Effects of Avian Influenza Virus Infection on the Transcriptome and the DNA Methylome in Two Genetically Distinct Chicken Lines using Next Generation Sequencing

Avian influenza virus (AIV) not only causes catastrophic losses to the commercial poultry industry, but also is a threat to human health. DNA methylation plays a significant role in gene regulation and disease. The objective of this study was to profile the host transcriptome and understand the effect of AIV infection on host DNA methylation in two genetically distinct highly inbred chicken lines (Fayoumi and Leghorn). Three-week old chickens were inoculated with 10⁷ EID50 of low-path H5N3 AIV, and lung and trachea were harvested four days later. Fayoumis had a significantly lower mean virus titer in the trachea than Leghorns (P < 0.05). Four cDNA lung library pools (infected and non-infected Leghorn, infected and non-infected Fayoumi) were prepared with 2 birds per pool, and sequenced by Illumina Genome Analyzer II, which yielded a total of 116 million reads of 75 bp. Gene expression levels of all annotated chicken genes were estimated using CLC Genomics Workbench. DESeq was used to identify differentially expressed transcripts between infected and non-infected birds (FDR < 0.05 and fold-change > 2). With AIV infection, there were 35 and 50 genes up-regulated, and 69 and 105 genes down-regulated, in Leghorn and Fayoumi birds, respectively. Host DNA methylation profiling at single-base resolution from the same eight birds were conducted. Identification of differentially methylated regions between infected and non-infected chickens is underway. Further analysis on the associations of chicken transcriptome and host DNA methylome will pave the way in understanding molecular mechanisms of genetic resistance to AIV infection in poultry.