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RNA deep sequencing reveals differential MicroRNA expression during development of sea urchin and sea star

Kadri, S and Hinman, VF and Benos, PV (2011) RNA deep sequencing reveals differential MicroRNA expression during development of sea urchin and sea star. PLoS ONE, 6 (12).

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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. © 2011 Kadri et al.


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Details

Item Type: Article
Status: Published
Creators/Authors:
CreatorsEmailPitt UsernameORCID
Kadri, S
Hinman, VF
Benos, PVbenos@pitt.eduBENOS
Contributors:
ContributionContributors NameEmailPitt UsernameORCID
EditorDupuy, DenisUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Date: 28 December 2011
Date Type: Publication
Journal or Publication Title: PLoS ONE
Volume: 6
Number: 12
DOI or Unique Handle: 10.1371/journal.pone.0029217
Schools and Programs: School of Medicine > Computational and Systems Biology
Refereed: Yes
MeSH Headings: Animals; Blotting, Northern; Gene Expression Regulation, Developmental; In Situ Hybridization; MicroRNAs--genetics; RNA--genetics; Sea Urchins--embryology; Starfish--growth & development
Other ID: NLM PMC3247247
PubMed Central ID: PMC3247247
PubMed ID: 22216218
Date Deposited: 13 Sep 2012 15:28
Last Modified: 26 Jan 2019 13:55
URI: http://d-scholarship.pitt.edu/id/eprint/14010

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