title: Disease-Associated Single-Nucleotide Polymorphisms From Noncoding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells.
abstract: OBJECTIVE
  Juvenile idiopathic arthritis (JIA) is considered a complex disease in which the environment interacts with inherited genes to produce a phenotype that shows broad interindividual variability. Twenty-four regions of genetic risk for JIA were identified in a recent genome-wide association study (GWAS); however, as is typical of the results of GWAS, most of the regions of genetic risk (22 of 24) were in noncoding regions of the genome. This study was undertaken to identify functional elements (other than genes) that might be located within the regions of genetic risk.
  
  
  METHODS
  We used paired-end RNA sequencing to identify noncoding RNAs (ncRNAs) located within 5 kb of disease-associated single-nucleotide polymorphisms (SNPs). In addition, we used chromatin immunoprecipitation (ChIP) followed by sequencing to identify epigenetic marks associated with enhancer function (H3K4me1 and H3K27ac) in human neutrophils to determine whether enhancer-associated histone marks were enriched in the linkage disequilibrium blocks that encompassed the 22 SNPs identified in the GWAS.
  
  
  RESULTS
  In human neutrophils, we identified H3K4me1 and/or H3K27ac marks in 15 of the 22 regions previously identified as risk loci for JIA. In CD4+ T cells, 18 regions had H3K4me1 and/or H3K27ac marks. In addition, we identified ncRNA transcripts at the rs4705862 and rs6894249 loci in human neutrophils.
  
  
  CONCLUSIONS
  Much of the genetic risk for JIA lies within or adjacent to regions of neutrophil and CD4+ T cell genomes that carry epigenetic marks associated with enhancer function and/or ncRNA transcripts. These findings are consistent with the hypothesis that JIA is fundamentally a disorder of gene regulation that includes both the innate and the adaptive immune system. Elucidating the specific roles of these noncoding elements within leukocyte genomes will be critical to our understanding of JIA pathogenesis.
authors.affiliation: University at Buffalo, Buffalo, New York.
authors.forename: Kaiyu
authors.initials: K
authors.lastname: Jiang
authors.affiliation: University at Buffalo, Buffalo, New York.
authors.forename: Lisha
authors.initials: L
authors.lastname: Zhu
authors.affiliation: University at Buffalo, Buffalo, New York.
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Buck
authors.affiliation: University at Buffalo, Buffalo, New York.
authors.forename: Yanmin
authors.initials: Y
authors.lastname: Chen
authors.affiliation: University at Buffalo, Buffalo, New York.
authors.forename: Bradley
authors.initials: B
authors.lastname: Carrier
authors.affiliation: University at Buffalo, Buffalo, New York.
authors.forename: Tao
authors.initials: T
authors.lastname: Liu
authors.affiliation: University at Buffalo, Buffalo, New York.
authors.forename: James N
authors.initials: JN
authors.lastname: Jarvis
mesh_terms: D000328:Adult; D001171:Arthritis, Juvenile / Q000235:genetics* / Q000473:pathology*; D015496:CD4-Positive T-Lymphocytes / Q000473:pathology*; D016022:Case-Control Studies; D002648:Child; D047369:Chromatin Immunoprecipitation; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D044127:Epigenesis, Genetic / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000235:genetics; D015894:Genome, Human / Q000235:genetics; D055106:Genome-Wide Association Study; D006657:Histones / Q000235:genetics; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics; D009504:Neutrophils / Q000473:pathology*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*
chemical_list: D006657:Histones; D022661:RNA, Untranslated
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