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The porcine microRNA transcriptome response to transmissible gastroenteritis virus infection.

Liu X, Zhu L, Liao S, Xu Z, Zhou Y - PLoS ONE (2015)

Bottom Line: Certain miRNAs were differentially regulated during TGEV infection. 59 unique miRNAs displayed significant differentially expression between the normal and TGEV-infected ST cell samples: 15 miRNAs were significantly up-regulated and 44 were significantly down-regulated.Stem-loop RT-PCR was carried out to determine the expression levels of specific miRNAs in the two samples, and the results were consistent with those of sequencing.This is the first report of the identification of ST cell miRNAs and the comprehensive analysis of the miRNA regulatory mechanism during TGEV infection, which revealed the miRNA molecular regulatory mechanisms for the viral infection, expression of viral genes and the expression of immune-related genes.

View Article: PubMed Central - PubMed

Affiliation: Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya' an, China; Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.

ABSTRACT
Transmissible gastroenteritis virus (TGEV; Coronaviridae family) causes huge economic losses to the swine industry. MicroRNAs (miRNAs) play a regulatory role in viral infection and may be involved in the mammalian immune response. Here, we report a comprehensive analysis of host miRNA expression in TGEV-infected swine testis (ST) cells. Deep sequencing generated 3,704,353 and 2,763,665 reads from uninfected ST cells and infected ST cells, respectively. The reads were aligned to known Sus scrofa pre-miRNAs in miRBase 19, identifying 284 annotated miRNAs. Certain miRNAs were differentially regulated during TGEV infection. 59 unique miRNAs displayed significant differentially expression between the normal and TGEV-infected ST cell samples: 15 miRNAs were significantly up-regulated and 44 were significantly down-regulated. Stem-loop RT-PCR was carried out to determine the expression levels of specific miRNAs in the two samples, and the results were consistent with those of sequencing. Gene ontology enrichment analysis of host target genes demonstrated that the differentially expressed miRNAs are involved in regulatory networks, including cellular process, metabolic process, immune system process. This is the first report of the identification of ST cell miRNAs and the comprehensive analysis of the miRNA regulatory mechanism during TGEV infection, which revealed the miRNA molecular regulatory mechanisms for the viral infection, expression of viral genes and the expression of immune-related genes. The results presented here will aid research on the prevention and treatment of viral diseases.

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Differentially expressed miRNAs directly targeted the 3' UTR or 5' UTR of the TGEV genome.ssc-miR-28–3p, ssc-miR-126–5p and ssc-miR-30b-5p target the 3' UTR of the TGEV genome (28297 bp–28571 bp), ssc-miR-2411 target the 5' UTR of the TGEV genome (1 bp–303 bp).
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pone.0120377.g005: Differentially expressed miRNAs directly targeted the 3' UTR or 5' UTR of the TGEV genome.ssc-miR-28–3p, ssc-miR-126–5p and ssc-miR-30b-5p target the 3' UTR of the TGEV genome (28297 bp–28571 bp), ssc-miR-2411 target the 5' UTR of the TGEV genome (1 bp–303 bp).

Mentions: The putative target genes of the 59 differentially expressed miRNAs (miRBase annotated) and 241 novel miRNAs were predicted using on-line miRNA target prediction tools to probe the biological roles of the miRNAs (S3 Table). To predict the putative TGEV targets for the differentially expressed miRNAs, the miRNA target gene database miRGen 3.0 was used with stringent criteria. The results showed that some of the differentially expressed miRNAs directly targeted the 3' UTR or 5' UTR of the TGEV genome: ssc-miR-28–3p, ssc-miR-126–5p and ssc-miR-30b-5p target the 3' UTR (28297 bp–28571 bp) and ssc-miR-2411 and chrX-16275 target the 5' UTR (1 bp–303 bp) (Fig. 5). This study also found a series of miRNAs that target host-encoded pre-miRNAs; for example, ssc-miR-9, ssc-miR-19a, ssc-miR-142–5p, ssc-miR-134 and ssc-miR-20c-5p all target ssc-mir-21. GO annotation was performed for the target genes of five designated differentially expressed miRNAs (miR-146b, miR-155–5p, miR-195, miR-124a and miR-1306–5p). The results showed that the differential expressed miRNAs and their target genes constituted a complex regulatory network: multiple miRNAs were linked through their common target genes. This complex regulatory network could regulate the expression of multiple genes through one miRNA, but could also regulate the expression of certain genes through several miRNAs in combination (S1 Fig. and S2 Fig.). For example, the significantly differentially expressed miRNAs, miR-9, miR-9–1 and miR-9–2 all target IL12A, but the immune-related gene IL7R was individually regulated by miR-140–3p. The in-depth analysis of the miRNA regulatory mechanism in gene expression will contribute to our understanding of the complexity of eukaryote genomes and gene regulatory networks.


The porcine microRNA transcriptome response to transmissible gastroenteritis virus infection.

Liu X, Zhu L, Liao S, Xu Z, Zhou Y - PLoS ONE (2015)

Differentially expressed miRNAs directly targeted the 3' UTR or 5' UTR of the TGEV genome.ssc-miR-28–3p, ssc-miR-126–5p and ssc-miR-30b-5p target the 3' UTR of the TGEV genome (28297 bp–28571 bp), ssc-miR-2411 target the 5' UTR of the TGEV genome (1 bp–303 bp).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4363316&req=5

pone.0120377.g005: Differentially expressed miRNAs directly targeted the 3' UTR or 5' UTR of the TGEV genome.ssc-miR-28–3p, ssc-miR-126–5p and ssc-miR-30b-5p target the 3' UTR of the TGEV genome (28297 bp–28571 bp), ssc-miR-2411 target the 5' UTR of the TGEV genome (1 bp–303 bp).
Mentions: The putative target genes of the 59 differentially expressed miRNAs (miRBase annotated) and 241 novel miRNAs were predicted using on-line miRNA target prediction tools to probe the biological roles of the miRNAs (S3 Table). To predict the putative TGEV targets for the differentially expressed miRNAs, the miRNA target gene database miRGen 3.0 was used with stringent criteria. The results showed that some of the differentially expressed miRNAs directly targeted the 3' UTR or 5' UTR of the TGEV genome: ssc-miR-28–3p, ssc-miR-126–5p and ssc-miR-30b-5p target the 3' UTR (28297 bp–28571 bp) and ssc-miR-2411 and chrX-16275 target the 5' UTR (1 bp–303 bp) (Fig. 5). This study also found a series of miRNAs that target host-encoded pre-miRNAs; for example, ssc-miR-9, ssc-miR-19a, ssc-miR-142–5p, ssc-miR-134 and ssc-miR-20c-5p all target ssc-mir-21. GO annotation was performed for the target genes of five designated differentially expressed miRNAs (miR-146b, miR-155–5p, miR-195, miR-124a and miR-1306–5p). The results showed that the differential expressed miRNAs and their target genes constituted a complex regulatory network: multiple miRNAs were linked through their common target genes. This complex regulatory network could regulate the expression of multiple genes through one miRNA, but could also regulate the expression of certain genes through several miRNAs in combination (S1 Fig. and S2 Fig.). For example, the significantly differentially expressed miRNAs, miR-9, miR-9–1 and miR-9–2 all target IL12A, but the immune-related gene IL7R was individually regulated by miR-140–3p. The in-depth analysis of the miRNA regulatory mechanism in gene expression will contribute to our understanding of the complexity of eukaryote genomes and gene regulatory networks.

Bottom Line: Certain miRNAs were differentially regulated during TGEV infection. 59 unique miRNAs displayed significant differentially expression between the normal and TGEV-infected ST cell samples: 15 miRNAs were significantly up-regulated and 44 were significantly down-regulated.Stem-loop RT-PCR was carried out to determine the expression levels of specific miRNAs in the two samples, and the results were consistent with those of sequencing.This is the first report of the identification of ST cell miRNAs and the comprehensive analysis of the miRNA regulatory mechanism during TGEV infection, which revealed the miRNA molecular regulatory mechanisms for the viral infection, expression of viral genes and the expression of immune-related genes.

View Article: PubMed Central - PubMed

Affiliation: Animal Biotechnology Center, College of Veterinary Medicine, Sichuan Agricultural University, Ya' an, China; Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America.

ABSTRACT
Transmissible gastroenteritis virus (TGEV; Coronaviridae family) causes huge economic losses to the swine industry. MicroRNAs (miRNAs) play a regulatory role in viral infection and may be involved in the mammalian immune response. Here, we report a comprehensive analysis of host miRNA expression in TGEV-infected swine testis (ST) cells. Deep sequencing generated 3,704,353 and 2,763,665 reads from uninfected ST cells and infected ST cells, respectively. The reads were aligned to known Sus scrofa pre-miRNAs in miRBase 19, identifying 284 annotated miRNAs. Certain miRNAs were differentially regulated during TGEV infection. 59 unique miRNAs displayed significant differentially expression between the normal and TGEV-infected ST cell samples: 15 miRNAs were significantly up-regulated and 44 were significantly down-regulated. Stem-loop RT-PCR was carried out to determine the expression levels of specific miRNAs in the two samples, and the results were consistent with those of sequencing. Gene ontology enrichment analysis of host target genes demonstrated that the differentially expressed miRNAs are involved in regulatory networks, including cellular process, metabolic process, immune system process. This is the first report of the identification of ST cell miRNAs and the comprehensive analysis of the miRNA regulatory mechanism during TGEV infection, which revealed the miRNA molecular regulatory mechanisms for the viral infection, expression of viral genes and the expression of immune-related genes. The results presented here will aid research on the prevention and treatment of viral diseases.

Show MeSH
Related in: MedlinePlus