleotide Sequencing*
  • Intestinal Mucosa / metabolism*
  • MicroRNAs / genetics*
  • Oligonucleotide Array Sequence Analysis
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Reproducibility of Results
  • Sea Cucumbers / genetics*
  • Sea Cucumbers / physiology*
  • Sequence Analysis, RNA

Substances

  • MicroRNAs
  • RNA, Messenger

Grant support

This work was supported by the National Natural Science Foundation (No. 31201972), Research Fund of young scholars for the Doctoral Program of Higher Education of China (No. 20120132120009) and Research fund for talented scholars Ocean University of China (No. 1400841212003). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.