Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in Ori
            <i>Lyt</i>

Forte, Eleonora; Li, Ming; Butun, Fatma Ayaloglu; Hu, Qiaolin; Borst, Eva Maria; Schipma, Matthew J.; Piunti, Andrea; Shilatifard, Ali; Terhune, Scott S.; Abecassis, Michael; Meier, Jeffery L.; Hummel, Mary

doi:10.1128/spectrum.03144-22

Cited by 3 publications

(6 citation statements)

References 92 publications

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“…OriLyts in herpesviruses are somewhat conserved, and KSHV OriLyts also contain the C/EBP CCCAT domains, supporting our finding of OriLyt-L as an RTA-inducible enhancer (115). Additionally, similar to KSHV, HCMV OriLyt gives rise to two ncRNAs (100). Thus, it can be envisioned as an enhancer, giving rise to ‘enhancer-derived lncRNA’ (116–118).…”

Section: Discussionmentioning

confidence: 99%

“…A strong enhancer is located upstream of the major immediate-early gene of Human Cytomegalovirus (HCMV) (98). Additional enhancers in HCMV are located in the short unique region (99) and OriLyt (100). Even the closest relative of KSHV, the Epstein Barr Virus (EBV), contains several enhancers, including the DR enhancer, which is both constitutive and lytically induced (101).…”

Section: Discussionmentioning

confidence: 99%

“…The OriLyt-R has been suggested to possess long-range transcriptional regulation properties based on loop formation with RTA promoter and the observation that a mutation in the RTA binding site within OriLyt- R abrogated RTA expression during exogenous RTA lytic induction (58). HCMV and EBV OriLyts have been previously reported to exhibit enhancer activities (100, 106). OriLyts in herpesviruses are somewhat conserved, and KSHV OriLyts also contain the C/EBP CCCAT domains, supporting our finding of OriLyt-L as an RTA-inducible enhancer (115).…”

Section: Discussionmentioning

confidence: 99%

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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%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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KSHV genome harbors both constitutive and lytically induced enhancers

Chowdhury,

Gurevich,

Shamay

2024

Preprint

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“…Both IE72 and IE86 bind HDAC3, which, in the case of the IE72-HDAC3 association, disrupts histone deacetylation ( 100 ), thus directly promoting active histone marks. Recently, Forte et al showed IE72 and IE86 recruit RNA polymerase II and H3K27ac to the Ori Lyt RNA4.9 promoter in lytically infected fibroblasts ( 138 ). Since Ori Lyt is a bi-directional promoter ( 139 ), Forte et al posit this IE-dependent H3K27ac enrichment at early times post-infection suggests this region functions as an enhancer element to influence E gene expression ( 138 ).…”

Section: Introductionmentioning

confidence: 99%

“…Recently, Forte et al showed IE72 and IE86 recruit RNA polymerase II and H3K27ac to the Ori Lyt RNA4.9 promoter in lytically infected fibroblasts ( 138 ). Since Ori Lyt is a bi-directional promoter ( 139 ), Forte et al posit this IE-dependent H3K27ac enrichment at early times post-infection suggests this region functions as an enhancer element to influence E gene expression ( 138 ). While intriguing, additional experiments are necessary to define this region of the Ori Lyt as an E gene enhancer element.…”

Section: Introductionmentioning

confidence: 99%

Chromatin control of human cytomegalovirus infection

Matthews

Groves

O’Connor

2023

mBio

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Human cytomegalovirus (HCMV) is a betaherpesvirus that establishes lifelong infection in its host and can cause severe comorbidities in individuals with suppressed or compromised immune systems. The lifecycle of HCMV consists of lytic and latent phases, largely dependent upon the cell type infected and whether transcription from the major immediate early locus can ensue. Control of this locus, which acts as a critical “switch” region from where the lytic gene expression cascade originates, as well as regulation of the additional ~235 kilobases of virus genome, occurs through chromatinization with cellular histone proteins after infection. Upon infection of a host cell, an initial intrinsic antiviral response represses gene expression from the incoming genome, which is relieved in permissive cells by viral and host factors in concert. Latency is established in a subset of hematopoietic cells, during which viral transcription is largely repressed while the genome is maintained. As these latently infected cells differentiate, the cellular milieu and epigenetic modifications change, giving rise to the initial stages of virus reactivation from latency. Thus, throughout the cycle of infection, chromatinization, chromatin modifiers, and the recruitment of specific transcription factors influence the expression of genes from the HCMV genome. In this review, we discuss epigenetic regulation of the HCMV genome during the different phases of infection, with an emphasis on recent reports that add to our current perspective.

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KSHV genome harbors both constitutive and lytically induced enhancers

Roy Chowdhury,

Gurevich,

Shamay

2024

J Virol

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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, 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 of the luciferase gene and tested their enhancer activity in infected and uninfected cells. A silencer was detected upstream of the latency-associated nuclear antigen promoter. Two constitutive enhancers were identified in the K12p-OriLyt-R and ORF29 Intron regions, 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. The 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-associated nuclear antigen (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. IMPORTANCE In this study, we performed a systematic functional assay to identify cis -regulatory elements within the genome of the oncogenic herpesvirus, Kaposi’s 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, one of which 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 the lytic gene locus. Utilizing CRISPR activation and interference techniques, we determined the connections between these enhancers and 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-associated nuclear antigen (LANA) with the activating effect of RTA to regulate latency to lytic transition.

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Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in Ori Lyt

Abstract: HCMV is an important human pathogen associated with complications in transplant patients and birth defects. The complex program of viral gene expression is regulated by both viral proteins and host factors.

Cited by 3 publications

References 92 publications

KSHV genome harbors both constitutive and lytically induced enhancers

KSHV genome harbors both constitutive and lytically induced enhancers

Chromatin control of human cytomegalovirus infection

KSHV genome harbors both constitutive and lytically induced enhancers

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