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Genome-wide identification of transcription factor ATOH1 target genes in adult small intestine and colon (ChIP-Seq)

ABSTRACT: We identify targets of ATOH1 binding in the adult intestinal epithelium.

ORGANISM(S): Mus musculus

PROVIDER: GSE82181 | GEO | 2017/01/05

SECONDARY ACCESSION(S): PRJNA324267

REPOSITORIES: GEO

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Genome-wide identification of transcription factor ATOH1 target genes in adult small intestine and colon.

Project description:We generated three mRNA expression profiles by RNA-Seq of (i) wild-type crypts, (ii) Atoh1 knockout crypts, and (iii) purified ATOH1-positive cells.

2017-01-05 | GSE82180 | GEO

Genome-wide identification of transcription factor ATOH1 target genes in adult small intestine and colon

Project description:Genome-wide identification of transcription factor ATOH1 target genes in adult small intestine and colon

| PRJNA324262 | ENA

Genome-wide identification of transcription factor ATOH1 target genes in adult small intestine and colon

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-01-05 | GSE82182 | GEO

Mediator Kinase Complexes Regulates ATOH1-Dependent Intestinal Differentiation

Project description:Cyclin Dependent Kinases CDK8 and CDK19 (Mediator kinase) are regulatory components of the Mediator complex, a highly conserved complex that fine tunes transcriptional output. While Mediator kinase has been implicated in the transcriptional control of key pathways necessary for development and growth, its function in vivo has not been well described. Herein, we report the consequences of complete ablation of both Cdk8/19 on tissue homeostasis. We show that intestinal epithelial specific deletion of Mediator kinase leads to a distinct defect in secretory progenitor differentiation with broad loss of the intestinal secretory cell types. Using a phospho-proteogenomic approach, we show that the Cdk8/19 kinase module interacts with and phosphorylates components of the chromatin remodeling complex Swi/Snf in intestinal epithelial cells. Genomic localisation of Swi/Snf and Mediator shows Cdk8/19-dependent genomic binding at distinct super-enhancer loci within key lineage specification genes, including the master regulator of secretory differentiation ATOH1. Using CRISPRi/CRISPRa, we identify a distinct Mediator- Swi/Snf bound enhancer element that is necessary and sufficient for ATOH1 expression in a Mediator-kinase dependent manner. As such, these studies uncover a newly described transcriptional mechanism of ATOH1-dependent intestinal cell specification that is dependent on the coordinated interaction of the chromatin remodeling complex Swi/Snf and Mediator complex.

2023-03-10 | PXD030212 | Pride

Phospho-regulation of Atoh1 is required for plasticity of secretory progenitors and tissue regeneration[intestine]

Project description:To define Atoh1 secretory signature, transcriptional profiling of secretory cells was performed. The expression profile of Atoh1+ cells from Atoh1(WT)CreERT2 R26RtdTom mice was determined by comparing tdTom+ (secretory) and tdTom- (absorptive) cells to define the baseline pro-secretory signature for small intestine (SI).

2018-08-06 | GSE115388 | GEO

A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics

Project description:Background and Aims: Single-cell transcriptomics offer unprecedented resolution of tissue function at the cellular level, yet studies analyzing healthy adult human small intestine and colon are sparse. Here, we present single-cell transcriptomics covering the duodenum, jejunum, ileum, and ascending, transverse, and descending colon from 3 humans. Methods: 12,590 single epithelial cells from three independently processed organ donors were evaluated for organ-specific lineage biomarkers, differentially regulated genes, receptors, and drug targets. Analyses focused on intrinsic cell properties and capacity for response to extrinsic signals along the gut axis across different humans. Results: Cells were assigned to 25 epithelial lineage clusters. Human intestinal stem cells (ISCs) are not specifically marked by many murine ISC markers. Lysozyme expression is not unique to human Paneth cells (PCs), and PCs lack expression of expected niche-factors. BEST4+ cells express NPY and show maturational differences between SI and colon. Tuft cells possess a broad ability to interact with the innate and adaptive immune systems through previously unreported receptors. Some classes of mucins, hormones, cell-junction, and nutrient absorption genes show unappreciated regional expression differences across lineages. Differential expression of receptors and drug targets across lineages reveals biological variation and potential for variegated responses. Conclusions: Our study identifies novel lineage marker genes; covers regional differences; shows important differences between mouse and human gut epithelium; and reveals insight into how the epithelium responds to the environment and drugs. This comprehensive cell atlas of the healthy adult human intestinal epithelium resolves likely functional differences across anatomical regions along the gastrointestinal tract and advances our understanding of human intestinal physiology.

2022-02-21 | GSE185224 | GEO

Gene expression profile of intestinal stem cells (ISCs) and ATOH1+ve cells in mice

Project description:Atoh1 is the master transcription factor of intestinal secretory cells. Lineage-tracing model of Atoh1+ve cells showed that the progeny of Atoh1+ve cells can develop into either LGR5+ve or LGR5-ve cells. Present analysis compared the gene expression profile of Atoh1+ve cell-derived LGR5+ve cells and LGR5-ve cells, compared to the resident LGR5+ve cell population of the mouse small intestine.

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Gene expression profile of colonic Atoh1+ve cells and their descendants in DSS-colitis mice

Project description:Atoh1 is the master transcription factor of secretory-type intestinal epithelial cells. By using a lineage-tracing model of Atoh1+ve cells, those Atoh1+ve epithelial cells and their descendants were collected from the colon of DSS-colitis mice or from the control mice, and subjected to global gene expression analysis.

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Phospho-regulation of Atoh1 is required for plasticity of secretory progenitors and tissue regeneration [colon]

2018-08-06 | GSE115378 | GEO

Gene expression induced by 5SA-Atoh1 in DLD1 cells

Project description:To investigate the function of Atoh1 in colon cancer cells. We have employed whole genome microarray expression profiling as a discovery platform to iedntify the gene expression induced by Atoh1 in colon cancer cells. Mutated Atoh1 (5SA-Atoh1) replaced 5 serine residues to Alanin for the protein stabilization were expressed in human colon cancer cellline; DLD1 cells. Triplicated RNAs were generated from GFP expressing DLD1 cells and 5SA-Atoh1 expressing DLD1 cell, respectively.

2012-04-10 | E-GEOD-37143 | biostudies-arrayexpress

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