title: Molecular effects of autoimmune-risk promoter polymorphisms on expression, exon choice, and translational efficiency of interferon regulatory factor 5.
abstract: The rs2004640 single nucleotide polymorphism and the CGGGG copy-number variant (rs77571059) are promoter polymorphisms within interferon regulatory factor 5 (IRF5). They have been implicated as susceptibility factors for several autoimmune diseases. IRF5 uses alternative promoter splicing, where any of 4 first exons begin the mRNA. The CGGGG indel is in exon 1A's promoter; the rs2004640 allele creates a splicing recognition site, enabling usage of exon 1B. This study aimed at characterizing alterations in IRF5 mRNA due to these polymorphisms. Cells with risk polymorphisms exhibited ~2-fold higher levels of IRF5 mRNA and protein, but demonstrated no change in mRNA stability. Quantitative PCR demonstrated decreased usage of exons 1C and 1D in cell lines with the risk polymorphisms. RNA folding analysis revealed a hairpin in exon 1B; mutational analysis showed that the hairpin shape decreased translation 5-fold. Although translation of mRNA that uses exon 1B is low due to a hairpin, increased IRF5 mRNA levels in individuals with the rs2004640 risk allele lead to higher overall protein expression. In addition, several new splice variants of IRF5 were sequenced. IRF5's promoter polymorphisms alter first exon usage and increase transcription levels. High levels of IRF5 may bias the immune system toward autoimmunity.
authors.affiliation: Department of Microbiology and Molecular Biology, Brigham Young University , Provo, Utah.
authors.forename: Daniel N
authors.initials: DN
authors.lastname: Clark
authors.forename: Jared P
authors.initials: JP
authors.lastname: Lambert
authors.forename: Rodney E
authors.initials: RE
authors.lastname: Till
authors.forename: Lissenya B
authors.initials: LB
authors.lastname: Argueta
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Greenhalgh
authors.forename: Brandon
authors.initials: B
authors.lastname: Henrie
authors.forename: Trieste
authors.initials: T
authors.lastname: Bills
authors.forename: Tyson F
authors.initials: TF
authors.lastname: Hawkley
authors.forename: Marinya G
authors.initials: MG
authors.lastname: Roznik
authors.forename: Jason M
authors.initials: JM
authors.lastname: Sloan
authors.forename: Vera
authors.initials: V
authors.lastname: Mayhew
authors.forename: Loc
authors.initials: L
authors.lastname: Woodland
authors.forename: Eric P
authors.initials: EP
authors.lastname: Nelson
authors.forename: Meng-Hsuan
authors.initials: MH
authors.lastname: Tsai
authors.forename: Brian D
authors.initials: BD
authors.lastname: Poole
mesh_terms: D001327:Autoimmune Diseases / Q000235:genetics* / Q000276:immunology; D002460:Cell Line; D005091:Exons / Q000235:genetics*; D005260:Female; D005786:Gene Expression Regulation / Q000235:genetics*; D005838:Genotype; D057809:HEK293 Cells; D064368:Healthy Volunteers; D006801:Humans; D050835:Interferon Regulatory Factors / Q000235:genetics* / Q000276:immunology; D008297:Male; D020641:Polymorphism, Single Nucleotide / Q000235:genetics* / Q000276:immunology; D011401:Promoter Regions, Genetic / Q000235:genetics* / Q000276:immunology; D014176:Protein Biosynthesis / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000276:immunology; D012307:Risk Factors
chemical_list: C431713:IRF5 protein, human; D050835:Interferon Regulatory Factors; D012333:RNA, Messenger