Kaiyu Jiang1, Haeja Kessler1, Yungki Park2,3, Marc Sudman4, Susan D Thompson4,5, James N Jarvis1,3. 1. Department of Pediatrics, Pediatric Rheumatology Research, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, United States of America. 2. Department of Biochemistry, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, United States of America. 3. Genetics, Genomics, & Bioinformatics Program, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, New York, United States of Americass. 4. Center for Autoimmune Genetics & Epigenetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America. 5. Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America.
Abstract
OBJECTIVE: The risk loci for juvenile idiopathic arthritis (JIA) consist of extended haplotypes that include functional elements in addition to canonical coding genes. As with most autoimmune diseases, the risk haplotypes for JIA are highly enriched for H3K4me1/H3K27ac histone marks, epigenetic signatures that typically identify poised or active enhancers. In this study, we test the hypothesis that genetic risk for JIA is exerted through altered enhancer-mediated gene regulation. METHODS: We mined publically available HiC and other chromatin conformation data to determine whether H3K27ac-marked regions in 25 JIA risk loci showed physical evidence of contact with gene promoters. We also used in vitro reporter assays to establish as proof-of-concept the idea that genetic variants in linkage disequilibrium with GWAS-identified tag SNPs alter enhancer function. RESULTS: All 25 loci examined showed multiple contact sites in the 4 different cell lines that we queried. These regions were characterized by HiC-defined loop structures that included 237 immune-related genes. Using in vitro assays, we found that a 657 bp, H3K4me1/H3K27-marked region within the first intron of IL2RA shows enhancer activity in reporter assays, and this activity is attenuated by SNPs on the IL2RA haplotype that we identified using whole genome sequencing of children with JIA. Similarly, we identified a 1,669 bp sequence in an intergenic region of the IL6R locus where SNPs identified in children with JIA increase enhancer function in reporter assays. CONCLUSIONS: These studies provide evidence that altered enhancer function contributes to genetic risk in JIA. Further studies to identify the specific target genes of genetically altered enhancers are warranted.
OBJECTIVE: The risk loci for juvenile idiopathic arthritis (JIA) consist of extended haplotypes that include functional elements in addition to canonical coding genes. As with most autoimmune diseases, the risk haplotypes for JIA are highly enriched for H3K4me1/H3K27ac histone marks, epigenetic signatures that typically identify poised or active enhancers. In this study, we test the hypothesis that genetic risk for JIA is exerted through altered enhancer-mediated gene regulation. METHODS: We mined publically available HiC and other chromatin conformation data to determine whether H3K27ac-marked regions in 25 JIA risk loci showed physical evidence of contact with gene promoters. We also used in vitro reporter assays to establish as proof-of-concept the idea that genetic variants in linkage disequilibrium with GWAS-identified tag SNPs alter enhancer function. RESULTS: All 25 loci examined showed multiple contact sites in the 4 different cell lines that we queried. These regions were characterized by HiC-defined loop structures that included 237 immune-related genes. Using in vitro assays, we found that a 657 bp, H3K4me1/H3K27-marked region within the first intron of IL2RA shows enhancer activity in reporter assays, and this activity is attenuated by SNPs on the IL2RA haplotype that we identified using whole genome sequencing of children with JIA. Similarly, we identified a 1,669 bp sequence in an intergenic region of the IL6R locus where SNPs identified in children with JIA increase enhancer function in reporter assays. CONCLUSIONS: These studies provide evidence that altered enhancer function contributes to genetic risk in JIA. Further studies to identify the specific target genes of genetically altered enhancers are warranted.
Authors: Douglas H Phanstiel; Kevin Van Bortle; Damek Spacek; Gaelen T Hess; Muhammad Saad Shamim; Ido Machol; Michael I Love; Erez Lieberman Aiden; Michael C Bassik; Michael P Snyder Journal: Mol Cell Date: 2017-09-07 Impact factor: 17.970
Authors: Richard C Pelikan; Jennifer A Kelly; Yao Fu; Caleb A Lareau; Kandice L Tessneer; Graham B Wiley; Mandi M Wiley; Stuart B Glenn; John B Harley; Joel M Guthridge; Judith A James; Martin J Aryee; Courtney Montgomery; Patrick M Gaffney Journal: Nat Commun Date: 2018-07-25 Impact factor: 17.694
Authors: Elizabeth A Crinzi; Emma K Haley; Kerry E Poppenberg; Kaiyu Jiang; Vincent M Tutino; James N Jarvis Journal: Front Immunol Date: 2022-09-29 Impact factor: 8.786