title: Many inflammatory bowel disease risk loci include regions that regulate gene expression in immune cells and the intestinal epithelium.
abstract: OBJECTIVE
  The contribution of genetic factors to the pathogenesis of inflammatory bowel disease (IBD) has been established by twin, targeted-sequencing, and genome-wide association studies. These studies identified many risk loci, and research is underway to identify causal variants. These studies have focused mainly on protein-coding genes. We investigated other functional elements in the human genome, such as regulatory regions.
  
  
  METHODS
  Using acetylated histone 3 lysine 27 chromatin immunoprecipitation and sequencing, we identified tens of thousands of potential regulatory regions that are active in intestinal epithelium (primary intestinal crypts and cultured organoids) isolated from resected material and from biopsies collected during ileo-colonoscopies and immune cells (monocytes, macrophages, CD34(+), CD4(+), and CD8(+)). We correlated these regions with susceptibility loci for IBD.
  
  
  RESULTS
  We have generated acetylated histone 3 lysine 27 profiles from primary intestinal epithelium and cultured organoids, which we have made publically available. We found that 45 of 163 single nucleotide polymorphisms (SNPs) associated with IBD overlap specifically with active regulatory elements. In addition, by taking strong linkage disequilibrium into account, another 47 IBD-associated SNPs colocalized with active regulatory elements through other SNPs in their vicinity. Altogether, 92 of 163 IBD-associated SNPs correlated with distinct active regulatory elements-a frequency 2.5- to 3.5-fold greater than that expected from random sampling. The variations in these SNPs often create or disrupt known binding motifs; they might affect the binding of transcriptional regulators to alter expression of regulated genes.
  
  
  CONCLUSIONS
  In addition to variants in protein coding genes, variants in noncoding DNA regulatory regions that are active in intestinal epithelium and immune cells are potentially involved in the pathogenesis of IBD.
authors: Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands.
authors: Michal
authors: M
authors: Mokry
authors: Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands.
authors: Sabine
authors: S
authors: Middendorp
authors: Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands.
authors: Caroline L
authors: CL
authors: Wiegerinck
authors: Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands; Hubrecht Institute for Stem Cell Research, Utrecht, The Netherlands.
authors: Merlijn
authors: M
authors: Witte
authors: Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands; Hubrecht Institute for Stem Cell Research, Utrecht, The Netherlands.
authors: Hans
authors: H
authors: Teunissen
authors: Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands.
authors: Claartje A
authors: CA
authors: Meddens
authors: Hubrecht Institute for Stem Cell Research, Utrecht, The Netherlands; Department of Medical Genetics, Medical Center Utrecht, Utrecht, The Netherlands.
authors: Edwin
authors: E
authors: Cuppen
authors: Hubrecht Institute for Stem Cell Research, Utrecht, The Netherlands.
authors: Hans
authors: H
authors: Clevers
authors: Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands. Electronic address: E.E.S.Nieuwenhuis@umcutrecht.nl.
authors: Edward E S
authors: EE
authors: Nieuwenhuis
mesh_terms: D000107:Acetylation; D000818:Animals; D030801:Animals, Genetically Modified; D047369:Chromatin Immunoprecipitation; D005786:Gene Expression Regulation; D056426:Genetic Loci; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D006657:Histones / Q000378:metabolism; D006801:Humans; D018928:Immunity, Mucosal / Q000235:genetics*; D015212:Inflammatory Bowel Diseases / Q000235:genetics* / Q000276:immunology / Q000378:metabolism; D007413:Intestinal Mucosa / Q000276:immunology* / Q000378:metabolism; D015810:Linkage Disequilibrium; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012045:Regulatory Sequences, Nucleic Acid; D015203:Reproducibility of Results; D012307:Risk Factors; D017422:Sequence Analysis, DNA; D015027:Zebrafish / Q000235:genetics
chemical_list: D006657:Histones
keywords: Chromatin Immunoprecipitation and Sequencing; Crohn's Disease; Enhancers; Ulcerative Colitis