{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,19]],"date-time":"2026-01-19T01:18:29Z","timestamp":1768785509176,"version":"3.49.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1009796","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,8,12]],"date-time":"2021-08-12T00:00:00Z","timestamp":1628726400000}}],"reference-count":40,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2021,8,2]],"date-time":"2021-08-02T00:00:00Z","timestamp":1627862400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"DOI":"10.13039\/100000738","name":"U.S. Department of Veterans Affairs","doi-asserted-by":"publisher","award":["Merit award I01 BX004434"],"award-info":[{"award-number":["Merit award I01 BX004434"]}],"id":[{"id":"10.13039\/100000738","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["R21-AI130453"],"award-info":[{"award-number":["R21-AI130453"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Science","doi-asserted-by":"crossref","award":["R35-GM126908"],"award-info":[{"award-number":["R35-GM126908"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000060","name":"national institute of allergy and infectious diseases","doi-asserted-by":"publisher","award":["T32-AI007533"],"award-info":[{"award-number":["T32-AI007533"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>Beta- and gammaherpesviruses late transcription factors (LTFs) target viral promoters containing a TATT sequence to drive transcription after viral DNA replication has begun. Human cytomegalovirus (HCMV), a betaherpesvirus, uses the UL87 LTF to bind both TATT and host RNA polymerase II (Pol II), whereas the UL79 LTF has been suggested to drive productive elongation. Here we apply integrated functional genomics (dTag system, PRO-Seq, ChIP-Seq, and promoter function assays) to uncover the contribution of diversity in LTF target sequences in determining degree and scope to which LTFs drive viral transcription. We characterize the DNA sequence patterns in LTF-responsive and -unresponsive promoter populations, determine where and when Pol II initiates transcription, identify sites of LTF binding genome-wide, and quantify change in nascent transcripts from individual promoters in relation to core promoter sequences, LTF loss, stage of infection, and viral DNA replication. We find that HCMV UL79 and UL87 LTFs function concordantly to initiate transcription from over half of all active viral promoters in late infection, while not appreciably affecting host transcription. Both LTFs act on and bind to viral early-late and late kinetic-class promoters. Over one-third of these core promoters lack the TATT and instead have a TATAT, TGTT, or YRYT. The TATT and non-TATT motifs are part of a sequence block with a sequence code that correlates with promoter transcription level. LTF occupancy of a TATATA palindrome shared by back-to-back promoters is linked to bidirectional transcription. We conclude that diversity in LTF target sequences shapes the LTF-transformative program that drives the viral early-to-late transcription switch.<\/jats:p>","DOI":"10.1371\/journal.ppat.1009796","type":"journal-article","created":{"date-parts":[[2021,8,2]],"date-time":"2021-08-02T17:39:25Z","timestamp":1627925965000},"page":"e1009796","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["Cytomegalovirus late transcription factor target sequence diversity orchestrates viral early to late transcription"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0396-4078","authenticated-orcid":true,"given":"Ming","family":"Li","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6236-0261","authenticated-orcid":true,"given":"Qiaolin","family":"Hu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Geoffrey","family":"Collins","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2146-5101","authenticated-orcid":true,"given":"Mrutyunjaya","family":"Parida","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5983-1605","authenticated-orcid":true,"given":"Christopher B.","family":"Ball","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David H.","family":"Price","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9491-1697","authenticated-orcid":true,"given":"Jeffery L.","family":"Meier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2021,8,2]]},"reference":[{"key":"ppat.1009796.ref001","unstructured":"Resource VP . [November 28, 2020]. Available from: https:\/\/www.viprbrc.org\/brc\/home.spg?decorator=vipr."},{"issue":"1","key":"ppat.1009796.ref002","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1016\/j.virusres.2006.01.002","article-title":"Topics in herpesvirus genomics and evolution","volume":"117","author":"DJ McGeoch","year":"2006","journal-title":"Virus Res"},{"issue":"11","key":"ppat.1009796.ref003","doi-asserted-by":"crossref","first-page":"6023","DOI":"10.1128\/JVI.00159-12","article-title":"The Epstein-Barr virus BcRF1 gene product is a TBP-like protein with an essential role in late gene expression","volume":"86","author":"H Gruffat","year":"2012","journal-title":"J Virol"},{"issue":"2","key":"ppat.1009796.ref004","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1016\/j.molcel.2014.11.026","article-title":"Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes","volume":"57","author":"ZH Davis","year":"2015","journal-title":"Mol Cell"},{"issue":"9","key":"ppat.1009796.ref005","doi-asserted-by":"crossref","first-page":"e1008843","DOI":"10.1371\/journal.ppat.1008843","article-title":"The gammaherpesviral TATA-box-binding protein directly interacts with the CTD of host RNA Pol II to direct late gene transcription","volume":"16","author":"AF Castaneda","year":"2020","journal-title":"PLoS Pathog"},{"issue":"8","key":"ppat.1009796.ref006","doi-asserted-by":"crossref","first-page":"e1004350","DOI":"10.1371\/journal.ppat.1004350","article-title":"Human cytomegalovirus pUL79 is an elongation factor of RNA polymerase II for viral gene transcription","volume":"10","author":"YC Perng","year":"2014","journal-title":"PLoS Pathog"},{"key":"ppat.1009796.ref007","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.01488-18","article-title":"The interaction between ORF18 and ORF30 are required for late gene expression in kaposis sarcoma-associaed herpesvirus","volume":"93","author":"AF Castaneda","year":"2019","journal-title":"J Virol"},{"key":"ppat.1009796.ref008","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1099\/jgv.0.000676","article-title":"Proteomic and phylogenetic coevolution analyses of pM79 and pM92 identify interactions with RNA polymerase II and delineate the murine cytomegalovirus late transcription complex","volume":"98","author":"TJ Chapa","year":"2017","journal-title":"J Gen Virol"},{"issue":"8","key":"ppat.1009796.ref009","doi-asserted-by":"crossref","first-page":"e1007980","DOI":"10.1371\/journal.ppat.1007980","article-title":"A single phosphoacceptor residue in BGLF3 is essential for transcription of Epstein-Barr virus late genes","volume":"15","author":"J Li","year":"2019","journal-title":"PLoS Pathog.PubMed Central PMCID"},{"issue":"8","key":"ppat.1009796.ref010","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.01707-18","article-title":"S-Like-Phase Cyclin-Dependent Kinases Stabilize the Epstein-Barr Virus BDLF4 Protein To Temporally Control Late Gene Transcription","volume":"93","author":"Y Sato","year":"2019","journal-title":"J Virol"},{"issue":"10","key":"ppat.1009796.ref011","doi-asserted-by":"crossref","first-page":"4841","DOI":"10.1128\/JVI.02344-10","article-title":"The human cytomegalovirus gene UL79 is required for the accumulation of late viral transcripts","volume":"85","author":"YC Perng","year":"2011","journal-title":"J Virol"},{"issue":"15","key":"ppat.1009796.ref012","doi-asserted-by":"crossref","first-page":"8651","DOI":"10.1128\/JVI.01052-13","article-title":"Cytomegalovirus UL91 is essential for transcription of viral true late (gamma2) genes.","volume":"87","author":"S Omoto","year":"2013","journal-title":"J Virol"},{"issue":"1","key":"ppat.1009796.ref013","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1128\/JVI.02983-13","article-title":"Transcription of true late (gamma2) cytomegalovirus genes requires UL92 function that is conserved among beta- and gammaherpesviruses","volume":"88","author":"S Omoto","year":"2014","journal-title":"J Virol"},{"issue":"13","key":"ppat.1009796.ref014","doi-asserted-by":"crossref","first-page":"6629","DOI":"10.1128\/JVI.00384-11","article-title":"The human cytomegalovirus gene products essential for late viral gene expression assemble into prereplication complexes before viral DNA replication","volume":"85","author":"H Isomura","year":"2011","journal-title":"J Virol"},{"issue":"19","key":"ppat.1009796.ref015","doi-asserted-by":"crossref","first-page":"9730","DOI":"10.1128\/JVI.00246-06","article-title":"ORF18 is a transfactor that is essential for late gene transcription of a gammaherpesvirus","volume":"80","author":"V Arumugaswami","year":"2006","journal-title":"J Virol"},{"issue":"12","key":"ppat.1009796.ref016","doi-asserted-by":"crossref","first-page":"6761","DOI":"10.1128\/JVI.02726-06","article-title":"Murine gammaherpesvirus 68 open reading frame 24 is required for late gene expression after DNA replication","volume":"81","author":"E Wong","year":"2007","journal-title":"J Virol"},{"issue":"5","key":"ppat.1009796.ref017","doi-asserted-by":"crossref","first-page":"2265","DOI":"10.1128\/JVI.01785-08","article-title":"ORF30 and ORF34 are essential for expression of late genes in murine gammaherpesvirus 68","volume":"83","author":"TT Wu","year":"2009","journal-title":"J Virol"},{"issue":"1","key":"ppat.1009796.ref018","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1128\/JVI.02684-13","article-title":"Murine cytomegalovirus protein pM92 is a conserved regulator of viral late gene expression","volume":"88","author":"TJ Chapa","year":"2014","journal-title":"J Virol"},{"issue":"6","key":"ppat.1009796.ref019","article-title":"Murine Cytomegalovirus Protein pM49 Interacts with pM95 and Is Critical for Viral Late Gene Expression","volume":"94","author":"T Han","year":"2020","journal-title":"J Virol"},{"issue":"2","key":"ppat.1009796.ref020","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.01300-19","article-title":"Kaposi\u2019s Sarcoma-Associated Herpesvirus ORF66 Is Essential for Late Gene Expression and Virus Production via Interaction with ORF34","volume":"94","author":"T Watanabe","year":"2020","journal-title":"J Virol"},{"issue":"6","key":"ppat.1009796.ref021","doi-asserted-by":"crossref","first-page":"e1007114","DOI":"10.1371\/journal.ppat.1007114","article-title":"CAGE-seq analysis of Epstein-Barr virus lytic gene transcription: 3 kinetic classes from 2 mechanisms","volume":"14","author":"R Djavadian","year":"2018","journal-title":"PLoS Pathog"},{"issue":"5","key":"ppat.1009796.ref022","doi-asserted-by":"crossref","first-page":"e1007774","DOI":"10.1371\/journal.ppat.1007774","article-title":"An integrative approach identifies direct targets of the late viral transcription complex and an expanded promoter recognition motif in Kaposi\u2019s sarcoma-associated herpesvirus","volume":"15","author":"D Nandakumar","year":"2019","journal-title":"PLoS Pathog"},{"key":"ppat.1009796.ref023","doi-asserted-by":"crossref","first-page":"869","DOI":"10.3389\/fmicb.2016.00869","article-title":"Herpesvirus Late Gene Expression: A Viral-Specific Pre-initiation Complex Is Key","volume":"7","author":"H Gruffat","year":"2016","journal-title":"Front Microbiol"},{"issue":"5","key":"ppat.1009796.ref024","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/s41589-018-0021-8","article-title":"The dTAG system for immediate and target-specific protein degradation","volume":"14","author":"B Nabet","year":"2018","journal-title":"Nat Chem Biol"},{"issue":"6241","key":"ppat.1009796.ref025","doi-asserted-by":"crossref","first-page":"1376","DOI":"10.1126\/science.aab1433","article-title":"DRUG DEVELOPMENT. Phthalimide conjugation as a strategy for in vivo target protein degradation","volume":"348","author":"GE Winter","year":"2015","journal-title":"Science"},{"issue":"4","key":"ppat.1009796.ref026","doi-asserted-by":"crossref","first-page":"e1008402","DOI":"10.1371\/journal.ppat.1008402","article-title":"Human cytomegalovirus IE2 drives transcription initiation from a select subset of late infection viral promoters by host RNA polymerase II","volume":"16","author":"M Li","year":"2020","journal-title":"PLoS Pathog"},{"issue":"1","key":"ppat.1009796.ref027","doi-asserted-by":"crossref","first-page":"4687","DOI":"10.1038\/s41467-020-18377-w","article-title":"Rapid and direct control of target protein levels with VHL-recruiting dTAG molecules","volume":"11","author":"B Nabet","year":"2020","journal-title":"Nat Commun."},{"issue":"6122","key":"ppat.1009796.ref028","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1126\/science.1229386","article-title":"Precise maps of RNA polymerase reveal how promoters direct initiation and pausing","volume":"339","author":"H Kwak","year":"2013","journal-title":"Science"},{"key":"ppat.1009796.ref029","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/mBio.02047-18","article-title":"Nucleotide resolution comparison of transcription of human cytomegalovirus and host genomes reveals universal use of RNA polymerase II elongation control driven by dissimilar core promoter elements","volume":"10","author":"M Parida","year":"2019","journal-title":"MBio"},{"key":"ppat.1009796.ref030","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1128\/jvi.66.2.1098-1108.1992","article-title":"Characterization of human cytomegalovirus UL84 early geme and identification of its putative protein product","volume":"66","author":"SY He","year":"1992","journal-title":"J Virol"},{"key":"ppat.1009796.ref031","doi-asserted-by":"crossref","first-page":"1783","DOI":"10.1128\/jvi.63.4.1783-1791.1989","article-title":"Regulation of cytomegalovirus late-gene expression: differential use of three start sites in the transcriptional activation of ICP36 gene expression","volume":"63","author":"FS Leach","year":"1989","journal-title":"J Virol"},{"issue":"4","key":"ppat.1009796.ref032","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1101\/gr.229518.117","article-title":"Genome-wide determinants of sequence-specific DNA binding of general regulatory factors","volume":"28","author":"MJ Rossi","year":"2018","journal-title":"Genome Res"},{"issue":"44","key":"ppat.1009796.ref033","doi-asserted-by":"crossref","first-page":"26404","DOI":"10.1074\/jbc.R115.651679","article-title":"Formaldehyde crosslinking: a tool for the study of chromatin complexes","volume":"290","author":"EA Hoffman","year":"2015","journal-title":"J Biol Chem"},{"issue":"6","key":"ppat.1009796.ref034","doi-asserted-by":"crossref","first-page":"3411","DOI":"10.1128\/JVI.01374-13","article-title":"Unconventional sequence requirement for viral late gene core promoters of murine gammaherpesvirus 68","volume":"88","author":"E Wong-Ho","year":"2014","journal-title":"J Virol"},{"key":"ppat.1009796.ref035","doi-asserted-by":"crossref","first-page":"13460","DOI":"10.1128\/JVI.78.24.13460-13469.2004","article-title":"Lytic cycle gene regulation of Epstein-Barr virus","volume":"78","author":"W Amon","year":"2003","journal-title":"J Virol"},{"issue":"24","key":"ppat.1009796.ref036","doi-asserted-by":"crossref","first-page":"12284","DOI":"10.1128\/JVI.00965-15","article-title":"Differentiation-Coupled Induction of Human Cytomegalovirus Replication by Union of the Major Enhancer Retinoic Acid, Cyclic AMP, and NF-kappaB Response Elements","volume":"89","author":"J Yuan","year":"2015","journal-title":"J Virol"},{"issue":"2","key":"ppat.1009796.ref037","doi-asserted-by":"crossref","first-page":"1246","DOI":"10.1128\/jvi.71.2.1246-1255.1997","article-title":"Effect of a modulator deletion on transcription of the human cytomegalovirus major immediate-early genes in infected undifferentiated and differentiated cells","volume":"71","author":"JL Meier","year":"1997","journal-title":"J Virol"},{"issue":"18","key":"ppat.1009796.ref038","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.ymeth.2019.02.003","article-title":"Use of the nuclear walk-on methodology to determine sites of RNA polymerase II initiation and pausing and quantify nascent RNAs in cells","volume":"159-160","author":"CB Ball","year":"2019","journal-title":"Methods"},{"issue":"6","key":"ppat.1009796.ref039","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"AR Quinalan","year":"2010","journal-title":"Bioinformatics"},{"issue":"6","key":"ppat.1009796.ref040","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The human genome browser at UCSC","volume":"12","author":"WJ Kent","year":"2002","journal-title":"Genome Res"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1009796","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,8,12]],"date-time":"2021-08-12T00:00:00Z","timestamp":1628726400000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1009796","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,8,12]],"date-time":"2021-08-12T19:21:35Z","timestamp":1628796095000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1009796"}},"subtitle":[],"editor":[{"given":"Britt A.","family":"Glaunsinger","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2021,8,2]]},"references-count":40,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2021,8,2]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1009796","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.ppat.1009796","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,8,2]]}}}