{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T02:29:19Z","timestamp":1792722559464,"version":"4.5.0"},"reference-count":112,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2027,2,6]],"date-time":"2027-02-06T00:00:00Z","timestamp":1801872000000},"content-version":"am","delay-in-days":342,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100000943","name":"Commonwealth Scientific and Industrial Research Organisation","doi-asserted-by":"publisher","award":["OD-232255"],"award-info":[{"award-number":["OD-232255"]}],"id":[{"id":"10.13039\/501100000943","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Developmental & Comparative Immunology"],"published-print":{"date-parts":[[2026,3]]},"DOI":"10.1016\/j.dci.2026.105561","type":"journal-article","created":{"date-parts":[[2026,2,3]],"date-time":"2026-02-03T15:51:58Z","timestamp":1770133918000},"page":"105561","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"special_numbering":"C","title":["Early innate immune response to highly pathogenic avian influenza and functional characterisation of the chicken IRF1 promoter"],"prefix":"10.1016","volume":"176","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1226-8798","authenticated-orcid":false,"given":"Aaron J.","family":"Smith","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sudip","family":"Dhakal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arjun","family":"Challagulla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kiran","family":"Krishnankutty Nair","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emiliana","family":"Weiss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristie","family":"Jenkins","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James W.","family":"Wynne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib1","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1111\/j.1863-2378.2007.01082.x","article-title":"Avian influenza\u2013diagnosis","volume":"55","author":"Alexander","year":"2008","journal-title":"Zoonoses Publ. Health"},{"issue":"15","key":"10.1016\/j.dci.2026.105561_bib2","doi-asserted-by":"crossref","first-page":"1591","DOI":"10.1016\/S0264-410X(02)00749-1","article-title":"A fish specific expression vector containing the interferon regulatory factor 1A (IRF1A) promoter for genetic immunization of fish","volume":"21","author":"Alonso","year":"2003","journal-title":"Vaccine"},{"issue":"7493","key":"10.1016\/j.dci.2026.105561_bib3","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1038\/nature12787","article-title":"An atlas of active enhancers across human cell types and tissues","volume":"507","author":"Andersson","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.dci.2026.105561_bib4","author":"Andrews"},{"issue":"8","key":"10.1016\/j.dci.2026.105561_bib5","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0105713","article-title":"TLR ligands induce antiviral responses in chicken macrophages","volume":"9","author":"Barjesteh","year":"2014","journal-title":"PLoS One"},{"issue":"11","key":"10.1016\/j.dci.2026.105561_bib6","doi-asserted-by":"crossref","first-page":"2005","DOI":"10.1016\/j.molimm.2010.04.015","article-title":"Regulation and function of interferon regulatory factors of Atlantic salmon","volume":"47","author":"Bergan","year":"2010","journal-title":"Mol. Immunol."},{"issue":"6","key":"10.1016\/j.dci.2026.105561_bib7","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.3390\/ani13061052","article-title":"Tissue tropism of H9N2 low-pathogenic avian influenza virus in broiler chickens by immunohistochemistry","volume":"13","author":"B\u00f3na","year":"2023","journal-title":"Animals"},{"issue":"Suppl. 4","key":"10.1016\/j.dci.2026.105561_bib8","article-title":"The biology of influenza viruses","volume":"26","author":"Bouvier","year":"2008","journal-title":"Vaccine"},{"issue":"4","key":"10.1016\/j.dci.2026.105561_bib9","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1016\/0022-2836(90)90223-9","article-title":"Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences","volume":"212","author":"Bucher","year":"1990","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.dci.2026.105561_bib10","doi-asserted-by":"crossref","first-page":"8718","DOI":"10.1128\/JVI.02403-10","article-title":"Antigenic drift in H5N1 avian influenza virus in poultry is driven by mutations in major antigenic sites of the hemagglutinin molecule analogous to those for human influenza virus","volume":"85","author":"Cattoli","year":"2011","journal-title":"J. Virol."},{"key":"10.1016\/j.dci.2026.105561_bib11","author":"Chatsuwan"},{"key":"10.1016\/j.dci.2026.105561_bib12","doi-asserted-by":"crossref","DOI":"10.1016\/j.dci.2021.103996","article-title":"IRF1 and IRF2 act as positive regulators in antiviral response of large yellow croaker (Larimichthys crocea) by induction of distinct subgroups of type I IFNs","volume":"118","author":"Chen","year":"2021","journal-title":"Dev. Comp. Immunol."},{"issue":"7","key":"10.1016\/j.dci.2026.105561_bib13","doi-asserted-by":"crossref","first-page":"1930","DOI":"10.4049\/jimmunol.1900293","article-title":"IRF7 is involved in both STING and MAVS mediating IFN-\u03b2 signaling in IRF3-lacking chickens","volume":"203","author":"Cheng","year":"2019","journal-title":"J. Immunol."},{"issue":"5","key":"10.1016\/j.dci.2026.105561_bib14","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1003358","article-title":"Colocalization of different influenza viral RNA segments in the cytoplasm before viral budding as shown by single-molecule sensitivity FISH analysis","volume":"9","author":"Chou","year":"2013","journal-title":"PLoS Pathog."},{"issue":"9101","key":"10.1016\/j.dci.2026.105561_bib15","doi-asserted-by":"crossref","first-page":"472","DOI":"10.1016\/S0140-6736(97)11212-0","article-title":"Human influenza A H5N1 virus related to a highly pathogenic avian influenza virus","volume":"351","author":"Claas","year":"1998","journal-title":"Lancet"},{"issue":"9","key":"10.1016\/j.dci.2026.105561_bib16","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1016\/j.dci.2009.04.001","article-title":"The avian toll-like receptor pathway\u2014Subtle differences amidst general conformity","volume":"33","author":"Cormican","year":"2009","journal-title":"Dev. Comp. Immunol."},{"issue":"6","key":"10.1016\/j.dci.2026.105561_bib17","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1080\/03079457.2012.732691","article-title":"Differential innate responses of chickens and ducks to low-pathogenic avian influenza","volume":"41","author":"Cornelissen","year":"2012","journal-title":"Avian Pathol."},{"issue":"5","key":"10.1016\/j.dci.2026.105561_bib18","doi-asserted-by":"crossref","first-page":"979","DOI":"10.4049\/jimmunol.2101147","article-title":"Duck CD8(+) T cell response to H5N1 highly pathogenic Avian influenza virus infection in vivo and in vitro","volume":"209","author":"Dai","year":"2022","journal-title":"J. Immunol."},{"key":"10.1016\/j.dci.2026.105561_bib19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13567-020-00793-x","article-title":"Systematic identification of chicken type I, II and III interferon-stimulated genes","volume":"51","author":"Dai","year":"2020","journal-title":"Vet. Res."},{"issue":"10","key":"10.1016\/j.dci.2026.105561_bib20","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1011685","article-title":"Dissection of key factors correlating with H5N1 avian influenza virus driven inflammatory lung injury of chicken identified by single-cell analysis","volume":"19","author":"Dai","year":"2023","journal-title":"PLoS Pathog."},{"issue":"5164","key":"10.1016\/j.dci.2026.105561_bib21","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1126\/science.8197455","article-title":"Jak-STAT pathways and transcriptional activation in response to IFNs and other extracellular signaling proteins","volume":"264","author":"Darnell","year":"1994","journal-title":"Science"},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib22","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib23","doi-asserted-by":"crossref","first-page":"29","DOI":"10.3109\/10409238.2011.628970","article-title":"NF-Y and the transcriptional activation of CCAAT promoters","volume":"47","author":"Dolfini","year":"2012","journal-title":"Crit. Rev. Biochem. Mol. Biol."},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib24","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1016\/j.celrep.2017.06.021","article-title":"Analysis of IAV replication and Co-infection dynamics by a versatile RNA viral genome labeling method","volume":"20","author":"Dou","year":"2017","journal-title":"Cell Rep."},{"issue":"D1","key":"10.1016\/j.dci.2026.105561_bib25","doi-asserted-by":"crossref","first-page":"D157","DOI":"10.1093\/nar\/gks1233","article-title":"EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era","volume":"41","author":"Dreos","year":"2013","journal-title":"Nucleic Acids Res."},{"issue":"3","key":"10.1016\/j.dci.2026.105561_bib26","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.4049\/jimmunol.1402415","article-title":"Zebrafish IRF1 regulates IFN antiviral response through binding to IFN\u03d51 and IFN\u03d53 promoters downstream of MyD88 signaling","volume":"194","author":"Feng","year":"2015","journal-title":"J. Immunol."},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib27","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/s13567-019-0638-y","article-title":"A balanced game: chicken macrophage response to ALV-J infection","volume":"50","author":"Feng","year":"2019","journal-title":"Vet. Res."},{"issue":"3","key":"10.1016\/j.dci.2026.105561_bib28","doi-asserted-by":"crossref","first-page":"451","DOI":"10.1016\/j.immuni.2019.07.007","article-title":"Differential activation of the transcription factor IRF1 underlies the distinct immune responses elicited by type I and type III interferons","volume":"51","author":"Forero","year":"2019","journal-title":"Immunity"},{"issue":"18","key":"10.1016\/j.dci.2026.105561_bib29","doi-asserted-by":"crossref","first-page":"5028","DOI":"10.1093\/emboj\/18.18.5028","article-title":"Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences","volume":"18","author":"Fujii","year":"1999","journal-title":"EMBO J."},{"key":"10.1016\/j.dci.2026.105561_bib30","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1016\/j.ijbiomac.2020.11.217","article-title":"Molecular and functional characterization of interferon regulatory factor 1 (IRF1) in amphibian Xenopus tropicalis","volume":"167","author":"Gan","year":"2021","journal-title":"Int. J. Biol. Macromol."},{"issue":"9","key":"10.1016\/j.dci.2026.105561_bib32","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0215495","article-title":"CiiiDER: a tool for predicting and analysing transcription factor binding sites","volume":"14","author":"Gearing","year":"2019","journal-title":"PLoS One"},{"issue":"21","key":"10.1016\/j.dci.2026.105561_bib33","doi-asserted-by":"crossref","first-page":"12408","DOI":"10.1074\/jbc.271.21.12408","article-title":"Application of genomic DNA affinity chromatography identifies multiple Interferon-\u03b1-regulated Stat2 complexes (\u2217)","volume":"271","author":"Ghislain","year":"1996","journal-title":"J. Biol. Chem."},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib34","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-17730-2","article-title":"Constitutively elevated levels of SOCS1 suppress innate responses in DF-1 immortalised chicken fibroblast cells","volume":"7","author":"Giotis","year":"2017","journal-title":"Sci. Rep."},{"issue":"9","key":"10.1016\/j.dci.2026.105561_bib35","doi-asserted-by":"crossref","first-page":"8350","DOI":"10.18632\/oncotarget.23615","article-title":"Proteomic analysis of chicken embryo fibroblast cells infected with recombinant H5N1 avian influenza viruses with and without NS1 eIF4GI binding domain","volume":"9","author":"Guo","year":"2017","journal-title":"Oncotarget"},{"issue":"2","key":"10.1016\/j.dci.2026.105561_bib36","first-page":"1500","article-title":"Structure and regulation of the human interferon regulatory factor 1 (IRF-1) and IRF-2 genes: implications for a gene network in the interferon system","volume":"14","author":"Harada","year":"1994","journal-title":"Mol. Cell Biol."},{"issue":"2","key":"10.1016\/j.dci.2026.105561_bib37","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1006\/viro.1998.9290","article-title":"The DF-1 chicken fibroblast cell line: transformation induced by diverse oncogenes and cell death resulting from infection by avian leukosis viruses","volume":"248","author":"Himly","year":"1998","journal-title":"Virology"},{"key":"10.1016\/j.dci.2026.105561_bib38","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2172-11-22","article-title":"Global characterization of interferon regulatory factor (IRF) genes in vertebrates: glimpse of the diversification in evolution","volume":"11","author":"Huang","year":"2010","journal-title":"BMC Immunol."},{"issue":"8","key":"10.1016\/j.dci.2026.105561_bib39","doi-asserted-by":"crossref","first-page":"2419","DOI":"10.1016\/j.molimm.2007.11.011","article-title":"Gene structures and promoter characteristics of interferon regulatory factor 1 (IRF-1), IRF-2 and IRF-7 from snakehead Channa argus","volume":"45","author":"Jia","year":"2008","journal-title":"Mol. Immunol."},{"issue":"2","key":"10.1016\/j.dci.2026.105561_bib40","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1186\/gb-2003-4-2-206","article-title":"Sp1- and Kr\u00fcppel-like transcription factors","volume":"4","author":"Kaczynski","year":"2003","journal-title":"Genome Biol."},{"issue":"10","key":"10.1016\/j.dci.2026.105561_bib41","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1111\/1348-0421.12443","article-title":"Highly pathogenic avian influenza H5N1 virus induces cytokine dysregulation with suppressed maturation of chicken monocyte\u2010derived dendritic cells","volume":"60","author":"Kalaiyarasu","year":"2016","journal-title":"Microbiol. Immunol."},{"issue":"9","key":"10.1016\/j.dci.2026.105561_bib42","doi-asserted-by":"crossref","first-page":"5397","DOI":"10.4049\/jimmunol.1003712","article-title":"Characterization of chicken MDA5 activity: regulation of IFN-\u03b2 in the absence of RIG-I functionality","volume":"186","author":"Karpala","year":"2011","journal-title":"J. Immunol."},{"key":"10.1016\/j.dci.2026.105561_bib43","article-title":"BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences","volume":"37","author":"Khan","year":"2020","journal-title":"Bioinformatics"},{"issue":"4","key":"10.1016\/j.dci.2026.105561_bib44","doi-asserted-by":"crossref","first-page":"245","DOI":"10.2141\/jpsa.0140203","article-title":"Genetically disparate Fayoumi chicken lines show different response to avian necrotic enteritis","volume":"52","author":"Kim","year":"2015","journal-title":"J. Poultry Sci."},{"issue":"7","key":"10.1016\/j.dci.2026.105561_bib45","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0133450","article-title":"Functional analysis of chicken IRF7 in response to dsRNA analog poly(I: C) by integrating overexpression and knockdown","volume":"10","author":"Kim","year":"2015","journal-title":"PLoS One"},{"key":"10.1016\/j.dci.2026.105561_bib46","doi-asserted-by":"crossref","first-page":"415","DOI":"10.3389\/fgene.2018.00415","article-title":"Overexpression of chicken IRF7 increased viral replication and programmed cell death to the Avian influenza virus infection through TGF-Beta\/FoxO signaling axis in DF-1","volume":"9","author":"Kim","year":"2018","journal-title":"Front. Genet."},{"issue":"3-4","key":"10.1016\/j.dci.2026.105561_bib47","first-page":"123","article-title":"Characterization of the chicken PKR: polymorphism of the gene and antiviral activity against vesicular stomatitis virus","volume":"51","author":"Ko","year":"2004","journal-title":"Jpn. J. Vet. Res."},{"key":"10.1016\/j.dci.2026.105561_bib48","article-title":"Fast gene set enrichment analysis","author":"Korotkevich","year":"2021","journal-title":"bioRxiv"},{"issue":"4","key":"10.1016\/j.dci.2026.105561_bib49","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"issue":"12","key":"10.1016\/j.dci.2026.105561_bib50","doi-asserted-by":"crossref","first-page":"1313","DOI":"10.1016\/S1357-2725(97)00094-0","article-title":"Transcriptional regulation by the Sp family proteins","volume":"29","author":"Lania","year":"1997","journal-title":"Int. J. Biochem. Cell Biol."},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib51","doi-asserted-by":"crossref","first-page":"133","DOI":"10.3390\/microorganisms10010133","article-title":"Interferon signaling in chickens plays a crucial role in inhibiting influenza replication in DF1 cells","volume":"10","author":"Layton","year":"2022","journal-title":"Microorganisms"},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib52","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.jviromet.2008.06.019","article-title":"Evaluation of chicken-origin (DF-1) and quail-origin (QT-6) fibroblast cell lines for replication of avian influenza viruses","volume":"153","author":"Lee","year":"2008","journal-title":"J. Virol. Methods"},{"key":"10.1016\/j.dci.2026.105561_bib53","doi-asserted-by":"crossref","first-page":"678","DOI":"10.3389\/fimmu.2020.00678","article-title":"Targeted knockout of MDA5 and TLR3 in the DF-1 chicken fibroblast cell line impairs innate immune response against RNA ligands","volume":"11","author":"Lee","year":"2020","journal-title":"Front. Immunol."},{"issue":"4","key":"10.1016\/j.dci.2026.105561_bib54","doi-asserted-by":"crossref","DOI":"10.1016\/j.cytox.2021.100056","article-title":"Interferon stimulated binding of ISRE is cell type specific and is predicted by homeostatic chromatin state","volume":"3","author":"Leviyang","year":"2021","journal-title":"Cytokine X"},{"key":"10.1016\/j.dci.2026.105561_bib55","article-title":"Diverse feather shape evolution enabled by coupling anisotropic signalling modules with self-organizing branching programme","volume":"8","author":"Li","year":"2017","journal-title":"Nat. Commun."},{"issue":"16","key":"10.1016\/j.dci.2026.105561_bib56","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib57","doi-asserted-by":"crossref","DOI":"10.1038\/srep18610","article-title":"Identification of climate factors related to human infection with avian influenza A H7N9 and H5N1 viruses in China","volume":"5","author":"Li","year":"2015","journal-title":"Sci. Rep."},{"issue":"10","key":"10.1016\/j.dci.2026.105561_bib58","doi-asserted-by":"crossref","first-page":"5790","DOI":"10.1074\/jbc.271.10.5790","article-title":"Formation of STAT1-STAT2 heterodimers and their role in the activation of IRF-1 gene transcription by Interferon-\u03b1(\u2217)","volume":"271","author":"Li","year":"1996","journal-title":"J. Biol. Chem."},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib59","doi-asserted-by":"crossref","first-page":"1558","DOI":"10.1038\/s41467-018-04013-1","article-title":"The molecular basis of JAK\/STAT inhibition by SOCS1","volume":"9","author":"Liau","year":"2018","journal-title":"Nat. Commun."},{"issue":"6","key":"10.1016\/j.dci.2026.105561_bib60","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The Molecular Signatures Database (MSigDB) hallmark gene set collection","volume":"1","author":"Liberzon","year":"2015","journal-title":"Cell Syst."},{"key":"10.1016\/j.dci.2026.105561_bib61","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1743-422X-9-7","article-title":"Highly pathogenic avian influenza virus H5N1 controls type I IFN induction in chicken macrophage HD-11 cells: a polygenic trait that involves NS1 and the polymerase complex","volume":"9","author":"Liniger","year":"2012","journal-title":"Virol. J."},{"issue":"2","key":"10.1016\/j.dci.2026.105561_bib62","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1128\/JVI.00742-11","article-title":"Chicken cells sense influenza A virus infection through MDA5 and CARDIF signaling involving LGP2","volume":"86","author":"Liniger","year":"2012","journal-title":"J. Virol."},{"issue":"2","key":"10.1016\/j.dci.2026.105561_bib63","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1007\/s11262-014-1151-z","article-title":"Comparative analysis of selected innate immune-related genes following infection of immortal DF-1 cells with highly pathogenic (H5N1) and low pathogenic (H9N2) avian influenza viruses","volume":"50","author":"Liu","year":"2015","journal-title":"Virus Genes"},{"key":"10.1016\/j.dci.2026.105561_bib64","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1016\/j.dci.2018.07.003","article-title":"Chicken interferon regulatory factor 1 (IRF1) involved in antiviral innate immunity via regulating IFN-\u03b2 production","volume":"88","author":"Liu","year":"2018","journal-title":"Dev. Comp. Immunol."},{"issue":"4","key":"10.1016\/j.dci.2026.105561_bib65","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":"Livak","year":"2001","journal-title":"Methods"},{"key":"10.1016\/j.dci.2026.105561_bib66","doi-asserted-by":"crossref","first-page":"471","DOI":"10.1007\/s11262-007-0187-8","article-title":"Virulence of H5N1 avian influenza virus enhanced by a 15-nucleotide deletion in the viral nonstructural gene","volume":"36","author":"Long","year":"2008","journal-title":"Virus Genes"},{"issue":"12","key":"10.1016\/j.dci.2026.105561_bib67","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"issue":"19","key":"10.1016\/j.dci.2026.105561_bib68","doi-asserted-by":"crossref","first-page":"16592","DOI":"10.1074\/jbc.M111440200","article-title":"Stimulation of IRF-7 gene expression by tumor necrosis factor \u03b1: requirement for NF\u03baB transcription factor and gene accessibility \u2217","volume":"277","author":"Lu","year":"2002","journal-title":"J. Biol. Chem."},{"issue":"5","key":"10.1016\/j.dci.2026.105561_bib69","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1111\/1348-0421.12588","article-title":"Dynamic analysis of expression of chemokine and cytokine gene responses to H5N1 and H9N2 avian influenza viruses in DF\u20101 cells","volume":"62","author":"Luo","year":"2018","journal-title":"Microbiol. Immunol."},{"issue":"5","key":"10.1016\/j.dci.2026.105561_bib70","doi-asserted-by":"crossref","first-page":"1135","DOI":"10.1093\/nar\/26.5.1135","article-title":"A survey of 178 NF-Y binding CCAAT boxes","volume":"26","author":"Mantovani","year":"1998","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib71","first-page":"3","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads [next generation sequencing","volume":"17","author":"Martin","year":"2011","journal-title":"small RNA; microRNA; adapter removal]"},{"issue":"11","key":"10.1016\/j.dci.2026.105561_bib72","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1292\/jvms.11-0517","article-title":"Biological effects of chicken type III interferon on expression of interferon-stimulated genes in chickens: comparison with type I and type II interferons","volume":"74","author":"Masuda","year":"2012","journal-title":"J. Vet. Med. Sci."},{"issue":"4","key":"10.1016\/j.dci.2026.105561_bib73","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1111\/j.1750-2659.2009.00089.x","article-title":"Understanding influenza transmission, immunity and pandemic threats","volume":"3","author":"Mathews","year":"2009","journal-title":"Influ. Respir. Viruses"},{"issue":"9","key":"10.1016\/j.dci.2026.105561_bib74","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1089\/104454900439782","article-title":"Cloning and promoter analysis of the chicken interferon regulatory factor-3 gene","volume":"19","author":"May","year":"2000","journal-title":"DNA Cell Biol."},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib75","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/S0303-7207(01)00593-7","article-title":"Sp1 is required for prolactin activation of the interferon regulatory factor-1 gene","volume":"184","author":"McAlexander","year":"2001","journal-title":"Mol. Cell. Endocrinol."},{"issue":"6","key":"10.1016\/j.dci.2026.105561_bib76","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1016\/S0092-8674(88)91307-4","article-title":"Regulated expression of a gene encoding a nuclear factor, IRF-1, that specifically binds to IFN-\u03b2 gene regulatory elements","volume":"54","author":"Miyamoto","year":"1988","journal-title":"Cell"},{"issue":"13","key":"10.1016\/j.dci.2026.105561_bib77","doi-asserted-by":"crossref","first-page":"12262","DOI":"10.1074\/jbc.M404260200","article-title":"Regulation of the transcriptional activity of the IRF7 promoter by a pathway independent of interferon signaling","volume":"280","author":"Ning","year":"2005","journal-title":"The Journal of Biological Chemistry"},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib78","doi-asserted-by":"crossref","first-page":"3072","DOI":"10.1038\/s41467-019-10905-7","article-title":"NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region","volume":"10","author":"Oldfield","year":"2019","journal-title":"Nat. Commun."},{"issue":"5","key":"10.1016\/j.dci.2026.105561_bib79","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1016\/j.molcel.2014.07.005","article-title":"Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors","volume":"55","author":"Oldfield","year":"2014","journal-title":"Mol. Cell"},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib80","doi-asserted-by":"crossref","first-page":"2232","DOI":"10.1038\/s41467-025-57338-z","article-title":"Cross-species and mammal-to-mammal transmission of clade 2.3. 4.4 b highly pathogenic avian influenza A\/H5N1 with PB2 adaptations","volume":"16","author":"Pardo-Roa","year":"2025","journal-title":"Nat. Commun."},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib81","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1002\/j.1460-2075.1994.tb06245.x","article-title":"Tyrosine phosphorylated p91 binds to a single element in the ISGF2\/IRF\u20101 promoter to mediate induction by IFN alpha and IFN gamma, and is likely to autoregulate the p91 gene","volume":"13","author":"Pine","year":"1994","journal-title":"EMBO J."},{"issue":"3","key":"10.1016\/j.dci.2026.105561_bib82","doi-asserted-by":"crossref","DOI":"10.3390\/genes13030435","article-title":"Network meta-analysis of chicken microarray data following Avian influenza Challenge-A comparison of highly and lowly pathogenic strains","volume":"13","author":"Pirbaluty","year":"2022","journal-title":"Genes (Basel)"},{"issue":"6","key":"10.1016\/j.dci.2026.105561_bib83","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":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.dci.2026.105561_bib101","series-title":"R: a Language and Environment for Statistical Computing","year":"2024"},{"issue":"4","key":"10.1016\/j.dci.2026.105561_bib84","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0153671","article-title":"Genome wide host gene expression analysis in chicken lungs infected with Avian influenza viruses","volume":"11","author":"Ranaware","year":"2016","journal-title":"PLoS One"},{"key":"10.1016\/j.dci.2026.105561_bib85","doi-asserted-by":"crossref","first-page":"2025","DOI":"10.3389\/fimmu.2018.02025","article-title":"Chickens expressing IFIT5 ameliorate clinical outcome and pathology of highly pathogenic avian influenza and velogenic newcastle disease viruses","volume":"9","author":"Rohaim","year":"2018","journal-title":"Front. Immunol."},{"key":"10.1016\/j.dci.2026.105561_bib86","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-017-3641-6","article-title":"Tissue and time specific expression pattern of interferon regulated genes in the chicken","volume":"18","author":"R\u00f6ll","year":"2017","journal-title":"BMC Genom."},{"key":"10.1016\/j.dci.2026.105561_bib87","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/j.fsi.2017.03.054","article-title":"Two type II IFN members, IFN-\u03b3 and IFN-\u03b3 related (rel), regulate differentially IRF1 and IRF11 in zebrafish","volume":"65","author":"Ruan","year":"2017","journal-title":"Fish Shellfish Immunol."},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib88","doi-asserted-by":"crossref","first-page":"6794","DOI":"10.1038\/s41598-018-24905-y","article-title":"Chicken interferon-induced protein with tetratricopeptide repeats 5 antagonizes replication of RNA viruses","volume":"8","author":"Santhakumar","year":"2018","journal-title":"Sci. Rep."},{"issue":"4","key":"10.1016\/j.dci.2026.105561_bib89","article-title":"Genome-wide classification of type I, type II and type III interferon-stimulated genes in chicken fibroblasts","volume":"7","author":"Santhakumar","year":"2019","journal-title":"Vaccines (Basel)"},{"key":"10.1016\/j.dci.2026.105561_bib90","doi-asserted-by":"crossref","first-page":"49","DOI":"10.3389\/fimmu.2017.00049","article-title":"Avian interferons and their antiviral effectors","volume":"8","author":"Santhakumar","year":"2017","journal-title":"Front. Immunol."},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib91","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1146\/annurev-virology-092818-015756","article-title":"Interferon-stimulated genes: what do they all do?","volume":"6","author":"Schoggins","year":"2019","journal-title":"Annual Rev. Virol."},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib92","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1006\/viro.1994.1464","article-title":"The chicken Mx promoter contains an ISRE motif and confers interferon inducibility to a reporter gene in chick and monkey cells","volume":"203","author":"Schumacher","year":"1994","journal-title":"Virology"},{"issue":"8","key":"10.1016\/j.dci.2026.105561_bib93","doi-asserted-by":"crossref","DOI":"10.3390\/ijms18081650","article-title":"Evolution of influenza A virus by mutation and Re-Assortment","volume":"18","author":"Shao","year":"2017","journal-title":"Int. J. Mol. Sci."},{"issue":"D1","key":"10.1016\/j.dci.2026.105561_bib94","doi-asserted-by":"crossref","first-page":"D39","DOI":"10.1093\/nar\/gkac907","article-title":"AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations","volume":"51","author":"Shen","year":"2022","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib95","first-page":"690","article-title":"A novel interferon-inducible domain: structural and functional analysis of the human interferon regulatory factor 1 gene promoter","volume":"13","author":"Sims","year":"1993","journal-title":"Mol. Cell Biol."},{"issue":"2","key":"10.1016\/j.dci.2026.105561_bib96","first-page":"275","article-title":"False discovery rates: a new deal","volume":"18","author":"Stephens","year":"2016","journal-title":"Biostatistics"},{"issue":"43","key":"10.1016\/j.dci.2026.105561_bib97","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"9","key":"10.1016\/j.dci.2026.105561_bib98","doi-asserted-by":"crossref","first-page":"2302","DOI":"10.1099\/vir.0.023267-0","article-title":"Phenotypes influencing the transmissibility of highly pathogenic avian influenza viruses in chickens","volume":"91","author":"Suzuki","year":"2010","journal-title":"J. Gen. Virol."},{"issue":"8","key":"10.1016\/j.dci.2026.105561_bib99","first-page":"4531","article-title":"Recognition DNA sequences of interferon regulatory factor 1 (IRF-1) and IRF-2, regulators of cell growth and the interferon system","volume":"13","author":"Tanaka","year":"1993","journal-title":"Mol. Cell Biol."},{"issue":"2","key":"10.1016\/j.dci.2026.105561_bib100","doi-asserted-by":"crossref","first-page":"292","DOI":"10.3390\/v14020292","article-title":"Transcriptomic profiling of mouse mast cells upon pathogenic avian H5N1 and pandemic H1N1 influenza a virus infection","volume":"14","author":"Tang","year":"2022","journal-title":"Viruses"},{"issue":"12","key":"10.1016\/j.dci.2026.105561_bib102","doi-asserted-by":"crossref","first-page":"1960","DOI":"10.1002\/2211-5463.12336","article-title":"The novel mitochondria localization of influenza A virus NS1 visualized by FlAsH labeling","volume":"7","author":"Tsai","year":"2017","journal-title":"FEBS Open Bio"},{"issue":"10","key":"10.1016\/j.dci.2026.105561_bib103","doi-asserted-by":"crossref","first-page":"1909","DOI":"10.3390\/v13101909","article-title":"Interaction between NS1 and cellular MAVS contributes to NS1 mitochondria targeting","volume":"13","author":"Tseng","year":"2021","journal-title":"Viruses"},{"issue":"2","key":"10.1016\/j.dci.2026.105561_bib104","doi-asserted-by":"crossref","first-page":"168","DOI":"10.3390\/pathogens12020168","article-title":"Zoonotic mutation of highly pathogenic Avian influenza H5N1 virus identified in the brain of multiple wild carnivore species","volume":"12","author":"Vreman","year":"2023","journal-title":"Pathogens"},{"key":"10.1016\/j.dci.2026.105561_bib105","doi-asserted-by":"crossref","DOI":"10.1016\/j.dci.2021.104026","article-title":"Chicken interferon regulatory factor 7 (IRF7) can control ALV-J virus infection by triggering type I interferon production through affecting genes related with innate immune signaling pathway","volume":"119","author":"Wang","year":"2021","journal-title":"Dev. Comp. Immunol."},{"issue":"4","key":"10.1016\/j.dci.2026.105561_bib106","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1556\/avet.2014.023","article-title":"Interferon regulatory factor 7-(IRF7-) mediated immune response affects Newcastle disease virus replication in chicken embryo fibroblasts","volume":"62","author":"Wang","year":"2014","journal-title":"Acta Vet. Hung."},{"key":"10.1016\/j.dci.2026.105561_bib107","article-title":"Evolutionary conservation and antiviral effect of interferon regulatory factor 1 (IRF1) in Tibetan frog Nanorana parkeri","volume":"33","author":"Wen","year":"2023","journal-title":"Gene Rep."},{"issue":"3","key":"10.1016\/j.dci.2026.105561_bib108","article-title":"clusterProfiler 4.0: a universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation"},{"issue":"7","key":"10.1016\/j.dci.2026.105561_bib109","doi-asserted-by":"crossref","DOI":"10.3390\/v14071506","article-title":"Avian IRF1 and IRF7 play overlapping and distinct roles in regulating IFN-dependent and -Independent antiviral responses to duck tembusu virus infection","volume":"14","author":"Xiang","year":"2022","journal-title":"Viruses"},{"issue":"6","key":"10.1016\/j.dci.2026.105561_bib110","doi-asserted-by":"crossref","first-page":"498","DOI":"10.3390\/v11060498","article-title":"Cholesterol-25-hydroxylase is a chicken ISG that restricts ALV-J infection by producing 25-hydroxycholesterol","volume":"11","author":"Xie","year":"2019","journal-title":"Viruses"},{"issue":"10","key":"10.1016\/j.dci.2026.105561_bib111","doi-asserted-by":"crossref","first-page":"1095","DOI":"10.1111\/imcb.12185","article-title":"IRF1 supports DNA binding of STAT1 by promoting its phosphorylation","volume":"96","author":"Zenke","year":"2018","journal-title":"Immunol. Cell Biol."},{"issue":"1","key":"10.1016\/j.dci.2026.105561_bib112","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1186\/s12920-018-0335-0","article-title":"Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection","volume":"11","author":"Zhang","year":"2018","journal-title":"BMC Med. Genom."},{"key":"10.1016\/j.dci.2026.105561_bib113","first-page":"1","article-title":"Negative regulators of inflammation response to the dynamic expression of cytokines in DF-1 and MDCK cells infected by avian influenza viruses","author":"Zhao","year":"2022","journal-title":"Inflammation"}],"container-title":["Developmental & Comparative Immunology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0145305X26000170?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0145305X26000170?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T09:30:07Z","timestamp":1773999007000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0145305X26000170"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3]]},"references-count":112,"alternative-id":["S0145305X26000170"],"URL":"https:\/\/doi.org\/10.1016\/j.dci.2026.105561","relation":{},"ISSN":["0145-305X"],"issn-type":[{"value":"0145-305X","type":"print"}],"subject":[],"published":{"date-parts":[[2026,3]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Early innate immune response to highly pathogenic avian influenza and functional characterisation of the chicken IRF1 promoter","name":"articletitle","label":"Article Title"},{"value":"Developmental & Comparative Immunology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.dci.2026.105561","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 Elsevier Ltd. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}],"article-number":"105561"}}