Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection
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 respo...
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ftdatacite:10.6084/m9.figshare.c.3772061 2023-05-15T15:31:01+02:00 Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection Andreassen, Rune Nardos Woldemariam Egeland, Ine Agafonov, Oleg Sindre, Hilde Høyheim, Bjørn 2017 https://dx.doi.org/10.6084/m9.figshare.c.3772061 https://figshare.com/collections/Identification_of_differentially_expressed_Atlantic_salmon_miRNAs_responding_to_salmonid_alphavirus_SAV_infection/3772061 unknown Figshare https://dx.doi.org/10.1186/s12864-017-3741-3 CC BY https://creativecommons.org/licenses/by/4.0 CC-BY Biophysics Microbiology FOS Biological sciences Genetics Molecular Biology Ecology Immunology FOS Clinical medicine 69999 Biological Sciences not elsewhere classified Infectious Diseases FOS Health sciences Computational Biology Collection article 2017 ftdatacite https://doi.org/10.6084/m9.figshare.c.3772061 https://doi.org/10.1186/s12864-017-3741-3 2021-11-05T12:55:41Z 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 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. Article in Journal/Newspaper Atlantic salmon DataCite Metadata Store (German National Library of Science and Technology) Sav’ ENVELOPE(156.400,156.400,68.817,68.817) |
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Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Biophysics Microbiology FOS Biological sciences Genetics Molecular Biology Ecology Immunology FOS Clinical medicine 69999 Biological Sciences not elsewhere classified Infectious Diseases FOS Health sciences Computational Biology |
spellingShingle |
Biophysics Microbiology FOS Biological sciences Genetics Molecular Biology Ecology Immunology FOS Clinical medicine 69999 Biological Sciences not elsewhere classified Infectious Diseases FOS Health sciences Computational Biology Andreassen, Rune Nardos Woldemariam Egeland, Ine Agafonov, Oleg Sindre, Hilde Høyheim, Bjørn Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection |
topic_facet |
Biophysics Microbiology FOS Biological sciences Genetics Molecular Biology Ecology Immunology FOS Clinical medicine 69999 Biological Sciences not elsewhere classified Infectious Diseases FOS Health sciences Computational Biology |
description |
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 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. |
format |
Article in Journal/Newspaper |
author |
Andreassen, Rune Nardos Woldemariam Egeland, Ine Agafonov, Oleg Sindre, Hilde Høyheim, Bjørn |
author_facet |
Andreassen, Rune Nardos Woldemariam Egeland, Ine Agafonov, Oleg Sindre, Hilde Høyheim, Bjørn |
author_sort |
Andreassen, Rune |
title |
Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection |
title_short |
Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection |
title_full |
Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection |
title_fullStr |
Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection |
title_full_unstemmed |
Identification of differentially expressed Atlantic salmon miRNAs responding to salmonid alphavirus (SAV) infection |
title_sort |
identification of differentially expressed atlantic salmon mirnas responding to salmonid alphavirus (sav) infection |
publisher |
Figshare |
publishDate |
2017 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.3772061 https://figshare.com/collections/Identification_of_differentially_expressed_Atlantic_salmon_miRNAs_responding_to_salmonid_alphavirus_SAV_infection/3772061 |
long_lat |
ENVELOPE(156.400,156.400,68.817,68.817) |
geographic |
Sav’ |
geographic_facet |
Sav’ |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
https://dx.doi.org/10.1186/s12864-017-3741-3 |
op_rights |
CC BY https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.3772061 https://doi.org/10.1186/s12864-017-3741-3 |
_version_ |
1766361507396845568 |