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Sample Preparation and Analysis of RNASeq-based Gene Expression Data from Zebrafish
Published on: October 27, 2017
Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection
Rune Andreassen1, Nardos Tesfaye Woldemariam2, Ine Østråt Egeland2
1Department of Pharmacy and Biomedical and Laboratory Sciences, Faculty of Health Sciences, Oslo and Akershus University College of Applied Sciences, Pilestredet 50, N-0130, Oslo, Norway. Rune.Andreassen@hioa.no.
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:
This study represents the first steps in exploring miRNAs important in viral-host interaction in Atlantic salmon. We identified several miRNAs responding to SAV infection. Some likely to prohibit harmful inflammation while other may promote an early immune response. Their predicted functions need to be validated and further studied in functional assays to fully understand their roles in immune homeostasis.
Insights
Researchers identified microRNAs (miRNAs) responding to salmonid alphavirus (SAV) infection in Atlantic salmon. These miRNAs may regulate inflammation, potentially explaining differences in SAV-induced mortality rates.
Area of Science:
- Aquatic Animal Health
- Molecular Biology
- Immunology
Background:
- MicroRNAs (miRNAs) are crucial regulators of gene expression, particularly in innate immune responses.
- No prior studies investigated miRNA roles in Atlantic salmon viral diseases.
- Salmonid alphavirus (SAV) causes significant mortality in Atlantic salmon aquaculture.
Purpose of the Study:
- To identify differentially expressed miRNAs in Atlantic salmon following SAV infection.
- To analyze the temporal expression patterns of these miRNAs in response to different SAV isolates.
- To predict the target genes and regulatory mechanisms of identified miRNAs in the immune response.
Main Methods:
- Differential expression analysis of miRNAs at various time points post-SAV infection.
- Bioinformatic analysis of miRNA genome sequences for cis-regulatory elements.
- In silico prediction of miRNA target genes within immune network pathways.
Main Results:
- Twenty differentially expressed miRNAs (DE miRNAs) were identified, with varying temporal expression patterns.
- Seventeen DE miRNAs were predicted to target 24 SAV-responsive immune genes, including IRF3 and IRF7.
- Upstream sequences of miRNA genes showed binding sites for immune transcription factors, suggesting TF-mediated regulation.
Conclusions:
- This study is the first to explore miRNAs in Atlantic salmon's viral-host interactions.
- Identified miRNAs may play roles in either promoting early immune responses or inhibiting excessive inflammation.
- Further functional validation is required to elucidate the precise roles of these miRNAs in immune homeostasis and SAV pathogenesis.
