{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T22:08:27Z","timestamp":1791151707070,"version":"4.1.0"},"reference-count":62,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2014,1,30]],"date-time":"2014-01-30T00:00:00Z","timestamp":1391040000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"DOI":"10.1371\/journal.ppat.1003896","type":"journal-article","created":{"date-parts":[[2014,1,30]],"date-time":"2014-01-30T17:05:07Z","timestamp":1391101507000},"page":"e1003896","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":73,"title":["RNA-seq Analysis of Host and Viral Gene Expression Highlights Interaction between Varicella Zoster Virus and Keratinocyte Differentiation"],"prefix":"10.1371","volume":"10","author":[{"given":"Meleri","family":"Jones","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Inga R.","family":"Dry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Frampton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manuraj","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ravinder K.","family":"Kanda","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael B.","family":"Yee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Kellam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Hollinshead","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul R.","family":"Kinchington","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edel A.","family":"O'Toole","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Judith","family":"Breuer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2014,1,30]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1152\/physrev.1997.77.2.397","article-title":"The epidermal keratinocyte as a model for the study of gene regulation and cell differentiation","volume":"77","author":"RL Eckert","year":"1997","journal-title":"Physiol Rev"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1016\/0092-8674(80)90094-X","article-title":"Changes in keratin gene expression during terminal differentiation of the keratinocyte","volume":"19","author":"E Fuchs","year":"1980","journal-title":"Cell"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"e7651","DOI":"10.1371\/journal.pone.0007651","article-title":"Dynamic and physical clustering of gene expression during epidermal barrier formation in differentiating keratinocytes","volume":"4","author":"JM Taylor","year":"2009","journal-title":"PLoS One"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1002\/jcb.20095","article-title":"Vitamin D regulated keratinocyte differentiation","volume":"92","author":"DD Bikle","year":"2004","journal-title":"J Cell Biochem"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1016\/S0303-7207(01)00452-X","article-title":"Calcium- and vitamin D-regulated keratinocyte differentiation","volume":"177","author":"DD Bikle","year":"2001","journal-title":"Mol Cell Endocrinol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nrm2636","article-title":"Epidermal homeostasis: a balancing act of stem cells in the skin","volume":"10","author":"C Blanpain","year":"2009","journal-title":"Nat Rev Mol Cell Biol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"398","DOI":"10.1038\/jid.2009.259","article-title":"BMP signaling induces cell-type-specific changes in gene expression programs of human keratinocytes and fibroblasts","volume":"130","author":"MY Fessing","year":"2010","journal-title":"J Invest Dermatol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1038\/jid.2010.268","article-title":"A comprehensive analysis of microRNA expression during human keratinocyte differentiation in vitro and in vivo","volume":"131","author":"J Hildebrand","year":"2011","journal-title":"J Invest Dermatol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1016\/j.tibs.2009.08.001","article-title":"The emerging roles of serine protease cascades in the epidermis","volume":"34","author":"P Ovaere","year":"2009","journal-title":"Trends Biochem Sci"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1002\/jmv.1890380406","article-title":"Replication of varicella zoster virus in primary human keratinocytes","volume":"38","author":"CJ Sexton","year":"1992","journal-title":"J Med Virol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"3238","DOI":"10.1128\/JVI.80.7.3238-3248.2006","article-title":"Varicella-zoster virus open reading frame 10 is a virulence determinant in skin cells but not in T cells in vivo","volume":"80","author":"X Che","year":"2006","journal-title":"J Virol"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"5825","DOI":"10.1128\/JVI.00303-08","article-title":"Functions of the ORF9-to-ORF12 gene cluster in varicella-zoster virus replication and in the pathogenesis of skin infection","volume":"82","author":"X Che","year":"2008","journal-title":"J Virol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1128\/JVI.72.2.965-974.1998","article-title":"Attenuation of the vaccine Oka strain of varicella-zoster virus and role of glycoprotein C in alphaherpesvirus virulence demonstrated in the SCID-hu mouse","volume":"72","author":"JF Moffat","year":"1998","journal-title":"J Virol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"5390","DOI":"10.1073\/pnas.82.16.5390","article-title":"Cell size as a determinant of the clone-forming ability of human keratinocytes","volume":"82","author":"Y Barrandon","year":"1985","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/0014-4827(83)90115-5","article-title":"Calcium regulation of cell-cell contact and differentiation of epidermal cells in culture. An ultrastructural study","volume":"143","author":"H Hennings","year":"1983","journal-title":"Exp Cell Res"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"W Huang da","year":"2009","journal-title":"Nat Protoc"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1033","DOI":"10.1016\/0092-8674(80)90094-X","article-title":"Changes in keratin gene expression during terminal differentiation of the keratinocyte","volume":"19","author":"E Fuchs","year":"1980","journal-title":"Cell"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1007\/s00418-008-0435-6","article-title":"The human keratins: biology and pathology","volume":"129","author":"R Moll","year":"2008","journal-title":"Histochem Cell Biol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"3904","DOI":"10.1128\/JVI.02137-08","article-title":"The replication cycle of varicella-zoster virus: analysis of the kinetics of viral protein expression, genome synthesis, and virion assembly at the single-cell level","volume":"83","author":"M Reichelt","year":"2009","journal-title":"J Virol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"4671","DOI":"10.1128\/AAC.49.11.4671-4680.2005","article-title":"Organotypic epithelial raft cultures as a model for evaluating compounds against alphaherpesviruses","volume":"49","author":"G Andrei","year":"2005","journal-title":"Antimicrob Agents Chemother"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1016\/j.bbamem.2007.07.014","article-title":"Desmosome structure, composition and function","volume":"1778","author":"D Garrod","year":"2008","journal-title":"Biochim Biophys Acta"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"10738","DOI":"10.1128\/JVI.78.19.10738-10746.2004","article-title":"The human papillomavirus type 8 E2 protein suppresses beta4-integrin expression in primary human keratinocytes","volume":"78","author":"M Oldak","year":"2004","journal-title":"J Virol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"2169","DOI":"10.1038\/jid.2011.295","article-title":"When activity requires breaking up: LEKTI proteolytic activation cascade for specific proteinase inhibition","volume":"131","author":"L Furio","year":"2011","journal-title":"J Invest Dermatol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/75977","article-title":"Mutations in SPINK5, encoding a serine protease inhibitor, cause Netherton syndrome","volume":"25","author":"S Chavanas","year":"2000","journal-title":"Nat Genet"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1111\/j.0022-202X.2004.22512.x","article-title":"Degradation of corneodesmosome proteins by two serine proteases of the kallikrein family, SCTE\/KLK5\/hK5 and SCCE\/KLK7\/hK7","volume":"122","author":"C Caubet","year":"2004","journal-title":"J Invest Dermatol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1038\/jid.2008.265","article-title":"Cadherin-mediated cell-cell contact regulates keratinocyte differentiation","volume":"129","author":"JL Charest","year":"2009","journal-title":"J Invest Dermatol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/nrg758","article-title":"Getting under the skin of epidermal morphogenesis","volume":"3","author":"E Fuchs","year":"2002","journal-title":"Nat Rev Genet"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"11501","DOI":"10.1128\/JVI.79.17.11501-11506.2005","article-title":"Replication of varicella-zoster virus in human skin organ culture","volume":"79","author":"SL Taylor","year":"2005","journal-title":"J Virol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"2473","DOI":"10.1099\/vir.0.19226-0","article-title":"Herpes simplex virus type 1 exhibits a tropism for basal entry in polarized epithelial cells","volume":"84","author":"M Schelhaas","year":"2003","journal-title":"J Gen Virol"},{"key":"ref30","first-page":"275","article-title":"Hair follicle involvement in herpes zoster: pathway of viral spread from ganglia to skin","volume":"428","author":"R Muraki","year":"1996","journal-title":"Virchows Arch"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1016\/j.cell.2004.11.007","article-title":"Mannose 6-phosphate receptor dependence of varicella zoster virus infection in vitro and in the epidermis during varicella and zoster","volume":"119","author":"JJ Chen","year":"2004","journal-title":"Cell"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"9544","DOI":"10.1128\/JVI.00668-06","article-title":"Delayed biosynthesis of varicella-zoster virus glycoprotein C: upregulation by hexamethylene bisacetamide and retinoic acid treatment of infected cells","volume":"80","author":"J Storlie","year":"2006","journal-title":"J Virol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.virol.2008.09.031","article-title":"Discordant varicella-zoster virus glycoprotein C expression and localization between cultured cells and human skin vesicles","volume":"382","author":"J Storlie","year":"2008","journal-title":"Virology"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"5113","DOI":"10.1128\/JVI.01956-05","article-title":"Inhibition of the NF-kappaB pathway by varicella-zoster virus in vitro and in human epidermal cells in vivo","volume":"80","author":"JO Jones","year":"2006","journal-title":"J Virol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"300","DOI":"10.3346\/jkms.2012.27.3.300","article-title":"Acute UV irradiation increases heparan sulfate proteoglycan levels in human skin","volume":"27","author":"JY Jung","year":"2012","journal-title":"J Korean Med Sci"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"6070","DOI":"10.1128\/JVI.66.10.6070-6080.1992","article-title":"Differentiation-induced and constitutive transcription of human papillomavirus type 31b in cell lines containing viral episomes","volume":"66","author":"M Hummel","year":"1992","journal-title":"J Virol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"13769","DOI":"10.1128\/JVI.79.21.13769-13777.2005","article-title":"Activation of Kaposi's sarcoma-associated herpesvirus lytic gene expression during epithelial differentiation","volume":"79","author":"AS Johnson","year":"2005","journal-title":"J Virol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"1995","DOI":"10.1016\/j.yexcr.2007.03.029","article-title":"Diseases of epidermal keratins and their linker proteins","volume":"313","author":"J Uitto","year":"2007","journal-title":"Exp Cell Res"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"3086","DOI":"10.1128\/MCB.19.4.3086","article-title":"Modulation of cell proliferation by cytokeratins K10 and K16","volume":"19","author":"JM Paramio","year":"1999","journal-title":"Mol Cell Biol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"x","DOI":"10.1111\/j.0022-202X.2004.23495.x","article-title":"The role of keratins in epidermal development and homeostasis\u2013going beyond the obvious","volume":"123","author":"PJ Koch","year":"2004","journal-title":"J Invest Dermatol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1111\/j.0022-202X.2004.23426.x","article-title":"Loss of keratin 10 leads to mitogen-activated protein kinase (MAPK) activation, increased keratinocyte turnover, and decreased tumor formation in mice","volume":"123","author":"J Reichelt","year":"2004","journal-title":"J Invest Dermatol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1750","DOI":"10.1242\/jcs.097139","article-title":"Deletion of K1\/K10 does not impair epidermal stratification but affects desmosomal structure and nuclear integrity","volume":"125","author":"L Wallace","year":"2012","journal-title":"J Cell Sci"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1622","DOI":"10.1038\/sj.jid.5700284","article-title":"Corneodesmosomal cadherins are preferential targets of stratum corneum trypsin- and chymotrypsin-like hyperactivity in Netherton syndrome","volume":"126","author":"P Descargues","year":"2006","journal-title":"J Invest Dermatol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"782","DOI":"10.1091\/mbc.E10-11-0879","article-title":"A decisive function of transforming growth factor-beta\/Smad signaling in tissue morphogenesis and differentiation of human HaCaT keratinocytes","volume":"22","author":"S Buschke","year":"2011","journal-title":"Mol Biol Cell"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1016\/j.antiviral.2005.06.011","article-title":"Viral and cellular gene transcription in fibroblasts infected with small plaque mutants of varicella-zoster virus","volume":"68","author":"JO Jones","year":"2005","journal-title":"Antiviral Res"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1083\/jcb.132.3.381","article-title":"Onset of re-epithelialization after skin injury correlates with a reorganization of keratin filaments in wound edge keratinocytes: defining a potential role for keratin 16","volume":"132","author":"RD Paladini","year":"1996","journal-title":"J Cell Biol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"6220","DOI":"10.1128\/JVI.02396-10","article-title":"Varicella-zoster virus (VZV) infection of neurons derived from human embryonic stem cells: direct demonstration of axonal infection, transport of VZV, and productive neuronal infection","volume":"85","author":"A Markus","year":"2011","journal-title":"J Virol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"6062","DOI":"10.1128\/JVI.77.10.6062-6065.2003","article-title":"Construction of varicella-zoster virus recombinants from parent Oka cosmids and demonstration that ORF65 protein is dispensable for infection of human skin and T cells in the SCID-hu mouse model","volume":"77","author":"T Niizuma","year":"2003","journal-title":"J Virol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"13200","DOI":"10.1128\/JVI.01148-07","article-title":"A self-excisable infectious bacterial artificial chromosome clone of varicella-zoster virus allows analysis of the essential tegument protein encoded by ORF9","volume":"81","author":"BK Tischer","year":"2007","journal-title":"J Virol"},{"key":"ref50","first-page":"79","article-title":"Varicella-Zoster Virus Open Reading Frame 66 Protein Kinase and Its Relationship to Alphaherpesvirus US3 Kinases","volume":"342","author":"A Erazo","year":"2010","journal-title":"Curr Top Microbiol Immunol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"191","DOI":"10.2144\/000112096","article-title":"Two-step red-mediated recombination for versatile high-efficiency markerless DNA manipulation in Escherichia coli","volume":"40","author":"BK Tischer","year":"2006","journal-title":"Biotechniques"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1089\/10763270152436508","article-title":"In vitro characterization of an artificial dermal scaffold","volume":"7","author":"NO Ojeh","year":"2001","journal-title":"Tissue Eng"},{"key":"ref53","first-page":"Unit 11 17","article-title":"Aligning short sequencing reads with Bowtie","volume":"Chapter 11","author":"B Langmead","year":"2010","journal-title":"Curr Protoc Bioinformatics"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"C Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"RC Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2010-11-3-r25","article-title":"A scaling normalization method for differential expression analysis of RNA-seq data","volume":"11","author":"MD Robinson","year":"2010","journal-title":"Genome Biol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"4288","DOI":"10.1093\/nar\/gks042","article-title":"Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation","volume":"40","author":"DJ McCarthy","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/S0076-6879(06)11009-5","article-title":"TM4 microarray software suite","volume":"411","author":"AI Saeed","year":"2006","journal-title":"Methods Enzymol"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"374","DOI":"10.2144\/03342mt01","article-title":"TM4: a free, open-source system for microarray data management and analysis","volume":"34","author":"AI Saeed","year":"2003","journal-title":"Biotechniques"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1038\/nbt.1754","article-title":"Integrative genomics viewer","volume":"29","author":"JT Robinson","year":"2011","journal-title":"Nat Biotechnol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method","volume":"25","author":"KJ Livak","year":"2001","journal-title":"Methods"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1004313","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2014,7,22]],"date-time":"2014-07-22T00:00:00Z","timestamp":1405987200000}}],"container-title":["PLoS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.ppat.1003896","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,14]],"date-time":"2020-08-14T17:56:06Z","timestamp":1597427766000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1003896"}},"subtitle":[],"editor":[{"given":"Roger D.","family":"Everett","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2014,1,30]]},"references-count":62,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2014,1,30]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1003896","relation":{},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,1,30]]}}}