Characterization of small RNAs in X. tropicalis gastrulae

Authors

  • Fernando Faunes,

    Corresponding author
    1. Center for Aging and Regeneration and Millennium Nucleus in Regenerative Biology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
    • Center for Aging and Regeneration and Millennium Nucleus in Regenerative Biology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
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    • Authors Fernando Faunes and Leonardo I. Almonacid contributed equally to this work.

  • Leonardo I. Almonacid,

    1. Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotheraphy, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
    2. Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
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    • Authors Fernando Faunes and Leonardo I. Almonacid contributed equally to this work.

  • Francisco Melo,

    1. Molecular Bioinformatics Laboratory, Millennium Institute on Immunology and Immunotheraphy, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
    2. Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
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  • Juan Larrain

    Corresponding author
    1. Center for Aging and Regeneration and Millennium Nucleus in Regenerative Biology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
    • Center for Aging and Regeneration and Millennium Nucleus in Regenerative Biology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile
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Errata

This article corrects:

  1. Characterization of small RNAs in Xenopus tropicalis gastrulae Volume 50, Issue 3, 260–270, Article first published online: 16 February 2012

  • The original version of this article publishing online 18 January 2012 was inadvertently created from an early revision of the submitted article and not from the accepted version. This corrected version has been prepared from the accepted version and should be considered authoritative. The publisher regrets the error.

Abstract

Here, we report and characterize deep sequencing data and bioinformatics analysis of small RNAs from X. tropicalis gastrula. A total of 17,553,124 reads with perfect match to the genome derived from 2,616,053 unique sequences were identified. Seventy-seven percent of theses sequences were not found in previous reports from X. tropicalis oocytes and somatic tissues. Bioinformatics analyses indicate that a large fraction of the small RNAs are PIWI-interacting RNAs. Up to 23.9% of small RNAs mapped to transposable elements and 27% to genic regions. Most of the abundant transposon-derived small RNAs are found in oocyte and gastrula libraries, suggesting that transposons also need to be silenced during early embryonic development. Importantly, novel clusters of piRNAs whose expression is activated after zygotic transcription begins were identified in the genome of X. tropicalis. Additionally, miRNAs were also identified and many of them are not present in oocytes, suggesting that miRNA expression is stage-specific. To the best of our knowledge, this is the first high throughput data release and bioinformatics characterization of small RNAs during Xenopus early embryonic development. genesis 50:572–58, 2012. © 2012 Wiley Periodicals, Inc.

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