TY - JOUR AU - Moldován, Norbert AU - Tombácz, Dóra AU - Szűcs, Attila AU - Csabai, Zsolt AU - Balázs, Zsolt AU - Kis, Emese AU - Molnar, J AU - Boldogkői, Zsolt TI - Third-generation Sequencing Reveals Extensive Polycistronism and Transcriptional Overlapping in a Baculovirus JF - SCIENTIFIC REPORTS J2 - SCI REP VL - 8 PY - 2018 IS - 1 PG - 11 SN - 2045-2322 DO - 10.1038/s41598-018-26955-8 UR - https://m2.mtmt.hu/api/publication/3383352 ID - 3383352 AB - The Autographa californica multiple nucleopolyhedrovirus (AcMNPV) is an insect-pathogen baculovirus. In this study, we applied the Oxford Nanopore Technologies platform for the analysis of the polyadenylated fraction of the viral transcriptome using both cDNA and direct RNA sequencing methods. We identified and annotated altogether 132 novel transcripts and transcript isoforms, including 4 coding and 4 non-coding RNA molecules, 47 length variants, 5 splice isoforms, as well as 23 polycistronic and 49 complex transcripts. All of the identified novel protein-coding genes were 5'-truncated forms of longer host genes. In this work, we demonstrated that in the case of transcript start site isoforms, the promoters and the initiator sequence of the longer and shorter variants belong to the same kinetic class. Long-read sequencing also revealed a complex meshwork of transcriptional overlaps, the function of which needs to be clarified. Additionally, we developed bioinformatics methods to improve the transcript annotation and to eliminate the non-specific transcription reads generated by template switching and false priming. LA - English DB - MTMT ER - TY - JOUR AU - Moldován, Norbert AU - Szűcs, Attila AU - Tombácz, Dóra AU - Balázs, Zsolt AU - Csabai, Zsolt AU - Michael, Snyder AU - Boldogkői, Zsolt TI - Multiplatform next-generation sequencing identifies novel RNA molecules and transcript isoforms of the endogenous retrovirus isolated from cultured cells JF - FEMS MICROBIOLOGY LETTERS J2 - FEMS MICROBIOL LETT VL - 365 PY - 2018 IS - 5 PG - 6 SN - 0378-1097 DO - 10.1093/femsle/fny013 UR - https://m2.mtmt.hu/api/publication/3319938 ID - 3319938 N1 - Megjegyzés-27406529 N1 Funding details: 5P50HG00773502 N1 Funding details: TAMOP-4.2.6-14/1 -288 N1 Funding details: 2015-18, MTA, Magyar Tudományos Akadémia N1 Funding details: SH/7/2/8, MTA, Magyar Tudományos Akadémia N1 Funding details: NINS, National Institutes of Natural Sciences N1 Funding text: This work was supported by the following: National Institutes of Health (NIH) Centers of Excellence in Genomic Science (CEGS)—Center for Personal Dynamic Regulomes: [grant number 5P50HG00773502 to MS]; TAMOP-Social Renewal Operational Programme: [grant number TAMOP-4.2.6-14/1 -288 to ZBo]; Bolyai Janos Scholarship of the Hungarian Academy of Sciences: [grant number 2015-18 to DT], and Swiss-Hungarian Co-operation Programme [grant number SH/7/2/8 to ZBo]. LA - English DB - MTMT ER - TY - JOUR AU - Moldován, Norbert AU - Tombácz, Dóra AU - Szűcs, Attila AU - Csabai, Zsolt AU - Michael, Snyder AU - Boldogkői, Zsolt TI - Multi-Platform Sequencing Approach Reveals a Novel Transcriptome Profile in Pseudorabies Virus JF - FRONTIERS IN MICROBIOLOGY J2 - FRONT MICROBIOL VL - 8 PY - 2018 PG - 13 SN - 1664-302X DO - 10.3389/fmicb.2017.02708 UR - https://m2.mtmt.hu/api/publication/3323833 ID - 3323833 LA - English DB - MTMT ER - TY - JOUR AU - Prazsák, István AU - Tombácz, Dóra AU - Szűcs, Attila AU - Dénes, Béla AU - Snyder, M AU - Boldogkői, Zsolt TI - Full Genome Sequence of the Western Reserve Strain of Vaccinia Virus Determined by Third-Generation Sequencing JF - GENOME ANNOUNCEMENTS J2 - GENOME ANNOUNC VL - 6 PY - 2018 IS - 11 PG - 2 SN - 2169-8287 DO - 10.1128/genomeA.01570-17 UR - https://m2.mtmt.hu/api/publication/3349644 ID - 3349644 AB - The vaccinia virus is a large, complex virus belonging to the Poxviridae family. Here, we report the complete, annotated genome sequence of the neurovirulent Western Reserve laboratory strain of this virus, which was sequenced on the Pacific Biosciences RS II and Oxford Nanopore MinION platforms. LA - English DB - MTMT ER - TY - JOUR AU - Prazsák, István AU - Moldován, Norbert AU - Balázs, Zsolt AU - Tombácz, Dóra AU - Megyeri, Klára AU - Szűcs, Attila AU - Csabai, Zsolt AU - Boldogkői, Zsolt TI - Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus JF - BMC GENOMICS J2 - BMC GENOMICS VL - 19 PY - 2018 IS - 1 PG - 20 SN - 1471-2164 DO - 10.1186/s12864-018-5267-8 UR - https://m2.mtmt.hu/api/publication/30338504 ID - 30338504 LA - English DB - MTMT ER - TY - JOUR AU - Tombácz, Dóra AU - Prazsák, István AU - Szűcs, Attila AU - Dénes, Béla AU - Snyder, Michael AU - Boldogkői, Zsolt TI - Dynamic Transcriptome Profiling Dataset of Vaccinia Virus Obtained from Long-read Sequencing Techniques JF - GIGASCIENCE J2 - GIGASCIENCE VL - 7 PY - 2018 IS - 12 PG - 17 SN - 2047-217X DO - 10.1093/gigascience/giy139 UR - https://m2.mtmt.hu/api/publication/30330053 ID - 30330053 AB - Poxviruses are large DNA viruses infecting humans and animals. Vaccinia virus (VACV) has been applied as a live vaccine for immunization against smallpox, which was eradicated by 1980 as a result of worldwide vaccination. VACV is the prototype of poxviruses in the investigation of the molecular pathogenesis of the virus. Short-read sequencing methods have revolutionized transcriptomics; but, they are not efficient in distinguishing between the RNA isoforms and transcript overlaps. Long-read sequencing (LRS) is much better suited to solve these problems, and also allow direct RNA sequencing. Despite the scientific relevance of VACV, no LRS data have been generated for the viral transcriptome so far.For the deep characterization of the VACV RNA profile, various LRS platforms and library preparation approaches were applied. The raw reads were mapped to the VACV reference genome and also to the host (Chlorocebus sabaeus) genome. In this study, we applied the Pacific Biosciences RSII and Sequel platforms, which altogether resulted in 937,531 mapped reads of inserts (1.42 Gb), while we obtained 2,160,348 aligned reads (1.75 Gb) from the different library preparation methods, using the MinION device from Oxford Nanopore Technologies.By applying cutting-edge technologies, we were able to generate a large dataset that can serve as a valuable resource for the investigation of the dynamic VACV transcriptome, the virus-host interactions and RNA base modifications. These data can provide useful information for novel gene annotations in the VACV genome. Our dataset can also be applied for analyzing the currently available LRS platforms, library preparation methods and bioinformatics pipelines. LA - English DB - MTMT ER - TY - JOUR AU - Balázs, Zsolt AU - Tombácz, Dóra AU - Szűcs, Attila AU - Csabai, Zsolt AU - Megyeri, Klára AU - Alexey, N Petrov AU - Michael, Snyder AU - Boldogkői, Zsolt TI - Long-Read Sequencing of Human Cytomegalovirus Transcriptome Reveals RNA Isoforms Carrying Distinct Coding Potentials JF - SCIENTIFIC REPORTS J2 - SCI REP VL - 7 PY - 2017 IS - 1 PG - 9 SN - 2045-2322 DO - 10.1038/s41598-017-16262-z UR - https://m2.mtmt.hu/api/publication/3294493 ID - 3294493 LA - English DB - MTMT ER - TY - JOUR AU - Moldován, Norbert AU - Balázs, Zsolt AU - Tombácz, Dóra AU - Csabai, Zsolt AU - Szűcs, Attila AU - Michael, Snyder AU - Boldogkői, Zsolt TI - Multi-platform Analysis Reveals a Complex Transcriptome Architecture of a Circovirus JF - VIRUS RESEARCH J2 - VIRUS RES VL - 237 PY - 2017 SP - 37 EP - 46 PG - 10 SN - 0168-1702 DO - 10.1016/j.virusres.2017.05.010 UR - https://m2.mtmt.hu/api/publication/3227970 ID - 3227970 LA - English DB - MTMT ER - TY - JOUR AU - Szűcs, Attila AU - Moldován, Norbert AU - Tombácz, Dóra AU - Csabai, Zsolt AU - Michael, Snyder AU - Boldogkői, Zsolt TI - Long-Read Sequencing Reveals a GC Pressure during the Evolution of Porcine Endogenous Retrovirus JF - GENOME ANNOUNCEMENTS J2 - GENOME ANNOUNC VL - 5 PY - 2017 IS - 40 PG - 2 SN - 2169-8287 DO - 10.1128/genomeA.01040-17 UR - https://m2.mtmt.hu/api/publication/3276338 ID - 3276338 LA - English DB - MTMT ER - TY - JOUR AU - Tombácz, Dóra AU - Balázs, Zsolt AU - Csabai, Zsolt AU - Moldován, Norbert AU - Szűcs, Attila AU - Donald, Sharon AU - Michael, Snyder AU - Boldogkői, Zsolt TI - Characterization of the Dynamic Transcriptome of a Herpesvirus with Long-read Single Molecule Real-Time Sequencing JF - SCIENTIFIC REPORTS J2 - SCI REP VL - 7 PY - 2017 PG - 13 SN - 2045-2322 DO - 10.1038/srep43751 UR - https://m2.mtmt.hu/api/publication/3180311 ID - 3180311 AB - Herpesvirus gene expression is co-ordinately regulated and sequentially ordered during productive infection. The viral genes can be classified into three distinct kinetic groups: immediate-early, early, and late classes. In this study, a massively parallel sequencing technique that is based on PacBio Single Molecule Real-time sequencing platform, was used for quantifying the poly(A) fraction of the lytic transcriptome of pseudorabies virus (PRV) throughout a 12- hour interval of productive infection on PK-15 cells. Other approaches, including microarray, real-time RT-PCR and Illumina sequencing are capable of detecting only the aggregate transcriptional activity of particular genomic regions, but not individual herpesvirus transcripts. However, SMRT sequencing allows for a distinction between transcript isoforms, including length- and splice variants, as well as between overlapping polycistronic RNA molecules. The non-amplified Isoform Sequencing (Iso-Seq) method was used to analyse the kinetic properties of the lytic PRV transcripts and to then classify them accordingly. Additionally, the present study demonstrates the general utility of long-read sequencing for the time-course analysis of global gene expression in practically any organism. LA - English DB - MTMT ER - TY - JOUR AU - Tombácz, Dóra AU - Csabai, Zsolt AU - Szűcs, Attila AU - Balázs, Zsolt AU - Moldován, Norbert AU - Donald, Sharon AU - MIchael, Snyder AU - Boldogkői, Zsolt TI - Long-Read Isoform Sequencing Reveals a Hidden Complexity of the Transcriptional Landscape of Herpes Simplex Virus Type 1 JF - FRONTIERS IN MICROBIOLOGY J2 - FRONT MICROBIOL VL - 8 PY - 2017 PG - 17 SN - 1664-302X DO - 10.3389/fmicb.2017.01079 UR - https://m2.mtmt.hu/api/publication/3235885 ID - 3235885 LA - English DB - MTMT ER - TY - JOUR AU - Tombácz, Dóra AU - Csabai, Zsolt AU - Oláh, Péter AU - Balázs, Zsolt AU - Likó, I AU - Zsigmond, Laura AU - Sharon, D AU - Snyder, M AU - Boldogkői, Zsolt TI - Full-Length Isoform Sequencing Reveals Novel Transcripts and Substantial Transcriptional Overlaps in a Herpesvirus JF - PLOS ONE J2 - PLOS ONE VL - 11 PY - 2016 IS - 9 PG - 29 SN - 1932-6203 DO - 10.1371/journal.pone.0162868 UR - https://m2.mtmt.hu/api/publication/3120595 ID - 3120595 N1 - * Megosztott szerzőség LA - English DB - MTMT ER - TY - JOUR AU - Oláh, Péter AU - Tombácz, Dóra AU - Póka, Nándor AU - Csabai, Zsolt AU - Prazsák, István AU - Boldogkői, Zsolt TI - Characterization of pseudorabies virus transcriptome by Illumina sequencing JF - BMC MICROBIOLOGY J2 - BMC MICROBIOL VL - 15 PY - 2015 IS - 1 PG - 9 SN - 1471-2180 DO - 10.1186/s12866-015-0470-0 UR - https://m2.mtmt.hu/api/publication/2927502 ID - 2927502 AB - BACKGROUND: Pseudorabies virus is a widely-studied model organism of the Herpesviridae family, with a compact genome arrangement of 72 known coding sequences. In order to obtain an up-to-date genetic map of the virus, a combination of RNA-sequencing approaches were applied, as recent advancements in high-throughput sequencing methods have provided a wealth of information on novel RNA species and transcript isoforms, revealing additional layers of transcriptome complexity in several viral species. RESULTS: The total RNA content and polyadenylation landscape of pseudorabies virus were characterized for the first time at high coverage by Illumina high-throughput sequencing of cDNA samples collected during the lytic infectious cycle. As anticipated, nearly all of the viral genome was transcribed, with the exception of loci in the large internal and terminal repeats, and several small intergenic repetitive sequences. Our findings included a small novel polyadenylated non-coding RNA near an origin of replication, and the single-base resolution mapping of 3' UTRs across the viral genome. Alternative polyadenylation sites were found in a number of genes and a novel alternative splice site was characterized in the ep0 gene, while previously known splicing events were confirmed, yielding no alternative splice isoforms. Additionally, we detected the active polyadenylation of transcripts earlier believed to be transcribed as part of polycistronic RNAs. CONCLUSION: To the best of our knowledge, the present work has furnished the highest-resolution transcriptome map of an alphaherpesvirus to date, and reveals further complexities of viral gene expression, with the identification of novel transcript boundaries, alternative splicing of the key transactivator EP0, and a highly abundant, novel non-coding RNA near the lytic replication origin. These advances provide a detailed genetic map of PRV for future research. LA - English DB - MTMT ER - TY - JOUR AU - Tombácz, Dóra AU - Csabai, Zsolt AU - Oláh, Péter AU - Havelda, Zoltán AU - Sharon, D AU - Snyder, M AU - Boldogkői, Zsolt TI - Characterization of novel transcripts in pseudorabies virus JF - VIRUSES J2 - VIRUSES-BASEL VL - 7 PY - 2015 IS - 5 SP - 2727 EP - 2744 PG - 18 SN - 1999-4915 DO - 10.3390/v7052727 UR - https://m2.mtmt.hu/api/publication/2912894 ID - 2912894 LA - English DB - MTMT ER - TY - JOUR AU - Tombácz, Dóra AU - Sharon, D AU - Oláh, Péter AU - Csabai, Zsolt AU - Snyder, M AU - Boldogkői, Zsolt TI - Strain Kaplan of Pseudorabies Virus Genome Sequenced by PacBio Single-Molecule Real-Time Sequencing Technology JF - GENOME ANNOUNCEMENTS J2 - GENOME ANNOUNC VL - 2 PY - 2014 IS - 4 PG - 2 SN - 2169-8287 DO - 10.1128/genomeA.00628-14 UR - https://m2.mtmt.hu/api/publication/2756561 ID - 2756561 AB - Pseudorabies virus (PRV) is a neurotropic herpesvirus that causes Aujeszky's disease in pigs. PRV strains are widely used as transsynaptic tracers for mapping neural circuits. We present here the complete and fully annotated genome sequence of strain Kaplan of PRV, determined by Pacific Biosciences RSII long-read sequencing technology. LA - English DB - MTMT ER - TY - JOUR AU - Takács, Irma AU - Tombácz, Dóra AU - Berta, B AU - Prazsák, István AU - Póka, Nándor AU - Boldogkői, Zsolt TI - The ICP22 protein selectively modifies the transcription of different kinetic classes of pseudorabies virus genes JF - BMC MOLECULAR BIOLOGY J2 - BMC MOL BIOL VL - 14 PY - 2013 PG - 12 SN - 1471-2199 DO - 10.1186/1471-2199-14-2 UR - https://m2.mtmt.hu/api/publication/2332154 ID - 2332154 AB - Background: Pseudorabies virus (PRV), an alpha-herpesvirus of swine, is a widely used model organism in investigations of the molecular pathomechanisms of the herpesviruses. This work is the continuation of our earlier studies, in which we investigated the effect of the abrogation of gene function on the viral transcriptome by knocking out PRV genes playing roles in the coordination of global gene expression of the virus. In this study, we deleted the us1 gene encoding the ICP22, an important viral regulatory protein, and analyzed the changes in the expression of other PRV genes.Results: A multi-timepoint real-time RT-PCR technique was applied to evaluate the impact of deletion of the PRV us1 gene on the overall transcription kinetics of viral genes. The mutation proved to exert a differential effect on the distinct kinetic classes of PRV genes at the various stages of lytic infection. In the us1 gene-deleted virus, all the kinetic classes of the genes were significantly down-regulated in the first hour of infection. After 2 to 6 h of infection, the late genes were severely suppressed, whereas the early genes were unaffected. In the late stage of infection, the early genes were selectively up-regulated. In the mutant virus, the transcription of the ie180 gene, the major coordinator of PRV gene expression, correlated closely with the transcription of other viral genes, a situation which was not found in the wild-type (wt) virus. A 4-h delay was observed in the commencement of DNA replication in the mutant virus as compared with the wt virus. The rate of transcription from a gene normalized to the relative copy number of the viral genome was observed to decline drastically following the initiation of DNA replication in both the wt and mutant backgrounds. Finally, the switch between the expressions of the early and late genes was demonstrated not to be controlled by DNA replication, as is widely believed, since the switch preceded the DNA replication.Conclusions: Our results show a strong dependence of PRV gene expression on the presence of functional us1 gene. ICP22 is shown to exert a differential effect on the distinct kinetic classes of PRV genes and to disrupt the close correlation between the transcription kinetics of ie180 and other PRV transcripts. Furthermore, DNA replication exerts a severe constraint on the viral transcription. © 2013 Takács et al; licensee BioMed Central Ltd. LA - English DB - MTMT ER - TY - JOUR AU - Boldogkői, Zsolt TI - Transcriptional interference networks coordinate the expression of functionally related genes clustered in the same genomic loci JF - FRONTIERS IN GENETICS J2 - FRONT GENET VL - 3 PY - 2012 PG - 17 SN - 1664-8021 DO - 10.3389/fgene.2012.00122 UR - https://m2.mtmt.hu/api/publication/2332155 ID - 2332155 AB - The regulation of gene expression is essential for normal functioning of biological systems in every form of life. Gene expression is primarily controlled at the level of transcription, especially at the phase of initiation. Non-coding RNAs are one of the major players at every level of genetic regulation, including the control of chromatin organization, transcription, various post-transcriptional processes, and translation. In this study, the Transcriptional Interference Network (TIN) hypothesis was put forward in an attempt to explain the global expression of antisense RNAs and the overall occurrence of tandem gene clusters in the genomes of various biological systems ranging from viruses to mammalian cells. The TIN hypothesis suggests the existence of a novel layer of genetic regulation, based on the interactions between the transcriptional machineries of neighboring genes at their overlapping regions, which are assumed to play a fundamental role in coordinating gene expression within a cluster of functionally linked genes. It is claimed that the transcriptional overlaps between adjacent genes are much more widespread in genomes than is thought today. The Waterfall model of the TIN hypothesis postulates a unidirectional effect of upstream genes on the transcription of downstream genes within a cluster of tandemly arrayed genes, while the Seesaw model proposes a mutual interdependence of gene expression between the oppositely oriented genes. The TIN represents an auto-regulatory system with an exquisitely timed and highly synchronized cascade of gene expression in functionally linked genes located in close physical proximity to each other. In this study, we focused on herpesviruses.The reason for this lies in the compressed nature of viral genes, which allows a tight regulation and an easier investigation of the transcriptional interactions between genes. However, I believe that the same or similar principles can be applied to cellular organisms too. © 2012 Boldogköi. LA - English DB - MTMT ER - TY - JOUR AU - Anderson, Bart R. AU - Muramatsu, Hiromi AU - Jha, Babal K. AU - Silverman, Robert H. AU - Weissman, Drew AU - Karikó, Katalin TI - Nucleoside modifications in RNA limit activation of 2'-5'-oligoadenylate synthetase and increase resistance to cleavage by RNase L JF - NUCLEIC ACIDS RESEARCH J2 - NUCLEIC ACIDS RES VL - 39 PY - 2011 IS - 21 SP - 9329 EP - 9338 PG - 10 SN - 0305-1048 DO - 10.1093/nar/gkr586 UR - https://m2.mtmt.hu/api/publication/32039143 ID - 32039143 N1 - Funding Agency and Grant Number: National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [R01AI50484, R21DE019059, T32GM07229, T32DK07748, T32RR007063, R01NS029331, R42HL87688, R01CA044059]; NATIONAL CANCER INSTITUTEUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Cancer Institute (NCI) [R01CA044059] Funding Source: NIH RePORTER; NATIONAL CENTER FOR RESEARCH RESOURCESUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Center for Research Resources (NCRR) [T32RR007063] Funding Source: NIH RePORTER; NATIONAL HEART, LUNG, AND BLOOD INSTITUTEUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Heart Lung & Blood Institute (NHLBI) [R42HL087688] Funding Source: NIH RePORTER; NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASESUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Allergy & Infectious Diseases (NIAID) [R01AI050484] Funding Source: NIH RePORTER; NATIONAL INSTITUTE OF DENTAL &CRANIOFACIAL RESEARCHUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Dental & Craniofacial Research (NIDCR) [R21DE019059] Funding Source: NIH RePORTER; NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASESUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Diabetes & Digestive & Kidney Diseases (NIDDK) [T32DK007748] Funding Source: NIH RePORTER; NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCESUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of General Medical Sciences (NIGMS) [T32GM007229] Funding Source: NIH RePORTER; NATIONAL INSTITUTE OF NEUROLOGICAL DISORDERS AND STROKEUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USANIH National Institute of Neurological Disorders & Stroke (NINDS) [R01NS029331] Funding Source: NIH RePORTER Funding text: National Institutes of Health (R01AI50484 and R21DE019059 to D.W.; T32GM07229, T32DK07748 and T32RR007063 to B.R.A.; R01NS029331 and R42HL87688 to K.K.; R01CA044059 to R.H.S). Funding for open access charge: National Institutes of Health (grant R42HL87688 to K.K.). Department of Medicine, University of Pennsylvania, 3610 Hamilton Walk, 522B Johnson Pavilion, Philadelphia, PA 19104, United States Department of Neurosurgery, 371 Stemmler Hall, University of Pennsylvania, Philadelphia, PA 19104, United States Department of Cancer Biology NB40, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, United States Cited By :99 Export Date: 28 May 2021 CODEN: NARHA Correspondence Address: Karikó, K.; Department of Neurosurgery, , Philadelphia, PA 19104, United States; email: kariko@mail.med.upenn.edu AB - The interferon-induced enzymes 2'-5'-oligoadenylate synthetase (OAS) and RNase L are key components of innate immunity involved in sensory and effector functions following viral infections. Upon binding target RNA, OAS is activated to produce 2'-5'-linked oligoadenylates (2-5A) that activate RNase L, which then cleaves single-stranded self and non-self RNA. Modified nucleosides that are present in cellular transcripts have been shown to suppress activation of several RNA sensors. Here, we demonstrate that in vitro transcribed, unmodified RNA activates OAS, induces RNase L-mediated ribosomal RNA (rRNA) cleavage and is rapidly cleaved by RNase L. In contrast, RNA containing modified nucleosides activates OAS less efficiently and induces limited rRNA cleavage. Nucleoside modifications also make RNA resistant to cleavage by RNase L. Examining translation in RNase L-/- cells and mice confirmed that RNase L activity reduces translation of unmodified mRNA, which is not observed with modified mRNA. Additionally, mRNA containing the nucleoside modification pseudouridine is translated longer and has an extended half-life. The observation that modified nucleosides in RNA reduce 2-5A pathway activation joins OAS and RNase L to the list of RNA sensors and effectors whose functions are limited when RNA is modified, confirming the role of nucleoside modifications in suppressing immune recognition of RNA. LA - English DB - MTMT ER - TY - JOUR AU - Tombácz, Dóra AU - Toth, JS AU - Petrovszki, P AU - Boldogkői, Zsolt TI - Whole-genome analysis of pseudorabies virus gene expression by real-time quantitative RT-PCR assay JF - BMC GENOMICS J2 - BMC GENOMICS VL - 10 PY - 2009 PG - 22 SN - 1471-2164 DO - 10.1186/1471-2164-10-491 UR - https://m2.mtmt.hu/api/publication/1882591 ID - 1882591 LA - English DB - MTMT ER - TY - JOUR AU - Karikó, Katalin AU - Buckstein, M. AU - Ni, H. AU - Weissman, D. TI - Suppression of RNA recognition by Toll-like receptors: The impact of nucleoside modification and the evolutionary origin of RNA JF - IMMUNITY J2 - IMMUNITY VL - 23 PY - 2005 IS - 2 SP - 165 EP - 175 PG - 11 SN - 1074-7613 DO - 10.1016/j.immuni.2005.06.008 UR - https://m2.mtmt.hu/api/publication/32039262 ID - 32039262 AB - DNA and RNA stimulate the mammalian innate immune system through activation of Toll-like receptors (TLRs). DNA containing methylated CpG motifs, however, is not stimulatory. Selected nucleosides in naturally occurring RNA are also methylated or otherwise modified, but the immunomodulatory effects of these alterations remain untested. We show that RNA signals through human TLR3, TLR7, and TLR8, but incorporation of modified nucleosides m5C, m6A, m5U, s2U, or pseudouridine ablates activity. Dendritic cells (DCs) exposed to such modified RNA express significantly less cytokines and activation markers than those treated with unmodified RNA. DCs and TLR-expressing cells are potently activated by bacterial and mitochondrial RNA, but not by mammalian total RNA, which is abundant in modified nucleosides. We conclude that nucleoside modifications suppress the potential of RNA to activate DCs. The innate immune system may therefore detect RNA lacking nucleoside modification as a means of selectively responding to bacteria or necrotic tissue. Copyright ©2005 by Elsevier Inc. LA - English DB - MTMT ER -