Genome-Wide Mapping of DNA Methylation in Chicken

Abstract

Cytosine DNA methylation is an important epigenetic modification termed as the fifth base that functions in diverse processes. Till now, the genome-wide DNA methylation maps of many organisms has been reported, such as human, Arabidopsis, rice and silkworm, but the methylation pattern of bird remains rarely studied. Here we show the genome-wide DNA methylation map of bird, using the chicken as a model organism and an immunocapturing approach followed by high-throughput sequencing. In both of the red jungle fowl and the avian broiler, DNA methylation was described separately for the liver and muscle tissue. Generally, chicken displays analogous methylation pattern with that of animals and plants. DNA methylation is enriched in the gene body regions and the repetitive sequences, and depleted in the transcription start site (TSS) and the transcription termination site (TTS). Most of the CpG islands in the chicken genome are kept in unmethylated state. Promoter methylation is negatively correlated with the gene expression level, indicating its suppressive role in regulating gene transcription. This work contributes to our understanding of epigenetics in birds.

Genome-Wide Epigenetic Studies in Chicken: A Review

“…This is consistent with the observation that average methylation patterns were the lowest in CpG islands that are localized in the promoters [75]. Slight methylation variations were observed along the gene body [74]. It was found that the methylation density in introns was higher than in untranslated transcribed regions (UTRs) and exons within the gene body [75].…”

“…These results followed the same trend as DNA methylation profile in human (for a review see [76]). Methylation level was shown to vary among tissues, the hepatic DNA of red jungle fowl being found to be less methylated than the one of the muscle [74]. This methylation variation between tissues could play a role in the regulation of gene expression during tissue differentiation [77].…”

“…In 2011, Li and colleagues provided the first global DNA methylation analysis in the liver and muscle tissues of red jungle fowl and avian broiler by MeDIP-seq [74]. They observed a decrease of DNA methylation level in the promoter region, especially at the transcription start site (TSS), and an increase in the gene body regions [74].…”

Evidence from pyrosequencing indicates that natural variation in animal personality is associated with DRD4 DNA methylation

“…This CGI contained a CG percentage of 73.5% and an observed to expected CpG ratio of 0.895. In mammals and chicken, approximately 50-65% of transcription starts sites (TSS) overlap with CGI predictions (Li et al 2011;Hu et al 2013;Long et al 2013), which is seen here for DRD4 too. However, the CGI in the great tit DRD4 shows features of both a TSS CGI but also gene body CGI as it overlaps TSS, exon 1 and part of intron 1.…”

Chicken domestication : Effects of tameness on brain gene expression and DNA methylation

“…The fact that WL but not RJF had a significant overlap between parental and offspring methylation patterns could also be an effect of the domestication process and importance of DNA methylation regulation on expression. The missing association between hypermethylation and downregulation of gene expression is puzzling, as previous studies have reported such correlations [157]. This could be explained by variation within promoters affecting interactions with methyl-CpG binding proteins in a complex manner [158].…”