Identification of differentially expressed miRNAs in chicken lung and trachea with avian influenza virus infection by a deep sequencing approach

Total RNAs were isolated from lung and trachea of low pathogenic H5N3 infected and non-infected SPF chickens at 4 days post-infection. A total of 278,398 and 340,726 reads were obtained from lung and trachea, respectively. And 377 miRNAs were detected in lungs and 149 in tracheae from a total of 474 distinct chicken miRNAs available at the miRBase, respectively. Seventy-three and thirty-six miRNAs were differentially expressed between infected and non-infected chickens in lungs and tracheae, respectively. There were more miRNAs highly expressed in non-infected tissues than in infected tissues. Interestingly, some of these differentially expressed miRNAs, including miR-146, have been previously reported to be associated with immune-related signal pathways in mammals.To our knowledge, this is the first study on miRNA gene expression in AIV infected chickens using a deep sequencing approach. During AIV infection, many host miRNAs were differentially regulated, supporting the hypothesis that certain miRNAs might be essential in the host-pathogen interactions. Elucidation of the mechanism of these miRNAs on the regulation of host-AIV interaction will lead to the development of new control strategies to prevent or treat AIV infections in poultry.Avian influenza virus (AIV) is a type A virus of the family Orthomyxovirida. Although wild aquatic birds such as water fowls and sea gulls are their natural reservoir [1], land-based birds including chickens may also be infected, which cause significant economic losses to the poultry industry, and raise a great public health threat due to potential host jump from animals to humans [2].miRNAs are non-coding, single-stranded RNAs of 19~23 nucleotides which represent a novel class of gene regulators and play important roles in a variety of biological processes in both plants and animals [3-5]. miRNAs modulate gene expression largely at the post-transcriptional level by different mechanisms including direct cleavage of targeted mRNAs