RNA Deep Sequencing Reveals Differential MicroRNA Expression during Development of Sea Urchin and Sea Star

Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
PLoS ONE (Impact Factor: 3.23). 12/2011; 6(12):e29217. DOI: 10.1371/journal.pone.0029217
Source: PubMed


microRNAs (miRNAs) are small (20-23 nt), non-coding single stranded RNA molecules that act as post-transcriptional regulators of mRNA gene expression. They have been implicated in regulation of developmental processes in diverse organisms. The echinoderms, Strongylocentrotus purpuratus (sea urchin) and Patiria miniata (sea star) are excellent model organisms for studying development with well-characterized transcriptional networks. However, to date, nothing is known about the role of miRNAs during development in these organisms, except that the genes that are involved in the miRNA biogenesis pathway are expressed during their developmental stages. In this paper, we used Illumina Genome Analyzer (Illumina, Inc.) to sequence small RNA libraries in mixed stage population of embryos from one to three days after fertilization of sea urchin and sea star (total of 22,670,000 reads). Analysis of these data revealed the miRNA populations in these two species. We found that 47 and 38 known miRNAs are expressed in sea urchin and sea star, respectively, during early development (32 in common). We also found 13 potentially novel miRNAs in the sea urchin embryonic library. miRNA expression is generally conserved between the two species during development, but 7 miRNAs are highly expressed in only one species. We expect that our two datasets will be a valuable resource for everyone working in the field of developmental biology and the regulatory networks that affect it. The computational pipeline to analyze Illumina reads is available at

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Available from: Veronica F Hinman
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    • "A common corollary is that the strand of the microRNA duplex that is seen to be more highly expressed is assumed to be the functional mature microRNA [21], [22]. The presumption that high expression leads to high activity is also evident in studies that use differential expression to identify microRNAs important in processes such as development or disease, which usually concentrate on microRNAs that are both highly and differentially expressed [23], [24]. This paradigm is supported by the observation that the over-expression of many microRNAs leads to dose-dependent decreases in the levels of target mRNAs [25], [26] and that the expression of microRNAs and their mRNA targets shows a weak negative correlation [27]. "
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    • "Lin28 transcripts accumulate in the esophagus, stomach, and PE in the early larva, and in the stomach, intestine, anus, and PE in the late larva, but not in the coelomic pouches. Importantly, a conserved let-7 miRNA was found in sea urchins (Kadri et al., 2011; Song et al., 2012), although its site of accumulation is not known, nor whether it is present in sea stars. "
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    • "The development of an ultrahigh-throughput sequencing RNA-Seq technique such as Illumina/Solexa, provided a powerful technology that greatly facilitated discovery and analysis of small RNAs, especially for an animal like the sea cucumber for which there is no genome background and no miRNA data in miRbase. This technology can generate several million small RNA sequences in each small RNA library in one run and has been successfully and increasingly used for non-model species like the sea star, Patiria miniata [21]. The RNA-Seq technique has the potential to overcome microarray limitations (lower throughput, high background noise, lower sensitivity and the miRNA sequence has to be known) and provide an expression profile with a greater and reproducible dynamic range. "
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