scholarly journals Genome-Wide DNA Methylome and Transcriptome Analysis of Porcine Testicular Cells Infected With Transmissible Gastroenteritis Virus

2022 ◽  
Vol 8 ◽  
Author(s):  
Jiayun Wu ◽  
Xiaoru Shi ◽  
Lisi Wu ◽  
Zhengchang Wu ◽  
Shenglong Wu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Ribosome Biogenesis ◽  
Transmissible Gastroenteritis Virus ◽  
Whole Genome Analysis ◽  
Testicular Cells ◽  
Gastroenteritis Virus ◽  
Expression Of Genes ◽  
Suckling Piglets ◽  
Transmissible Gastroenteritis ◽  
Methylation Patterns

Transmissible gastroenteritis virus (TGEV) is a porcine pathogen causing highly communicable gastrointestinal infection that are lethal for suckling piglets. In an attempt to delineate the pathogenic mechanism of TGEV-infected porcine testicular cells (ST cells), we conducted a whole genome analysis of DNA methylation and expression in ST cells through reduced bisulfate-seq and RNA-seq. We examined alterations in the methylation patterns and recognized 1764 distinct methylation sites. 385 differentially expressed genes (DEGs) were enriched in the viral defense and ribosome biogenesis pathways. Integrative analysis identified two crucial genes (EMILIN2, RIPOR3), these two genes expression were negatively correlated to promoter methylation. In conclusion, alterations in DNA methylation and differential expression of genes reveal that their potential functional interactions in TGEV infection. Our data highlights the epigenetic and transcriptomic landscapes in TGEV-infected ST cells and provides a reliable dataset for screening TGEV resistance genes and genetic markers.

scholarly journals Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection

2019 ◽  
Author(s):  
Xuelian Ma ◽  
Xiaomin Zhao ◽  
Kaili Wang ◽  
Xiaoyi Tang ◽  
Jianxiong Guo ◽  
...  
Keyword(s):  
Inflammatory Response ◽  
Messenger Rna ◽  
Binding Proteins ◽  
Differentially Expressed ◽  
Transmissible Gastroenteritis Virus ◽  
Intestinal Epithelial ◽  
Antisense Gene ◽  
Gastroenteritis Virus ◽  
Expression Of Genes ◽  
Transmissible Gastroenteritis

Abstract Abstract Background: Transmissible gastroenteritis virus (TGEV) infection can cause acute inflammation. Long noncoding RNAs (lncRNAs) play important roles in a number of biological process including inflammation response. However, whether lncRNAs participate in TGEV-induced inflammation in porcine intestinal epithelial cells (IPECs) is largely unknown. Results: In this study, the next-generation sequencing (NGS) technology was used to analyze the profiles of lncRNAs in Mock and TGEV-infected porcine intestinal epithelial cell-jejunum 2 (IPEC-J2) cell line. A total of 106 lncRNAs were differentially expressed. Many differentially expressed lncRNAs act as elements to competitively attach microRNAs (miRNAs) which target to messenger RNA (mRNAs ) to mediate expression of genes that related to Toll-like receptors (TLRs), NOD-like receptors (NLRs), Tumor necrosis factor (TNF), and RIG-I-like receptor s (RLRs) pathways. Functional analysis of the binding proteins and the up/down-stream genes of the differentially expressed lncRNAs revealed that lncRNAs were principally related to inflammatory response. Meanwhile, we found that the differentially expressed lncRNA TCONS_00058367 might lead to a reduction of phosphorylation of transcription factor p65 (p-p65) in TGEV-infected IPEC-J2 cells by negatively regulating its antisense gene romyelocytic leukemia (PML ). Conclusions: The data showed that differentially expressed lncRNAs might be involved in inflammatory response induced by TGEV through acting as miRNA sponges, regulating their up/down-stream genes, or directly binding proteins.

scholarly journals Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection

2019 ◽  
Author(s):  
Xuelian Ma ◽  
Xiaomin Zhao ◽  
Kaili Wang ◽  
Xiaoyi Tang ◽  
Jianxiong Guo ◽  
...  
Keyword(s):  
Immune Response ◽  
Binding Proteins ◽  
Differentially Expressed ◽  
Transmissible Gastroenteritis Virus ◽  
Intestinal Epithelial ◽  
Antisense Gene ◽  
Gastroenteritis Virus ◽  
Expression Of Genes ◽  
Transmissible Gastroenteritis ◽  
Mirna Sponges

Abstract Abstract Background: Transmissible gastroenteritis virus (TGEV) infection can activate the immune response and cause inflammation. Long noncoding RNAs (lncRNAs) play important roles in antiviral innate immune response. However, whether lncRNAs participate in TGEV-induced inflammation in porcine intestinal epithelial cells (IPECs) is largely unknown. Results: In this study, the next-generation sequencing (NGS) technology was used to analyze the profiles of lncRNAs in Mock and TGEV-infected porcine intestinal epithelial cell-jejunum 2 (IPEC-J2) cell line. A total of 106 lncRNAs were differentially expressed. Many differentially expressed lncRNAs act as elements to competitively attach miRNAs with mRNAs to mediate expression of genes that related to Toll-like receptor, NOD-like receptor, TNF, and RIG-I-like receptor pathways. Functional analysis of the binding proteins and the up/down-stream genes of the differentially expressed lncRNAs revealed that lncRNAs were principally related to immune response. Meanwhile, we found that the differentially expressed lncRNA TCONS_00058367 might lead to a reduction of p-p65 in TGEV-infected IPEC-J2 cells by negatively regulating its antisense gene PML. Conclusions: The data showed that differentially expressed lncRNAs might be involved in immune response induced by TGEV through acting as miRNA sponges, regulating their up/down-stream genes, or directly binding proteins.

scholarly journals Identification and analysis of long non-coding RNAs that are involved in inflammatory process in response to transmissible gastroenteritis virus infection

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Xuelian Ma ◽  
Xiaomin Zhao ◽  
Kaili Wang ◽  
Xiaoyi Tang ◽  
Jianxiong Guo ◽  
...  
Keyword(s):  
Inflammatory Response ◽  
Messenger Rna ◽  
Binding Proteins ◽  
Differentially Expressed ◽  
Transmissible Gastroenteritis Virus ◽  
Intestinal Epithelial ◽  
Antisense Gene ◽  
Gastroenteritis Virus ◽  
Expression Of Genes ◽  
Transmissible Gastroenteritis

Abstract Background Transmissible gastroenteritis virus (TGEV) infection can cause acute inflammation. Long noncoding RNAs (lncRNAs) play important roles in a number of biological process including inflammation response. However, whether lncRNAs participate in TGEV-induced inflammation in porcine intestinal epithelial cells (IPECs) is largely unknown. Results In this study, the next-generation sequencing (NGS) technology was used to analyze the profiles of lncRNAs in Mock and TGEV-infected porcine intestinal epithelial cell-jejunum 2 (IPEC-J2) cell line. A total of 106 lncRNAs were differentially expressed. Many differentially expressed lncRNAs act as elements to competitively attach microRNAs (miRNAs) which target to messenger RNA (mRNAs) to mediate expression of genes that related to toll-like receptors (TLRs), NOD-like receptors (NLRs), tumor necrosis factor (TNF), and RIG-I-like receptors (RLRs) pathways. Functional analysis of the binding proteins and the up/down-stream genes of the differentially expressed lncRNAs revealed that lncRNAs were principally related to inflammatory response. Meanwhile, we found that the differentially expressed lncRNA TCONS_00058367 might lead to a reduction of phosphorylation of transcription factor p65 (p-p65) in TGEV-infected IPEC-J2 cells by negatively regulating its antisense gene promyelocytic leukemia (PML). Conclusions The data showed that differentially expressed lncRNAs might be involved in inflammatory response induced by TGEV through acting as miRNA sponges, regulating their up/down-stream genes, or directly binding proteins.

scholarly journals Reverse Genetic Analysis of the Transcription Regulatory Sequence of the Coronavirus Transmissible Gastroenteritis Virus

2004 ◽  
Vol 78 (11) ◽  
pp. 6061-6066 ◽  
Author(s):  
Kristopher M. Curtis ◽  
Boyd Yount ◽  
Amy C. Sims ◽  
Ralph S. Baric
Keyword(s):  
Genetic Analysis ◽  
Full Length ◽  
Transmissible Gastroenteritis Virus ◽  
Regulatory Sequence ◽  
Reverse Genetic ◽  
Conserved Sequence ◽  
Gastroenteritis Virus ◽  
Flanking Sequences ◽  
Transmissible Gastroenteritis ◽  
Discontinuous Transcription

ABSTRACT Coronavirus discontinuous transcription uses a highly conserved sequence (CS) in the joining of leader and body RNAs. Using a full-length infectious construct of transmissable gastroenteritis virus, the present study demonstrates that subgenomic transcription is heavily influenced by upstream flanking sequences and supports a mechanism of transcription attenuation that is regulated in part by a larger domain composed of primarily upstream flanking sequences which select appropriately positioned CS elements for synthesis of subgenomic RNAs.

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