TY - JOUR AU - Torma, Gábor AU - Tombácz, Dóra AU - Moldován, Norbert AU - Fülöp, Ádám AU - Prazsák, István AU - Csabai, Zsolt AU - Michael, Snyder AU - Boldogkői, Zsolt TI - Dual isoform sequencing reveals complex transcriptomic and epitranscriptomic landscapes of a prototype baculovirus JF - SCIENTIFIC REPORTS J2 - SCI REP VL - 12 PY - 2022 IS - 1 PG - 16 SN - 2045-2322 DO - 10.1038/s41598-022-05457-8 UR - https://m2.mtmt.hu/api/publication/32618973 ID - 32618973 N1 - Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Szeged, 6720, Hungary Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, United States Cited By :2 Export Date: 20 February 2024 Correspondence Address: Boldogkői, Z.; Department of Medical Biology, Hungary; email: boldogkoi.zsolt@med.u-szeged.hu LA - English DB - MTMT ER - TY - JOUR AU - Fülöp, Ádám AU - Torma, Gábor AU - Moldován, Norbert AU - Szenthe, Kálmán AU - Bánáti, Ferenc AU - Almsarrhad, Islam AU - Csabai, Zsolt AU - Tombácz, Dóra AU - Minárovits, János AU - Boldogkői, Zsolt TI - Integrative profiling of Epstein–Barr virus transcriptome using a multiplatform approach JF - VIROLOGY JOURNAL J2 - VIROL J VL - 19 PY - 2022 IS - 1 PG - 17 SN - 1743-422X DO - 10.1186/s12985-021-01734-6 UR - https://m2.mtmt.hu/api/publication/32581214 ID - 32581214 AB - Background Epstein-Barr virus (EBV) is an important human pathogenic gammaherpesvirus with carcinogenic potential. The EBV transcriptome has previously been analyzed using both Illumina-based short read-sequencing and Pacific Biosciences RS II-based long-read sequencing technologies. Since the various sequencing methods have distinct strengths and limitations, the use of multiplatform approaches have proven to be valuable. The aim of this study is to provide a more complete picture on the transcriptomic architecture of EBV. Methods In this work, we apply the Oxford Nanopore Technologies MinION (long-read sequencing) platform for the generation of novel transcriptomic data, and integrate these with other's data generated by another LRS approach, Pacific BioSciences RSII sequencing and Illumina CAGE-Seq and Poly(A)-Seq approaches. Both amplified and non-amplified cDNA sequencings were applied for the generation of sequencing reads, including both oligo-d(T) and random oligonucleotide-primed reverse transcription. EBV transcripts are identified and annotated using the LoRTIA software suite developed in our laboratory. Results This study detected novel genes embedded into longer host genes containing 5 '-truncated in-frame open reading frames, which potentially encode N-terminally truncated proteins. We also detected a number of novel non-coding RNAs and transcript length isoforms encoded by the same genes but differing in their start and/or end sites. This study also reports the discovery of novel splice isoforms, many of which may represent altered coding potential, and of novel replication-origin-associated transcripts. Additionally, novel mono- and multigenic transcripts were identified. An intricate meshwork of transcriptional overlaps was revealed. Conclusions An integrative approach applying multi-technique sequencing technologies is suitable for reliable identification of complex transcriptomes because each techniques has different advantages and limitations, and the they can be used for the validation of the results obtained by a particular approach. LA - English DB - MTMT ER - TY - JOUR AU - Tombácz, Dóra AU - Prazsák, István AU - Torma, Gábor AU - Csabai, Zsolt AU - Balázs, Zsolt AU - Moldován, Norbert AU - Dénes, Béla AU - Snyder, Michael AU - Boldogkői, Zsolt TI - Time-Course Transcriptome Profiling of a Poxvirus Using Long-Read Full-Length Assay JF - PATHOGENS J2 - PATHOGENS VL - 10 PY - 2021 IS - 8 PG - 17 SN - 2076-0817 DO - 10.3390/pathogens10080919 UR - https://m2.mtmt.hu/api/publication/32109464 ID - 32109464 LA - English DB - MTMT ER - TY - JOUR AU - Kakuk, Balázs AU - Tombácz, Dóra AU - Balázs, Zsolt AU - Moldován, Norbert AU - Csabai, Zsolt AU - Torma, Gábor AU - Megyeri, Klára AU - Snyder, Michael AU - Boldogkői, Zsolt TI - Combined nanopore and single-molecule real-time sequencing survey of human betaherpesvirus 5 transcriptome JF - SCIENTIFIC REPORTS J2 - SCI REP VL - 11 PY - 2021 IS - 1 PG - 14 SN - 2045-2322 DO - 10.1038/s41598-021-93593-y UR - https://m2.mtmt.hu/api/publication/32109459 ID - 32109459 N1 - Department of Medical Biology, Faculty of Medicine, University of Szeged, Somogyi B. u. 4, Szeged, 6720, Hungary MTA-SZTE Momentum GeMiNI Research Group, University of Szeged, Somogyi B. u. 4, Szeged, 6720, Hungary Department of Genetics, School of Medicine, Stanford University, 300 Pasteur Dr, Stanford, CA, United States Department of Medical Microbiology and Immunobiology, Faculty of Medicine, University of Szeged, Szeged, 6720, Hungary Cited By :4 Export Date: 20 June 2023 Correspondence Address: Boldogkői, Z.; Department of Medical Biology, Somogyi B. u. 4, Hungary; email: boldogkoi.zsolt@med.u-szeged.hu Chemicals/CAS: DNA, Complementary; RNA, Messenger Funding details: 4675 Funding details: National Institutes of Health, NIH, 5P50HG00773502 Funding details: Magyar Tudományos Akadémia, MTA, LP-2020/8 Funding details: Wigner Fizikai Kutatóközpont, Magyar Tudományos Akadémia, Lendület (Momentum) I Program LP-2020/8 Funding details: National Research, Development and Innovation Office, FK 128252, K 128247 Funding text 1: The study was supported by National Research, Development and Innovation Office (Grant numbers: FK 128252 to DT, K 128247 to ZBo), Magyar Tudományos Akadémia (Grant number: Lendület (Momentum) I Program LP-2020/8 to DT), NIH Centers of Excellence in Genomic Science Center for Personal Dynamic Regu-lomes (Grant number: 5P50HG00773502 to MS), University of Szeged Open Access Fund (Grant number: 4675). LA - English DB - MTMT ER - TY - JOUR AU - Maróti, Zoltán AU - Tombácz, Dóra AU - Moldován, Norbert AU - Torma, Gábor AU - Jefferson, Victoria A. AU - Csabai, Zsolt AU - Gulyás, Gábor AU - Dörmő, Ákos AU - Boldogkői, Miklós AU - Kalmár, Tibor AU - Meyer, Florencia AU - Boldogkői, Zsolt TI - Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing JF - SCIENTIFIC REPORTS J2 - SCI REP VL - 11 PY - 2021 IS - 1 PG - 11 SN - 2045-2322 DO - 10.1038/s41598-021-93142-7 UR - https://m2.mtmt.hu/api/publication/32109423 ID - 32109423 LA - English DB - MTMT ER - TY - JOUR AU - Maróti, Zoltán AU - Tombácz, Dóra AU - Prazsák, István AU - Moldován, Norbert AU - Csabai, Zsolt AU - Torma, Gábor AU - Balázs, Zsolt AU - Kalmár, Tibor AU - Dénes, Béla AU - Snyder, Michael AU - Boldogkői, Zsolt TI - Time-course transcriptome analysis of host cell response to poxvirus infection using a dual long-read sequencing approach JF - BMC RESEARCH NOTES J2 - BMC RES NOTES VL - 14 PY - 2021 IS - 1 PG - 7 SN - 1756-0500 DO - 10.1186/s13104-021-05657-x UR - https://m2.mtmt.hu/api/publication/32080152 ID - 32080152 LA - English DB - MTMT ER - TY - JOUR AU - Tombácz, Dóra AU - Moldován, Norbert AU - Torma, Gábor AU - Nagy, Tibor AU - Hornyák, Ákos AU - Csabai, Zsolt AU - Gulyás, Gábor AU - Boldogkői, Miklós AU - Jefferson, Victoria A. AU - Zádori, Zoltán AU - Meyer, Florencia AU - Boldogkői, Zsolt TI - Dynamic Transcriptome Sequencing of Bovine Alphaherpesvirus Type 1 and Host Cells Carried Out by a Multi-Technique Approach JF - FRONTIERS IN GENETICS J2 - FRONT GENET VL - 12 PY - 2021 PG - 8 SN - 1664-8021 DO - 10.3389/fgene.2021.619056 UR - https://m2.mtmt.hu/api/publication/31989778 ID - 31989778 LA - English DB - MTMT ER - TY - JOUR AU - Torma, Gábor AU - Tombácz, Dóra AU - Csabai, Zsolt AU - Moldován, Norbert AU - Mészáros, István AU - Zádori, Zoltán AU - Boldogkői, Zsolt TI - Combined Short and Long-Read Sequencing Reveals a Complex Transcriptomic Architecture of African Swine Fever Virus JF - VIRUSES J2 - VIRUSES-BASEL VL - 13 PY - 2021 IS - 4 PG - 21 SN - 1999-4915 DO - 10.3390/v13040579 UR - https://m2.mtmt.hu/api/publication/31940598 ID - 31940598 LA - English DB - MTMT ER - TY - JOUR AU - Moldován, Norbert AU - Torma, Gábor AU - Gulyás, Gábor AU - Hornyák, Ákos AU - Zádori, Zoltán AU - Jefferson, Victoria A. AU - Csabai, Zsolt AU - Boldogkői, Miklós AU - Tombácz, Dóra AU - Meyer, Florencia AU - Boldogkői, Zsolt TI - Time-course profiling of bovine alphaherpesvirus 1.1 transcriptome using multiplatform sequencing JF - SCIENTIFIC REPORTS J2 - SCI REP VL - 10 PY - 2020 IS - 1 PG - 14 SN - 2045-2322 DO - 10.1038/s41598-020-77520-1 UR - https://m2.mtmt.hu/api/publication/31672953 ID - 31672953 LA - English DB - MTMT ER - TY - JOUR AU - Tombácz, Dóra AU - Prazsák, István AU - Csabai, Zsolt AU - Moldován, Norbert AU - Dénes, Béla AU - Snyder, Michael AU - Boldogkői, Zsolt TI - Long-read assays shed new light on the transcriptome complexity of a viral pathogen. JF - SCIENTIFIC REPORTS J2 - SCI REP VL - 10 PY - 2020 IS - 1 PG - 13 SN - 2045-2322 DO - 10.1038/s41598-020-70794-5 UR - https://m2.mtmt.hu/api/publication/31406099 ID - 31406099 AB - Characterization of global transcriptomes using conventional short-read sequencing is challenging due to the insensitivity of these platforms to transcripts isoforms, multigenic RNA molecules, and transcriptional overlaps. Long-read sequencing (LRS) can overcome these limitations by reading full-length transcripts. Employment of these technologies has led to the redefinition of transcriptional complexities in reported organisms. In this study, we applied LRS platforms from Pacific Biosciences and Oxford Nanopore Technologies to profile the vaccinia virus (VACV) transcriptome. We performed cDNA and direct RNA sequencing analyses and revealed an extremely complex transcriptional landscape of this virus. In particular, VACV genes produce large numbers of transcript isoforms that vary in their start and termination sites. A significant fraction of VACV transcripts start or end within coding regions of neighbouring genes. This study provides new insights into the transcriptomic profile of this viral pathogen. LA - English DB - MTMT ER -