Identification of three new cis-regulatory IRF5 polymorphisms: in vitro studies
1 Laboratorio Investigacion 10 and Rheumatology Unit, Instituto de Investigacion Sanitaria, Hospital Clinico Universitario de Santiago, Travesia Choupana, s/n. Santiago de Compostela 15706, Spain
2 Department of Human Genetics, McGill University, Stewart Biology Building, 1205 Dr Penfield Avenue, Montreal, QC, H3A 1B1, Canada
3 Department of Medicine, University of Santiago de Compostela, Rúa de San Francisco, s/n. Santiago de Compostela 15782, Spain
Arthritis Research & Therapy 2013, 15:R82 doi:10.1186/ar4262Published: 13 August 2013
Polymorphisms in the interferon regulatory factor 5 (IRF5) gene are associated with susceptibility to systemic lupus erythematosus, rheumatoid arthritis and other diseases through independent risk and protective haplotypes. Several functional polymorphisms are already known, but they do not account for the protective haplotypes that are tagged by the minor allele of rs729302.
Polymorphisms in linkage disequilibrium (LD) with rs729302 or particularly associated with IRF5 expression were selected for functional screening, which involved electrophoretic mobility shift assays (EMSAs) and reporter gene assays.
A total of 54 single-nucleotide polymorphisms in the 5' region of IRF5 were genotyped. Twenty-four of them were selected for functional screening because of their high LD with rs729302 or protective haplotypes. In addition, two polymorphisms were selected for their prominent association with IRF5 expression. Seven of these twenty-six polymorphisms showed reproducible allele differences in EMSA. The seven were subsequently analyzed in gene reporter assays, and three of them showed significant differences between their two alleles: rs729302, rs13245639 and rs11269962. Haplotypes including the cis-regulatory polymorphisms correlated very well with IRF5 mRNA expression in an analysis based on previous data.
We have found that three polymorphisms in LD with the protective haplotypes of IRF5 have differential allele effects in EMSA and in reporter gene assays. Identification of these cis-regulatory polymorphisms will allow more accurate analysis of transcriptional regulation of IRF5 expression, more powerful genetic association studies and deeper insight into the role of IRF5 in disease susceptibility.