Comprehensive Genomic Characterization Analysis of lncRNAs in Cells With Porcine Delta Coronavirus Infection.

Junli Liu,Juan Li,Tianqi Yu,Yulan Jin,Jiyong Zhou,Yan Yan,Jinyan Gu,Liuyang Du,Fangfang Wang

doi:10.3389/fmicb.2019.03036

Abstract

Porcine delta coronavirus (PDCoV) is a novel emerging enterocytetropic virus causing diarrhea, vomiting, dehydration, and mortality in suckling piglets. Long non-coding RNAs (lncRNAs) are known to be important regulators during virus infection. Here, we describe a comprehensive transcriptome profile of lncRNA in PDCoV-infected swine testicular (ST) cells. In total, 1,308 annotated and 1,190 novel lncRNA candidate sequences were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these lncRNAs might be involved in numerous biological processes. Clustering analysis of differentially expressed lncRNAs showed that 454 annotated and 376 novel lncRNAs were regulated after PDCoV infection. Furthermore, we constructed a lncRNA-protein-coding gene co-expression interaction network. The KEGG analysis of the co-expressed genes showed that these differentially expressed lncRNAs were enriched in pathways related to metabolism and TNF signaling. Our study provided comprehensive information about lncRNAs that would be a useful resource for studying the pathogenesis of and designing antiviral therapy for PDCoV infection.

Highlights

Long non-coding RNAs, which are transcripts larger than 200 nt in length that lack protein-coding ability, have previously been described in mammalian cells (Kapranov et al, 2007; Mattick and Rinn, 2015)
To identify the Long non-coding RNAs (lncRNAs) in Porcine delta coronavirus (PDCoV)-infected cells, we sequenced the transcriptomes of the swine testicular (ST) cells with or without PDCoV infection using high-throughput RNA sequencing
The results showed that protein-coding genes associated with differentially expressed (DE) lncRNAs were mainly enriched in terms of molecular function and cellular component, primarily under the category of nucleic acid binding and intracellular membranebounded organelle (Figure 4B)

Summary

Introduction

Long non-coding RNAs (lncRNAs), which are transcripts larger than 200 nt in length that lack protein-coding ability, have previously been described in mammalian cells (Kapranov et al, 2007; Mattick and Rinn, 2015). Emerging evidence shows that non-coding RNAs have a regulatory role in multiple cellular processes, such as genomic imprinting, chromatin modification, and alternative splicing of RNA (Mercer et al, 2009). Some diseases such as cancer and neurological disorders are related to the dysregulated expression of lncRNA (Qureshi et al, 2010; Tsai et al, 2011). NRAV can promote influenza virus replication and virulence through negatively lncRNAs Profiling During PDCoV Infection regulating the initial transcription of varieties of interferonstimulated genes (ISGs) (Ouyang et al, 2014). Large amounts of data have proved that several lncRNAs are involved in different kinds of virus infection, the mechanisms by which they act are still largely unknown

Methods

Results

Discussion

Conclusion