Identification of herpesvirus transcripts from genomic regions around the replication origins
Abstract Long-read sequencing (LRS) techniques enable the identification of full-length RNA molecules in a single run eliminating the need for additional assembly steps. LRS research has exposed unanticipated transcriptomic complexity in various organisms, including viruses. Herpesviruses are known...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-09-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-43344-y |
| _version_ | 1827723350900736000 |
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| author | Gábor Torma Dóra Tombácz Zsolt Csabai Islam A. A. Almsarrhad Gergely Ármin Nagy Balázs Kakuk Gábor Gulyás Lauren McKenzie Spires Ishaan Gupta Ádám Fülöp Ákos Dörmő István Prazsák Máté Mizik Virág Éva Dani Viktor Csányi Ákos Harangozó Zoltán Zádori Zsolt Toth Zsolt Boldogkői |
| author_facet | Gábor Torma Dóra Tombácz Zsolt Csabai Islam A. A. Almsarrhad Gergely Ármin Nagy Balázs Kakuk Gábor Gulyás Lauren McKenzie Spires Ishaan Gupta Ádám Fülöp Ákos Dörmő István Prazsák Máté Mizik Virág Éva Dani Viktor Csányi Ákos Harangozó Zoltán Zádori Zsolt Toth Zsolt Boldogkői |
| author_sort | Gábor Torma |
| collection | DOAJ |
| description | Abstract Long-read sequencing (LRS) techniques enable the identification of full-length RNA molecules in a single run eliminating the need for additional assembly steps. LRS research has exposed unanticipated transcriptomic complexity in various organisms, including viruses. Herpesviruses are known to produce a range of transcripts, either close to or overlapping replication origins (Oris) and neighboring genes related to transcription or replication, which possess confirmed or potential regulatory roles. In our research, we employed both new and previously published LRS and short-read sequencing datasets to uncover additional Ori-proximal transcripts in nine herpesviruses from all three subfamilies (alpha, beta and gamma). We discovered novel long non-coding RNAs, as well as splice and length isoforms of mRNAs. Moreover, our analysis uncovered an intricate network of transcriptional overlaps within the examined genomic regions. We demonstrated that herpesviruses display distinct patterns of transcriptional overlaps in the vicinity of or at the Oris. Our findings suggest the existence of a ‘super regulatory center’ in the genome of alphaherpesviruses that governs the initiation of both DNA replication and global transcription through multilayered interactions among the molecular machineries. |
| first_indexed | 2024-03-10T21:59:02Z |
| format | Article |
| id | doaj.art-06e84a45cae64350bc7931c004d3aef5 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-10T21:59:02Z |
| publishDate | 2023-09-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-06e84a45cae64350bc7931c004d3aef52023-11-19T12:59:42ZengNature PortfolioScientific Reports2045-23222023-09-0113112510.1038/s41598-023-43344-yIdentification of herpesvirus transcripts from genomic regions around the replication originsGábor Torma0Dóra Tombácz1Zsolt Csabai2Islam A. A. Almsarrhad3Gergely Ármin Nagy4Balázs Kakuk5Gábor Gulyás6Lauren McKenzie Spires7Ishaan Gupta8Ádám Fülöp9Ákos Dörmő10István Prazsák11Máté Mizik12Virág Éva Dani13Viktor Csányi14Ákos Harangozó15Zoltán Zádori16Zsolt Toth17Zsolt Boldogkői18Department of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Oral Biology, University of Florida College of DentistryDepartment of Biochemical Engineering and Biotechnology, Indian Institute of TechnologyDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedHUN-REN Veterinary Medical Research Institute HUDepartment of Oral Biology, University of Florida College of DentistryDepartment of Medical Biology, Albert Szent-Györgyi Medical School, University of SzegedAbstract Long-read sequencing (LRS) techniques enable the identification of full-length RNA molecules in a single run eliminating the need for additional assembly steps. LRS research has exposed unanticipated transcriptomic complexity in various organisms, including viruses. Herpesviruses are known to produce a range of transcripts, either close to or overlapping replication origins (Oris) and neighboring genes related to transcription or replication, which possess confirmed or potential regulatory roles. In our research, we employed both new and previously published LRS and short-read sequencing datasets to uncover additional Ori-proximal transcripts in nine herpesviruses from all three subfamilies (alpha, beta and gamma). We discovered novel long non-coding RNAs, as well as splice and length isoforms of mRNAs. Moreover, our analysis uncovered an intricate network of transcriptional overlaps within the examined genomic regions. We demonstrated that herpesviruses display distinct patterns of transcriptional overlaps in the vicinity of or at the Oris. Our findings suggest the existence of a ‘super regulatory center’ in the genome of alphaherpesviruses that governs the initiation of both DNA replication and global transcription through multilayered interactions among the molecular machineries.https://doi.org/10.1038/s41598-023-43344-y |
| spellingShingle | Gábor Torma Dóra Tombácz Zsolt Csabai Islam A. A. Almsarrhad Gergely Ármin Nagy Balázs Kakuk Gábor Gulyás Lauren McKenzie Spires Ishaan Gupta Ádám Fülöp Ákos Dörmő István Prazsák Máté Mizik Virág Éva Dani Viktor Csányi Ákos Harangozó Zoltán Zádori Zsolt Toth Zsolt Boldogkői Identification of herpesvirus transcripts from genomic regions around the replication origins Scientific Reports |
| title | Identification of herpesvirus transcripts from genomic regions around the replication origins |
| title_full | Identification of herpesvirus transcripts from genomic regions around the replication origins |
| title_fullStr | Identification of herpesvirus transcripts from genomic regions around the replication origins |
| title_full_unstemmed | Identification of herpesvirus transcripts from genomic regions around the replication origins |
| title_short | Identification of herpesvirus transcripts from genomic regions around the replication origins |
| title_sort | identification of herpesvirus transcripts from genomic regions around the replication origins |
| url | https://doi.org/10.1038/s41598-023-43344-y |
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