Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies

Research output: Contribution to journalJournal article – Annual report year: 2018Researchpeer-review

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  • Author: Boyd, Mette

    University of Copenhagen

  • Author: Thodberg, Malte

    University of Copenhagen

  • Author: Vitezic, Morana

    University of Copenhagen

  • Author: Bornholdt, Jette

    University of Copenhagen

  • Author: Vitting-Seerup, Kristoffer

    University of Copenhagen

  • Author: Chen, Yun

    University of Copenhagen

  • Author: Coskun, Mehmet

    University of Copenhagen

  • Author: Li, Yuan

    University of Copenhagen, Denmark

  • Author: Lo, Bobby Zhao Sheng

    University of Copenhagen

  • Author: Klausen, Pia

    University of Copenhagen

  • Author: Jan Schweiger, Pawel

    University of Copenhagen

  • Author: Pedersen, Anders Gorm

    Disease Intelligence and Molecular Evolution, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800, Kgs. Lyngby, Denmark

  • Author: Rapin, Nicolas

    University of Copenhagen, Denmark

  • Author: Skovgaard, Kerstin

    Department of Biotechnology and Biomedicine, Technical University of Denmark, Kemitorvet, 2800, Kgs. Lyngby, Denmark

  • Author: Dahlgaard, Katja

    Roskilde University

  • Author: Andersson, Robin

    University of Copenhagen

  • Author: Terkelsen, Thilde Bagger

    University of Copenhagen

  • Author: Lilje, Berit

    University of Copenhagen

  • Author: Troelsen, Jesper Thorvald

    Roskilde University

  • Author: Petersen, Andreas Munk

    University of Copenhagen

  • Author: Jensen, Kim Bak

    University of Copenhagen, Denmark

  • Author: Gögenur, Ismail

    Zealand University Hospital

  • Author: Thielsen, Peter

    University of Copenhagen

  • Author: Seidelin, Jakob Benedict

    University of Copenhagen

  • Author: Nielsen, Ole Haagen

    University of Copenhagen, Denmark

  • Author: Bjerrum, Jacob Tveiten

    University of Copenhagen

  • Author: Sandelin, Albin

    University of Copenhagen

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Inflammatory bowel disease (IBD) is a chronic intestinal disorder, with two main types: Crohn's disease (CD) and ulcerative colitis (UC), whose molecular pathology is not well understood. The majority of IBD-associated SNPs are located in non-coding regions and are hard to characterize since regulatory regions in IBD are not known. Here we profile transcription start sites (TSSs) and enhancers in the descending colon of 94 IBD patients and controls. IBD-upregulated promoters and enhancers are highly enriched for IBD-associated SNPs and are bound by the same transcription factors. IBD-specific TSSs are associated to genes with roles in both inflammatory cascades and gut epithelia while TSSs distinguishing UC and CD are associated to gut epithelia functions. We find that as few as 35 TSSs can distinguish active CD, UC, and controls with 85% accuracy in an independent cohort. Our data constitute a foundation for understanding the molecular pathology, gene regulation, and genetics of IBD.

Original languageEnglish
Article number1661
JournalNature Communications
Volume9
Issue number1
Number of pages19
ISSN2041-1723
DOIs
Publication statusPublished - 2018

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This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give
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