1. RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star
- Author
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Veronica F. Hinman, Panayiotis V. Benos, and Sabah Kadri
- Subjects
Evolutionary Genetics ,Small RNA ,lcsh:Medicine ,Genetic Networks ,Transcriptomes ,Starfish ,0302 clinical medicine ,Pattern Formation ,lcsh:Science ,Genome Evolution ,Sea urchin ,In Situ Hybridization ,0303 health sciences ,education.field_of_study ,Multidisciplinary ,Ecology ,biology ,Gene Expression Regulation, Developmental ,Genomics ,69999 Biological Sciences not elsewhere classified ,Research Article ,Population ,Deep sequencing ,03 medical and health sciences ,Genome Analysis Tools ,biology.animal ,Animals ,education ,Biology ,Gene ,030304 developmental biology ,Evolutionary Biology ,Sequence Assembly Tools ,Evolutionary Developmental Biology ,lcsh:R ,Genomic Evolution ,Molecular Development ,Comparative Genomics ,Blotting, Northern ,biology.organism_classification ,Strongylocentrotus purpuratus ,Molecular biology ,Signaling ,MicroRNAs ,Evolutionary biology ,Sea Urchins ,FOS: Biological sciences ,RNA ,lcsh:Q ,Genome Expression Analysis ,Organism Development ,Developmental biology ,030217 neurology & neurosurgery ,Developmental Biology - 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 http://www.benoslab.pitt.edu/services.html.
- Published
- 2011
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