Comparative epigenomic profiling of the DNA methylome in mouse and Zebrafish uncovers high interspecies divergence

Chi Zhang, Yujin Hoshida, Kirsten Sadler Edepli

    Research output: Contribution to journalArticle

    Abstract

    The DNA methylation landscape is dynamically patterned during development and distinct methylation patterns distinguish healthy from diseased cells. However, whether tissue-specific methylation patterns are conserved across species is not known. We used comparative methylome analysisof base-resolution DNA methylation profiles from the liver and brain ofmouse and zebrafish generated by reduced representation bisulfite sequencing to identify the conserved and divergent aspects of the methylome in these commonly used vertebrate model organisms. On average, 24% of CpGs are methylated in mouse livers and the pattern of methylation was highly concordant among four male mice from two different strains. The same level of methylation (24.2%) was identified in mouse brain. In striking contrast, zebrafish had 63 and 70% of CpG methylation in the liver and brain, respectively. This is attributed, in part, to the higher percentage of the zebrafish genome occupied by transposable elements (52% vs. 45%in mice). Thus, the species identity was more significant in determining methylome patterning than was the similarity in organ function. Conserved features of the methylome across tissues and species was the exclusion of methylation from promoters and from CpG islands near transcriptionstart sites, and the clustering of methylated CpGs in gene bodies and intragenic regions. These data suggest that DNA methylation reflects species-specific genome structure, and supports the notion that DNA methylation in non-promoter regions may contribute to genome evolution.

    Original languageEnglish (US)
    Article number110
    JournalFrontiers in Genetics
    Volume7
    Issue numberJUN
    DOIs
    StatePublished - Jun 17 2016

    Fingerprint

    DNA Fingerprinting
    Zebrafish
    Epigenomics
    Methylation
    DNA Methylation
    Genome
    Liver
    Brain
    Body Regions
    CpG Islands
    DNA Transposable Elements
    Cluster Analysis
    Vertebrates
    Genes

    Keywords

    • Brain
    • Comparative epigenomics
    • DNA methylation
    • Liver
    • Mouse
    • Zebrafish

    ASJC Scopus subject areas

    • Molecular Medicine
    • Genetics
    • Genetics(clinical)

    Cite this

    Comparative epigenomic profiling of the DNA methylome in mouse and Zebrafish uncovers high interspecies divergence. / Zhang, Chi; Hoshida, Yujin; Sadler Edepli, Kirsten.

    In: Frontiers in Genetics, Vol. 7, No. JUN, 110, 17.06.2016.

    Research output: Contribution to journalArticle

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