ArticleMolecular and cellular biology2014
Chromatin profiling reveals regulatory network shifts and a protective role for hepatocyte nuclear factor 4α during colitis.
Article in Molecular and cellular biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 47 citations in OpenAlex.
- Review
- Opposing lineage specifiers induce a protumor hybrid identity state in lung adenocarcinoma.Genes & development · 2025Article
- Early subclinical stages of the inflammatory bowel diseases: insights from human and animal studies.American journal of physiology. Gastrointestinal and liver physiology · 2025Review
- Stress-induced mucin 13 reductions drive intestinal microbiome shifts and despair behaviors.Brain, behavior, and immunity · 2024Article
- Article
- Transcription factor HNF4α2 promotes osteogenesis and prevents bone abnormalities in mice with renal osteodystrophy.The Journal of clinical investigation · 2023Article
- Inference on autoregulation in gene expression with variance-to-mean ratio.Journal of mathematical biology · 2023Article
- Epithelial HNF4A shapes the intraepithelial lymphocyte compartment via direct regulation of immune signaling molecules.The Journal of experimental medicine · 2022Article
- Transcriptional Integration of Distinct Microbial and Nutritional Signals by the Small Intestinal Epithelium.Cellular and molecular gastroenterology and hepatology · 2022Article
- Therapeutic Potential of HNF4α in End-stage Liver Disease.Organogenesis · 2021Review
- The miR-223/nuclear factor I-A axis regulates inflammation and cellular functions in intestinal tissues with necrotizing enterocolitis.FEBS open bio · 2021Article
- STAT1 epigenetically regulates LCP2 and TNFAIP2 by recruiting EP300 to contribute to the pathogenesis of inflammatory bowel disease.Clinical epigenetics · 2021Article
- Transcriptional programmes underlying cellular identity and microbial responsiveness in the intestinal epithelium.Nature reviews. Gastroenterology & hepatology · 2021Review
- Genomic Analysis of Oral Lichen Planus and Related Oral Microbiome Pathogens.Pathogens (Basel, Switzerland) · 2020Article
- Review
- HNF4 factors control chromatin accessibility and are redundantly required for maturation of the fetal intestine.Development (Cambridge, England) · 2019Article
- The role of lineage specifiers in pancreatic ductal adenocarcinoma.Journal of gastrointestinal oncology · 2018Review
- DNA methylome and transcriptome alterations and cancer prevention by curcumin in colitis-accelerated colon cancer in mice.Carcinogenesis · 2018Article
- An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression.Genome biology · 2018Article
- Microenvironment and tumor cells: two targets for new molecular therapies of hepatocellular carcinoma.Translational gastroenterology and hepatology · 2018Review
Corrections and comments
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Authors and funding
19 authors at 5 institutions in 2 countries.
Funding
Abstract
Transcriptional regulatory mechanisms likely contribute to the etiology of inflammatory bowel disease (IBD), as genetic variants associated with the disease are disproportionately found at regulatory elements. However, the transcription factors regulating colonic inflammation are unclear. To identify these transcription factors, we mapped epigenomic changes in the colonic epithelium upon inflammation. Epigenetic marks at transcriptional regulatory elements responded dynamically to inflammation and indicated a shift in epithelial transcriptional factor networks. Active enhancer chromatin structure at regulatory regions bound by the transcription factor hepatocyte nuclear factor 4α (HNF4A) was reduced during colitis. In agreement, upon an inflammatory stimulus, HNF4A was downregulated and showed a reduced ability to bind chromatin. Genetic variants that confer a predisposition to IBD map to HNF4A binding sites in the human colon cell line CaCo2, suggesting impaired HNF4A binding could underlie genetic susceptibility to IBD. Despite reduced HNF4A binding during inflammation, a temporal knockout model revealed HNF4A still actively protects against inflammatory phenotypes and promotes immune regulatory gene expression in the inflamed colonic epithelium. These findings highlight the potential for HNF4A agonists as IBD therapeutics.
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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.