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Genome-Wide Classification of Type I, Type II and Type III Interferon-Stimulated Genes in Chicken Fibroblasts

Diwakar Santhakumar, Mohammed A. Rohaim, Muhammad Munir
doi: https://doi.org/10.1101/793448
Diwakar Santhakumar
1Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK; ; ;
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  • For correspondence: d.santhakumar@lancaster.ac.uk m.a.rohaim@lancaster.ac.uk muhammad.munir@lancaster.ac.uk
Mohammed A. Rohaim
1Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK; ; ;
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  • For correspondence: d.santhakumar@lancaster.ac.uk m.a.rohaim@lancaster.ac.uk muhammad.munir@lancaster.ac.uk
Muhammad Munir
1Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, LA1 4YG, UK; ; ;
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  • For correspondence: muhammad.munir@lancaster.ac.uk d.santhakumar@lancaster.ac.uk m.a.rohaim@lancaster.ac.uk muhammad.munir@lancaster.ac.uk
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Abstract

Interferons (IFNs) play central roles in establishing innate immunity and mediating adaptive immunity against multiple pathogens. Three known types of IFNs identify their cognate receptors, initiate cascades of signalling events and eventually result in the induction of myriad of IFN-stimulated genes (ISGs). These ISGs perform multitude of functions and cumulatively corroborate a bespoke antiviral state to safeguard hosts against invading viruses. Owing to unique nature of chicken’s immune system and lack of foundational profiling information on the nature and dynamic expression of IFN-specific ISGs at the genome scale, we performed a systematic and extensive analysis of type I, II and III IFN-induced genes in chicken. Employing pan-IFN responsive chicken fibroblasts coupled with transcriptomics we observed an overwhelming over-representation of up-regulated ISGs by all types of IFNs. Intriguingly, prediction of IFN-stimulated response element (ISRE) and gamma-IFN activation sequence (GAS) revealed a substantial number of GAS motifs in selective significantly induced ISGs in chicken. Extensive comparative, genome-wide and differential expression analysis of ISGs under equivalent signalling input catalogue a set of genes that were either IFN-specific or independent of types of IFNs used to prime fibroblasts. These comprehensive datasets, first of their kinds in chicken, will establish foundations to elucidate the mechanisms of actions and breadth of antiviral action of ISGs which may propose alternative avenues for the targeted antiviral therapy against viruses of poultry and public health importance.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 04, 2019.
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Genome-Wide Classification of Type I, Type II and Type III Interferon-Stimulated Genes in Chicken Fibroblasts
Diwakar Santhakumar, Mohammed A. Rohaim, Muhammad Munir
bioRxiv 793448; doi: https://doi.org/10.1101/793448
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Genome-Wide Classification of Type I, Type II and Type III Interferon-Stimulated Genes in Chicken Fibroblasts
Diwakar Santhakumar, Mohammed A. Rohaim, Muhammad Munir
bioRxiv 793448; doi: https://doi.org/10.1101/793448

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