Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection

• Published in: BMC Genomics
• Main Authors: Rune Andreassen, Nardos Tesfaye Woldemariam, Ine Østråt Egeland, Oleg Agafonov, Hilde Sindre, Bjørn Høyheim
• Format: Article in Journal/Newspaper
• Language: English
• Published: BMC 2017
• Subjects: miRNA; Virus; Atlantic salmon; Innate immune response; Biotechnology; TP248.13-248.65; Genetics; QH426-470; Sav’
• Online Access: https://doi.org/10.1186/s12864-017-3741-3; https://doaj.org/article/e3603a2c2100485aad70ffc5a710a3f4

Abstract Background MicroRNAs (miRNAs) control multiple biological processes including the innate immune responses by negative post-transcriptional regulation of gene expression. As there were no studies on the role(s) of miRNAs in viral diseases in Atlantic salmon, we aimed to identify miRNAs responding to salmonid alphavirus (SAV) infection. Their expression were studied at different time points post infection with SAV isolates associated with different mortalities. Furthermore, the genome sequences of the identified miRNAs were analysed to reveal putative cis-regulatory elements, and, finally, their putative target genes were predicted. Results Twenty differentially expressed miRNAs (DE miRNAs) were identified. The expression of the majority of these increased post infection with maximum levels reached after the viral load were stabilized or decreasing. On the other hand, some miRNAs (e.g. the miRNA-21 family) showed decreased expression at the early time points post infection. There were significant differences in the temporal expression of individual miRNA associated with different SAV isolates. Target gene prediction in SAV responsive immune network genes showed that seventeen of the DE miRNAs could target 24 genes (e.g. IRF3, IRF7). Applying the Atlantic salmon transcriptome as input 28 more immune network genes were revealed as putative targets (e.g. IRF5, IRF4). The majority of the predicted target genes promote inflammatory response. The upstream sequences of the miRNA genes revealed a high density of cis-regulatory sequences known as binding sites for immune network transcription factors (TFs). A high expression in the late phase could therefore be due to increased transcription promoted by immune response activated TFs. Based on the in silico target predictions, we discuss their putative roles as early promotors or late inhibitors of inflammation. We propose that the differences in expressions associated with different SAV isolates could contribute to their differences in mortality rates. Conclusions ...