{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,23]],"date-time":"2026-08-23T15:39:28Z","timestamp":1787499568791,"version":"build-2736575974"},"reference-count":104,"publisher":"The Company of Biologists","issue":"5","license":[{"start":{"date-parts":[[2020,11,9]],"date-time":"2020-11-09T00:00:00Z","timestamp":1604880000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.biologists.com\/user-licence-1-1\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","doi-asserted-by":"crossref","award":["31003A_179256\/1"],"award-info":[{"award-number":["31003A_179256\/1"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Kanton Zurich"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,3,1]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>In clonal cultures, not all cells are equally susceptible to virus infection, and the mechanisms underlying this are poorly understood. Here, we developed image-based single-cell measurements to scrutinize the heterogeneity of adenovirus (AdV) infection. AdV delivers, transcribes and replicates a linear double-stranded DNA genome in the nucleus. We measured the abundance of viral transcripts using single-molecule RNA fluorescence in situ hybridization (FISH) and the incoming 5-ethynyl-2\u2032-deoxycytidine (EdC)-tagged viral genomes using a copper(I)-catalyzed azide\u2013alkyne cycloaddition (click) reaction. Surprisingly, expression of the immediate early gene E1A only moderately correlated with the number of viral genomes in the cell nucleus. Intranuclear genome-to-genome heterogeneity was found at the level of viral transcription and, in accordance, individual genomes exhibited heterogeneous replication activity. By analyzing the cell cycle state, we found that G1 cells exhibited the highest E1A gene expression and displayed increased correlation between E1A gene expression and viral genome copy numbers. The combined image-based single-molecule procedures described here are ideally suited to explore the cell-to-cell variability in viral gene expression in a range of different settings, including the innate immune response.<\/jats:p>\n                  <jats:p>This article has an associated First Person interview with the first author of the paper.<\/jats:p>","DOI":"10.1242\/jcs.252544","type":"journal-article","created":{"date-parts":[[2020,9,11]],"date-time":"2020-09-11T15:05:13Z","timestamp":1599836713000},"source":"Crossref","is-referenced-by-count":20,"title":["Cell-to-cell and genome-to-genome variability of adenovirus transcription tuned by the cell cycle"],"prefix":"10.1242","volume":"134","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3276-3008","authenticated-orcid":false,"given":"Maarit","family":"Suomalainen","sequence":"first","affiliation":[{"name":"Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7450-607X","authenticated-orcid":false,"given":"Vibhu","family":"Prasad","sequence":"additional","affiliation":[{"name":"Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8502-4129","authenticated-orcid":false,"given":"Abhilash","family":"Kannan","sequence":"additional","affiliation":[{"name":"Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2278-120X","authenticated-orcid":false,"given":"Urs F.","family":"Greber","sequence":"additional","affiliation":[{"name":"Department of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"237","published-online":{"date-parts":[[2020,11,9]]},"reference":[{"key":"2022051110093521900_JCS252544C1","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1007\/978-1-4939-0888-2_10","article-title":"Cell cycle regulation during viral infection","volume":"1170","author":"Bagga","year":"2014","journal-title":"Methods Mol. Biol."},{"key":"2022051110093521900_JCS252544C2","doi-asserted-by":"publisher","first-page":"1127","DOI":"10.1038\/nmeth.2657","article-title":"Image-based transcriptomics in thousands of single human cells at single-molecule resolution","volume":"10","author":"Battich","year":"2013","journal-title":"Nat. Methods"},{"key":"2022051110093521900_JCS252544C3","doi-asserted-by":"publisher","first-page":"1596","DOI":"10.1016\/j.cell.2015.11.018","article-title":"Control of Transcript Variability in Single Mammalian Cells","volume":"163","author":"Battich","year":"2015","journal-title":"Cell"},{"key":"2022051110093521900_JCS252544C4","doi-asserted-by":"publisher","first-page":"3785","DOI":"10.1016\/j.celrep.2019.11.064","article-title":"The E3 Ubiquitin Ligase Mind Bomb 1 Controls Adenovirus Genome Release at the Nuclear Pore Complex","volume":"29","author":"Bauer","year":"2019","journal-title":"Cell Rep."},{"key":"2022051110093521900_JCS252544C5","doi-asserted-by":"publisher","first-page":"d1369","DOI":"10.2741\/ben","article-title":"Adenovirus and cell cycle control","volume":"7","author":"Ben-Israel","year":"2002","journal-title":"Front. Biosci."},{"key":"2022051110093521900_JCS252544C6","doi-asserted-by":"publisher","first-page":"e18311.","DOI":"10.7554\/eLife.18311","article-title":"A systematic view on influenza induced host shutoff","volume":"5","author":"Bercovich-Kinori","year":"2016","journal-title":"eLife"},{"key":"2022051110093521900_JCS252544C7","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1146\/annurev.ge.20.120186.000401","article-title":"Adenovirus promoters and E1A transactivation","volume":"20","author":"Berk","year":"1986","journal-title":"Annu. Rev. Genet."},{"key":"2022051110093521900_JCS252544C8","doi-asserted-by":"publisher","first-page":"7673","DOI":"10.1038\/sj.onc.1209040","article-title":"Recent lessons in gene expression, cell cycle control, and cell biology from adenovirus","volume":"24","author":"Berk","year":"2005","journal-title":"Oncogene"},{"key":"2022051110093521900_JCS252544C9","doi-asserted-by":"publisher","first-page":"387","DOI":"10.1016\/0042-6822(84)90175-2","article-title":"Accumulation of early and intermediate mRNA species during subgroup C adenovirus productive infections","volume":"136","author":"Binger","year":"1984","journal-title":"Virology"},{"key":"2022051110093521900_JCS252544C10","doi-asserted-by":"publisher","first-page":"6555","DOI":"10.1093\/nar\/20.24.6555","article-title":"Different binding site requirements for binding and activation for the bipartite enhancer factor EF-1A","volume":"20","author":"Bolwig","year":"1992","journal-title":"Nucleic Acids Res."},{"key":"2022051110093521900_JCS252544C11","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1016\/S0378-1119(97)00178-9","article-title":"Serum-dependent and cell cycle-dependent expression from a cytomegalovirus-based mammalian expression vector","volume":"194","author":"Brightwell","year":"1997","journal-title":"Gene"},{"key":"2022051110093521900_JCS252544C12","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1038\/nbt.3102","article-title":"Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells","volume":"33","author":"Buettner","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"2022051110093521900_JCS252544C13","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1016\/j.chom.2011.07.006","article-title":"Drifting motions of the adenovirus receptor Car and immobile integrins initiate virus uncoating and membrane lytic protein exposure","volume":"10","author":"Burckhardt","year":"2011","journal-title":"Cell Host Microbe"},{"key":"2022051110093521900_JCS252544C14","doi-asserted-by":"publisher","first-page":"R100","DOI":"10.1186\/gb-2006-7-10-r100","article-title":"CellProfiler: image analysis software for identifying and quantifying cell phenotypes","volume":"7","author":"Carpenter","year":"2006","journal-title":"Genome Biol."},{"key":"2022051110093521900_JCS252544C15","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1016\/S0076-6879(00)18072-3","article-title":"Sensitive and high-resolution detection of RNA in situ","volume":"318","author":"Chartrand","year":"2000","journal-title":"Methods Enzymol."},{"key":"2022051110093521900_JCS252544C16","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1016\/j.virol.2007.08.012","article-title":"Transcription releases protein VII from adenovirus chromatin","volume":"369","author":"Chen","year":"2007","journal-title":"Virology"},{"key":"2022051110093521900_JCS252544C17","doi-asserted-by":"crossref","first-page":"aaa6090","DOI":"10.1126\/science.aaa6090","article-title":"RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells","volume":"348","author":"Chen","year":"2015","journal-title":"Science"},{"key":"2022051110093521900_JCS252544C18","doi-asserted-by":"publisher","first-page":"e13617","DOI":"10.7554\/eLife.13617","article-title":"RNA Polymerase II cluster dynamics predict mRNA output in living cells","volume":"5","author":"Cho","year":"2016","journal-title":"eLife"},{"key":"2022051110093521900_JCS252544C19","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1126\/science.aar4199","article-title":"Mediator and RNA polymerase II clusters associate in transcription-dependent condensates","volume":"361","author":"Cho","year":"2018","journal-title":"Science"},{"key":"2022051110093521900_JCS252544C20","doi-asserted-by":"publisher","first-page":"eaar2555","DOI":"10.1126\/science.aar2555","article-title":"Imaging dynamic and selective low-complexity domain interactions that control gene transcription","volume":"361","author":"Chong","year":"2018","journal-title":"Science"},{"key":"2022051110093521900_JCS252544C21","doi-asserted-by":"publisher","first-page":"664","DOI":"10.1126\/science.1239053","article-title":"Real-time dynamics of RNA polymerase II clustering in live human cells","volume":"341","author":"Cisse","year":"2013","journal-title":"Science"},{"key":"2022051110093521900_JCS252544C22","doi-asserted-by":"publisher","first-page":"e0211192","DOI":"10.1371\/journal.pone.0211192","article-title":"Temporal dynamics of adenovirus 5 gene expression in normal human cells","volume":"14","author":"Crisostomo","year":"2019","journal-title":"PLoS One"},{"key":"2022051110093521900_JCS252544C23","doi-asserted-by":"publisher","first-page":"e46339","DOI":"10.7554\/eLife.46339","article-title":"HSV-1 single cell analysis reveals anti-viral and developmental programs activation in distinct sub-populations","volume":"8","author":"Drayman","year":"2019","journal-title":"eLife"},{"key":"2022051110093521900_JCS252544C24","doi-asserted-by":"publisher","first-page":"615","DOI":"10.1038\/labinvest.2017.13","article-title":"Blue intensity matters for cell cycle profiling in fluorescence DAPI-stained images","volume":"97","author":"Ferro","year":"2017","journal-title":"Lab. Investig."},{"key":"2022051110093521900_JCS252544C25","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1016\/0022-2836(76)90263-1","article-title":"Adenovirus transcription. V. Quantitation of viral RNA sequences in adenovirus 2-infected and transformed cells","volume":"106","author":"Flint","year":"1976","journal-title":"J. Mol. Biol."},{"key":"2022051110093521900_JCS252544C26","doi-asserted-by":"publisher","first-page":"2369","DOI":"10.1093\/nar\/gkr1076","article-title":"Chromatin structure of adenovirus DNA throughout infection","volume":"40","author":"Giberson","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2022051110093521900_JCS252544C27","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1016\/0168-1702(88)90051-2","article-title":"Detailed kinetics of adenovirus type-5 steady-state transcripts during early infection","volume":"9","author":"Glenn","year":"1988","journal-title":"Virus Res."},{"key":"2022051110093521900_JCS252544C28","doi-asserted-by":"publisher","first-page":"942","DOI":"10.1016\/j.celrep.2018.03.102","article-title":"Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated Hiv-Infected Cells","volume":"23","author":"Golumbeanu","year":"2018","journal-title":"Cell Rep."},{"key":"2022051110093521900_JCS252544C29","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1016\/0092-8674(93)90382-Z","article-title":"Stepwise dismantling of adenovirus 2 during entry into cells","volume":"75","author":"Greber","year":"1993","journal-title":"Cell"},{"key":"2022051110093521900_JCS252544C30","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1016\/S0014-5793(03)01336-X","article-title":"Ternary complex formation between DNA-adenovirus core protein VII and TAF-Ibeta\/SET, an acidic molecular chaperone","volume":"555","author":"Haruki","year":"2003","journal-title":"FEBS Lett."},{"key":"2022051110093521900_JCS252544C31","doi-asserted-by":"publisher","first-page":"3214","DOI":"10.1128\/MCB.5.11.3214","article-title":"Sequence-independent autoregulation of the adenovirus type 5 E1A transcription unit","volume":"5","author":"Hearing","year":"1985","journal-title":"Mol. Cell. Biol."},{"key":"2022051110093521900_JCS252544C32","doi-asserted-by":"publisher","first-page":"15062","DOI":"10.1073\/pnas.1908962116","article-title":"Large distances separate coregulated genes in living Drosophila embryos","volume":"116","author":"Heist","year":"2019","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2022051110093521900_JCS252544C33","doi-asserted-by":"publisher","first-page":"8938","DOI":"10.1038\/ncomms9938","article-title":"Single-cell analysis and stochastic modelling unveil large cell-to-cell variability in influenza A virus infection","volume":"6","author":"Heldt","year":"2015","journal-title":"Nat. Commun."},{"key":"2022051110093521900_JCS252544C34","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1089\/hum.2014.001","article-title":"Innate Immunity to Adenovirus","volume":"25","author":"Hendrickx","year":"2014","journal-title":"Hum. Gene. Ther."},{"key":"2022051110093521900_JCS252544C35","doi-asserted-by":"publisher","first-page":"a013003","DOI":"10.1101\/cshperspect.a013003","article-title":"Adenovirus DNA replication","volume":"5","author":"Hoeben","year":"2013","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"2022051110093521900_JCS252544C36","doi-asserted-by":"publisher","first-page":"295","DOI":"10.1006\/viro.1996.8349","article-title":"Adenovirus E1B 19K protein is required for efficient DNA replication in U937 cells","volume":"227","author":"Hu","year":"1997","journal-title":"Virology"},{"key":"2022051110093521900_JCS252544C37","doi-asserted-by":"publisher","first-page":"17831","DOI":"10.1073\/pnas.0407786101","article-title":"Viral DNA synthesis-dependent titration of a cellular repressor activates transcription of the human adenovirus type 2 IVa2 gene","volume":"101","author":"Iftode","year":"2004","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2022051110093521900_JCS252544C38","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-9-482","article-title":"CellProfiler Analyst: data exploration and analysis software for complex image-based screens","volume":"9","author":"Jones","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2022051110093521900_JCS252544C39","doi-asserted-by":"publisher","first-page":"4135","DOI":"10.1128\/JVI.02540-10","article-title":"Adenovirus core protein VII protects the viral genome from a DNA damage response at early times after infection","volume":"85","author":"Karen","year":"2011","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C40","doi-asserted-by":"publisher","first-page":"13554","DOI":"10.1128\/JVI.02337-12","article-title":"Reduced infectivity of adenovirus type 5 particles and degradation of entering viral genomes associated with incomplete processing of the preterminal protein","volume":"86","author":"Kato","year":"2012","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C41","doi-asserted-by":"publisher","first-page":"e02241-17","DOI":"10.1128\/JVI.02241-17","article-title":"Visualization of Arenavirus RNA Species in Individual Cells by Single-Molecule Fluorescence In Situ Hybridization Suggests a Model of Cyclical Infection and Clearance during Persistence","volume":"92","author":"King","year":"2018","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C42","doi-asserted-by":"publisher","first-page":"e00390-18","DOI":"10.1128\/mBio.00390-18","article-title":"Hacking the Cell: Network Intrusion and Exploitation by Adenovirus E1A","volume":"9","author":"King","year":"2018","journal-title":"MBio."},{"key":"2022051110093521900_JCS252544C43","doi-asserted-by":"publisher","first-page":"889","DOI":"10.1093\/nar\/gkq783","article-title":"Cellular and viral chromatin proteins are positive factors in the regulation of adenovirus gene expression","volume":"39","author":"Komatsu","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2022051110093521900_JCS252544C44","doi-asserted-by":"publisher","first-page":"e00166-17","DOI":"10.1128\/JVI.00166-17","article-title":"Simultaneous Single-Cell In Situ Analysis of Human Adenovirus Type 5 DNA and mRNA Expression Patterns in Lytic and Persistent Infection","volume":"91","author":"Krzywkowski","year":"2017","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C45","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1038\/s41586-018-0836-1","article-title":"Genomic encoding of transcriptional burst kinetics","volume":"565","author":"Larsson","year":"2019","journal-title":"Nature"},{"key":"2022051110093521900_JCS252544C46","doi-asserted-by":"publisher","first-page":"5349","DOI":"10.1128\/JVI.64.11.5349-5359.1990","article-title":"Adenovirus E1A and E1B genes are regulated posttranscriptionally in human lymphoid cells","volume":"64","author":"Lavery","year":"1990","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C47","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1038\/nmeth.2372","article-title":"Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation","volume":"10","author":"Levesque","year":"2013","journal-title":"Nat. Methods"},{"key":"2022051110093521900_JCS252544C48","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1016\/j.cell.2019.05.029","article-title":"Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells","volume":"178","author":"Li","year":"2019","journal-title":"Cell"},{"key":"2022051110093521900_JCS252544C49","doi-asserted-by":"publisher","first-page":"619","DOI":"10.1016\/j.chom.2016.04.008","article-title":"Epigenetics and Genetics of Viral Latency","volume":"19","author":"Lieberman","year":"2016","journal-title":"Cell Host Microbe"},{"key":"2022051110093521900_JCS252544C50","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1128\/CMR.00116-13","article-title":"Adenovirus infections in immunocompetent and immunocompromised patients","volume":"27","author":"Lion","year":"2014","journal-title":"Clin. Microbiol. Rev."},{"key":"2022051110093521900_JCS252544C51","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1038\/nmeth.2892","article-title":"Single-cell in situ RNA profiling by sequential hybridization","volume":"11","author":"Lubeck","year":"2014","journal-title":"Nat. Methods"},{"key":"2022051110093521900_JCS252544C52","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1016\/j.chom.2015.06.006","article-title":"Co-option of Membrane Wounding Enables Virus Penetration into Cells","volume":"18","author":"Luisoni","year":"2015","journal-title":"Cell Host Microbe"},{"key":"2022051110093521900_JCS252544C53","doi-asserted-by":"publisher","first-page":"R58","DOI":"10.1186\/gb-2007-8-4-r58","article-title":"Adenovirus type 5 exerts genome-wide control over cellular programs governing proliferation, quiescence, and survival","volume":"8","author":"Miller","year":"2007","journal-title":"Genome Biol."},{"key":"2022051110093521900_JCS252544C54","doi-asserted-by":"publisher","first-page":"4222","DOI":"10.1128\/JVI.06399-11","article-title":"Characterization of the 55-residue protein encoded by the 9S E1A mRNA of species C adenovirus","volume":"86","author":"Miller","year":"2012","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C55","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1038\/295380a0","article-title":"Resolving the functions of overlapping viral genes by site-specific mutagenesis at a mRNA splice site","volume":"295","author":"Montell","year":"1982","journal-title":"Nature"},{"key":"2022051110093521900_JCS252544C56","doi-asserted-by":"publisher","first-page":"4268","DOI":"10.1038\/s41467-018-06739-4","article-title":"Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin","volume":"9","author":"Moreau","year":"2018","journal-title":"Nat. Commun."},{"key":"2022051110093521900_JCS252544C57","doi-asserted-by":"publisher","first-page":"7096","DOI":"10.1128\/JVI.00107-10","article-title":"Adenovirus late-phase infection is controlled by a novel L4 promoter","volume":"84","author":"Morris","year":"2010","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C58","doi-asserted-by":"publisher","first-page":"e1007849","DOI":"10.1371\/journal.ppat.1007849","article-title":"Multidimensional analysis of Gammaherpesvirus RNA expression reveals unexpected heterogeneity of gene expression","volume":"15","author":"Oko","year":"2019","journal-title":"PLoS Pathog."},{"key":"2022051110093521900_JCS252544C59","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.virol.2005.09.028","article-title":"Viral persistence: parameters, mechanisms and future predictions","volume":"344","author":"Oldstone","year":"2006","journal-title":"Virology"},{"key":"2022051110093521900_JCS252544C60","doi-asserted-by":"publisher","first-page":"e1006455","DOI":"10.1371\/journal.ppat.1006455","article-title":"The adenovirus major core protein VII is dispensable for virion assembly but is essential for lytic infection","volume":"13","author":"Ostapchuk","year":"2017","journal-title":"PLoS Pathog."},{"key":"2022051110093521900_JCS252544C61","doi-asserted-by":"publisher","first-page":"7252","DOI":"10.1128\/JVI.00104-08","article-title":"Intrinsic structural disorder in adenovirus E1A: a viral molecular hub linking multiple diverse processes","volume":"82","author":"Pelka","year":"2008","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C62","doi-asserted-by":"publisher","first-page":"e04114","DOI":"10.7554\/eLife.04114","article-title":"Quantitative microscopy of functional HIV post-entry complexes reveals association of replication with the viral capsid","volume":"3","author":"Peng","year":"2014","journal-title":"eLife"},{"key":"2022051110093521900_JCS252544C63","doi-asserted-by":"publisher","first-page":"39","DOI":"10.2202\/1544-6115.1585","article-title":"Permutation P-values should never be zero: calculating exact P-values when permutations are randomly drawn","volume":"9","author":"Phipson","year":"2010","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"2022051110093521900_JCS252544C64","doi-asserted-by":"publisher","first-page":"3419","DOI":"10.1002\/1873-3468.13690","article-title":"Imaging the adenovirus infection cycle","volume":"593","author":"Pied","year":"2019","journal-title":"FEBS Lett."},{"key":"2022051110093521900_JCS252544C65","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1021\/acsinfecdis.7b00009","article-title":"Cell Cycle-Dependent Kinase Cdk9 Is a Postexposure Drug Target against Human Adenoviruses","volume":"3","author":"Prasad","year":"2017","journal-title":"ACS Infect Dis."},{"key":"2022051110093521900_JCS252544C66","doi-asserted-by":"publisher","first-page":"1997","DOI":"10.1038\/s41467-020-15844-2","article-title":"The UPR sensor IRE1alpha and the adenovirus E3-19K glycoprotein sustain persistent and lytic infections","volume":"11","author":"Prasad","year":"2020","journal-title":"Nat. Commun."},{"key":"2022051110093521900_JCS252544C67","doi-asserted-by":"publisher","first-page":"13086","DOI":"10.1128\/JVI.02156-14","article-title":"Chemical Induction of Unfolded Protein Response Enhances Cancer Cell Killing through Lytic Virus Infection","volume":"88","author":"Prasad","year":"2014","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C68","doi-asserted-by":"publisher","first-page":"1882","DOI":"10.1038\/s41467-017-01693-z","article-title":"Multiplex single-cell visualization of nucleic acids and protein during HIV infection","volume":"8","author":"Puray-Chavez","year":"2017","journal-title":"Nat. Commun."},{"key":"2022051110093521900_JCS252544C69","doi-asserted-by":"publisher","first-page":"e309","DOI":"10.1371\/journal.pbio.0040309","article-title":"Stochastic mRNA synthesis in mammalian cells","volume":"4","author":"Raj","year":"2006","journal-title":"PLoS Biol."},{"key":"2022051110093521900_JCS252544C70","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1016\/0042-6822(83)90274-X","article-title":"Monoclonal antibodies which recognize native and denatured forms of the adenovirus DNA-binding protein","volume":"128","author":"Reich","year":"1983","journal-title":"Virology"},{"key":"2022051110093521900_JCS252544C71","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.cell.2018.11.026","article-title":"Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity","volume":"176","author":"Rodriguez","year":"2019","journal-title":"Cell"},{"key":"2022051110093521900_JCS252544C72","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1038\/nprot.2015.016","article-title":"Cell cycle staging of individual cells by fluorescence microscopy","volume":"10","author":"Roukos","year":"2015","journal-title":"Nat. Protoc."},{"key":"2022051110093521900_JCS252544C73","doi-asserted-by":"publisher","first-page":"e32303","DOI":"10.7554\/eLife.32303","article-title":"Extreme heterogeneity of influenza virus infection in single cells","volume":"7","author":"Russell","year":"2018","journal-title":"eLife"},{"key":"2022051110093521900_JCS252544C74","doi-asserted-by":"publisher","first-page":"e00500-19","DOI":"10.1128\/JVI.00500-19","article-title":"Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity","volume":"93","author":"Russell","year":"2019","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C75","doi-asserted-by":"publisher","first-page":"eaar3958","DOI":"10.1126\/science.aar3958","article-title":"Coactivator condensation at super-enhancers links phase separation and gene control","volume":"361","author":"Sabari","year":"2018","journal-title":"Science"},{"key":"2022051110093521900_JCS252544C76","doi-asserted-by":"publisher","first-page":"487","DOI":"10.1016\/j.cell.2007.12.033","article-title":"Visualizing spatiotemporal dynamics of multicellular cell-cycle progression","volume":"132","author":"Sakaue-Sawano","year":"2008","journal-title":"Cell"},{"key":"2022051110093521900_JCS252544C77","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat. Methods"},{"key":"2022051110093521900_JCS252544C78","doi-asserted-by":"publisher","first-page":"1282","DOI":"10.1158\/0008-5472.CAN-05-1484","article-title":"Adenovirus-induced extracellular signal-regulated kinase phosphorylation during the late phase of infection enhances viral protein levels and virus progeny","volume":"66","author":"Sch\u00fcmann","year":"2006","journal-title":"Cancer Res."},{"key":"2022051110093521900_JCS252544C79","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/j.cell.2018.05.035","article-title":"Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH","volume":"174","author":"Shah","year":"2018","journal-title":"Cell"},{"key":"2022051110093521900_JCS252544C80","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1016\/0092-8674(80)90568-1","article-title":"Transcripts from the adenovirus-2 major late promoter yield a single early family of 3\u2032 coterminal mRNAs and five late families","volume":"22","author":"Shaw","year":"1980","journal-title":"Cell"},{"key":"2022051110093521900_JCS252544C81","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1016\/0022-2836(78)90048-7","article-title":"Regulation of the appearance of cytoplasmic RNAs from region 1 of the adenovirus 2 genome","volume":"126","author":"Spector","year":"1978","journal-title":"J. Mol. Biol."},{"key":"2022051110093521900_JCS252544C82","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1016\/j.cels.2018.05.008","article-title":"Dissection of Influenza Infection In Vivo by Single-Cell RNA Sequencing","volume":"6","author":"Steuerman","year":"2018","journal-title":"Cell Syst."},{"key":"2022051110093521900_JCS252544C83","doi-asserted-by":"publisher","first-page":"e1006914","DOI":"10.1371\/journal.ppat.1006914","article-title":"Lung macrophage scavenger receptor SR-A6 (MARCO) is an adenovirus type-specific virus entry receptor","volume":"14","author":"Stichling","year":"2018","journal-title":"PLoS Pathog."},{"key":"2022051110093521900_JCS252544C84","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1016\/j.chom.2011.08.010","article-title":"Kinesin-1-mediated capsid disassembly and disruption of the nuclear pore complex promote virus infection","volume":"10","author":"Strunze","year":"2011","journal-title":"Cell Host Microbe"},{"key":"2022051110093521900_JCS252544C85","doi-asserted-by":"publisher","first-page":"12367","DOI":"10.1128\/JVI.01833-13","article-title":"A direct and versatile assay measuring membrane penetration of adenovirus in single cells","volume":"87","author":"Suomalainen","year":"2013","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C86","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1006\/viro.2002.1406","article-title":"Evaluation of accuracy and precision of adenovirus absorptivity at 260 nm under conditions of complete DNA disruption","volume":"295","author":"Sweeney","year":"2002","journal-title":"Virology"},{"key":"2022051110093521900_JCS252544C87","doi-asserted-by":"publisher","first-page":"1802","DOI":"10.1001\/jama.2018.3795","article-title":"Chronic Hepatitis B Infection: A Review","volume":"319","author":"Tang","year":"2018","journal-title":"JAMA"},{"key":"2022051110093521900_JCS252544C88","doi-asserted-by":"publisher","first-page":"E1366","DOI":"10.1073\/pnas.1714790115","article-title":"Superresolution imaging of individual replication forks reveals unexpected prodrug resistance mechanism","volume":"115","author":"Triemer","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2022051110093521900_JCS252544C89","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1038\/nmeth.1321","article-title":"Imaging intracellular RNA distribution and dynamics in living cells","volume":"6","author":"Tyagi","year":"2009","journal-title":"Nat. Methods"},{"key":"2022051110093521900_JCS252544C90","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.cell.2018.10.056","article-title":"Low-Fidelity Assembly of Influenza A Virus Promotes Escape from Host Cells","volume":"176","author":"Vahey","year":"2019","journal-title":"Cell"},{"key":"2022051110093521900_JCS252544C91","doi-asserted-by":"publisher","first-page":"12320","DOI":"10.1128\/JVI.78.22.12320-12332.2004","article-title":"Postentry neutralization of adenovirus type 5 by an antihexon antibody","volume":"78","author":"Varghese","year":"2004","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C92","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1128\/JVI.60.2.353-362.1986","article-title":"Identification of two nuclear subclasses of the adenovirus type 5-encoded DNA-binding protein","volume":"60","author":"Voelkerding","year":"1986","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C93","doi-asserted-by":"publisher","first-page":"468","DOI":"10.1016\/j.chom.2013.09.004","article-title":"Tracking viral genomes in host cells at single-molecule resolution","volume":"14","author":"Wang","year":"2013","journal-title":"Cell Host Microbe"},{"key":"2022051110093521900_JCS252544C94","doi-asserted-by":"publisher","first-page":"2185","DOI":"10.1242\/jcs.203794","article-title":"The nuclear export factor CRM1 controls juxta-nuclear microtubule-dependent virus transport","volume":"130","author":"Wang","year":"2017","journal-title":"J. Cell Sci."},{"key":"2022051110093521900_JCS252544C95","doi-asserted-by":"publisher","first-page":"e1005800","DOI":"10.1371\/journal.ppat.1005800","article-title":"Single-Molecule FISH Reveals Non-selective Packaging of Rift Valley Fever Virus Genome Segments","volume":"12","author":"Wichgers Schreur","year":"2016","journal-title":"PLoS Pathog."},{"key":"2022051110093521900_JCS252544C96","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1016\/0022-2836(81)90537-4","article-title":"Control of messenger RNA concentration by differential cytoplasmic half-life. Adenovirus messenger RNAs from transcription units 1A and 1B","volume":"148","author":"Wilson","year":"1981","journal-title":"J. Mol. Biol."},{"key":"2022051110093521900_JCS252544C97","doi-asserted-by":"publisher","first-page":"e00179-18.","DOI":"10.1128\/JVI.00179-18","article-title":"Single-Cell Analysis of the Impact of Host Cell Heterogeneity on Infection with Foot-and-Mouth Disease Virus","volume":"92","author":"Xin","year":"2018","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C98","doi-asserted-by":"publisher","first-page":"2474","DOI":"10.1128\/JVI.79.4.2474-2483.2005","article-title":"Adenovirus protein VII functions throughout early phase and interacts with cellular proteins SET and pp32","volume":"79","author":"Xue","year":"2005","journal-title":"J. Virol."},{"key":"2022051110093521900_JCS252544C99","doi-asserted-by":"publisher","first-page":"e0138760","DOI":"10.1371\/journal.pone.0138760","article-title":"Plaque2.0 \u2013 A High-Throughput Analysis Framework to Score Virus-Cell Transmission and Clonal Cell Expansion","volume":"10","author":"Yakimovich","year":"2015","journal-title":"PLoS One"},{"key":"2022051110093521900_JCS252544C100","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1006\/viro.2001.1204","article-title":"Critical role for SV40 small-t antigen in human cell transformation","volume":"290","author":"Yu","year":"2001","journal-title":"Virology"},{"key":"2022051110093521900_JCS252544C101","doi-asserted-by":"publisher","first-page":"e32942","DOI":"10.7554\/eLife.32942","article-title":"Single-cell transcriptional dynamics of flavivirus infection","volume":"7","author":"Zanini","year":"2018","journal-title":"eLife"},{"key":"2022051110093521900_JCS252544C102","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1016\/j.virol.2011.12.006","article-title":"The transcriptome of the adenovirus infected cell","volume":"424","author":"Zhao","year":"2012","journal-title":"Virology"},{"key":"2022051110093521900_JCS252544C103","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1016\/j.virol.2014.04.006","article-title":"A new look at adenovirus splicing","volume":"456-457","author":"Zhao","year":"2014","journal-title":"Virology"},{"key":"2022051110093521900_JCS252544C104","doi-asserted-by":"publisher","first-page":"e1005415","DOI":"10.1371\/journal.ppat.1005415","article-title":"E2F\/Rb Family Proteins Mediate Interferon Induced Repression of Adenovirus Immediate Early Transcription to Promote Persistent Viral Infection","volume":"12","author":"Zheng","year":"2016","journal-title":"PLoS Pathog."}],"container-title":["Journal of Cell Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1242\/jcs.252544","content-type":"unspecified","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/journals.biologists.com\/jcs\/article-pdf\/doi\/10.1242\/jcs.252544\/2142306\/jcs252544.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/journals.biologists.com\/jcs\/article-pdf\/doi\/10.1242\/jcs.252544\/2063578\/jcs_252544v1.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/journals.biologists.com\/jcs\/article-pdf\/doi\/10.1242\/jcs.252544\/2142306\/jcs252544.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,5,11]],"date-time":"2022-05-11T06:14:09Z","timestamp":1652249649000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.biologists.com\/jcs\/article\/134\/5\/jcs252544\/223977\/Cell-to-cell-and-genome-to-genome-variability-of"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,11,9]]},"references-count":104,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2021,3,1]]}},"URL":"https:\/\/doi.org\/10.1242\/jcs.252544","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.02.27.967471","asserted-by":"object"}]},"ISSN":["0021-9533","1477-9137"],"issn-type":[{"value":"0021-9533","type":"print"},{"value":"1477-9137","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,11,9]]},"article-number":"jcs252544"}}