Identification of herpesvirus transcripts from genomic regions around the replication origins

Torma, Gábor; Tombácz, Dóra; Csabai, Zsolt; Almsarrhad, Islam A. A.; Nagy, Gergely Ármin; Kakuk, Balázs; Gulyás, Gábor; Spires, Lauren McKenzie; Gupta, Ishaan; Fülöp, Ádám; Dörmő, Ákos; Prazsák, István; Mizik, Máté; Dani, Virág Éva; Csányi, Viktor; Harangozó, Ákos; Zádori, Zoltán; Toth, Zsolt; Boldogkői, Zsolt

doi:10.1038/s41598-023-43344-y

Cited by 5 publications

(2 citation statements)

References 109 publications

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“…Within the OriLyt-R region, there are two enhancers: one constitutive and one lytically induced. This entire region is active during latency and is further induced by RTA during the lytic cycle (107)(108)(109). The K12 promoter is flanked by OriLyt-R ( 108).…”

Section: Discussionmentioning

confidence: 99%

KSHV genome harbors both constitutive and lytically induced enhancers

Chowdhury,

Gurevich,

Shamay

2024

Preprint

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Kaposi’s sarcoma-associated herpesvirus (KSHV) belongs to the gamma-herpesvirus family and is a well-known human oncogenic virus. In infected cells, the viral genome of 165 kbp is circular DNA wrapped in chromatin. The tight control of gene expression is critical for latency, the transition into the lytic phase, and the development of viral-associated malignancies. Distal cis-regulatory elements (CRE), such as enhancers and silencers, can regulate gene expression in a position and orientation-independent manner. Open chromatin is another characteristic feature of enhancers. To systematically search for enhancers, we cloned all the open chromatin regions in the KSHV genome downstream to the luciferase gene and tested their enhancer activity in infected and uninfected cells. A silencer was detected upstream of the latency promoter (LANAp). Two constitutive enhancers were identified in the K12p-OriLyt-R and ORF29 Intron region, where ORF29 Intron is a tissue-specific enhancer. The following promoters: OriLyt-L, PANp, ALTp, and the Terminal Repeats (TRs) acted as lytically induced enhancers. Expression of the Replication and Transcription Activator (RTA), the master regulator of the lytic cycle, was sufficient to induce the activity of lytic enhancers in uninfected cells. We propose that the TRs that span about 24 kbp region serve as a “viral super-enhancer” that integrates the repressive effect of the latency protein LANA with the activating effect of RTA. Utilizing CRISPR activation and interference techniques, we determined the connections between these enhancers and their regulated genes. The silencer and enhancers described here provide an additional layer to the complex gene regulation of herpesviruses.ImportanceIn this study, we performed a systematic functional assay to identify cis-regulatory elements within the genome of the oncogenic herpesvirus, Kaposi sarcoma-associated herpesvirus (KSHV). Similar to other herpesviruses, KSHV presents both latent and lytic phases. Therefore, our assays were performed in uninfected cells, during latent infection, and under lytic conditions. We identified two constitutive enhancers, where one seems to be a tissue- specific enhancer. In addition, four lytically induced enhancers, which are all responsive to the Replication and Transcription Activator (RTA), were identified. Furthermore, a silencer was identified between the major latency promoter and lytic genes locus. Utilizing CRISPR activation and interference techniques, we determined the connections between these enhancers with their regulated genes. The terminal repeats spanning a region of about 24 kbp, seem like a “viral super-enhancer” that integrates the repressive effect of the latency protein LANA with the activating effect of RTA to regulate latency to lytic transition.

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Section: Discussionmentioning

confidence: 99%

KSHV genome harbors both constitutive and lytically induced enhancers

Chowdhury,

Gurevich,

Shamay

2024

Preprint

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“…This includes the regulation of RNA primer synthesis through hybridization with DNA sequences or forming hybrids with mRNA. This hybridization process initiates their degradation through RNase H, thereby inhibiting replication and protein translation ( Torma et al, 2023 ). In VZV, aside from LAT and ORF63, no other VZV mRNA expression was detected during infection.…”

Section: The Models For Studying Latent Infections Of Alphaherpesvirusesmentioning

confidence: 99%

Advances in the immunoescape mechanisms exploited by alphaherpesviruses

Wang,

Ma,

Wang

et al. 2024

Front. Microbiol.

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Alphaherpesviruses, categorized as viruses with linear DNA composed of two complementary strands, can potentially to induce diseases in both humans and animals as pathogens. Mature viral particles comprise of a core, capsid, tegument, and envelope. While herpesvirus infection can elicit robust immune and inflammatory reactions in the host, its persistence stems from its prolonged interaction with the host, fostering a diverse array of immunoescape mechanisms. In recent years, significant advancements have been achieved in comprehending the immunoescape tactics employed by alphaherpesviruses, including pseudorabies virus (PRV), herpes simplex virus (HSV), varicella-zoster virus (VZV), feline herpesvirus (FeHV), equine herpesvirus (EHV), and caprine herpesvirus type I (CpHV-1). Researchers have unveiled the intricate adaptive mechanisms existing between viruses and their natural hosts. This review endeavors to illuminate the research advancements concerning the immunoescape mechanisms of alphaherpesviruses by delineating the pertinent proteins and genes involved in virus immunity. It aims to furnish valuable insights for further research on related mechanisms and vaccine development, ultimately contributing to virus control and containment efforts.

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Long-read Transcriptomics of Caviid Gammaherpesvirus 1: Compiling a Comprehensive RNA Atlas

Torma,

Dörmő,

Fülöp

et al. 2024

Preprint

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Caviid gammaherpesvirus 1 (CaGHV-1), formerly known as the guinea pig herpes-like virus, is an oncogenic gammaherpesvirus with a sequenced genome but an as-yet uncharacterized transcriptome. Using nanopore long-read RNA sequencing, we annotated the CaGHV-1 genome and constructed a detailed transcriptomic atlas. Our findings reveal diverse viral mRNAs and non-coding RNAs, along with mapped promoter elements for each viral gene. We demonstrated that the CaGHV-1 RTA lytic cycle transcription factor activates its own promoter, similar to KSHV, and that the CaGHV-1 ORF50 promoter responds to RTA proteins from other gammaherpesviruses, highlighting the evolutionary conservation of RTA-mediated transcriptional mechanisms. Additionally, our analysis uncovered extensive transcriptional overlap within the viral genome, suggesting a role in regulating global gene expression. Given its tumorigenic properties, broad host range, and non-human pathogenicity, this work establishes CaGHV-1 as a promising small animal model for investigating human gammaherpesvirus pathogenesis.

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Identification of herpesvirus transcripts from genomic regions around the replication origins

Cited by 5 publications

References 109 publications

KSHV genome harbors both constitutive and lytically induced enhancers

KSHV genome harbors both constitutive and lytically induced enhancers

Advances in the immunoescape mechanisms exploited by alphaherpesviruses

Long-read Transcriptomics of Caviid Gammaherpesvirus 1: Compiling a Comprehensive RNA Atlas

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