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

Ying Wang1, Vinayak Brahmakshatriya1, Huifeng Zhu2, Blanca Lupiani3, Sanjay M Reddy3, Byung-Jun Yoon4, Preethi H Gunaratne2, Jong Hwan Kim2, Rui Chen5, Junjun Wang6 and Huaijun Zhou1*

Author Affiliations

1 Department of Poultry Science, Texas A&M University College Station, TX 77843-2472, USA

2 Department of Biology & Biochemistry, University of Houston, Houston, TX 77204, USA

3 Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843-4467, USA

4 Department of Electrical and Computer Engineering, Texas A&M University College Station, TX 77840, USA

5 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston 77030, TX, USA

6 State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing, 100193, PR China

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BMC Genomics 2009, 10:512  doi:10.1186/1471-2164-10-512

Published: 5 November 2009



MicroRNAs (miRNAs) play critical roles in a wide spectrum of biological processes and have been shown to be important effectors in the intricate host-pathogen interaction networks. Avian influenza virus (AIV) not only causes significant economic losses in poultry production, but also is of great concern to human health. The objective of this study was to identify miRNAs associated with AIV infections in chickens.


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.