A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo

Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Osamu Ohara, Takashi Kuramoto, Mikita Suyama

    Research output: Contribution to journalArticle

    2 Citations (Scopus)

    Abstract

    Background: Head spot is one of the phenotypes identified in the KFRS4/Kyo rat strain. Although previous linkage analysis suggested that Ednrb, which is frequently involved in coat color variations in various animals, could be the gene responsible for this phenotype, no mutations have been identified in its coding region. Results: To identify mutations causative of this phenotype in KFRS4/Kyo, we analyzed target capture sequencing data that we recently generated. Our target capture method has a unique feature, i.e., it covers not only exonic regions but also conserved non-coding sequences (CNSs) among vertebrates; therefore, it has the potential to detect regulatory mutations. We identified a deletion of approximately 50kb in length approximately 50kb upstream of Ednrb. A comparative analysis with the epigenomic data in the corresponding region in humans and mice showed that one of the CNSs might be an enhancer. Further comparison with Hi-C data, which provide information about chromosome conformation, indicated that the putative enhancer is spatially close to the promoter of Ednrb, suggesting that it acts as an enhancer of Ednrb. Conclusions: These in silico data analyses strongly suggest that the identified deletion in the intergenic region upstream of Ednrb, which might contain a melanocyte-specific enhancer, is the mutation causative of the head spot phenotype in the KFRS4/Kyo rat strain.

    Original languageEnglish
    Article number29
    JournalBMC Genetics
    Volume18
    Issue number1
    DOIs
    Publication statusPublished - Mar 29 2017

    Fingerprint

    Intergenic DNA
    Head
    Phenotype
    Mutation
    Melanocytes
    Epigenomics
    Computer Simulation
    Vertebrates
    Color
    Chromosomes
    Genes

    All Science Journal Classification (ASJC) codes

    • Genetics
    • Genetics(clinical)

    Cite this

    A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo. / Yoshihara, Minako; Sato, Tetsuya; Saito, Daisuke; Ohara, Osamu; Kuramoto, Takashi; Suyama, Mikita.

    In: BMC Genetics, Vol. 18, No. 1, 29, 29.03.2017.

    Research output: Contribution to journalArticle

    Yoshihara, Minako ; Sato, Tetsuya ; Saito, Daisuke ; Ohara, Osamu ; Kuramoto, Takashi ; Suyama, Mikita. / A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo. In: BMC Genetics. 2017 ; Vol. 18, No. 1.
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    abstract = "Background: Head spot is one of the phenotypes identified in the KFRS4/Kyo rat strain. Although previous linkage analysis suggested that Ednrb, which is frequently involved in coat color variations in various animals, could be the gene responsible for this phenotype, no mutations have been identified in its coding region. Results: To identify mutations causative of this phenotype in KFRS4/Kyo, we analyzed target capture sequencing data that we recently generated. Our target capture method has a unique feature, i.e., it covers not only exonic regions but also conserved non-coding sequences (CNSs) among vertebrates; therefore, it has the potential to detect regulatory mutations. We identified a deletion of approximately 50kb in length approximately 50kb upstream of Ednrb. A comparative analysis with the epigenomic data in the corresponding region in humans and mice showed that one of the CNSs might be an enhancer. Further comparison with Hi-C data, which provide information about chromosome conformation, indicated that the putative enhancer is spatially close to the promoter of Ednrb, suggesting that it acts as an enhancer of Ednrb. Conclusions: These in silico data analyses strongly suggest that the identified deletion in the intergenic region upstream of Ednrb, which might contain a melanocyte-specific enhancer, is the mutation causative of the head spot phenotype in the KFRS4/Kyo rat strain.",
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    AU - Saito, Daisuke

    AU - Ohara, Osamu

    AU - Kuramoto, Takashi

    AU - Suyama, Mikita

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