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BMC Genomics. 2020 Feb 4;21(1):123. doi: 10.1186/s12864-020-6539-7.

Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings.

Wu F1,2, Lu F1,2, Fan X1,3, Chao J1,4, Liu C1,2, Pan Q1,2, Sun H1,2, Zhang X5,6.

Author information

1
Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China.
2
Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, China.
3
Academy of Animal Sciences, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet Province, China.
4
College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui Province, China.
5
Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu Province, China. xiaofei0804@sina.com.
6
Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing, Jiangsu Province, China. xiaofei0804@sina.com.

Abstract

BACKGROUND:

Duck hepatitis A virus type 3 (DHAV-3) is one of the most harmful pathogens in the duck industry. However, the molecular mechanism underlying DHAV-3 infection in ducklings remains poorly understood. To study the genetic regulatory network for miRNA-mRNA and the signaling pathways involved in DHAV-3 infection in ducklings, we conducted global miRNA and mRNA expression profiling of duckling liver tissues infected with lethal DHAV-3 by high-throughput sequencing.

RESULTS:

We found 156 differentially expressed miRNAs (DEMs) and 7717 differentially expressed genes (DEGs) in livers of mock-infected and DHAV-3-infected duckling. A total of 19,606 miRNA-mRNA pairs with negatively correlated expression patterns were identified in miRNA-mRNA networks constructed on the basis of these DEMs and DEGs. Moreover, immune-related pathways, including the cytokine-cytokine receptor interaction, apoptosis, Toll-like receptor, Jak-STAT, and RIG-I-like receptor signaling pathway, were significantly enriched through analyzing functions of mRNAs in the network in response to DHAV-3 infection. Furthermore, apl-miR-32-5p, apl-miR-125-5p, apl-miR-128-3p, apl-miR-460-5p, and novel-m0012-3p were identified as potential regulators in the immune-related signaling pathways during DHAV-3 infection. And some host miRNAs were predicted to target the DHAV-3 genome.

CONCLUSIONS:

This is the first integrated analysis of miRNA and mRNA in DHAV-3-infected ducklings. The results indicated the important roles of miRNAs in regulating immune response genes and revealed the immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver. These findings increase our knowledge of the roles of miRNAs and their target genes in DHAV-3 replication and pathogenesis. They also aid in the understanding of host-virus interactions.

KEYWORDS:

Duck hepatitis a virus type 3; Host-virus interactions; Innate immune response; Transcriptome; miRNA; miRNA-mRNA network

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