Abstract
BackgroundDNA 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.MethodsThe 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.ResultsThe 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2098-8) contains supplementary material, which is available to authorized users.
Highlights
DNA cytosine methylation is an important epigenetic modification that has significant effects on a variety of biological processes in animals
To validate MethylC-seq results, we randomly examined methylation level of 165 mCGs, 61 mCHHs and 42 mCHGs using bisulphite PCR sequencing (BS-PCR)
We found that in the differentially methylated regions (DMR), the methylation level of Fayoumi was higher than Leghorn and the BS-PCR validation result displayed an even more pronounced difference
Summary
DNA cytosine methylation is an important epigenetic modification that has significant effects on a variety of biological processes in animals. DNA methylation is a central epigenetic modification that occurs in most eukaryotic organisms and plays a crucial role in transcriptional regulation. This epigenetic mark is involved in many cellular processes, including embryogenesis, transposon silencing, genomic imprinting, X chromosome inactivation, and tumorigenesis [1,2,3]. Of the many approaches to profile genome-wide DNA methylation patterns, MethylC-seq is considered the current “gold standard” [4, 5]. Single-base resolution DNA cytosine methylome maps for Arabidopsis, human, silkworm, and chicken have been generated by MethylC-seq [3, 6,7,8,9]
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