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Examination of whole genome DNA methylation status of two chicken breeds


ABSTRACT: We report the genome-wide DNA methylation mapping of chicken by methylated DNA immunoprecipitation following by highthroughput sequencing, and the gene expression profile of chicken by RNA-seq. For meDIP-seq, about 17,202,074 to 27,501,760 reads were generated for the tissue and liver tissues of the red jungle fowl and the avian broiler each. We found that compared with the red jungle fowl, DNA methylation in muscle tissue of the avian broiler, showed dramatically decline on a genome-wide scale. Furthermore, the length of the highly methylated regions (HMRs) has become shorter in the avian broiler, which has suffered intense artificial selection. In addition to the global changes in DNA methylation, transcriptome-wide analysis of the two breeds of chicken revealed that the patterns of gene expression in the domestic chicken have undergone a specific bias towards a pattern that is more suited to human-made environments with variable expression in certain gene functions, such as immune response and fatty acid metabolism. Our results demonstrated a potential role of epigenetic modification in animal domestication besides the genetic variations. Overall design: Examination of whole genome DNA methylation status in liver and muscle of two chicken breeds.

INSTRUMENT(S): Illumina Genome Analyzer (Gallus gallus)

ORGANISM(S): Gallus gallus  

SUBMITTER: qinghe li   

PROVIDER: GSE21167 | GEO |

SECONDARY ACCESSION(S): PRJNA129665

REPOSITORIES: GEO

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