{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,10]],"date-time":"2026-01-10T08:05:35Z","timestamp":1768032335972,"version":"3.49.0"},"update-to":[{"DOI":"10.1371\/journal.ppat.1007389","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,11,13]],"date-time":"2018-11-13T00:00:00Z","timestamp":1542067200000}}],"reference-count":57,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2018,11,1]],"date-time":"2018-11-01T00:00:00Z","timestamp":1541030400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["CA16038"],"award-info":[{"award-number":["CA16038"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100013874","name":"Hope Funds for Cancer Research","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100013874","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"DOI":"10.1371\/journal.ppat.1007389","type":"journal-article","created":{"date-parts":[[2018,11,1]],"date-time":"2018-11-01T17:57:51Z","timestamp":1541095071000},"page":"e1007389","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":21,"title":["Two herpesviral noncoding PAN RNAs are functionally homologous but do not associate with common chromatin loci"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1289-4454","authenticated-orcid":true,"given":"Johanna B.","family":"Withers","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1804-6915","authenticated-orcid":true,"given":"Eric S.","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3699-7394","authenticated-orcid":true,"given":"Tenaya K.","family":"Vallery","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Therese A.","family":"Yario","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0534-8722","authenticated-orcid":true,"given":"Joan A.","family":"Steitz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2018,11,1]]},"reference":[{"issue":"10","key":"ref1","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1038\/nrc2888","article-title":"Kaposi's sarcoma and its associated herpesvirus","volume":"10","author":"EA Mesri","year":"2010","journal-title":"Nat rev cancer"},{"issue":"10","key":"ref2","doi-asserted-by":"crossref","first-page":"e1002300","DOI":"10.1371\/journal.ppat.1002300","article-title":"A viral nuclear noncoding RNA binds re-localized poly(A) binding protein and is required for late KSHV gene expression","volume":"7","author":"S Borah","year":"2011","journal-title":"PLoS Pathog"},{"issue":"21","key":"ref3","doi-asserted-by":"crossref","first-page":"11883","DOI":"10.1073\/pnas.93.21.11883","article-title":"Polyadenylylated nuclear RNA encoded by Kaposi sarcoma-associated herpesvirus","volume":"93","author":"R Sun","year":"1996","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"ref4","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1128\/JVI.71.2.1207-1212.1997","article-title":"Characterization of ribonucleoprotein complexes containing an abundant polyadenylated nuclear RNA encoded by Kaposi's sarcoma-associated herpesvirus (human herpesvirus 8)","volume":"71","author":"W Zhong","year":"1997","journal-title":"J Virol"},{"issue":"6008","key":"ref5","doi-asserted-by":"crossref","first-page":"1244","DOI":"10.1126\/science.1195858","article-title":"Poly(A) tail recognition by a viral RNA element through assembly of a triple helix","volume":"330","author":"RM Mitton-Fry","year":"2010","journal-title":"Science"},{"issue":"47","key":"ref6","doi-asserted-by":"crossref","first-page":"19202","DOI":"10.1073\/pnas.1217338109","article-title":"Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MENbeta noncoding RNAs","volume":"109","author":"JA Brown","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"10","key":"ref7","doi-asserted-by":"crossref","first-page":"1831","DOI":"10.1038\/sj.emboj.7600662","article-title":"A Kaposi's sarcoma virus RNA element that increases the nuclear abundance of intronless transcripts","volume":"24","author":"NK Conrad","year":"2005","journal-title":"EMBO J"},{"issue":"1","key":"ref8","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.celrep.2012.05.020","article-title":"Conservation of a triple-helix-forming RNA stability element in noncoding and genomic RNAs of diverse viruses","volume":"2","author":"KT Tycowski","year":"2012","journal-title":"Cell Rep"},{"issue":"24","key":"ref9","doi-asserted-by":"crossref","first-page":"13290","DOI":"10.1128\/JVI.05886-11","article-title":"Kaposi's sarcoma-associated herpesvirus noncoding polyadenylated nuclear RNA interacts with virus- and host cell-encoded proteins and suppresses expression of genes involved in immune modulation","volume":"85","author":"CC Rossetto","year":"2011","journal-title":"J Virol"},{"issue":"5","key":"ref10","doi-asserted-by":"crossref","first-page":"e1002680","DOI":"10.1371\/journal.ppat.1002680","article-title":"KSHV PAN RNA associates with demethylases UTX and JMJD3 to activate lytic replication through a physical interaction with the virus genome","volume":"8","author":"CC Rossetto","year":"2012","journal-title":"PLoS Pathog"},{"issue":"10","key":"ref11","doi-asserted-by":"crossref","first-page":"5540","DOI":"10.1128\/JVI.03111-12","article-title":"Regulation of viral and cellular gene expression by Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA","volume":"87","author":"CC Rossetto","year":"2013","journal-title":"J Virol"},{"issue":"3","key":"ref12","doi-asserted-by":"crossref","first-page":"1843","DOI":"10.1128\/JVI.03251-13","article-title":"A lytic viral long noncoding RNA modulates the function of a latent protein","volume":"88","author":"M Campbell","year":"2014","journal-title":"J Virol"},{"issue":"4","key":"ref13","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1016\/j.molcel.2011.08.027","article-title":"Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions","volume":"44","author":"C Chu","year":"2011","journal-title":"Mol Cell"},{"issue":"1","key":"ref14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.tig.2005.10.003","article-title":"Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function","volume":"22","author":"KC Pang","year":"2006","journal-title":"Trends Genet"},{"issue":"7","key":"ref15","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1016\/j.cell.2011.11.055","article-title":"Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution","volume":"147","author":"I Ulitsky","year":"2011","journal-title":"Cell"},{"issue":"6","key":"ref16","doi-asserted-by":"crossref","first-page":"943","DOI":"10.1016\/j.molcel.2006.10.029","article-title":"Identification of a rapid mammalian deadenylation-dependent decay pathway and its inhibition by a viral RNA element","volume":"24","author":"NK Conrad","year":"2006","journal-title":"Mol Cell"},{"issue":"1","key":"ref17","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1128\/JVI.71.1.527-538.1997","article-title":"Characterization of an abundant, unique 1.7-kilobase bovine herpesvirus 4 (BHV-4) late RNA and mapping of a BHV-4 IE2 transactivator-binding site in its promoter-regulatory region","volume":"71","author":"R Bermudez-Cruz","year":"1997","journal-title":"J Virol"},{"issue":"1","key":"ref18","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.chom.2017.06.009","article-title":"Persistent KSHV infection increases EBV-associated tumor formation in vivo via enhanced EBV lytic gene expression","volume":"22","author":"D McHugh","year":"2017","journal-title":"Cell Host Microbe"},{"issue":"5","key":"ref19","doi-asserted-by":"crossref","first-page":"3127","DOI":"10.1128\/JVI.79.5.3127-3138.2005","article-title":"The latency-associated nuclear antigen of rhesus monkey rhadinovirus inhibits viral replication through repression of Orf50\/Rta transcriptional activation","volume":"79","author":"SM DeWire","year":"2005","journal-title":"J Virol"},{"key":"ref20","doi-asserted-by":"crossref","DOI":"10.1002\/0471142727.mb2125s101","article-title":"Capture hybridization analysis of RNA targets (CHART)","author":"MD Simon","year":"2013","journal-title":"Curr Protoc Mol Biol"},{"issue":"8","key":"ref21","doi-asserted-by":"crossref","first-page":"5806","DOI":"10.1074\/jbc.M111.289496","article-title":"Protein arginine methyltransferase 1-directed methylation of Kaposi sarcoma-associated herpesvirus latency-associated nuclear antigen","volume":"287","author":"M Campbell","year":"2012","journal-title":"The Journal of biological chemistry"},{"issue":"3","key":"ref22","doi-asserted-by":"crossref","first-page":"1789","DOI":"10.1128\/JVI.02283-12","article-title":"CTCF regulates Kaposi's sarcoma-associated herpesvirus latency transcription by nucleosome displacement and RNA polymerase programming","volume":"87","author":"H Kang","year":"2013","journal-title":"J Virol"},{"issue":"5","key":"ref23","doi-asserted-by":"crossref","first-page":"1943","DOI":"10.1128\/JVI.02060-10","article-title":"Functional characterization of Kaposi's sarcoma-associated herpesvirus open reading frame K8 by bacterial artificial chromosome-based mutagenesis","volume":"85","author":"Y Wang","year":"2011","journal-title":"J Virol"},{"issue":"14","key":"ref24","doi-asserted-by":"crossref","first-page":"12023","DOI":"10.1074\/jbc.M108026200","article-title":"Transcriptional regulation of Kaposi's sarcoma-associated herpesvirus-encoded oncogene viral interferon regulatory factor by a novel transcriptional silencer, Tis","volume":"277","author":"XP Wang","year":"2002","journal-title":"The Journal of biological chemistry"},{"issue":"7","key":"ref25","doi-asserted-by":"crossref","first-page":"3888","DOI":"10.1128\/JVI.03597-14","article-title":"Complete genome sequence of Pig-tailed macaque rhadinovirus 2 and its evolutionary relationship with rhesus macaque rhadinovirus and human herpesvirus 8\/Kaposi's sarcoma-associated herpesvirus","volume":"89","author":"AG Bruce","year":"2015","journal-title":"J Virol"},{"issue":"7","key":"ref26","doi-asserted-by":"crossref","first-page":"3644","DOI":"10.1128\/JVI.80.7.3644-3649.2006","article-title":"Infection and persistence of rhesus monkey rhadinovirus in immortalized B-cell lines","volume":"80","author":"JP Bilello","year":"2006","journal-title":"J Virol"},{"issue":"6","key":"ref27","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1016\/j.cbpa.2006.09.020","article-title":"Interactions between macromolecules and ions: The Hofmeister series","volume":"10","author":"Y Zhang","year":"2006","journal-title":"Curr Opin Chem Biol"},{"issue":"2","key":"ref28","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1016\/j.molcel.2008.08.022","article-title":"Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation","volume":"32","author":"RR Pandey","year":"2008","journal-title":"Mol Cell"},{"issue":"11","key":"ref29","doi-asserted-by":"crossref","first-page":"3713","DOI":"10.1128\/MCB.02263-07","article-title":"Kcnq1ot1\/Lit1 noncoding RNA mediates transcriptional silencing by targeting to the perinucleolar region","volume":"28","author":"F Mohammad","year":"2008","journal-title":"Molecular and cellular biology"},{"issue":"1","key":"ref30","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1128\/JVI.02157-15","article-title":"Interaction between ORF24 and ORF34 in the Kaposi's sarcoma-associated herpesvirus late gene transcription factor complex is essential for viral late gene expression","volume":"90","author":"ZH Davis","year":"2016","journal-title":"J Virol"},{"issue":"21","key":"ref31","doi-asserted-by":"crossref","first-page":"12825","DOI":"10.1128\/JVI.02139-14","article-title":"Epstein-Barr virus late gene transcription depends on the assembly of a virus-specific preinitiation complex","volume":"88","author":"V Aubry","year":"2014","journal-title":"J Virol"},{"issue":"5","key":"ref32","doi-asserted-by":"crossref","first-page":"2609","DOI":"10.1128\/JVI.78.5.2609-2614.2004","article-title":"Requirement of a 12-base-pair TATT-containing sequence and viral lytic DNA replication in activation of the Kaposi's sarcoma-associated herpesvirus K8.1 late promoter","volume":"78","author":"S Tang","year":"2004","journal-title":"J Virol"},{"issue":"11","key":"ref33","doi-asserted-by":"crossref","first-page":"6148","DOI":"10.1128\/JVI.00272-15","article-title":"Association of Kaposi's sarcoma-associated herpesvirus ORF31 with ORF34 and ORF24 Is critical for late gene expression","volume":"89","author":"K Brulois","year":"2015","journal-title":"J Virol"},{"issue":"10","key":"ref34","doi-asserted-by":"crossref","first-page":"5000","DOI":"10.1128\/JVI.76.10.5000-5013.2002","article-title":"Characterization of interactions between RTA and the promoter of polyadenylated nuclear RNA in Kaposi's sarcoma-associated herpesvirus\/human herpesvirus 8","volume":"76","author":"MJ Song","year":"2002","journal-title":"J Virol"},{"issue":"2","key":"ref35","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1006\/dbio.1995.1080","article-title":"Differential binding of oocyte-type and somatic-type 5S rRNA to TFIIIA and ribosomal protein L5 in Xenopus oocytes: specialization for storage versus mobilization","volume":"168","author":"LA Allison","year":"1995","journal-title":"Dev Biol"},{"issue":"1","key":"ref36","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/0012-1606(91)90485-L","article-title":"RNA-protein interactions of stored 5S RNA with TFIIIA and ribosomal protein L5 during Xenopus oogenesis","volume":"144","author":"LA Allison","year":"1991","journal-title":"Dev Biol"},{"issue":"4","key":"ref37","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1111\/gtc.12218","article-title":"Exportin-5 mediates nuclear export of SRP RNA in vertebrates","volume":"20","author":"T Takeiwa","year":"2015","journal-title":"Genes Cells"},{"issue":"1","key":"ref38","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1261\/rna.7189205","article-title":"Nuclear export of metazoan replication-dependent histone mRNAs is dependent on RNA length and is mediated by TAP","volume":"11","author":"JA Erkmann","year":"2005","journal-title":"RNA"},{"issue":"1","key":"ref39","doi-asserted-by":"crossref","DOI":"10.3390\/pathogens6010011","article-title":"Quantitative analysis of the KSHV transcriptome following primary infection of blood and lymphatic endothelial cells","volume":"6","author":"AG Bruce","year":"2017","journal-title":"Pathogens"},{"issue":"7","key":"ref40","doi-asserted-by":"crossref","first-page":"3931","DOI":"10.1073\/pnas.95.7.3931","article-title":"Herpes simplex virus 1 induces and blocks apoptosis at multiple steps during infection and protects cells from exogenous inducers in a cell-type-dependent manner","volume":"95","author":"V Galvan","year":"1998","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"ref41","doi-asserted-by":"crossref","first-page":"e1006865","DOI":"10.1371\/journal.ppat.1006865","article-title":"Conditional mutagenesis in vivo reveals cell type- and infection stage-specific requirements for LANA in chronic MHV68 infection.","volume":"14","author":"E Salinas","year":"2018","journal-title":"PLoS Pathog"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.virusres.2015.06.012","article-title":"New insights into the expression and functions of the Kaposi's sarcoma-associated herpesvirus long noncoding PAN RNA","volume":"212","author":"NK Conrad","year":"2016","journal-title":"Virus Res"},{"key":"ref43","article-title":"KSHV mRNA accumulation in nuclear foci is influenced by viral DNA replication and the viral noncoding PAN RNA","author":"TK Vallery","year":"2018","journal-title":"J Virol"},{"issue":"11","key":"ref44","doi-asserted-by":"crossref","first-page":"6805","DOI":"10.1093\/nar\/gkx241","article-title":"Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA: a structural scaffold for nuclear, cytoplasmic and viral proteins","volume":"45","author":"J Sztuba-Solinska","year":"2017","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"ref45","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1016\/j.tig.2011.03.003","article-title":"Forkhead transcription factors: key players in health and disease","volume":"27","author":"BA Benayoun","year":"2011","journal-title":"Trends Genet"},{"issue":"2","key":"ref46","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1128\/MCB.05504-11","article-title":"The forkhead transcription factor FOXK2 promotes AP-1-mediated transcriptional regulation","volume":"32","author":"Z Ji","year":"2012","journal-title":"Molecular and cellular biology"},{"issue":"3","key":"ref47","doi-asserted-by":"crossref","first-page":"1404","DOI":"10.1128\/JVI.02046-13","article-title":"DNA virus replication compartments","volume":"88","author":"M Schmid","year":"2014","journal-title":"J Virol"},{"issue":"1","key":"ref48","doi-asserted-by":"crossref","first-page":"e1003847","DOI":"10.1371\/journal.ppat.1003847","article-title":"KSHV 2.0: a comprehensive annotation of the Kaposi's sarcoma-associated herpesvirus genome using next-generation sequencing reveals novel genomic and functional features","volume":"10","author":"C Arias","year":"2014","journal-title":"PLoS Pathog"},{"issue":"22","key":"ref49","doi-asserted-by":"crossref","first-page":"19126","DOI":"10.1074\/jbc.M101777200","article-title":"A mechanism regulating proteolysis of specific proteins during renal tubular cell growth","volume":"276","author":"HA Franch","year":"2001","journal-title":"The Journal of biological chemistry"},{"issue":"21","key":"ref50","doi-asserted-by":"crossref","first-page":"4996","DOI":"10.1128\/MCB.00600-10","article-title":"binding protein restricts gene expression via hyperadenylation and nuclear retention of mRNA","volume":"30","author":"GR Kumar","year":"2010","journal-title":"Molecular and cellular biology"},{"issue":"3","key":"ref51","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1038\/nm0396-342","article-title":"Lytic growth of Kaposi's sarcoma-associated herpesvirus (human herpesvirus 8) in culture","volume":"2","author":"R Renne","year":"1996","journal-title":"Nat Med"},{"issue":"15","key":"ref52","doi-asserted-by":"crossref","first-page":"8490","DOI":"10.1128\/JVI.00742-14","article-title":"Identification of properties of the Kaposi's sarcoma-associated herpesvirus latent origin of replication that are essential for the efficient establishment and maintenance of intact plasmids","volume":"88","author":"P Shrestha","year":"2014","journal-title":"J Virol"},{"issue":"4","key":"ref53","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/j.cell.2015.01.015","article-title":"EBV noncoding RNA binds nascent RNA to drive host PAX5 to viral DNA","volume":"160","author":"N Lee","year":"2015","journal-title":"Cell"},{"issue":"9","key":"ref54","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Y Zhang","year":"2008","journal-title":"Genome Biol"},{"issue":"7414","key":"ref55","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","year":"2012","journal-title":"Nature"},{"issue":"6","key":"ref56","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 Quinlan","year":"2010","journal-title":"Bioinformatics"},{"issue":"8","key":"ref57","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.7150\/ijbs.7.1145","article-title":"Stability of a long noncoding viral RNA depends on a 9-nt core element at the RNA 5' end to interact with viral ORF57 and cellular PABPC1","volume":"7","author":"MJ Massimelli","year":"2011","journal-title":"International journal of biological sciences"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1007389","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,11,13]],"date-time":"2018-11-13T00:00:00Z","timestamp":1542067200000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.ppat.1007389","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,14]],"date-time":"2020-11-14T13:23:04Z","timestamp":1605360184000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1007389"}},"subtitle":[],"editor":[{"given":"Britt A.","family":"Glaunsinger","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,11,1]]},"references-count":57,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2018,11,1]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1007389","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.ppat.1007389","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,11,1]]}}}