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Transcriptome profiling of genes involved in neural tube closure during human embryonic development using long serial analysis of gene expression (long-SAGE)§

Authors

  • Deidre R. Krupp,

    1. Center for Human Genetics, Department of Medicine, Duke University Medical Center, Durham, North Carolina
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    • D.R. Krupp and P-T. Xu contributed equally to this article.

  • Pu-Ting Xu,

    1. Center for Human Genetics, Department of Medicine, Duke University Medical Center, Durham, North Carolina
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    • D.R. Krupp and P-T. Xu contributed equally to this article.

  • Sophie Thomas,

    1. Department of Genetics and INSERM U781, Hôpital Necker Enfants Malades, Université Paris Descartes, Paris, France
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  • Andrew Dellinger,

    1. Center for Human Genetics, Department of Medicine, Duke University Medical Center, Durham, North Carolina
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  • Heather C. Etchevers,

    1. INSERM U910, Université de la Méditerranée Faculté de Médecine, Marseille, France
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  • Michel Vekemans,

    1. Department of Genetics and INSERM U781, Hôpital Necker Enfants Malades, Université Paris Descartes, Paris, France
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  • John R. Gilbert,

    1. Center for Human Genetics, Department of Medicine, Duke University Medical Center, Durham, North Carolina
    2. The Miami Institute for Human Genomics and Department of Human Genetics, University of Miami, Miami, Florida
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  • Marcy C. Speer,

    1. Center for Human Genetics, Department of Medicine, Duke University Medical Center, Durham, North Carolina
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  • Allison E. Ashley-Koch,

    1. Center for Human Genetics, Department of Medicine, Duke University Medical Center, Durham, North Carolina
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    • A.E. Ashley-Koch and S. G. Gregory are joint senior authors.

  • Simon G. Gregory

    Corresponding author
    1. Center for Human Genetics, Department of Medicine, Duke University Medical Center, Durham, North Carolina
    • Duke Center for Human Genetics, 905 S. LaSalle Street, DUMC 3445, Durham, NC 27710
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    • A.E. Ashley-Koch and S. G. Gregory are joint senior authors.


  • Supported National Institutes of Health grant R01-NS039818.

  • M.C. Speer is deceased.

  • §

    The expression data from this study is in the process of being submitted to the Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/).

  • This article was published online on 18 July 2012. Subsequently, it was determined that supplemental materials had been omitted, and the article was corrected on 21 September 2012.

Abstract

BACKGROUND

Neural tube defects (NTDs) are common human birth defects with a complex etiology. To develop a comprehensive knowledge of the genes expressed during normal neurulation, we established transcriptomes from human neural tube fragments during and after neurulation using long Serial Analysis of Gene Expression (long-SAGE).

METHODS

Rostral and caudal neural tubes were dissected from normal human embryos aged between 26 and 32 days of gestation. Tissues from the same region and Carnegie stage were pooled (n ≥ 4) and total RNA extracted to construct four long-SAGE libraries. Tags were mapped using the UniGene Homo sapiens 17 bp tag-to-gene best mapping set. Differentially expressed genes were identified by chi-square or Fisher's exact test, and validation was performed for a subset of those transcripts using in situ hybridization. In silico analyses were performed with BinGO and EXPANDER.

RESULTS

We observed most genes to be similarly regulated in rostral and caudal regions, but expression profiles differed during and after closure. In silico analysis found similar enrichments in both regions for biologic process terms, transcription factor binding and miRNA target motifs. Twelve genes potentially expressing alternate isoforms by region or developmental stage, and the microRNAs miR-339-5p, miR-141/200a, miR-23ab, and miR-129/129-5p are among several potential candidates identified here for future research.

CONCLUSIONS

Time appears to influence gene expression in the developing central nervous system more than location. These data provide a novel complement to traditional strategies of identifying genes associated with human NTDs and offer unique insight into the genes associated with normal human neurulation. Birth Defects Research (Part A) 94:683–692, 2012. © 2012 Wiley Periodicals, Inc.

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