Journal article
Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies
University of Copenhagen1
Department of Bio and Health Informatics, Technical University of Denmark2
Disease Intelligence and Molecular Evolution, Department of Bio and Health Informatics, Technical University of Denmark3
Department of Biotechnology and Biomedicine, Technical University of Denmark4
Roskilde University5
Sjællands Universitetshospital6
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.
| Language: | English |
|---|---|
| Publisher: | Nature Publishing Group UK |
| Year: | 2018 |
| Pages: | 1661 |
| ISSN: | 20411723 |
| Types: | Journal article |
| DOI: | 10.1038/s41467-018-03766-z |
| ORCIDs: | Pedersen, Anders Gorm , 0000-0001-5208-8874 , 0000-0003-1516-879X , 0000-0001-6569-1664 , 0000-0002-7109-7378 , 0000-0002-7994-9600 , 0000-0002-6450-0608 , 0000-0003-3230-7966 , 0000-0003-4612-8635 and Skovgaard, Kerstin |
