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Genome-Wide DNA Methylome Variation in Two Genetically Distinct Chicken Lines Using MethylC-Seq
BMC Genomics
  • Jinxiu Li, China Agricultural University
  • Rujiao Li, Chinese Academy of Sciences
  • Ying Wang, University of California - Davis
  • Xiaoxiang Hu, China Agricultural University
  • Yiqiang Zhao, China Agricultural University
  • Li LI, China Agricultural University
  • Chungang Feng, China Agricultural University
  • Xiaorong Gu, China Agricultural University
  • Fang Liang, Chinese Academy of Sciences
  • Susan J. Lamont, Iowa State University
  • Songnian Hu, Chinese Academy of Sciences
  • Huaijun Zhou, University of California - Davis
  • Ning Li, China Agricultural University
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DNA cytosine methylation is an important epigenetic modification that has significant effects on a variety of biological processes in animals. Avian species hold a crucial position in evolutionary history. In this study, we used whole-genome bisulfite sequencing (MethylC-seq) to generate single base methylation profiles of lungs in two genetically distinct and highly inbred chicken lines (Fayoumi and Leghorn) that differ in genetic resistance to multiple pathogens, and we explored the potential regulatory role of DNA methylation associated with immune response differences between the two chicken lines. The MethylC-seq was used to generate single base DNA methylation profiles of Fayoumi and Leghorn birds. In addition, transcriptome profiling using RNA–seq from the same chickens and tissues were obtained to interrogate how DNA methylation regulates gene transcription on a genome-wide scale. The general DNA methylation pattern across different regions of genes was conserved compared to other species except for hyper-methylation of repeat elements, which was not observed in chicken. The methylation level of miRNA and pseudogene promoters was high, which indicates that silencing of these genes may be partially due to promoter hyper-methylation. Interestingly, the promoter regions of more recently evolved genes tended to be more highly methylated, whereas the gene body regions of evolutionarily conserved genes were more highly methylated than those of more recently evolved genes. Immune-related GO (Gene Ontology) terms were significantly enriched from genes within the differentially methylated regions (DMR) between Fayoumi and Leghorn, which implicates DNA methylation as one of the regulatory mechanisms modulating immune response differences between these lines. This study establishes a single-base resolution DNA methylation profile of chicken lung and suggests a regulatory role of DNA methylation in controlling gene expression and maintaining genome transcription stability. Furthermore, profiling the DNA methylomes of two genetic lines that differ in disease resistance provides a unique opportunity to investigate the potential role of DNA methylation in host disease resistance. Our study provides a foundation for future studies on epigenetic modulation of host immune response to pathogens in chickens.

This article is from BMC Genomics 16 (2015): 851, doi:10.1186/s12864-015-2098-8. Posted with permission.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Jinxiu Li, et al.
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Jinxiu Li, Rujiao Li, Ying Wang, Xiaoxiang Hu, et al.. "Genome-Wide DNA Methylome Variation in Two Genetically Distinct Chicken Lines Using MethylC-Seq" BMC Genomics Vol. 16 (2015) p. 1 - 13
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