title: Deciphering the modulation of gene expression by type I and II interferons combining 4sU-tagging, translational arrest and in silico promoter analysis.
abstract: 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.
authors.affiliation: 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.
authors.forename: Mirko
authors.initials: M
authors.lastname: Trilling
authors.forename: Nicolás
authors.initials: N
authors.lastname: Bellora
authors.forename: Andrzej J
authors.initials: AJ
authors.lastname: Rutkowski
authors.forename: Miranda
authors.initials: M
authors.lastname: de Graaf
authors.forename: Paul
authors.initials: P
authors.lastname: Dickinson
authors.forename: Kevin
authors.initials: K
authors.lastname: Robertson
authors.forename: Olivia
authors.initials: O
authors.lastname: Prazeres da Costa
authors.forename: Peter
authors.initials: P
authors.lastname: Ghazal
authors.forename: Caroline C
authors.initials: CC
authors.lastname: Friedel
authors.forename: M Mar
authors.initials: MM
authors.lastname: Albà
authors.forename: Lars
authors.initials: L
authors.lastname: Dölken
mesh_terms: D000818:Animals; D002478:Cells, Cultured; D003198:Computer Simulation; D003513:Cycloheximide / Q000494:pharmacology; D025461:Feedback, Physiological; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000187:drug effects; D016898:Interferon-alpha / Q000494:pharmacology*; D007371:Interferon-gamma / Q000494:pharmacology*; D008264:Macrophages / Q000187:drug effects / Q000378:metabolism; D051379:Mice; D041681:NIH 3T3 Cells; D011401:Promoter Regions, Genetic; D011500:Protein Synthesis Inhibitors / Q000494:pharmacology; D020218:Response Elements; D050794:STAT1 Transcription Factor / Q000502:physiology; D013891:Thiouridine; D014158:Transcription, Genetic / Q000187:drug effects
chemical_list: D016898:Interferon-alpha; D011500:Protein Synthesis Inhibitors; D050794:STAT1 Transcription Factor; D013891:Thiouridine; D007371:Interferon-gamma; D003513:Cycloheximide