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.
Highlights
DNA methylation is a stable epigenetic modification found in most of the eukaryotes that plays a crucial role in many biological processes, including gene expression regulation, gene imprinting and transposon silencing in mammals and plants [1,2,3]
A range of 17,202,074 to 27,501,760 raw reads were generated for the four samples respectively and more than 85% of the reads were mapped and about 65% of the reads in each sample were uniquely mapped to the chicken genome in each sample (Table 1)
We carried out bis-seq for 8 randomly selected regions in the chicken genome, and the bis-seq results were feckly consistent with the meDIP-seq results (Fig. 1B, Fig S1 and Fig S2)
Summary
DNA methylation is a stable epigenetic modification found in most of the eukaryotes that plays a crucial role in many biological processes, including gene expression regulation, gene imprinting and transposon silencing in mammals and plants [1,2,3]. Cytosine DNA methylation occurs mostly at the CpG dinucleotides except for the CpGs in CpG islands [4]. Many genome-wide DNA methylation profiles and their functional analysis have been reported, there is little knowledge about the DNA methylation patterns in birds [5,6,7,8,9]. There are many approaches to decipher a genome-wide DNA methylation profile, including methylated DNA immunoprecipitation-sequencing/chip (meDIP-seq/chip), bisulfite-sequencing (bis-seq) and some enzyme digestion based techniques. MeDIP uses an antibody which can recognizes methylated cytosines and pulls down the methylated fractions, MeDIP-chip was used to provide the first comprehensive DNA methylation map of an entire Arabidopsis thaliana genome [3]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
