RNAs expression analyses in commercially used Marek’s disease vaccine viruses to identify their Latency associated transcripts splicing patterns
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PROVIDER: PRJNA1246595 | ENA |
REPOSITORIES: ENA
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Project description:Circular RNAs (circRNAs) are covalently closed RNA molecules, supporting a wide diversity of functions. While aberrant circRNA expression stands as a recognized hallmark of cancer development, our attention has turned to investigate their role in viral infections, specifically Mardivirus Gallidalpha 2 (GaHV-2, MDV) infection. In a previous study focused on the virulent GaHV-2, RB-1B strain, we extensively cataloged circRNAs produced from virulence genes, notably from the MEQ-vIL-8 locus and the Latency Associated Transcripts (LATs) gene. Building upon this groundwork, our current investigation uncovers novel loci expressing viral circRNAs in distinct stages of GaHV-2 infection. Furthermore, we extend our focus to viral circRNA signatures in three commonly used MDV vaccines, the avirulent GaHV-2 (CVI988- Rispens strain), non-oncogenic Mardivirus Gallidalpha 3 (GaHV-3), and non-oncogenic Mardivirus Meleagridalpha 1 (MeHV-1) commercially called Herpesvirus of Turkey (HVT). In these vaccine viruses, we identified viral circRNA expression from a locus antisense to the immediate early ICP4 gene a conserved feature across the three species. This region has been characterized herein for the first time in term of candidate LATs exons and introns for GaHV-3 and MeHV-1. Potential LATs circRNAs were then deeply analyzed and we observed both similarities and distinctions when compared to those of the virulent GaHV-2. Another conserved gene, encoding the DNA packaging protein, was identified as a source of circRNAs in all three species. Eventually, different levels of circRNAs expression were found from the meq locus between virulent and avirulent GaHV-2 strains. Our findings highlight a conserved pattern of viral derived circRNA expression in these related avian alphaherpesviruses. This conservation underscores the potential significance of these transcripts in completing the viral cycle and facilitating viral spread.
2025-08-22 | GSE293852 | GEO
Project description:Circular RNAs (circRNAs) are covalently closed RNA molecules, supporting a wide diversity of functions. While aberrant circRNA expression stands as a recognized hallmark of cancer development, our attention has turned to investigate their role in viral infections, specifically Mardivirus Gallidalpha 2 (GaHV-2, MDV) infection. In a previous study focused on the virulent GaHV-2, RB-1B strain, we extensively cataloged circRNAs produced from virulence genes, notably from the MEQ-vIL-8 locus and the Latency Associated Transcripts (LATs) gene. Building upon this groundwork, our current investigation uncovers novel loci expressing viral circRNAs in distinct stages of GaHV-2 infection. Furthermore, we extend our focus to viral circRNA signatures in three commonly used MDV vaccines, the avirulent GaHV-2 (CVI988- Rispens strain), non-oncogenic Mardivirus Gallidalpha 3 (GaHV-3), and non-oncogenic Mardivirus Meleagridalpha 1 (MeHV-1) commercially called Herpesvirus of Turkey (HVT). In these vaccine viruses, we identified viral circRNA expression from a locus antisense to the immediate early ICP4 gene a conserved feature across the three species. This region has been characterized herein for the first time in term of candidate LATs exons and introns for GaHV-3 and MeHV-1. Potential LATs circRNAs were then deeply analyzed and we observed both similarities and distinctions when compared to those of the virulent GaHV-2. Another conserved gene, encoding the DNA packaging protein, was identified as a source of circRNAs in all three species. Eventually, different levels of circRNAs expression were found from the meq locus between virulent and avirulent GaHV-2 strains. Our findings highlight a conserved pattern of viral derived circRNA expression in these related avian alphaherpesviruses. This conservation underscores the potential significance of these transcripts in completing the viral cycle and facilitating viral spread.
2025-08-22 | GSE293847 | GEO
Project description:Conserved and distinct expression of circular RNAs in commercially used Marek’s disease vaccine viruses
| PRJNA1246573 | ENA
Project description:Herpes simplex viruses (HSVs) cause cold sores and genital herpes and can establish lifelong latent infection in neurons. An engineered oncolytic HSV (oHSV) has recently been approved to treat tumors in clinics. HSV latency-associated transcripts (LATs) are associated with the latent infection, but LAT transcriptional regulation was seldom reported. For a better treatment of HSV infection and tumors, here we sequenced the LAT encoding DNA and LAT transcription regulatory region of our recently isolated new strain HSV-1-LXMW and did comparative analysis of the sequences together with those of other four HSV-1 and two HSV-2 strains. Phylogenetic analysis of LATs revealed that HSV-1-LXMW is evolutionarily close to HSV-1-17 from MRC University, Glasgow, UK. For the first time, Using a weight matrix-based program Match and multi-sequences alignment of the 6 HSV strains, we identified HSV LAT transcription regulatory sequences that bind to 9 transcription factors: AP-1, C-REL, Comp1, E2F, Hairy, HFH-3, Kr, TCF11/MAFG, v-Myb. Interestingly, these transcription regulatory sequences and factors are either conserved or unique among LATs of HSV-1 and HSV-2, suggesting they are potentially functional. Furthermore, literature analysis found that the transcription factors v-myb and AP-1 family member JunD are functional in regulating HSV gene transcription, including LAT transcription. For the first time, we discovered seven novel transcription factors and their corresponding transcription regulatory sequences of HSV LATs. Based on our findings and other reports, we proposed potential mechanisms of the initiation and maintenance of HSV latent infection. Our findings may have significant implication in our understanding of HSV latency and engineering of better oncolytic HSVs.
| S-EPMC7097949 | biostudies-literature
Project description:Background: Marek’s disease (MD) is a highly contagious, lymphomatous disease of chickens induced by a herpesvirus, Marek’s disease virus (MDV) that is the cause of major annual losses to the poultry industry. MD pathogenesis involves multiple stages including an early cytolytic phase and latency, and transitions between these stages are governed by several host and environmental factors. The success of vaccination strategies has led to the increased virulence of MDV and selective breeding of naturally resistant chickens is seen as a viable alternative. While multiple gene expression studies have been performed in resistant and susceptible populations, little is known about the epigenetic effects of infection. Results: In this study, we investigated temporal chromatin signatures induced by MDV by analyzing early cytolytic and latent phases of infection in the bursa of Fabricius of MD-resistant and –susceptible birds. Major global variations in chromatin marks were observed at different stages of MD in the two lines. Differential H3K27me3 marks were associated with immune-related pathways, such as MAP kinase signaling, focal adhesion and neuroactive ligand receptor interaction, and suggested varying degrees of silencing in response to infection. Immune-related microRNAs, e.g. gga-miR-155 and gga-miR-10b, bore chromatin signatures, which suggested their contribution to MD-susceptibility. Finally, several members of the focal adhesion pathway, e.g. THBS4 and ITGA1, showed marked concordance between gene expression and chromatin marks indicating putative epigenetic regulation in response to MDV infection. Conclusions: Our comprehensive analysis of chromatin signatures, therefore, revealed further clues about the epigenetic effects of MDV infection although further studies are necessary to elucidate the functional implications of the observed variations in histone modifications. Total of 32 samples analyzed; 2 histone modifications - H3K4me3 and H3K27me3 x 2 chicken lines with varying resistance to MD - L63 and L72 x 2 time-points of disease progression - 5 and 10 days post infection x 2 conditions - infected and control x 2 biological replicates
2015-04-17 | E-GEOD-65961 | biostudies-arrayexpress
Project description:Two wild house mice lines were genetically selected for short and long attack latency. Mice with an attack latency <50s or >600s were considered short attack latency mice (SAL) and long attack latency mice(LAL) respectively. RNA from the hippocampus of 14 SAL or 14 LAL mice was pooled and used as input material for the SAGE libraries. Keywords: other
2003-10-30 | E-GEOD-786 | biostudies-arrayexpress
Project description:Deciphering the molecular pathogenesis of virally induced cancers is challenging due, in part, to the heterogeneity of both viral and host gene expression. Epstein-Barr Virus (EBV) is a ubiquitous herpesvirus prevalent in B-cell lymphomas of the immune suppressed. EBV infection of primary human B cells leads to their immortalization into lymphoblastoid cell lines (LCLs) serving as a model of these lymphomas. In previous studies, our lab has described a temporal model for immortalization with an initial phase characterized by expression of the Epstein-Barr Nuclear Antigens (EBNAs), high c-Myc activity, and hyper-proliferation in the absence of the Latent Membrane Proteins (LMPs), called latency IIb. This is followed by the long-term outgrowth of LCLs expressing the EBNAs along with the LMPs, particularly the NFkB-activating LMP1, defining latency III. LCLs, however, express a broad distribution of LMP1 such that a subset of these cells expresses LMP1 at levels seen in latency IIb, making it difficult to distinguish these two latency states. In this study, we performed mRNA-Seq on early EBV-infected latency IIb cells and latency III LCLs sorted by NFkB activity. We found that latency IIb transcriptomes clustered independently from latency III independent of NFkB. We identified and validated mRNAs defining these latency states. Indeed, we were able to distinguish latency IIb cells from LCLs expressing low levels of LMP1 using multiplex RNA-FISH targeting EBV EBNA2, LMP1, and human CCR7 or MGST1. This study defines latency IIb as a bona fide latency state independent from latency III and identifies biomarkers for understanding EBV-associated tumor heterogeneity
2019-06-04 | GSE132138 | GEO
Project description:Ancient Marek’s disease virus
| PRJEB64489 | ENA
Project description:Industrialized tomato production faced a decrease in flavours and nutritional values due to conventional breeding and growth conditions. We addressed the question, whether commercially used tomato cultivars grown in a hydroponic system can be mycorrhizal leading to improved fruit quality. Comparing green and red fruits from non-mycorrhizal and mycorrhizal plants, differentially expressed genes (DEGs) should be found possibly being involved in processes regulating fruit maturation and nutrition.
2020-11-06 | E-MTAB-9419 | biostudies-arrayexpress