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. 2017 Mar 4;14(1):45.
doi: 10.1186/s12985-017-0718-4.

Transcriptional profiling of host cell responses to encephalomyocarditis virus (EMCV)

Jia Wei  1   2 , Haixia Zhang  1 , Xiangrong Li  1 , Qiongyi Li  1   2 , Zhongren Ma  3 , Jialin Bai  3 , Zilin Qiao  3 , Ruofei Feng  4   5
Affiliations

Transcriptional profiling of host cell responses to encephalomyocarditis virus (EMCV)

Jia Wei et al. Virol J. .

Abstract

Backgroud: Encephalomyocarditis virus (EMCV) has been discovered on pig farms worldwide and can cause myocarditis in piglets and reproductive failure in sows. However, little is known about the host transcriptional responses to infection and host-pathogen interactions.

Methods: In this study, transcription profiling was performed by Illumina RNA-Sequencing (RNA-seq) to identify EMCV induced differentially expressed genes in BHK-21 cells at serial time points (12, 24, and 30 h post infection (hpi)), using mock infected cells as control.

Results: We identified 237, 241, and 207 differentially expressed genes (DEGs) respectively, majority of which were up-regulated. A large number of DEGs clustered into host defense, cellular signaling and metabolism categories. Moreover, short time series expression analysis revealed that 12 hpi was an important time point for expression change, indicating host virus resistance.

Conclusions: This RNA-seq analysis provides the first data for understanding the network of virus host interactions under EMCV infection in vitro, and for identifying host components which involved in the virus infection course.

Keywords: Encephalomyocarditis virus (EMCV); Host transcriptional responses; Transcriptome analysis.

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Figures

Fig. 1
Fig. 1
Quantification of EMCV RNA copies in infected BHK-21 cells. Numbers of EMCV RNA copies in infected BHK-21 cells at 12, 24, and 30 hpi were determined by Real-time quantitative PCR
Fig. 2
Fig. 2
GO annotation of DEGs at 30 h after EMCV infection. The x-axis represents the functional groups, while the y-axis represents the number of genes
Fig. 3
Fig. 3
KEGG enrichment analysis of DEGs at 30 h after EMCV infection. The x-axis represents the enrichment factor, while y-axis represents enrichment KEGG pathways
Fig. 4
Fig. 4
STEM analysis of short time series gene expression during EMCV infection. The number in each profile box represents the profile ID number. Statistically significant temporal expression profiles are highlighted in color (P < 0.05). Non-white profiles of the same color grouped together based on similarity to form a single cluster. Four time points are 0, 12, 24, and 30 h post infection
Fig. 5
Fig. 5
Relative Quantification of DEGs by real-time PCR for verification. Real-time PCR relative expression levels of selected genes (purple) at 30 hpi were compared with RNA-seq data (pink) at the same time point. The x-axis represents DEGs, while y-axis represents normalized fold changes of transcripts
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