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01.12.2018 | Research | Ausgabe 1/2018 Open Access

Virology Journal 1/2018

MicroRNA transcriptome analysis of porcine vital organ responses to immunosuppressive porcine cytomegalovirus infection

Zeitschrift:
Virology Journal > Ausgabe 1/2018
Autoren:
Xiao Liu, Haoche Wei, Shan Liao, Jianheng Ye, Ling Zhu, Zhiwen Xu
Wichtige Hinweise

Electronic supplementary material

The online version of this article (https://​doi.​org/​10.​1186/​s12985-018-0922-x) contains supplementary material, which is available to authorized users.

Abstract

Background

Porcine cytomegalovirus (PCMV) is an immunosuppressive virus that mainly inhibits T-lymphocyte and macrophage immune functions; it has significantly damaged the farming industry. Although recent studies have shown that miRNAs play important roles in immune responses, the regulatory mechanisms of miRNAs during immunosuppressive virus infection remain unclear.

Methods

In this study, porcine small-RNA transcriptomes of PCMV-infected and uninfected vital organs were first characterised by high-throughput sequencing. miRDeep2 software was used to predict novel pig-encoded miRNAs. To verify the accuracy of the high-throughput sequencing results, stem-loop qRT-PCR was performed on 12 significantly DE miRNAs.
The physical and functional interactions between the immune-related target genes of the DE miRNAs in PCMV-infected organs were analysed using the STRING database.

Results

In total, 306 annotated and 295 novel miRNAs were identified from PCMV-infected and uninfected porcine organs, respectively, through alignment with known Sus scrofa pre-miRNAs. Overall, 92, 107, 95, 77 and 111 miRNAs were significantly differentially expressed in lung, liver, spleen, kidney and thymus after PCMV infection, respectively.
According to Gene Ontology enrichment analysis, target genes of the differentially expressed miRNAs associated with immune system processes, regulation of biological processes and metabolic processes were enriched in every sample. Integrated expression analysis of the differentially expressed miRNAs and their target mRNAs in PCMV-infected thymus showed that the significant differential expression of specific miRNAs under the pressure of PCMV infection in central immune organs interfered with the expression of genes involved in important immune-related signalling pathways, thus promoting the viral infection.

Conclusions

This is the first comprehensive analysis of the responses of host small-RNA transcriptomes to PCMV infection in vital porcine organs. It provides new insights into the regulatory mechanisms of miRNAs during infection by immunosuppressive viruses.
Zusatzmaterial
Additional file 1: Figure S1. Length distribution of total sRNAs. Figure S2. Pie charts of sRNA percentages. Figure S3. Top 10 miRNA reads. Figure S4. GO functional enrichment annotations for the target genes of DE miRNAs. Table S1. Overview of miRNA high-throughput sequencing data. Table S2. Expression profiles of miRNAs. Table S3. Differentially expressed miRNAs. Table S4. Target prediction for DE miRNAs. Table S5. Integrated expression analysis of DE miRNAs and their target mRNA. Table S6. DE miRNAs in vivo and vitro under viral infection. Table S7. Primers used for stem-loop qRT-PCR. (DOCX 2983 kb)
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