Defining the Temporal Transcriptomic Landscape of a Viral Pathogen through Nanopore and CAGE sequencing

Defining the Temporal Transcriptomic Landscape of a Viral Pathogen through Nanopore and CAGE sequencing | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Defining the Temporal Transcriptomic Landscape of a Viral Pathogen through Nanopore and CAGE sequencing Dóra Tombácz, Balázs Kakuk, Gábor Torma, Ádám Fülöp, Ákos Dörmő, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4648105/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract A member of the Varicellovirus genus of herpesviruses, equid alphaherpesvirus 1 (EHV-1) was subjected to timescale profiling in this research. We employed cap analysis gene expression sequencing (CAGE-Seq) on Illumina platform to determine the transcript start sites alongside long-read direct cDNA sequencing (dcDNA-Seq) on Oxford Nanopore Technology platform to detect full-length viral transcripts. Samples were collected at nine distinct stages of the viral lifecycle, with triplicates taken at each stage. We also applied protein synthesis inhibition to determine the immediate-early gene expression of the virus. Analysis of the time-course expression of the viral transcripts using dcDNA-Seq allowed their kinetic categorization. Moreover, the EHV-1 transcriptome was reannotated using CAGE-Seq, long-read dcDNA-Seq, and our previous data obtained from native RNA sequencing. Biological sciences/Genetics Biological sciences/Microbiology Equid herpesvirus 1 EHV-1 transcriptome long-read sequencing nanopore sequencing direct cDNA-sequencing CAGE-Seq kinetic classes Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementaryFilles.zip Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4648105","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":329762537,"identity":"d18ae745-1991-4863-87c9-7625ad9f1afe","order_by":0,"name":"Dóra Tombácz","email":"","orcid":"","institution":"University of Szeged","correspondingAuthor":false,"prefix":"","firstName":"Dóra","middleName":"","lastName":"Tombácz","suffix":""},{"id":329762542,"identity":"7265e74b-7af5-4466-a8fb-48f93fea44db","order_by":1,"name":"Balázs Kakuk","email":"","orcid":"","institution":"University of 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