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

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 http://www.benoslab.pitt.edu/services.html.

微小RNA（microRNAs, miRNAs）是一类长度为20~23 nt的非编码单链RNA分子，可作为mRNA基因表达的转录后调控因子。它们已被证实参与调控多种生物的发育过程。棘皮动物中的紫海胆（Strongylocentrotus purpuratus, sea urchin）和海星（Patiria miniata, sea star）是研究发育的优秀模式生物，其转录调控网络已得到充分解析。然而迄今为止，除了已知miRNA生物合成通路相关基因在二者的发育阶段中存在表达外，人们对这两种生物发育过程中miRNA的功能仍一无所知。本研究使用Illumina基因组分析仪（Illumina公司），对海胆和海星受精后1至3天的混合发育阶段胚胎的小RNA文库进行测序，共获得22670000条读段。对上述数据的分析揭示了这两个物种的miRNA表达谱。研究发现，在早期发育阶段，海胆和海星中分别有47种和38种已知miRNA得以表达，其中32种为二者共有。此外，在海胆胚胎文库中还发现了13种潜在的新型miRNA。发育过程中，两个物种的miRNA表达模式总体保守，但有7种miRNA仅在其中一个物种中呈高表达。本研究产生的两套数据集将为从事发育生物学及其调控网络研究的科研人员提供宝贵的研究资源。用于分析Illumina读段的计算流程可在http://www.benoslab.pitt.edu/services.html获取。