ArticleGenome biology2016
Systematic analysis of chromatin interactions at disease associated loci links novel candidate genes to inflammatory bowel disease.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
33 citing papers in PubMed, 46 citations in OpenAlex.
- Human colon stem cells are the predominant epithelial responders to bacterial antigens.Frontiers in immunology · 2025Article
- Liver-specific loss ofAutophagy reports · 2025Article
- Translation of genome-wide association study: from genomic signals to biological insights.Frontiers in genetics · 2024Review
- Autophagy genes in biology and disease.Nature reviews. Genetics · 2023Review
- Translating non-coding genetic associations into a better understanding of immune-mediated disease.Disease models & mechanisms · 2023Review
- Shifts in intestinal microbiota and improvement of sheep immune response to resist Salmonella infection using Toll-like receptor 4 (TLR4) overexpression.Frontiers in microbiology · 2023Article
- 3D genome organization and epigenetic regulation in autoimmune diseases.Frontiers in immunology · 2023Review
- Chromosome conformation capture approaches to investigate 3D genome architecture in Ankylosing Spondylitis.Frontiers in genetics · 2023Article
- Interplay between Serotonin, Immune Response, and Intestinal Dysbiosis in Inflammatory Bowel Disease.International journal of molecular sciences · 2022Review
- An optimized 4C-seq protocol based on cistrome and epigenome data in the mouse RAW264.7 macrophage cell line.STAR protocols · 2022Article
- Transcriptional Integration of Distinct Microbial and Nutritional Signals by the Small Intestinal Epithelium.Cellular and molecular gastroenterology and hepatology · 2022Article
- Moments in autophagy and disease: Past and present.Molecular aspects of medicine · 2021Review
- Ketogenic diet alleviates colitis by reduction of colonic group 3 innate lymphoid cells through altering gut microbiome.Signal transduction and targeted therapy · 2021Article
- Epigenomic and transcriptomic analysis of chronic inflammatory diseases.Genes & genomics · 2021Review
- Transcriptional programmes underlying cellular identity and microbial responsiveness in the intestinal epithelium.Nature reviews. Gastroenterology & hepatology · 2021Review
- Chromatin Conformation in Development and Disease.Frontiers in cell and developmental biology · 2021Review
- Review
- Autophagy and disease: unanswered questions.Cell death and differentiation · 2020Review
- Saikosaponin C exerts anti-HBV effects by attenuating HNF1α and HNF4α expression to suppress HBV pgRNA synthesis.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2019Article
- Long-range interactions between proximal and distal regulatory regions in maize.Nature communications · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 5 institutions in 5 countries.
Funding
Abstract
backgroundGenome-wide association studies (GWAS) have revealed many susceptibility loci for complex genetic diseases. For most loci, the causal genes have not been identified. Currently, the identification of candidate genes is predominantly based on genes that localize close to or within identified loci. We have recently shown that 92 of the 163 inflammatory bowel disease (IBD)-loci co-localize with non-coding DNA regulatory elements (DREs). Mutations in DREs can contribute to IBD pathogenesis through dysregulation of gene expression. Consequently, genes that are regulated by these 92 DREs are to be considered as candidate genes. This study uses circular chromosome conformation capture-sequencing (4C-seq) to systematically analyze chromatin-interactions at IBD susceptibility loci that localize to regulatory DNA.
resultsUsing 4C-seq, we identify genomic regions that physically interact with the 92 DRE that were found at IBD susceptibility loci. Since the activity of regulatory elements is cell-type specific, 4C-seq was performed in monocytes, lymphocytes, and intestinal epithelial cells. Altogether, we identified 902 novel IBD candidate genes. These include genes specific for IBD-subtypes and many noteworthy genes including ATG9A and IL10RA. We show that expression of many novel candidate genes is genotype-dependent and that these genes are upregulated during intestinal inflammation in IBD. Furthermore, we identify HNF4α as a potential key upstream regulator of IBD candidate genes.
conclusionsWe reveal many novel and relevant IBD candidate genes, pathways, and regulators. Our approach complements classical candidate gene identification, links novel genes to IBD and can be applied to any existing GWAS data.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.