Comprehensive profiling analysis of the N6-methyladenosine-modified circular RNA transcriptome in cultured cells infected with Marek’s disease virus

Abstract

Marek’s disease virus (MDV) induces severe immunosuppression and lymphomagenesis in the chicken, its natural host, and results in a condition that investigated the pathogenesis of MDV and have begun to focus on the expression profiling of circular RNAs (circRNAs). However, little is known about how the expression of circRNAs is referred to as Marek’s disease. Previous reports have is regulated during MDV replication. Here, we carried out a comprehensive profiling analysis of N6-methyladenosine (m6A) modification on the circRNA transcriptome in infected and uninfected chicken embryonic fibroblast (CEF) cells. Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) revealed that m6A modification was highly conserved in circRNAs. Comparing to the uninfected group, the number of peaks and conserved motifs were not significantly different in cells that were infected with MDV, although reduced abundance of circRNA m6A modifications. However, gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) pathway analyses revealed that the insulin signaling pathway was associated with the regulation of m6A modified circRNAs in MDV infection. This is the first report to describe alterations in the transcriptome-wide profiling of m6A modified circRNAs in MDV-infected CEF cells.

Marek’s Disease Virus Virulence Genes Encode Circular RNAs

“…While previous studies have reported on the expression of host circRNAs during MDV infection ( 20 , 47 ), no study has addressed the expression of MDV-encoded circRNAs until now. Thus, we investigated MDV-encoded circRNAs from two transcriptional units involved in viral pathogenesis and tumorigenesis, namely, the meq oncogene and the LATs.…”

“…The bioinformatic pipeline was also applied to another set of high-throughput RNAseq data obtained from an independent experiment investigating MDV in vitro productive infection and focusing on host circRNAs dysregulation ( 47 ). This RNAseq data set (accession number GSE166240 ) from infected chicken embryo fibroblasts (CEF) was processed to map back-spliced junctions over the MDV genome.…”

“…Two data sets from previous experiments ( 20 , 47 ) were downloaded from the SRA database (GEO accession numbers: GSE138600 and GSE166240 ). The first set of data (( 20 ); data available under GSE138600 ) was obtained from infected chickens with (TA + ) and without (TA − ) MDV-induced T CD4 + lymphomas and was analyzed through our pipeline.…”

“…The first set of data (( 20 ); data available under GSE138600 ) was obtained from infected chickens with (TA + ) and without (TA − ) MDV-induced T CD4 + lymphomas and was analyzed through our pipeline. The second set of data (( 47 ); data available under GSE166240 ) were gathered from chicken embryonic fibroblasts (CEF) infected by the Md5 strain of MDV. All the data obtained from this experiment were analyzed through our pipeline.…”

Fully Attenuated meq and pp38 Double Gene Deletion Mutant Virus Confers Superior Immunological Protection against Highly Virulent Marek’s Disease Virus Infection

“…Importantly, the m 6 A modification may regulate the immune system to facilitate viral replication ( 53 ). We have also reported alterations in transcriptome-wide m 6 A modification in chicken lncRNAs and circRNAs ( 54 , 55 ). Recently, we found spatiotemporal changes of mRNA m 6 A modification in distinct MDV infection phases (unpublished data).…”