The long non-coding RNA expression profile of Coxsackievirus A16 infected RD cells identified by RNA-seq

Abstract

Coxsackievirus A16 (CVA16) is one of major pathogens of hand, foot and mouth disease (HFMD) in children. Long non-coding RNAs (IncRNAs) have been implicated in various biological processes, but they have not been associated with CVA16 infection. In this study, we comprehensively characterized the landscape of IncRNAs of normal and CVA16 infected rhabdomyosarcoma (RD) cells using RNA-Seq to investigate the functional relevance of IncRNAs. We showed that a total of 760 IncRNAs were upregulated and 1210 IncRNAs were downregulated. Out of these dysregulated IncRNAs, 43.64% were intergenic, 22.31% were sense, 15.89% were intronic, 8.67% were bidirectional, 5.59% were antisense, 3.85% were sRNA host IncRNAs and 0.05% were enhancer. Six dysregulated IncRNAs were validated by quantitative PCR assays and the secondary structures of these IncRNAs were projected. Moreover, we conducted a bioinformatics analysis of an IncRNAs (ENST00000602478) to elucidate the diversity of modification and functions of IncRNAs. In summary, the current study compared the dysregulated IncRNAs profile upon CVA16 challenge and illustrated the intricate relationship between coding and IncRNAs transcripts. These results may not only provide a complete picture of transcription in CVA16 infected cells but also provide novel molecular targets for treatments of HFMD.

Global identification and analysis revealed differentially expressed lncRNAs associated with meiosis and low fertility in autotetraploid rice

“…The genes transcribed within a 100 kb window upstream or downstream of lncRNAs were considered as potential cis target genes [79]. The second algorithm was used to identify potential trans targets based on RNA sequence complementarity (mRNA-lncRNA) and RNA duplex energy prediction [80,81]. Based on the RNA duplex energy (Free energy < − 50) assessed by RIsearch algorithms [82], the differentially expressed genes and lncRNAs were considered as potentially involved in trans-interaction.…”

HDAC6, A Novel Cargo for Autophagic Clearance of Stress Granules, Mediates the Repression of the Type I Interferon Response During Coxsackievirus A16 Infection

“…Previously, we focused on the molecular epidemiology and pathogenic mechanism of CA16 and found that CA16 infection induces apoptosis (Zhu et al, 2013) and regulates long noncoding RNA (lncRNA) (Shi et al, 2016), which regulates viral replication (Zhu et al, 2013;Shi et al, 2016). In this study, we found that granulophagy occurred during CA16 infection and facilitated viral replication, and CA16-induced granulophagy also repressed the antiviral response.…”

Autophagy triggered by MAVS inhibits Coxsackievirus A16 replication

“…The cells were maintained at 37°C and 5% CO 2 . CA16 is a laboratory strain that has been completely sequenced and belongs to the B1 genotype (Shi et al, 2015(Shi et al, , 2016. Plasmids expressing the His-tagged fulllength MAVS and deletion mutants lacking either the CARD-like domain (∆CARD) or the transmembrane domain (∆TM) were amplified by PCR and cloned into the pcDNA 6/V5-His B vector (Thermo Fisher Scientific, USA).…”