Single Base Resolution DNA Methylome Between Avian Influenza Virus Resistant and Susceptible Chickens

Avian influenza virus cause serious disease in a wide variety of birds and mammals.  To investigate whether avian influenza virus (AIV) will affect host epigenetic modification and identify DNA methylation differences between AIV resistant and susceptible breeds, we use genomic DNA bisulfite sequencing (BS-Seq) to compare DNA methylation between infected and non-infected AIV resistant (Fayoumi) and susceptible (Leghorn) chickens.

Here we report the first chicken whole-genome DNA methylation profile at single-base resolution. Total of 278.54 Gb sequences were generated from eight samples at four groups (2 samples per group).An average read depth of 15.2X for each sample were obtained after filtering. The bisulfite conversion rates for all samples were over 99%. Of all methylcytosins 96.24% were in the CG contexts, 0.86% in the CHG contexts and 2.89% in the CHH contexts. Most of mCG sites we obtained were highly methylated. Both absolute and relative methylation levels were higher within gene than 5’ upstream and 3’ downstream regions. Gene ontology analysis suggest that promoter unmethylated genes were enriched in binding and catalytic activity, and cellular and metabolic process, while promoter methylated genes were enriched in establishment of localization such as cell member and extracellular part, and transducer, transporter and receptor activity. Similar with other animals and plants, promoter DNA methylation and gene expression levels is negative correlation, but gene body methylation can increase gene expression. Our results indicate that DNA methylation is prevailing in chicken genome, and it plays an important role in gene expression regulation.