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: 3.53). 12/2011; 6(12):e29217. DOI: 10.1371/journal.pone.0029217
Source: PubMed

ABSTRACT 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, Aug 05, 2015
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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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    Developmental Dynamics 04/2014; 243(4). DOI:10.1002/dvdy.24038 · 2.67 Impact Factor
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    • "miRNAs (for reviews see Bartel, 2004, 2009; Carthew and Sontheimer, 2009; Berezikov, 2011; Huntzinger and Izaurralde, 2011; Starega‐ Roslan et al., 2011) are a class of endogenously transcribed small RNAs $22 nt long that regulate the translation of messenger RNA targets via complementarity between the mature miRNA gene product and the sequence of the target mRNA, and in doing so are important in the regulation of numerous biological processes including cellular pluripotency and differentiation (Li and He, 2012). Most metazoan model systems have been sampled for their respective miRNA repertoires, including the hemichordate Saccoglossus kowalevskii, the echinoid Strongylocentrotus purpuratus, and the starfish Patiria miniata (Wheeler et al., 2009; Campo‐Paysaa et al., 2011; Kadri et al., 2011), and it has become clear that miRNAs show five interesting properties that make them good candidates to help resolve phylogenetic controversies: (1) The processes of miRNA biogenesis enables the identification of novel miRNAs without prior knowledge of sequence; (2) miRNA families are continuously being added to metazoan genomes through evolutionary time; (3) Most taxa show low levels of secondary miRNA gene loss such that for roughly every 11 miRNA families gained in a phylogenetic lineage there is a single miRNA family loss; (4) miRNAs show very low substitution rates in the mature miRNA sequence; and finally (5) There is an exceeding small chance for the convergent evolution of the same miRNA sequence (Sperling and Peterson, 2009). miRNAs have been used to address particularly difficult phylogenetic problems, ranging from sponge interrelationships (Sperling et al., 2010), to ecdysozoan interrelationships (Rota‐Stabellli et al., 2010; Campbell et al., 2011), to vertebrate interrelationships (Heimberg et al., 2010; Lyson et al., 2011), to the phylogenetic placement of enigmatic taxa like myzostomids (Helm et al., 2012). "
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    ABSTRACT: The abundance of an mRNA in a cell depends on its overall rates of synthesis and decay. RNA stability is an important element in the regulation of gene expression, and is achieved by a variety of processes including specific recruitment of nucleases and RNAi-associated mechanisms. These mechanisms are particularly important in stem cells, which, in many cases, have attenuated transcription. Here we report that mRNA injected into fertilized eggs of the sea urchin is selectively retained in the small micromeres,which contribute to the germline in this organism, beginning in blastulae, when compared to adjacent somatic cells. We show that modification of this exogenous RNA using cap analogs and poly-adenosine tail deletions do not affect its selective retention in the small micromeres, but removal of the cap or of the 3'-untranslated region eliminates any selective mRNA retention in the germline. Our results illuminate a likely ancient mechanism used by stem cells to prolong the lifespan of RNAs - either through RNA protection or by the absence of basic RNA degradation mechanisms, which are employed by most other cells of an organism. Mol. Reprod. Dev. © 2013 Wiley Periodicals, Inc.
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