Chicken interferome: avian interferon-stimulated genes identified by microarray and RNA-seq of primary chick embryo fibroblasts treated with a chicken type I interferon (IFN-α)

Abstract

Viruses that infect birds pose major threats—to the global supply of chicken, the major, universally-acceptable meat, and as zoonotic agents (e.g. avian influenza viruses H5N1 and H7N9). Controlling these viruses in birds as well as understanding their emergence into, and transmission amongst, humans will require considerable ingenuity and understanding of how different species defend themselves. The type I interferon-coordinated response constitutes the major antiviral innate defence. Although interferon was discovered in chicken cells, details of the response, particularly the identity of hundreds of stimulated genes, are far better described in mammals. Viruses induce interferon-stimulated genes but they also regulate the expression of many hundreds of cellular metabolic and structural genes to facilitate their replication. This study focusses on the potentially anti-viral genes by identifying those induced just by interferon in primary chick embryo fibroblasts. Three transcriptomic technologies were exploited: RNA-seq, a classical 3′-biased chicken microarray and a high density, “sense target”, whole transcriptome chicken microarray, with each recognising 120–150 regulated genes (curated for duplication and incorrect assignment of some microarray probesets). Overall, the results are considered robust because 128 of the compiled, curated list of 193 regulated genes were detected by two, or more, of the technologies.Electronic supplementary materialThe online version of this article (doi:10.1186/s13567-016-0363-8) contains supplementary material, which is available to authorized users.

Tissue and time specific expression pattern of interferon regulated genes in the chicken

“…In agreement with our observation Giotis and colleagues analyzed IRGs in IFNα treated chicken embryo fibroblasts (CEF) and they also identified many potential chicken IRGs with no equivalent in the Interferome database [29]. Partly, annotation problems could be a reason as entries in the database and the chicken genome use a different nomenclature, hence mammalian IRGs were not found on the array.…”

“…The finding of so many additional differentially expressed genes might have been facilitated by the usage of a strong stimulation and the high sensitivity of the array. Furthermore, we analyzed both increased and reduced expression of target genes, while many other approaches were only focused on positively affected, so called “Interferon Stimulated Genes” (ISGs) [13, 29]. Among the 30 most affected genes in the spleen were eight with reduced expression and only one of them ( SFTPA1 ) was also identified in the database search.…”

“…Here we provide a comprehensive list of chicken IRGs and show that in addition to common IRGs shared between mammals and chickens unique chicken IRGs could be identified. This information together with recently published in vitro studies will allow large scale functional screens of IRGs as recently reported in mammals [29]. …”

Differential gene expression in chicken primary B cells infected ex vivo with attenuated and very virulent strains of infectious bursal disease virus (IBDV)

“…One limitation of the enrichment analysis is that it relies on a comparison with mammalian gene counterparts. Previously, we have defined chicken ISGs using DNA microarrays and RNA sequencing in CEFs stimulated with recombinant chicken IFNa [26], and we have made the full list of chicken ISGs publicly available at http:// cisbic.bioinformatics.ic.ac.uk/skinner. To confirm and extend the enrichment analysis observations, we compared the relative expression of known chicken ISGs between cells infected with the two virus strains.…”

Interferons: application in veterinary medicine

“…Завдяки останнім досягненням генної інженерії з'явилися нові можливості для ви-користання інтерферону з лікувальною метою, в тому числі й у ветеринарії [44,98,103]. До-слідники відкрили нові молекулярні агенти, які активують гени інтерферону і таким чином стимулюють продукцію інтерферону в організ-мі.…”