{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T18:03:59Z","timestamp":1789581839637,"version":"build-2803163510"},"reference-count":155,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH","award":["R01 AI 141968"],"award-info":[{"award-number":["R01 AI 141968"]}]},{"name":"NIH","award":["R01 AI 048633"],"award-info":[{"award-number":["R01 AI 048633"]}]},{"name":"NIH","award":["R21 AI 148926"],"award-info":[{"award-number":["R21 AI 148926"]}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>We used precision nuclear run-on with sequencing (PRO-seq) in conjunction with quantitative RT-qPCR to map transcription, and transcript abundance in terminally differentiated LUHMES neurons before (mock) and after infection with Herpes Simplex Virus 1 (HSV-1). Initial PRO-seq analysis of cellular transcription demonstrated that the mock-infected differentiated LUHMES neurons expressed genes associated with differentiated neurons. This gene set included transcription of genes related to dopaminergic signaling, cell adhesion, and neuronal cell differentiation. By contrast, epithelial cells transcribed genes involved in cell cycle progression and DNA damage repair. PRO-Seq analysis of HSV-1-infected LUHMES neurons indicated only modest transcription of viral genomes. Additionally, genes of LUHMES neurons maintained RNA polymerase II (Pol II) promoter proximal pausing whereas we previously showed HSV-1 infection decreases promoter-proximal pausing on genes of epithelial cells. PRO-Seq and RT-qPCRanalysis were performed during a time course of infection, spanning both acute and latent phases. The results from the acute infection demonstrated slower rates of transcription, viral mRNA accumulation, and viral genome replication compared to undifferentiated, non-neuronal cells. RT-qPCR indicated that steady-state transcripts from all viral gene kinetic classes increased in abundance from 1 h to 24 h post-infection. This accumulation correlated with an increase in transcription on the same genes as demonstrated by PRO-seq. In contrast, the latent phase of infection was distinguished by high levels of transcription on all viral genes, but very low viral transcript abundance. These results indicate that viral gene transcription initiation does not correlate with viral transcript abundance during the latent phase, and suggest that blocks to RNA polymerase processivity and other components of the RNA life cycle likely contribute to maintenance of latency in LUHMES neurons.<\/jats:p>","DOI":"10.1371\/journal.ppat.1014603","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T17:37:38Z","timestamp":1789580258000},"page":"e1014603","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Analysis of host and viral nascent and steady-state RNA levels in a human neuronal model of herpes simplex virus 1 infection"],"prefix":"10.1371","volume":"22","author":[{"given":"Claire H.","family":"Birkenheuer","sequence":"first","affiliation":[{"name":"Cornell University Baker Institute for Animal Health","place":["Ithaca, New York, United States of America"],"department":["Department of Microbiology and Immunology"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Terri G.","family":"Edwards","sequence":"additional","affiliation":[{"name":"University of Florida","place":["Gainesville, Florida, United States of America"],"department":["Department of Molecular Genetics and Microbiology"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David C.","family":"Bloom","sequence":"additional","affiliation":[{"name":"University of Florida","place":["Gainesville, Florida, United States of America"],"department":["Department of Molecular Genetics and Microbiology"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6397-2830","authenticated-orcid":true,"given":"Joel D.","family":"Baines","sequence":"additional","affiliation":[{"name":"Cornell University Baker Institute for Animal Health","place":["Ithaca, New York, United States of America"],"department":["Department of Microbiology and Immunology"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,9,16]]},"reference":[{"key":"ppat.1014603.ref001","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511545313.033","article-title":"Pathogenesis and disease.","volume-title":"Human herpesviruses: biology, therapy, and immunoprophylaxis","author":"R Whitley","year":"2007"},{"key":"ppat.1014603.ref002","first-page":"2381","article-title":"The Family Herpesviridae: A Brief Introduction.","volume-title":"Fields Virology","author":"B Roizman","year":"2001","edition":"4"},{"issue":"1","key":"ppat.1014603.ref003","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1128\/jvi.14.1.8-19.1974","article-title":"Regulation of herpesvirus macromolecular synthesis. 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Sawtell","year":"2016","journal-title":"F1000Res"},{"issue":"6","key":"ppat.1014603.ref022","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.02210-18","article-title":"Lund Human Mesencephalic (LUHMES) Neuronal Cell Line Supports Herpes Simplex Virus 1 Latency In Vitro","volume":"93","author":"TG Edwards","year":"2019","journal-title":"J Virol"},{"issue":"12","key":"ppat.1014603.ref023","doi-asserted-by":"crossref","first-page":"6056","DOI":"10.1128\/JVI.02661-07","article-title":"During herpes simplex virus type 1 infection of rabbits, the ability to express the latency-associated transcript increases latent-phase transcription of lytic genes","volume":"82","author":"NV Giordani","year":"2008","journal-title":"J Virol"},{"issue":"12","key":"ppat.1014603.ref024","doi-asserted-by":"crossref","DOI":"10.1128\/jvi.00508-22","article-title":"DLK-Dependent Biphasic Reactivation of Herpes Simplex Virus Latency Established in the Absence of Antivirals","volume":"96","author":"S Dochnal","year":"2022","journal-title":"J Virol"},{"issue":"6648","key":"ppat.1014603.ref025","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1038\/38444","article-title":"Crystal structure of the nucleosome core particle at 2.8 A resolution","volume":"389","author":"K Luger","year":"1997","journal-title":"Nature"},{"issue":"6","key":"ppat.1014603.ref026","first-page":"704","article-title":"Nucleosomes: the structural quantum in chromosomes","volume":"66","author":"DE Olins","year":"1978","journal-title":"Am Sci"},{"issue":"3","key":"ppat.1014603.ref027","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/S0092-8674(00)81958-3","article-title":"Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosome","volume":"98","author":"RD Kornberg","year":"1999","journal-title":"Cell"},{"issue":"1","key":"ppat.1014603.ref028","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/s12915-021-00949-x","article-title":"Characterizing RNA 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Wu","year":"2024","journal-title":"Nat Commun"},{"issue":"18","key":"ppat.1014603.ref035","doi-asserted-by":"crossref","first-page":"10747","DOI":"10.1093\/nar\/gkae764","article-title":"Striving for clarity in language about gene expression","volume":"52","author":"ASG Cunningham","year":"2024","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"ppat.1014603.ref036","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1016\/j.tig.2012.02.005","article-title":"Overcoming the nucleosome barrier during transcript elongation","volume":"28","author":"SJ Petesch","year":"2012","journal-title":"Trends Genet"},{"issue":"9","key":"ppat.1014603.ref037","doi-asserted-by":"crossref","first-page":"664","DOI":"10.1016\/j.tig.2020.05.008","article-title":"Termination of Transcription by RNA Polymerase II: BOOM!","volume":"36","author":"JD Eaton","year":"2020","journal-title":"Trends 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Kwak","year":"2013","journal-title":"Science"},{"issue":"8","key":"ppat.1014603.ref044","doi-asserted-by":"crossref","first-page":"1455","DOI":"10.1038\/nprot.2016.086","article-title":"Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)","volume":"11","author":"DB Mahat","year":"2016","journal-title":"Nat Protoc"},{"issue":"6","key":"ppat.1014603.ref045","doi-asserted-by":"crossref","DOI":"10.1128\/jvi.00712-24","article-title":"Aberrant RNA polymerase initiation and processivity on the genome of a herpes simplex virus 1 mutant lacking ICP27","volume":"98","author":"CH Birkenheuer","year":"2024","journal-title":"J Virol"},{"issue":"8","key":"ppat.1014603.ref046","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.02184-17","article-title":"Herpes Simplex Virus 1 Dramatically Alters Loading and Positioning of RNA Polymerase II on Host Genes Early in Infection","volume":"92","author":"CH Birkenheuer","year":"2018","journal-title":"J Virol"},{"key":"ppat.1014603.ref047","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.00796-20","article-title":"Herpes Simplex Virus 1 Strains 17syn and KOS(M) Differ Greatly in Their Ability to Reactivate from Human Neurons In Vitro","volume":"94","author":"TR Grams","year":"2020","journal-title":"J Virol"},{"issue":"2","key":"ppat.1014603.ref048","doi-asserted-by":"crossref","DOI":"10.1128\/jvi.01935-22","article-title":"HSV-1 LAT Promoter Deletion Viruses Exhibit Strain-Specific and LAT-Dependent Epigenetic Regulation of Latent Viral Genomes in Human Neurons","volume":"97","author":"TR Grams","year":"2023","journal-title":"J Virol"},{"issue":"12","key":"ppat.1014603.ref049","doi-asserted-by":"crossref","DOI":"10.1128\/jvi.01438-23","article-title":"A viral lncRNA tethers HSV-1 genomes at the nuclear periphery to establish viral latency","volume":"97","author":"TR Grams","year":"2023","journal-title":"J Virol"},{"key":"ppat.1014603.ref050","doi-asserted-by":"crossref","first-page":"104621","DOI":"10.1016\/j.antiviral.2019.104621","article-title":"Virtual screening identified compounds that bind to cyclin dependent kinase 2 and prevent herpes simplex virus type 1 replication and reactivation in neurons","volume":"172","author":"DJ Viegas","year":"2019","journal-title":"Antiviral Res"},{"issue":"13","key":"ppat.1014603.ref051","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.00415-19","article-title":"The CCCTC Binding Factor, CTRL2, Modulates Heterochromatin Deposition and the Establishment of Herpes Simplex Virus 1 Latency In Vivo","volume":"93","author":"SD Washington","year":"2019","journal-title":"J Virol"},{"issue":"5","key":"ppat.1014603.ref052","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1111\/j.1471-4159.2011.07255.x","article-title":"Rapid, complete and large-scale generation of post-mitotic neurons from the human LUHMES cell line","volume":"119","author":"D Scholz","year":"2011","journal-title":"J Neurochem"},{"issue":"5","key":"ppat.1014603.ref053","doi-asserted-by":"crossref","DOI":"10.1128\/jvi.02191-21","article-title":"ICP22 of Herpes Simplex Virus 1 Decreases RNA Polymerase Processivity","volume":"96","author":"CH Birkenheuer","year":"2022","journal-title":"J Virol"},{"issue":"22","key":"ppat.1014603.ref054","article-title":"Immediate Early Proteins of Herpes Simplex Virus Transiently Repress Viral Transcription before Subsequent Activation","volume":"96","author":"LEM Dunn","year":"2022","journal-title":"J Virol"},{"issue":"5","key":"ppat.1014603.ref055","doi-asserted-by":"crossref","first-page":"1272","DOI":"10.3390\/v5051272","article-title":"The dynamics of HCF-1 modulation of herpes simplex virus chromatin during initiation of infection","volume":"5","author":"JL 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Hargett","year":"2006","journal-title":"The Journal of Virology"},{"issue":"23","key":"ppat.1014603.ref059","doi-asserted-by":"crossref","first-page":"11954","DOI":"10.1128\/JVI.01639-15","article-title":"Differential Reovirus-Specific and Herpesvirus-Specific Activator Protein 1 Activation of Secretogranin II Leads to Altered Virus Secretion","volume":"89","author":"AR Berard","year":"2015","journal-title":"J Virol"},{"issue":"1","key":"ppat.1014603.ref060","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1016\/j.yexcr.2005.04.016","article-title":"Activation of c-Jun N-terminal kinase (JNK) pathway by HSV-1 immediate early protein ICP0","volume":"308","author":"L Diao","year":"2005","journal-title":"Exp Cell Res"},{"issue":"4","key":"ppat.1014603.ref061","doi-asserted-by":"crossref","first-page":"706","DOI":"10.9734\/BMRJ\/2013\/4817","article-title":"Induction of Transcription Factor Early Growth Response Protein 1 during HSV-1 Infection Promotes Viral Replication in Corneal Cells","volume":"3","author":"SC Hsia","year":"2013","journal-title":"Br Microbiol Res J"},{"issue":"11","key":"ppat.1014603.ref062","doi-asserted-by":"crossref","first-page":"2296","DOI":"10.3390\/v13112296","article-title":"Stress Induced Transcription Factors Transactivate the Herpes Simplex Virus 1 Infected Cell Protein 27 (ICP27) Transcriptional Enhancer","volume":"13","author":"JB Ostler","year":"2021","journal-title":"Viruses"},{"issue":"10","key":"ppat.1014603.ref063","doi-asserted-by":"crossref","DOI":"10.1128\/MCB.00171-21","article-title":"The Herpes Simplex Virus 1 Protein ICP4 Acts as both an Activator and a Repressor of Host Genome Transcription during Infection","volume":"41","author":"T Rivas","year":"2021","journal-title":"Mol Cell Biol"},{"issue":"5","key":"ppat.1014603.ref064","doi-asserted-by":"crossref","first-page":"2503","DOI":"10.1128\/JVI.02665-15","article-title":"Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II 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Zhang","year":"2026","journal-title":"Biometrics"},{"issue":"17","key":"ppat.1014603.ref071","doi-asserted-by":"crossref","first-page":"8105","DOI":"10.1128\/JVI.75.17.8105-8116.2001","article-title":"RNAs extracted from herpes simplex virus 1 virions: apparent selectivity of viral but not cellular RNAs packaged in virions","volume":"75","author":"MT Sciortino","year":"2001","journal-title":"J Virol"},{"issue":"12","key":"ppat.1014603.ref072","doi-asserted-by":"crossref","first-page":"8318","DOI":"10.1073\/pnas.122231699","article-title":"Of the three tegument proteins that package mRNA in herpes simplex virions, one (VP22) transports the mRNA to uninfected cells for expression prior to viral infection","volume":"99","author":"MT Sciortino","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ppat.1014603.ref073","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1016\/S0168-1702(01)00355-0","article-title":"Assessment of the subcellular localization of the herpes 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interacts with the lytic HSV-1 genome to promote viral transcription","volume":"7","author":"F Lang","year":"2017","journal-title":"Sci Rep"},{"issue":"11","key":"ppat.1014603.ref077","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.00173-18","article-title":"Depletion of the Insulator Protein CTCF Results in Herpes Simplex Virus 1 Reactivation In Vivo","volume":"92","author":"SD Washington","year":"2018","journal-title":"J Virol"},{"issue":"11","key":"ppat.1014603.ref078","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.00364-21","article-title":"Cohesin subunit Rad21 binds to the HSV-1 genome near CTCF insulator sites during latency in vivo","volume":"95","author":"P Singh","year":"2021","journal-title":"J Virol"},{"issue":"5","key":"ppat.1014603.ref079","doi-asserted-by":"crossref","first-page":"4250","DOI":"10.1128\/JVI.72.5.4250-4264.1998","article-title":"A virus with a mutation in the ICP4-binding site in the L\/ST promoter of herpes simplex virus type 1, but not a virus with a mutation in open reading frame P, exhibits cell-type-specific expression of gamma(1)34.5 transcripts and latency-associated transcripts","volume":"72","author":"LY Lee","year":"1998","journal-title":"J Virol"},{"issue":"19","key":"ppat.1014603.ref080","doi-asserted-by":"crossref","first-page":"10423","DOI":"10.1073\/pnas.93.19.10423","article-title":"Open reading frame P--a herpes simplex virus gene repressed during productive infection encodes a protein that binds a splicing factor and reduces synthesis of viral proteins made from spliced mRNA","volume":"93","author":"R Bruni","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"3","key":"ppat.1014603.ref081","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1009441","article-title":"Viral infection of human neurons triggers strain-specific differences in host neuronal and viral transcriptomes","volume":"17","author":"CA Mangold","year":"2021","journal-title":"PLoS Pathog"},{"issue":"23","key":"ppat.1014603.ref082","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.00958-17","article-title":"Differentiated Human SH-SY5Y Cells Provide a Reductionist Model of Herpes Simplex Virus 1 Neurotropism","volume":"91","author":"MM Shipley","year":"2017","journal-title":"J Virol"},{"key":"ppat.1014603.ref083","first-page":"45","article-title":"Individual HSV transcripts. Characterization of specific genes.","volume-title":"The Herpesviruses","author":"EK. Wagner","year":"1984"},{"issue":"4","key":"ppat.1014603.ref084","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1128\/jvi.10.4.675-682.1972","article-title":"Transcription of the herpes simplex virus genome in human cells","volume":"10","author":"EK Wagner","year":"1972","journal-title":"J Virol"},{"issue":"1","key":"ppat.1014603.ref085","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1006\/viro.1998.9036","article-title":"Atypical splicing of the latency-associated transcripts of herpes simplex type 1","volume":"243","author":"TT Wu","year":"1998","journal-title":"Virology"},{"issue":"10","key":"ppat.1014603.ref086","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1012621","article-title":"The HSV-1 encoded CCCTC-binding factor, CTRL2, impacts the nature of viral chromatin during HSV-1 lytic infection","volume":"20","author":"P Singh","year":"2024","journal-title":"PLoS Pathog"},{"issue":"12","key":"ppat.1014603.ref087","doi-asserted-by":"crossref","first-page":"1123","DOI":"10.1080\/14787210.2024.2420329","article-title":"The opportunities and challenges of epigenetic approaches to manage herpes simplex infections","volume":"22","author":"SM Saddoris","year":"2024","journal-title":"Expert Rev Anti Infect Ther"},{"issue":"11","key":"ppat.1014603.ref088","doi-asserted-by":"crossref","DOI":"10.1128\/jvi.01258-24","article-title":"Lytic promoter activity during herpes simplex virus latency is dependent on genome location","volume":"98","author":"N Singh","year":"2024","journal-title":"J Virol"},{"issue":"3","key":"ppat.1014603.ref089","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1038\/s41588-022-01026-x","article-title":"Prediction of histone post-translational modification patterns based on nascent transcription data","volume":"54","author":"Z Wang","year":"2022","journal-title":"Nat Genet"},{"issue":"10","key":"ppat.1014603.ref090","doi-asserted-by":"crossref","DOI":"10.1016\/j.molcel.2023.04.014","article-title":"Co-transcriptional genome surveillance by HUSH is coupled to termination machinery","volume":"83","author":"AL Spencley","year":"2023","journal-title":"Mol Cell"},{"issue":"1","key":"ppat.1014603.ref091","doi-asserted-by":"crossref","first-page":"2762","DOI":"10.1038\/s41467-023-38359-y","article-title":"The NELF pausing checkpoint mediates the functional divergence of Cdk9","volume":"14","author":"M DeBerardine","year":"2023","journal-title":"Nat Commun"},{"issue":"4","key":"ppat.1014603.ref092","doi-asserted-by":"crossref","DOI":"10.1016\/j.chom.2017.03.007","article-title":"Transcriptional Elongation of HSV Immediate Early Genes by the Super Elongation Complex Drives Lytic Infection and Reactivation from Latency","volume":"21","author":"R Alfonso-Dunn","year":"2017","journal-title":"Cell Host Microbe"},{"issue":"5909","key":"ppat.1014603.ref093","doi-asserted-by":"crossref","first-page":"1845","DOI":"10.1126\/science.1162228","article-title":"Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters","volume":"322","author":"LJ Core","year":"2008","journal-title":"Science"},{"issue":"1","key":"ppat.1014603.ref094","article-title":"Discovering Transcriptional Regulatory Elements From Run-On and Sequencing Data Using the Web-Based dREG Gateway","volume":"66","author":"T Chu","year":"2019","journal-title":"Curr Protoc Bioinformatics"},{"issue":"6","key":"ppat.1014603.ref095","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1000116","article-title":"Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes","volume":"4","author":"CR Farthing","year":"2008","journal-title":"PLoS Genet"},{"key":"ppat.1014603.ref096","unstructured":"Andrews S. SeqMonk (1.48.1). Babraham Institute."},{"issue":"5","key":"ppat.1014603.ref097","doi-asserted-by":"crossref","first-page":"2503","DOI":"10.1128\/JVI.02665-15","article-title":"Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome","volume":"90","author":"RG Abrisch","year":"2015","journal-title":"J Virol"},{"issue":"12","key":"ppat.1014603.ref098","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"MI Love","year":"2014","journal-title":"Genome Biol"},{"key":"ppat.1014603.ref099","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkac194","article-title":"DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)","volume":"50","author":"BT Sherman","year":"2022","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"ppat.1014603.ref100","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"H Thorvaldsd\u00f3ttir","year":"2013","journal-title":"Brief Bioinform"},{"key":"ppat.1014603.ref101","unstructured":"SAS. SAS JMP (JMP PRO 14.1.0). 2018."},{"issue":"1","key":"ppat.1014603.ref102","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"DW Huang","year":"2009","journal-title":"Nat Protoc"},{"key":"ppat.1014603.ref103","article-title":"Participation of the TBP\u2010associated factors (TAFs) in cell differentiation","volume":"239","author":"JP Luna\u2010Arias","year":"2024","journal-title":"Journal Cellular Physiology"},{"key":"ppat.1014603.ref104","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1004939","article-title":"Selective recruitment of nuclear factors to productively replicating herpes simplex virus genomes","volume":"11","author":"JA Dembowski","year":"2015","journal-title":"PLoS 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Virol"},{"key":"ppat.1014603.ref108","doi-asserted-by":"crossref","first-page":"2383","DOI":"10.1101\/gad.4.12b.2383","article-title":"Interactions of the Oct-1 POU subdomains with specific DNA sequences and with the HSV alpha-trans-activator protein","volume":"4","author":"TM Kristie","year":"1990","journal-title":"Genes Dev"},{"issue":"24","key":"ppat.1014603.ref109","doi-asserted-by":"crossref","first-page":"4135","DOI":"10.1128\/MCB.00477-15","article-title":"Genomic Determinants of THAP11\/ZNF143\/HCFC1 Complex Recruitment to Chromatin","volume":"35","author":"A Vinckevicius","year":"2015","journal-title":"Mol Cell Biol"},{"issue":"22","key":"ppat.1014603.ref110","doi-asserted-by":"crossref","first-page":"5260","DOI":"10.1128\/MCB.00484-10","article-title":"Chromatin loading of E2F-MLL complex by cancer-associated coregulator ANCCA via reading a specific histone mark","volume":"30","author":"AS Revenko","year":"2010","journal-title":"Mol Cell Biol"},{"issue":"10","key":"ppat.1014603.ref111","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/s41419-020-03094-5","article-title":"HCF-1 promotes cell cycle progression by regulating the expression of CDC42","volume":"11","author":"P Xiang","year":"2020","journal-title":"Cell Death Dis"},{"issue":"1","key":"ppat.1014603.ref112","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1006166","article-title":"Replication-Coupled Recruitment of Viral and Cellular Factors to Herpes Simplex Virus Type 1 Replication Forks for the Maintenance and Expression of Viral Genomes","volume":"13","author":"JA Dembowski","year":"2017","journal-title":"PLoS Pathog"},{"issue":"4","key":"ppat.1014603.ref113","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1111\/1348-0421.13120","article-title":"MYBBP1A is required for efficient replication and gene expression of herpes simplex virus 1","volume":"68","author":"M Nobe","year":"2024","journal-title":"Microbiol Immunol"},{"issue":"3","key":"ppat.1014603.ref114","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1016\/j.jmb.2006.11.099","article-title":"MYBBP1a is a novel repressor of NF-kappaB","volume":"366","author":"HR Owen","year":"2007","journal-title":"J Mol Biol"},{"issue":"3","key":"ppat.1014603.ref115","doi-asserted-by":"crossref","first-page":"278","DOI":"10.1101\/gad.1152204","article-title":"Suppression of mitochondrial respiration through recruitment of p160 myb binding protein to PGC-1alpha: modulation by p38 MAPK","volume":"18","author":"M Fan","year":"2004","journal-title":"Genes Dev"},{"issue":"29","key":"ppat.1014603.ref116","doi-asserted-by":"crossref","first-page":"12163","DOI":"10.1073\/pnas.0705245104","article-title":"Interaction of herpes simplex virus RNase with VP16 and VP22 is required for the accumulation of the protein but not for accumulation of mRNA","volume":"104","author":"B Taddeo","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"9","key":"ppat.1014603.ref117","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.3390\/pathogens12091126","article-title":"HSV-1 Triggers an Antiviral Transcriptional Response during Viral Replication That Is Completely Abrogated in PKR-\/- Cells","volume":"12","author":"R Pennisi","year":"2023","journal-title":"Pathogens"},{"issue":"7887","key":"ppat.1014603.ref118","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1038\/s41586-021-04054-5","article-title":"Self-guarding of MORC3 enables virulence factor-triggered immunity","volume":"600","author":"MM Gaidt","year":"2021","journal-title":"Nature"},{"issue":"14","key":"ppat.1014603.ref119","doi-asserted-by":"crossref","first-page":"5150","DOI":"10.3390\/ijms21145150","article-title":"Herpes Simplex Virus Type 1 Interactions with the Interferon System","volume":"21","author":"K Danastas","year":"2020","journal-title":"Int J Mol 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1 lacking the virion host shutoff gene","volume":"99","author":"B Taddeo","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ppat.1014603.ref123","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1016\/S0168-1702(02)00058-8","article-title":"Transactivation of the human endogenous retrovirus K long terminal repeat by herpes simplex virus type 1 immediate early protein 0","volume":"86","author":"HJ Kwun","year":"2002","journal-title":"Virus Res"},{"key":"ppat.1014603.ref124","doi-asserted-by":"crossref","first-page":"121986","DOI":"10.1016\/j.lfs.2023.121986","article-title":"Mediator complex in neurological disease","volume":"329","author":"C Schiano","year":"2023","journal-title":"Life Sci"},{"issue":"1","key":"ppat.1014603.ref125","doi-asserted-by":"crossref","DOI":"10.1101\/mcs.a006124","article-title":"MED13L-related intellectual disability due to paternal germinal mosaicism","volume":"8","author":"B Bessenyei","year":"2022","journal-title":"Cold Spring Harb Mol Case Stud"},{"issue":"16","key":"ppat.1014603.ref126","doi-asserted-by":"crossref","DOI":"10.15252\/embj.2019102509","article-title":"The SAGA complex regulates early steps in transcription via its deubiquitylase module subunit USP22","volume":"40","author":"TJ Stanek","year":"2021","journal-title":"EMBO J"},{"issue":"18","key":"ppat.1014603.ref127","doi-asserted-by":"crossref","first-page":"2119","DOI":"10.1101\/gad.285775.116","article-title":"Functional interplay between Mediator and TFIIB in preinitiation complex assembly in relation to promoter architecture","volume":"30","author":"T Eychenne","year":"2016","journal-title":"Genes Dev"},{"issue":"5","key":"ppat.1014603.ref128","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1016\/j.cub.2017.01.056","article-title":"The CDK8 Complex and Proneural Proteins Together Drive Neurogenesis from a Mesodermal Lineage","volume":"27","author":"S Luo","year":"2017","journal-title":"Curr Biol"},{"issue":"10","key":"ppat.1014603.ref129","doi-asserted-by":"crossref","first-page":"5450","DOI":"10.1128\/JVI.00464-15","article-title":"Retroviral cyclin controls cyclin-dependent kinase 8-mediated transcription elongation and reinitiation","volume":"89","author":"CH Birkenheuer","year":"2015","journal-title":"J Virol"},{"issue":"1","key":"ppat.1014603.ref130","doi-asserted-by":"crossref","first-page":"3326","DOI":"10.1038\/s41467-024-47623-8","article-title":"Cdk8\/CDK19 promotes mitochondrial fission through Drp1 phosphorylation and can phenotypically suppress pink1 deficiency in Drosophila","volume":"15","author":"JZ Liao","year":"2024","journal-title":"Nat Commun"},{"issue":"4","key":"ppat.1014603.ref131","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1010422","article-title":"Exploitation of the Mediator complex by viruses","volume":"18","author":"J Rovnak","year":"2022","journal-title":"PLoS Pathog"},{"issue":"22","key":"ppat.1014603.ref132","doi-asserted-by":"crossref","first-page":"10124","DOI":"10.1093\/nar\/gkt796","article-title":"The head module of Mediator directs activation of preloaded RNAPII in vivo","volume":"41","author":"SK Lee","year":"2013","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"ppat.1014603.ref133","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1530\/REP-18-0508","article-title":"MED20 is essential for early embryogenesis and regulates NANOG expression","volume":"157","author":"W Cui","year":"2019","journal-title":"Reproduction"},{"issue":"2","key":"ppat.1014603.ref134","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1038\/s41594-022-00883-8","article-title":"Signal-induced enhancer activation requires Ku70 to read topoisomerase1-DNA covalent complexes","volume":"30","author":"Y Tan","year":"2023","journal-title":"Nat Struct Mol Biol"},{"issue":"1","key":"ppat.1014603.ref135","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1016\/j.cell.2011.06.005","article-title":"Human mediator subunit MED26 functions as a docking site for transcription elongation factors","volume":"146","author":"H Takahashi","year":"2011","journal-title":"Cell"},{"key":"ppat.1014603.ref136","doi-asserted-by":"crossref","first-page":"591","DOI":"10.3389\/fneur.2018.00591","article-title":"Genome-Wide Association Study in Vestibular Neuritis: Involvement of the Host Factor for HSV-1 Replication","volume":"9","author":"D Rujescu","year":"2018","journal-title":"Front Neurol"},{"issue":"7861","key":"ppat.1014603.ref137","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1038\/s41586-021-03555-7","article-title":"Structure of the human Mediator-RNA polymerase II pre-initiation complex","volume":"594","author":"S Rengachari","year":"2021","journal-title":"Nature"},{"issue":"9","key":"ppat.1014603.ref138","article-title":"Mediator complex proximal Tail subunit MED30 is critical for Mediator core stability and cardiomyocyte transcriptional network","volume":"17","author":"C Tan","year":"2021","journal-title":"PLoS Genet"},{"issue":"4","key":"ppat.1014603.ref139","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1002\/jcb.240190404","article-title":"Regulation of herpes simplex virus gene transcription in vitro","volume":"19","author":"TW Beck","year":"1982","journal-title":"J Cell Biochem"},{"issue":"3","key":"ppat.1014603.ref140","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1099\/0022-1317-33-3-471","article-title":"The effects of herpes simplex virus type 1 on cellular DNA-dependent RNA polymerase activities","volume":"33","author":"CM Preston","year":"1976","journal-title":"J Gen Virol"},{"issue":"2","key":"ppat.1014603.ref141","doi-asserted-by":"crossref","first-page":"988","DOI":"10.1128\/jvi.68.2.988-1001.1994","article-title":"RNA polymerase II is aberrantly phosphorylated and localized to viral replication compartments following herpes simplex virus infection","volume":"68","author":"SA Rice","year":"1994","journal-title":"J Virol"},{"issue":"5","key":"ppat.1014603.ref142","doi-asserted-by":"crossref","first-page":"1032","DOI":"10.3390\/v15051032","article-title":"The Archer and the Prey: The Duality of PAF1C in Antiviral Immunity","volume":"15","author":"MW Kenaston","year":"2023","journal-title":"Viruses"},{"issue":"7720","key":"ppat.1014603.ref143","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1038\/s41586-018-0440-4","article-title":"Structure of activated transcription complex Pol II-DSIF-PAF-SPT6","volume":"560","author":"SM Vos","year":"2018","journal-title":"Nature"},{"issue":"2","key":"ppat.1014603.ref144","doi-asserted-by":"crossref","first-page":"262","DOI":"10.3390\/microorganisms12020262","article-title":"A Revision of Herpes Simplex Virus Type 1 Transcription: First, Repress; Then, Express","volume":"12","author":"LEM Dunn","year":"2024","journal-title":"Microorganisms"},{"issue":"37","key":"ppat.1014603.ref145","doi-asserted-by":"crossref","first-page":"15489","DOI":"10.1074\/jbc.M117.806000","article-title":"CDK9 and SPT5 proteins are specifically required for expression of herpes simplex virus 1 replication-dependent late genes","volume":"292","author":"Z Zhao","year":"2017","journal-title":"J Biol Chem"},{"issue":"14","key":"ppat.1014603.ref146","doi-asserted-by":"crossref","first-page":"166657","DOI":"10.1016\/j.jmb.2020.09.016","article-title":"Mechanisms of Transcription Elongation Factor DSIF (Spt4-Spt5)","volume":"433","author":"T-M Decker","year":"2021","journal-title":"J Mol Biol"},{"issue":"7720","key":"ppat.1014603.ref147","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1038\/s41586-018-0442-2","article-title":"Structure of paused transcription complex Pol II-DSIF-NELF","volume":"560","author":"SM 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