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H3K27ac profiling in control and DSS-treated colonic epithelium

ABSTRACT: We determined changes in enhancer chromatin that occur during colonic inflammation, found that dynamic chromatin regions are enriched for HNF4A binding motirfs, and then measured HNF4A binidng by ChIP-seq in each condition.

ORGANISM(S): Mus musculus

PROVIDER: GSE52426 | GEO | 2014/06/30

SECONDARY ACCESSION(S): PRJNA228913

REPOSITORIES: GEO

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H3K27ac profiling in control and DSS-treated colonic epithelium

Project description:We determined changes in enhancer chromatin that occur during colonic inflammation, found that dynamic chromatin regions are enriched for HNF4A binding motirfs, and then measured HNF4A binidng by ChIP-seq in each condition. Examination of H3K27ac histone modification in normal and DSS-treated colon, examination of HNF4A binding by ChIP-seq in normal and DSS-treated colon epithelium

2014-06-30 | E-GEOD-52426 | biostudies-arrayexpress

Claudin-based barrier differentiation in the colonic epithelial crypt niche involves Hopx/Klf4 and Tcf7l2/Hnf4-alpha cascades

2016-07-23 | GSE84742 | GEO

Claudin-based barrier differentiation in the colonic epithelial crypt niche involves Hopx/Klf4 and Tcf7l2/Hnf4-alpha cascades

Project description:Analysis of the complex expression of claudin genes and transcription factors during intestinal epithelial cell differentiation across the crypt-to-surface colonic axis. Characterization of the complex expression gradients of transcription factors Hopx, Hnf4a, Klf4 and Tcfl2 and 12 claudin genes. In vitro confirmatory methods identified two pathways that stimulate claudin expression; Hopx/Klf4 activation of Cldn4, 7 and 15, and Tcf7l2/Hnf4a upregulation of Cldn23. Chromatin Immunoprecipitation confirmed a Tcf7l2/Hnf4a/Claudin23 cascade. Hnf4a conditional knockout mice fail to induce Cldn23 during colonocyte differentiation. The distal colon tissue was obtained from 4 male, 10-12 week old, C57BL/6 (WT) mice. The Arcturus Laser Capture Microdissection (LCM) system (Applied Biosystems/Life Technologies) was used to isolate crypt-base and surface cell populations providing two samples per mouse (crypt-base and surface). This resulted in 8 total samples for microarray analysis.

2016-07-23 | E-GEOD-84742 | biostudies-arrayexpress

Colonic gene expression data of acute and chronic dextran sodium sulphate (DSS) colitis mice

Project description:The lack of suitable animal models reflecting chronically relapsing inflammation and tissue remodeling have hindered fibrosis research in inflammatory bowel diseases (IBD). This study investigated changes in connective tissue in a chronic murine model using different cycles of dextran sodium sulphate (DSS) to mimic the relapsing nature of the disease. We used whole gene expression arrays to study differences in colonic gene expression levels between acute and more chronic DSS colitis, Acute and chronic relapsing colonic inflammation was induced in C57BL6 female mice using several cycles of exposure to DSS in drinking water, followed by recovery phases. Total RNA, extracted from snap frozen colon from five mice per condition was used to analyze mRNA expression via Affymetrix Mouse Gene 1.0 ST arrays.

2013-09-03 | E-GEOD-42768 | biostudies-arrayexpress

H3K27Ac ChIP-seq of colonic intestine epithelium from Vil-CreER;MTA2F/F (MTA2KO) and Wild Type mice

Project description:Understanding the enhancer activity in MTA2 regulates colonic intestine epithelial fate and tissue plasticity.

2024-03-07 | GSE245751 | GEO

Transcriptomic anlaysis of the early response of the colonic epithelium to colitis induction by dextran sodium sulfate (DSS)

Project description:We compared the transcriptional signatures of the colonic mucosa from control mice (WT) versus mice deficient for the epithelial pantetheinase Vnn1 (Vnn1KO) or overexpressing Vnn1 specifically in intestinal epithelial cells (VIVA transgenic mice), during the development of DSS-induced colitis.

2022-11-24 | GSE174166 | GEO

Development of gene expression signatures for colonic lamina propria DCs of CD300a deficient mice

Project description:To further development of our gene expression approach to CD300a deficiency on dendritic cells (DCs) in colonic lamina propria, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish CD300a deficiency on DCs in colonic lamina propria from those of WT mice. Colonic lamina propria DCs were obtained by cell sorter from WT and CD300a deficient mice raised under SPF and GF condition. Expression of Ifnb1 was significantly higher in CD300a deficient DCs, quantified in the same RNA samples by real-time PCR. Gene expression in WT and CD300a colonic lamina propria DCs raised under SPF and GF conditions were measured. Colonic lamina propria cells were obtained from 5 mice in each conditions. Takara-Bio

2015-04-10 | E-GEOD-67696 | biostudies-arrayexpress

HNF4A regulation of transcription profiles in the mouse ileal and colonic epithelial cells

Project description:Purpose: HNF4A is a highly conserved nuclear receptor that has been associated with inflammatory bowel diseases. The goal of this study is to determine and compare transcriptional regulation by HNF4A in the small intestine and large intestine in mice. Methods: Intestinal epithelial cells (IECs) were flow sorted from the ileum and colon of WT and HNF4A IEC-specific KO mice at 21~22 days old and sequenced for transcriptome. Differentially expressed genes in the illeum and colon respectively comparing the WT and HNF4A IEC-KO were determined. Results: HNF4A regulates expression of hundreds of genes in both ileal and colonic IECs. However, many of the DE genes and the magnitude of changes are location specific. In general, a more significant dependancy on HNF4A is found in the colon. HNF4A is particularly required for the expression of a set of immune signaling molecules that are critical for the IEC-intrapithelial lymphocyte crosstalk. Those molecules include members of the butyrophilin-like molecules (Btnl1, Btnl2, Btnl4, and Btnl6) and MHC-I like molecule H2-T3 etc. Expression of the immune signaling molecules was validated by qPCR. Further comparison with HNF4A ChIP-seq datasets and validation with ChIP-qPCR confirmed that those genes are also direct HNF4A targets.

2022-06-30 | GSE199416 | GEO

single nuclei transcriptomics of colonic epithelium

Project description:FOXA1 and FOXA2 are essentail transcription factors for proper gut development. In adults, they play a role in the differentiation of intestinal secretory cells and were also reporeted to directly activate Muc2 transcription. Here we show that deletion of Foxa1 and Foxa2 in mouse intestinal epithelium leads to a downregulation of glycosylation genes in the colon and to a massive change of the colonic surface glycans, which in turn leads to dysbiosis and to inflammatory bowel disease. In order to associate this phenotype with a specific colonic lineage, we generated cell specific gene sets by performing single nuclei RNA-seq on colonic tissue from control mice. Gene set enrichment analysis demonstrated major changes in Goblet cell genes following Foxa1/2 deletion, including glycosylation genes. However, other lineages were also affected. We concluded that vertebrates shape a favorable microbiome by establishing a glycocalyx to nurture specific bacterial taxa through control of the epithelial glycosylation program by the FoxA transcription factors.

2024-05-14 | GSE263631 | GEO

Temporal transcriptional profiles of colonic tissue during DSS-induce colitis

Project description:Inflammation dramatically alters the gut microenvironment. To investigate the transcriptome changes the temporal profile of multiple signaling pathways throughout the progression of colitis, we collected the colonic tissue at a series of time points during DSS colitis for bulk RNA sequencing.

2022-09-06 | GSE210405 | GEO

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