Open Access Open Badges Research article

Identification of three new cis-regulatory IRF5 polymorphisms: in vitro studies

Elisa Alonso-Perez1, Romina Fernandez-Poceiro1, Emilie Lalonde2, Tony Kwan2, Manuel Calaza1, Juan J Gomez-Reino13, Jacek Majewski2 and Antonio Gonzalez1*

Author Affiliations

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

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Arthritis Research & Therapy 2013, 15:R82  doi:10.1186/ar4262

Published: 13 August 2013

Additional files

Additional file 1:

Note S1: IRF5 haplotypes defined in previous studies and their relationship with systemic lupus erythematosus susceptibility and IRF5 expression. Note S2: RNA-seq study of the IRF5 transcriptome and detection of potential cis-regulatory polymorphisms.

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Additional file 2:

Table S1 Polymorphisms included in our analysis with indication of their genomic position, relationship with known genes, alleles and minor allele frequency (MAF) and whether they were present in HapMap and in the 1000 Genomes database. Table S2 Oligonucleotides used for genotyping. Table S3: Three polymorphisms included in the study for their association with IRF5 expression level or known cis-regulatory effect. Table S4: Polymorphisms analyzed by electrophoretic mobility shift assay with indication of the oligonucleotides used as probes. Table S5: Primers used to generate the inserts included in the plasmid vectors for reporter gene assays. Table S6: Pairwise linkage disequilibrium relationship between the analyzed polymorphisms.

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Additional file 3:

Figure S1 Western blot showing expression of IRF5 in WIL2 NS cells. Figure S2 Relationship of the r2 values between rs729302 and the other single-nucleotide polymorphisms included in our study obtained in our samples and in phase 1 of the 1000 Genomes projec. Figure S3 Functional analysis of the positive control: the CGGGG indel. Figure S4 Lack of difference between the two alleles of rs4728142 in electrophoretic mobility shift assay.

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