The RNA Epitranscriptome of DNA Viruses

Polyadenylated nuclear (PAN) RNA is a non-coding transcript involved in Kaposis sarcoma-associated herpesvirus (KSHV) lytic reactivation and regulation of cellular and viral gene expression. We have shown that PAN RNA has a dynamic secondary structure and protein binding profiles that can be influenced by the epitranscriptomic modifications. N6-methyladenosine (m6A) is an abundant signature found in viral and virus-encoded RNAs. Here, we combined an antibody-independent next generation mapping with direct RNA sequencing to elucidate the m6A landscape of PAN RNA during the KSHV latent and lytic stages of infection. Using a newly developed method, termed Selenium-modified deoxythymidine triphosphate reverse transcription and Ligation Assisted PCR analysis of m6A (SLAP), we gained insight into the fraction of modification at identified sites. Using comprehensive proteomic approaches, we identified writers, erasers, and readers that regulate the m6A status of PAN. We verified the temporal and spatial subcellular availability of the methylome components for PAN modification by performing confocal microscopy analysis. Additionally, the RNA biochemical probing outlined structural alterations invoked by m6A in the context of full-length PAN RNA. This work represents the first comprehensive overview of the dynamic interplay between the cellular epitranscriptomic machinery and a specific viral RNA.

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“…1 and 3). Thus, it is feasible that the YTHDF2 association with PAN might be involved in the regulation of PAN RNA turnover (98,105,106).…”

Section: Discussionmentioning

confidence: 99%

The m⁶A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication

Martin

Gan

Toomer

et al. 2021

Preprint

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“…Moreover, the methylation pattern has also been elucidated in the transcripts of numerous DNA viruses, such as hepatitis B virus (HBV) and Kaposi’s sarcoma‐associated herpesvirus (KSHV) (Ye et al , 2017; Hesser et al , 2018; Imam et al , 2018; Tan et al , 2018; Baquero‐Perez et al , 2019). Crucially, the m 6 A machinery was reported to regulate viral replication and infectivity (Gonzales‐van Horn & Sarnow, 2017; Tan & Gao, 2018; Tirumuru & Wu, 2019).…”

Section: Introductionmentioning

confidence: 99%

N(6)‐methyladenosine‐binding protein YTHDF1 suppresses EBV replication and promotes EBV RNA decay

Xia

Wang

et al. 2021

EMBO Reports

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N6‐methyladenosine (m6A) modification of mRNA mediates diverse cellular and viral functions. Infection with Epstein–Barr virus (EBV) is causally associated with nasopharyngeal carcinoma (NPC), 10% of gastric carcinoma, and various B‐cell lymphomas, in which the viral latent and lytic phases both play vital roles. Here, we show that EBV transcripts exhibit differential m6A modification in human NPC biopsies, patient‐derived xenograft tissues, and cells at different EBV infection stages. m6A‐modified EBV transcripts are recognized and destabilized by the YTHDF1 protein, which leads to the m6A‐dependent suppression of EBV infection and replication. Mechanistically, YTHDF1 hastens viral RNA decapping and mediates RNA decay by recruiting RNA degradation complexes, including ZAP, DDX17, and DCP2, thereby post‐transcriptionally downregulating the expression of EBV genes. Taken together, our results reveal the critical roles of m6A modifications and their reader YTHDF1 in EBV replication. These findings contribute novel targets for the treatment of EBV‐associated cancers.

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“…Methylated adenosine was firstly discovered a few decades ago in hepatoma cells ( Desrosiers et al, 1974 ) and encountered in a wide range of species including human ( Dominissini et al, 2012 ; Meyer and Jaffrey, 2017 ; Wang et al, 2017 ), mouse ( Mouse Genome Sequencing Consortium et al, 2002 ; Dominissini et al, 2012 ; Jain et al, 2018 ), plant ( Martínez-Pérez et al, 2017 ; Yue et al, 2019 ), yeast ( Agarwala et al, 2012 ), and bacteria ( Deng et al, 2015 ). Intriguingly, m6A marks are also encoded in wide arrays of viral transcripts of both DNA and RNA viruses ( Krug et al, 1976 ; Narayan et al, 1987 ; Courtney et al, 2017 ; Kennedy et al, 2017 ; Tan and Gao, 2018 ; Dang et al, 2019 ; Wu et al, 2019 ). The m6A has recently been attributed to RNA metabolism pathways including splicing, stability, translation, and secondary structure ( Niu et al, 2013 ; Li and Mason, 2014 ; Meyer and Jaffrey, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Structural and Virus Regulatory Insights Into Avian N6-Methyladenosine (m6A) Machinery

Bayoumi

Rohaim

Munir

2020

Front. Cell Dev. Biol.

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The addition of a methyl group to the N6 position of adenosine (m6A) is the most common posttranscriptional RNA modification, and it regulates most steps of RNA metabolism including splicing, stability, translation, nuclear-export, and RNA structures. Besides cellular RNA, m6A modifications have also been detected on viral RNA. A range of recent studies have demonstrated the crucial roles of m6A in the virushost interactions; however, m6A cellular machineries are only characterized in limited mammalian species. Herein, we aim to present comprehensive evolutionary insights into major m6A writers, erasers, and readers and draw a comparative structural analysis between avian and mammalian m6A-associated machineries. The comparative collinearity on the chromosomal scale revealed that the majority of m6A-related genes were found less syntenic even among avian species. Genetic analysis of avian m6A erasers revealed a distinct phylogenetic clustering compared to mammalian orthologs and shared a weak percent (55%) identity with mammalian species with low identity percentage (55%). The overall comparative three-dimensional (3D) structure analyses among different mammalian species were maintained through synonymous structural mutations. Unlike erasers, the putative 3D structures in the active sites as for the aromatic cage in YTH-domain of YTHDC1 and two pivotal loops in MTD-domains in METTL3 exhibited structural alterations in chicken. In conjunction with in silico investigations, influenza viruses significantly downregulated gene the transcription of m6A writers and erasers, whereas m6A readers were moderately regulated in chicken fibroblasts. In light of these findings, future detailed biochemical and crystallographic studies are warranted to define the roles of m6A machinery in regulating both viral and cellular RNA metabolism in avian species.

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The RNA Epitranscriptome of DNA Viruses

Cited by 38 publications

References 95 publications

The m⁶A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication

The m⁶A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication

N(6)‐methyladenosine‐binding protein YTHDF1 suppresses EBV replication and promotes EBV RNA decay

Structural and Virus Regulatory Insights Into Avian N6-Methyladenosine (m6A) Machinery

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The RNA Epitranscriptome of DNA Viruses

Cited by 38 publications

References 95 publications

The m6A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication

The m6A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication

N(6)‐methyladenosine‐binding protein YTHDF1 suppresses EBV replication and promotes EBV RNA decay

Structural and Virus Regulatory Insights Into Avian N6-Methyladenosine (m6A) Machinery

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The m⁶A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication

The m⁶A landscape of polyadenylated nuclear (PAN) RNA and its related methylome in the context of KSHV replication