{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T06:03:25Z","timestamp":1791266605429,"version":"4.1.0"},"reference-count":54,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2016,2,1]],"date-time":"2016-02-01T00:00:00Z","timestamp":1454284800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100002839","name":"Charit\u00e9 Universit\u00e4tsmedizin Berlin","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100002839","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Virol"],"published-print":{"date-parts":[[2016,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>Adeno-associated virus (AAV) is recognized for its bipartite life cycle with productive replication dependent on coinfection with adenovirus (Ad) and AAV latency being established in the absence of a helper virus. The shift from latent to Ad-dependent AAV replication is mostly regulated at the transcriptional level. The current AAV transcription map displays highly expressed transcripts as found upon coinfection with Ad. So far, AAV transcripts have only been characterized on the plus strand of the AAV single-stranded DNA genome. The AAV minus strand is assumed not to be transcribed. Here, we apply Illumina-based RNA sequencing (RNA-Seq) to characterize the entire AAV2 transcriptome in the absence or presence of Ad. We find known and identify novel AAV transcripts, including additional splice variants, the most abundant of which leads to expression of a novel 18-kDa Rep\/VP fusion protein. Furthermore, we identify for the first time transcription on the AAV minus strand with clustered reads upstream of the p5 promoter, confirmed by 5\u02c8 rapid amplification of cDNA ends and RNase protection assays. The p5 promoter displays considerable activity in both directions, a finding indicative of divergent transcription. Upon infection with AAV alone, low-level transcription of both AAV strands is detectable and is strongly stimulated upon coinfection with Ad.<\/jats:p>\n          <jats:p>\n            <jats:bold>IMPORTANCE<\/jats:bold>\n            Next-generation sequencing (NGS) allows unbiased genome-wide analyses of transcription profiles, used here for an in depth analysis of the AAV2 transcriptome during latency and productive infection. RNA-Seq analysis led to the discovery of novel AAV transcripts and splice variants, including a derived, novel 18-kDa Rep\/VP fusion protein. Unexpectedly, transcription from the AAV minus strand was discovered, indicative of divergent transcription from the p5 promoter. This finding opens the door for novel concepts of the switch between AAV latency and productive replication. In the absence of a suitable animal model to study AAV\n            <jats:italic>in vivo<\/jats:italic>\n            , combined\n            <jats:italic>in cellulae<\/jats:italic>\n            and\n            <jats:italic>in silico<\/jats:italic>\n            studies will help to forward the understanding of the unique, bipartite AAV life cycle.\n          <\/jats:p>","DOI":"10.1128\/jvi.02750-15","type":"journal-article","created":{"date-parts":[[2015,11,12]],"date-time":"2015-11-12T02:28:54Z","timestamp":1447295334000},"page":"1278-1289","update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":42,"title":["A Comprehensive RNA Sequencing Analysis of the Adeno-Associated Virus (AAV) Type 2 Transcriptome Reveals Novel AAV Transcripts, Splice Variants, and Derived Proteins"],"prefix":"10.1128","volume":"90","author":[{"given":"Catrin","family":"Stutika","sequence":"first","affiliation":[{"name":"Institute of Virology, Campus Benjamin Franklin, Charit\u00e9 Medical School, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Gogol-D\u00f6ring","sequence":"additional","affiliation":[{"name":"German Centre for Integrative Biodiversity Research, Halle-Jena-Leipzig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Botschen","sequence":"additional","affiliation":[{"name":"Institute of Virology, Campus Benjamin Franklin, Charit\u00e9 Medical School, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mario","family":"Mietzsch","sequence":"additional","affiliation":[{"name":"Institute of Virology, Campus Benjamin Franklin, Charit\u00e9 Medical School, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stefan","family":"Weger","sequence":"additional","affiliation":[{"name":"Institute of Virology, Campus Benjamin Franklin, Charit\u00e9 Medical School, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mirjam","family":"Feldkamp","sequence":"additional","affiliation":[{"name":"Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Centrum f\u00fcr Molekulare Medizin, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Chen","sequence":"additional","affiliation":[{"name":"Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbr\u00fcck-Centrum f\u00fcr Molekulare Medizin, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Regine","family":"Heilbronn","sequence":"additional","affiliation":[{"name":"Institute of Virology, Campus Benjamin Franklin, Charit\u00e9 Medical School, Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.58.4.1410"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.45.2.555-564.1983"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1001673107"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/0092-8674(80)90171-3"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.41.2.518-526.1982"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.76.2.625"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.76.11.5567"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.62.9.3356-3363.1988"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1432-1033.1981.tb06443.x"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.74.21.9878-9888.2000"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.76.24.12435-12447.2002"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.35.2.560-565.1980"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.36.1.79-92.1980"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature11233"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2014.04.006"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.06991-11"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.64.6.3012-3018.1990"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01356-14"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.03371-13"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.65.5.2476-2483.1991"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1099\/vir.0.000034"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.1923"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000502"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0097-8485(01)00099-7"},{"key":"e_1_3_2_26_2","first-page":"52","article-title":"Studies on the relationship between adeno-associated virus type I (AAV-1) and adenoviruses. I","volume":"32","author":"Casto BC","year":"1967","unstructured":"Casto BC, Atchison RW, Hammon WM. 1967. Studies on the relationship between adeno-associated virus type I (AAV-1) and adenoviruses. I. Replication of AAV-1 in certain cell cultures and its effect on helper adenovirus. Virology 32:52\u201359.","journal-title":"Replication of AAV-1 in certain cell cultures and its effect on helper adenovirus. Virology"},{"key":"e_1_3_2_27_2","first-page":"452","article-title":"Studies on the relationship between adeno-associated virus type 1 (AAV-1) and adenoviruses. II","volume":"33","author":"Casto BC","year":"1967","unstructured":"Casto BC, Armstrong JA, Atchison RW, Hammon WM. 1967. Studies on the relationship between adeno-associated virus type 1 (AAV-1) and adenoviruses. II. Inhibition of adenovirus plaques by AAV; its nature and specificity. Virology 33:452\u2013458.","journal-title":"Inhibition of adenovirus plaques by AAV; its nature and specificity. Virology"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.70.3.1845-1854.1996"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.00198-06"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0021-9258(18)53762-5"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.74.18.8732-8739.2000"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.2741\/2912"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.01717-12"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0104596"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/7.5.919"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.71.2.1079-1088.1997"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.63.10.4450-4454.1989"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1101\/gad.17268411"},{"key":"e_1_3_2_39_2","first-page":"359","article-title":"Chromosomal latency and expression at map unit 96 of a wild-type plus adeno-associated virus (AAV)\/Neo vector and identification of p81, a new AAV transcriptional promoter","volume":"2","author":"Hermonat PL","year":"1999","unstructured":"Hermonat PL, Santin AD, De Greve J, De Rijcke M, Bishop BM, Han L, Mane M, Kokorina N. 1999. Chromosomal latency and expression at map unit 96 of a wild-type plus adeno-associated virus (AAV)\/Neo vector and identification of p81, a new AAV transcriptional promoter. J Hum Virol 2:359\u2013368.","journal-title":"J Hum Virol"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.4161\/cc.8.16.9305"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.gde.2011.11.002"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2014.12.029"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2015.04.006"},{"key":"e_1_3_2_44_2","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.1372"},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.1162253"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0800250105"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/11.4.1019"},{"key":"e_1_3_2_48_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.59.3.564-573.1986"},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.72.3.1834-1843.1998"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.virol.2006.01.039"},{"key":"e_1_3_2_51_2","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.61.8.2395-2406.1987"},{"key":"e_1_3_2_52_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.78.23.12929-12939.2004"},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1128\/JVI.02430-05"},{"key":"e_1_3_2_54_2","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2009-04-215756"},{"key":"e_1_3_2_55_2","doi-asserted-by":"publisher","DOI":"10.1006\/viro.2001.1217"}],"container-title":["Journal of Virology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JVI.02750-15","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JVI.02750-15","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T14:14:31Z","timestamp":1646489671000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JVI.02750-15"}},"subtitle":[],"editor":[{"given":"L.","family":"Banks","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2016,2]]},"references-count":54,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2016,2]]}},"alternative-id":["10.1128\/JVI.02750-15"],"URL":"https:\/\/doi.org\/10.1128\/jvi.02750-15","relation":{},"ISSN":["0022-538X","1098-5514"],"issn-type":[{"value":"0022-538X","type":"print"},{"value":"1098-5514","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,2]]},"assertion":[{"value":"2015-10-28","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2015-11-06","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2016-01-15","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}