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Nucleic Acids Res. 2013 Sep;41(17):8107-25. doi: 10.1093/nar/gkt589. Epub 2013 Jul 5.

Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis.

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Institute for Virology, University Hospital in Essen, University of Duisburg-Essen, Essen, D-45147, Germany, Computational Genomics Group, IMIM-UPF Research Programme on Biomedical Informatics, Barcelona Biomedical Research Park (PRBB), Barcelona 08003, Spain, Department of Medicine, University of Cambridge, Box 157, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK, Division of Pathway Medicine, University of Edinburgh Medical School, Edinburgh, EH16 4SB, Scotland, UK, SynthSys, University of Edinburgh, Edinburgh, EH9 3JU Scotland, UK, Institute of Medical Microbiology, Technical University Munich, Munich 81675, Germany, Institute for Informatics, Ludwig-Maximilians-University Munich, Munich 80333, Germany and Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain.


Interferons (IFN) play a pivotal role in innate immunity, orchestrating a cell-intrinsic anti-pathogenic state and stimulating adaptive immune responses. The complex interplay between the primary response to IFNs and its modulation by positive and negative feedback loops is incompletely understood. Here, we implement the combination of high-resolution gene-expression profiling of nascent RNA with translational inhibition of secondary feedback by cycloheximide. Unexpectedly, this approach revealed a prominent role of negative feedback mechanisms during the immediate (≤60 min) IFNα response. In contrast, a more complex picture involving both negative and positive feedback loops was observed on IFNγ treatment. IFNγ-induced repression of genes associated with regulation of gene expression, cellular development, apoptosis and cell growth resulted from cycloheximide-resistant primary IFNγ signalling. In silico promoter analysis revealed significant overrepresentation of SP1/SP3-binding sites and/or GC-rich stretches. Although signal transducer and activator of transcription 1 (STAT1)-binding sites were not overrepresented, repression was lost in absence of STAT1. Interestingly, basal expression of the majority of these IFNγ-repressed genes was dependent on STAT1 in IFN-naïve fibroblasts. Finally, IFNγ-mediated repression was also found to be evident in primary murine macrophages. IFN-repressed genes include negative regulators of innate and stress response, and their decrease may thus aid the establishment of a signalling perceptive milieu.

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