Informatic and genomic analysis of melanocyte cDNA libraries as a resource for the study of melanocyte development and function

Authors

  • Laura L. Baxter,

    1. Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20855, USA
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  • Benjamin J. Hsu,

    1. Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20855, USA
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  • Lowell Umayam,

    1. Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20855, USA
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  • Tyra G. Wolfsberg,

    1. Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20855, USA
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  • Denise M. Larson,

    1. Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20855, USA
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  • Martin C. Frith,

    1. ARC Centre in Bioinformatics and Institute for Molecular Bioscience, the University of Queensland, Brisbane, QLD 4072, Australia
    2. Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1–7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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  • Jun Kawai,

    1. Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1–7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
    2. Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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  • Yoshihide Hayashizaki,

    1. Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1–7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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  • Piero Carninci,

    1. Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1–7-22, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
    2. Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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  • William J. Pavan

    1. Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20855, USA
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*Address correspondence to Dr William J. Pavan,
e-mail: bpavan@mail.nih.gov

Summary

As part of the RIKEN mouse encyclopedia project, two cDNA libraries were prepared from melanocyte-derived cell lines, using techniques of full-length clone selection and subtraction/normalization to enrich for rare transcripts. End sequencing showed that these libraries display over 83% complete coding sequence at the 5′ end and 96–97% complete coding sequence at the 3′ end. Evaluation of the libraries, derived from B16F10Y tumor cells and melan-c cells, revealed that they contain clones for a majority of the genes previously demonstrated to function in melanocyte biology. Analysis of genomic locations for transcripts revealed that the distribution of melanocyte genes is non-random throughout the genome. Three genomic regions identified that showed significant clustering of melanocyte-expressed genes contain one or more genes previously shown to regulate melanocyte development or function. A catalog of genes expressed in these libraries is presented, providing a valuable resource of cDNA clones and sequence information that can be used for identification of new genes important for melanocyte development, function, and disease.

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