title: Functional relevance of the IRF-1 promoter polymorphism rs2549009 on transcriptional activity in a native genomic environment.
abstract: Interferon regulatory factor-1 (IRF-1), a transcription regulator involved both in inducing and in mediating the effects of interferon, is encoded by a highly polymorphic gene in different ethnic populations. Some of these genetic variations have been described to be associated to disease traits in hepatitis C virus and in human immunodeficiency virus infection, including one single-nucleotide polymorphism rs2549009 within the promoter region. This study aimed at investigating the functional relevance of rs2549009 on IRF-1 transcriptional activity in peripheral blood mononuclear cells in its natural genomic environment. Haplotype-specific chromatin immunoprecipitation using antibodies directed against both the transcriptionally inactive and active RNA polymerase II (RNAPII) and allele-specific transcript quantification techniques were applied to ex vivo-derived samples from healthy heterozygous donors. Inactive serine 5 phosphorylated RNAPII was found to be preferentially bound to the rs2549009 A allele in all donors investigated. Active serine 2 phosphorylated (ser2-P) RNAPII, in contrast, was found to be precipitable, depending on the donor, preferentially either with the A or the G promoter variants or without any preference. The ratio of rs2549009 A/G promoter variants engaged by ser2-P RNAPII was closely related to the relative frequency of the respective IRF-1 transcripts, and relative allelic expression was found to be associated to total IRF-1 gene expression. These results provide evidence for a bidirectional IRF-1 gene expression imbalance that appears not to be solely controlled by rs2549009 in cis and may rely on a yet unidentified variant or haplotype or on environmental control in trans.
authors.affiliation: Department of Gastroenterology and Endocrinology, University Medical Center Goettingen, Georg-August-Universitaet, Robert-Koch-Strasse 40, Goettingen, Germany.
authors.forename: Jasmin
authors.initials: J
authors.lastname: Mertens
authors.forename: Giuliano
authors.initials: G
authors.lastname: Ramadori
authors.forename: Sabine
authors.initials: S
authors.lastname: Mihm
mesh_terms: D000328:Adult; D000483:Alleles; D047369:Chromatin Immunoprecipitation; D005260:Female; D015870:Gene Expression; D014644:Genetic Variation; D006239:Haplotypes; D006801:Humans; D050856:Interferon Regulatory Factor-1 / Q000235:genetics* / Q000378:metabolism*; D007963:Leukocytes, Mononuclear / Q000378:metabolism; D008297:Male; D008875:Middle Aged; D010768:Phosphoserine / Q000378:metabolism; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000276:immunology / Q000378:metabolism; D050436:Regulatory Elements, Transcriptional; D014158:Transcription, Genetic
chemical_list: D050856:Interferon Regulatory Factor-1; D010768:Phosphoserine; D012319:RNA Polymerase II