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Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq
- Source :
- BMC genomics, vol 16, iss 1, BMC Genomics
- Publication Year :
- 2015
- Publisher :
- Springer Science and Business Media LLC, 2015.
-
Abstract
- Background 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. Methods 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. Results 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. Conclusions 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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2098-8) contains supplementary material, which is available to authorized users.
- Subjects :
- Epigenomics
Bisulfite sequencing
Medical and Health Sciences
Repetitive Sequences
Epigenesis, Genetic
MethylC-seq
2.1 Biological and endogenous factors
Aetiology
Promoter Regions, Genetic
Lung
Regulation of gene expression
Genetics
Base Composition
Genome
DNA methylation
High-Throughput Nucleotide Sequencing
Methylation
Biological Sciences
Epigenetics
Pseudogenes
Research Article
Biotechnology
Evolution
Bioinformatics
Biology
Evolution, Molecular
Promoter Regions
Genetic
Information and Computing Sciences
Animals
Gene
Repetitive Sequences, Nucleic Acid
Nucleic Acid
Gene Expression Profiling
Human Genome
Immunity
Computational Biology
Molecular
Molecular Sequence Annotation
Differentially methylated regions
Gene Expression Regulation
CpG Islands
Generic health relevance
Transcriptome
Chickens
Epigenesis
Genome-Wide Association Study
Subjects
Details
- ISSN :
- 14712164
- Volume :
- 16
- Database :
- OpenAIRE
- Journal :
- BMC Genomics
- Accession number :
- edsair.doi.dedup.....377a897b462ee264c5f4752b90a09498