KSHV 3.0: a state-of-the-art annotation of the Kaposi’s sarcoma-associated herpesvirus transcriptome using cross-platform sequencing
ABSTRACTKaposi’s sarcoma-associated herpesvirus (KSHV) is a large, oncogenic DNA virus belonging to the gammaherpesvirus subfamily. KSHV has been extensively studied with various high-throughput RNA-sequencing approaches to map the transcription start and end sites, the splice junctions, and the tra...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2024-02-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/msystems.01007-23 |
| _version_ | 1827346450678284288 |
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| author | István Prazsák Dóra Tombácz Ádám Fülöp Gábor Torma Gábor Gulyás Ákos Dörmő Balázs Kakuk Lauren McKenzie Spires Zsolt Toth Zsolt Boldogkői |
| author_facet | István Prazsák Dóra Tombácz Ádám Fülöp Gábor Torma Gábor Gulyás Ákos Dörmő Balázs Kakuk Lauren McKenzie Spires Zsolt Toth Zsolt Boldogkői |
| author_sort | István Prazsák |
| collection | DOAJ |
| description | ABSTRACTKaposi’s sarcoma-associated herpesvirus (KSHV) is a large, oncogenic DNA virus belonging to the gammaherpesvirus subfamily. KSHV has been extensively studied with various high-throughput RNA-sequencing approaches to map the transcription start and end sites, the splice junctions, and the translation initiation sites. Despite these efforts, the comprehensive annotation of the viral transcriptome remains incomplete. In the present study, we generated a long-read sequencing data set of the lytic and latent KSHV transcriptome using native RNA and direct cDNA-sequencing methods. This was supplemented with Cap Analysis of Gene Expression sequencing based on a short-read platform. We also utilized data sets from previous publications for our analysis. As a result of this combined approach, we have identified a number of novel viral transcripts and RNA isoforms and have either corroborated or improved the annotation of previously identified viral RNA molecules, thereby notably enhancing our comprehension of the transcriptomic architecture of the KSHV genome. We also evaluated the coding capability of transcripts previously thought to be non-coding by integrating our data on the viral transcripts with translatomic information from other publications.IMPORTANCEDeciphering the viral transcriptome of Kaposi’s sarcoma-associated herpesvirus is of great importance because we can gain insight into the molecular mechanism of viral replication and pathogenesis, which can help develop potential targets for antiviral interventions. Specifically, the identification of substantial transcriptional overlaps by this work suggests the existence of a genome-wide interference between transcriptional machineries. This finding indicates the presence of a novel regulatory layer, potentially controlling the expression of viral genes. |
| first_indexed | 2024-03-07T23:31:17Z |
| format | Article |
| id | doaj.art-1b10e36e87124544aba3dfca738982d7 |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-03-07T23:31:17Z |
| publishDate | 2024-02-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-1b10e36e87124544aba3dfca738982d72024-02-20T14:00:48ZengAmerican Society for MicrobiologymSystems2379-50772024-02-019210.1128/msystems.01007-23KSHV 3.0: a state-of-the-art annotation of the Kaposi’s sarcoma-associated herpesvirus transcriptome using cross-platform sequencingIstván Prazsák0Dóra Tombácz1Ádám Fülöp2Gábor Torma3Gábor Gulyás4Ákos Dörmő5Balázs Kakuk6Lauren McKenzie Spires7Zsolt Toth8Zsolt Boldogkői9Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, HungaryDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, HungaryDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, HungaryDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, HungaryDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, HungaryDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, HungaryDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, HungaryDepartment of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USADepartment of Oral Biology, University of Florida College of Dentistry, Gainesville, Florida, USADepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, HungaryABSTRACTKaposi’s sarcoma-associated herpesvirus (KSHV) is a large, oncogenic DNA virus belonging to the gammaherpesvirus subfamily. KSHV has been extensively studied with various high-throughput RNA-sequencing approaches to map the transcription start and end sites, the splice junctions, and the translation initiation sites. Despite these efforts, the comprehensive annotation of the viral transcriptome remains incomplete. In the present study, we generated a long-read sequencing data set of the lytic and latent KSHV transcriptome using native RNA and direct cDNA-sequencing methods. This was supplemented with Cap Analysis of Gene Expression sequencing based on a short-read platform. We also utilized data sets from previous publications for our analysis. As a result of this combined approach, we have identified a number of novel viral transcripts and RNA isoforms and have either corroborated or improved the annotation of previously identified viral RNA molecules, thereby notably enhancing our comprehension of the transcriptomic architecture of the KSHV genome. We also evaluated the coding capability of transcripts previously thought to be non-coding by integrating our data on the viral transcripts with translatomic information from other publications.IMPORTANCEDeciphering the viral transcriptome of Kaposi’s sarcoma-associated herpesvirus is of great importance because we can gain insight into the molecular mechanism of viral replication and pathogenesis, which can help develop potential targets for antiviral interventions. Specifically, the identification of substantial transcriptional overlaps by this work suggests the existence of a genome-wide interference between transcriptional machineries. This finding indicates the presence of a novel regulatory layer, potentially controlling the expression of viral genes.https://journals.asm.org/doi/10.1128/msystems.01007-23Kaposi’s sarcoma-associated herpesvirus (KSHV)herpesvirusestranscriptomenanopore sequencingCAGETSS |
| spellingShingle | István Prazsák Dóra Tombácz Ádám Fülöp Gábor Torma Gábor Gulyás Ákos Dörmő Balázs Kakuk Lauren McKenzie Spires Zsolt Toth Zsolt Boldogkői KSHV 3.0: a state-of-the-art annotation of the Kaposi’s sarcoma-associated herpesvirus transcriptome using cross-platform sequencing mSystems Kaposi’s sarcoma-associated herpesvirus (KSHV) herpesviruses transcriptome nanopore sequencing CAGE TSS |
| title | KSHV 3.0: a state-of-the-art annotation of the Kaposi’s sarcoma-associated herpesvirus transcriptome using cross-platform sequencing |
| title_full | KSHV 3.0: a state-of-the-art annotation of the Kaposi’s sarcoma-associated herpesvirus transcriptome using cross-platform sequencing |
| title_fullStr | KSHV 3.0: a state-of-the-art annotation of the Kaposi’s sarcoma-associated herpesvirus transcriptome using cross-platform sequencing |
| title_full_unstemmed | KSHV 3.0: a state-of-the-art annotation of the Kaposi’s sarcoma-associated herpesvirus transcriptome using cross-platform sequencing |
| title_short | KSHV 3.0: a state-of-the-art annotation of the Kaposi’s sarcoma-associated herpesvirus transcriptome using cross-platform sequencing |
| title_sort | kshv 3 0 a state of the art annotation of the kaposi s sarcoma associated herpesvirus transcriptome using cross platform sequencing |
| topic | Kaposi’s sarcoma-associated herpesvirus (KSHV) herpesviruses transcriptome nanopore sequencing CAGE TSS |
| url | https://journals.asm.org/doi/10.1128/msystems.01007-23 |
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