Identification of three new cis-regulatory IRF5 polymorphisms: in vitro studies
Arthritis Research & Therapy 2013, 15:R82 doi:10.1186/ar4262Published: 13 August 2013
Polymorphisms in IRF5 (interferon regulatory factor 5) are associated with susceptibility to systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) 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 (EMSA) and reporter gene assays.
A total of 54 SNPs in the 5' region of IRF5 were genotyped. Twenty three of them were selected for functional screening due to their high LD with rs729302 or protective haplotypes. In addition, two polymorphisms were selected due to their prominent association with IRF5 expression. Six of these 25 polymorphisms showed reproducible allele differences in EMSA. The six were subsequently analyzed in gene reporter assays and three of them showed significant differences between their two alleles, rs13245639, rs12706860 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 a deeper insight into the role of IRF5 in disease susceptibility.