Chromatin accessibility in the mouse intestinal epithelium across different regions and life stages
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE134579 | GEO | 2022/07/08
REPOSITORIES: GEO
Similar Datasets
Project description:Genes encoding transcription factors function as hubs in gene regulatory networks because they encode DNA-binding proteins, which bind to promoters that carry their binding sites. In the present work we have studied gene regulatory networks defined by genes with transcripts belonging to different mRNA abundance classes in the small intestinal epithelial cell. The focus is the rewiring that occurs in transcription factor hubs in these networks during the differentiation of the small intestinal epithelial cell while it migrates along the crypt-villus axis and during its development from a fetal endodermal cell to a mature adult villus epithelial cell. We have generated transcriptome data for mouse small intestinal villus, crypt and fetal intestinal epithelial cells. In addition we have generated metabolome data from crypt and villus cells. Our results show that the intestinal crypt transcription factor hubs that are rewired during differentiation are involved in the cell cycle process (E2F, NF-Y) and stem cell maintenance (c-Myc). In contrast the villi are dominated by a HNF-4 villus hub, which is rewired during differentiation by the addition of network genes with relevance for lipoprotein synthesis and lipid absorption. Moreover, we have identified a villus NF-kB hub, which was revealed by comparison of the villus and endoderm transcriptomes. The rewiring of the NF-kB villus hub during intestinal development reflects transcriptional activity established by host and microflora interactions. To aid in the mining of our results we have developed a web portal (http://gastro.imbg.ku.dk/mousecv/) allowing easy linkage between the transcriptomic data, biological processes and functions. Experiment Overall Design: Four different sample categories were analyzed. Experiment Overall Design: 1) Small intestinal crypts isolated form 12-weeks old C57BL/6 mice. These samples are in triplicates. Experiment Overall Design: 2) Small intestinal villi isolated form 12-weeks old C57BL/6 mice. These samples are in triplicates. Experiment Overall Design: 3) Embryonic day 12 mesenchyme. These samples are in quadruplicate. each sample is derived from a pool of mesenchymes (10-40) Experiment Overall Design: 4) Embryonic day 12 endoderm. These samples are in quadruplicate. each sample is derived from a pool of endoderms (10-40)
2008-06-12 | E-GEOD-3216 | biostudies-arrayexpress
Project description:Regeneration of skeletal muscle depends on a population of adult stem cells (satellite cells) that remain quiescent throughout life. Satellite cell regenerative functions decline in geriatric satellite cells, compared to old cells are incapable of maintaining their normal quiescent state in muscle homeostatic conditions, and this irreversibly affects their intrinsic regenerative and self-renewal capacities. In geriatric mice, resting satellite cells lose reversible quiescence by switching to an irreversible pre-senescence state, caused by derepression of p16INK4a. Young Bmi1-deficient satellite cells shares similar features.
2013-12-31 | GSE53727 | GEO
Project description:We investigated genome-wide analysis of 5-hydroxymethylcytosine (5hmC) distribution in mouse intestinal stem and differentiated cells using hydroxyMethylated DNA immunoprecipitation (hMeDIP) followed by sequencing. Genomic DNA from mouse intestinal stem (Lgr5+) and villus differentiated cells were sonicated, immunoprecipitated by a 5hmC antibody, and sequenced in order to identify differential hydroxymethylated regions and genes.
2016-11-23 | E-MTAB-5202 | biostudies-arrayexpress
Project description:The small intestinal crypt exhibits a defined spatial organisation involving multiple cell types that undergo continuous proliferation and differentiation while migrating towards the villus. We have built a multi-scale agent-based model (ABM), with individual cells interacting in the crypt geometry, which reproduces the self-organizing stable behaviour reported for the crypt. In our ABM, spatial organization emerges from the dynamic interaction of multiple signalling pathways, which include the Wnt, Notch, BMP and RNF43/ZNRF3 pathways that orchestrate cellular fate and mechanisms of contact inhibition of proliferation as well as feedback loops that regulate the expansion of the niche and size of the crypt. Moreover, this dynamic signalling network interacts with the main cell cycle proteins, governing the progression of each cell across the division stages.
2024-11-22 | MODEL2212120002 | BioModels
Project description:The mammalian intestine is a self-renewing organ that processes ingested food, absorbing nutrients from a sea of biochemical, mechanical, and pathogenic insults. To understand the developmental specification of diverse cell types in the small intestine, we performed time-resolved single-cell transcriptomics across five stages intestinal development: embryonic days (E) 12.5, 14.5, 16.5, and 18.5, and postnatal day (P) 1.5. By dissociating cells from whole organ preparations, we captured the full range of cellular diversity across all intestinal cell lineages. This allowed us to reconstruct the mesenchymal differentiation trajectory and identify the specific genetic programs that give rise to the diverse musculature of the gut wall and villus stroma.
2023-01-12 | GSE222122 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE41541: Expression data from mouse proximal intestinal epithelial Lgr5(hi) stem cells and differentiated villus cells (enterocytes from Atoh1 conditional knockout) GSE41542: H3K79me2 ChIP-seq in mouse proximal intestinal Lgr5(hi) stem cells and villus cells GSE41710: Global gene expression analysis of Dot1l-deficient and control intestinal villus cells in mouse Refer to individual Series
2012-10-13 | E-GEOD-41543 | biostudies-arrayexpress
Project description:The small intestinal epithelium mediates vital functions of nutrient absorption and host defense. The spatial organization of the epithelial cells along the crypt-villus axis segregates them into regions of specialized function. However, many of the mechanisms governing intestinal epithelial cell migration and the coordination of interactions with adjacent cells and the extracellular matrix are not fully understood. We have evaluated in vivo gene expression patterns of ileal epithelial cells in healthy human subjects, isolated by laser capture microdissection from either the villus epithelial or crypt cell regions of the small intestinal mucosa. Expression profiles in villus epithelium and Paneth cell lineages were determined by quantitative real-time PCR, DNA microarray, and immunohistochemistry based methods. Relative expression levels of selected epithelial biomarkers were compared between the ileum, jejunum, duodenum, colon, stomach, and esophagus. Previously established biomarkers as well as a novel and distinct set of genes believed to be linked to epithelial cell motility, adhesion, and differentiation were found to be enriched in each of the two corresponding cell populations. Additionally, high baseline expression levels of innate antimicrobials, alpha defensin 5 (HD5) and regenerating islet-derived 3 alpha (Reg3A), were detected exclusively within the small bowel, most notably in the ileum, in comparison to other sites along the gastrointestinal tract. Our findings provide new and important insights regarding the molecular machinery employed by small intestinal epithelial cells to mediate their function and spatial organization in vivo. Experiment Overall Design: Surgical specimens of human intestinal mucosa were obtained from 4 individuals undergoing surgery for colon cancer, bowel obstruction, or other non-inflammatory conditions. The samples were fixed overnight in 4% (w/v) paraformaldehyde, dehydrated in a graded alcohol series and paraffin-embedded. At least 500 epithelial cells from the crypt or upper villus regions were then captured by LCMD from unstained 6µm thick sections using a PALM MicroLaser System Total RNA was extracted for microarray-based gene expression analysis.
2008-04-07 | E-GEOD-10629 | biostudies-arrayexpress
Project description:Using full-genome arrays, the expression of all XMEs was examined during fetal (gestation day (GD) 19), neonatal (postnatal day (PND) 7), prepubescent (PND30), middle age (12 mon), and old age (18 and 24 mon) in the C57Bl6/J mouse liver and compared to young adults. Fetal and neonatal life stages had a dramatic effect on XME expression compared to the relatively minor effects of old age. At all life stages except PND30 down-regulated genes outnumbered up-regulated genes. The altered XMEs included those in all of the major metabolic phases including phase I (alcohol and aldehyde dehydrogenase and Cyp genes), phase II (aldo-keto reductase, glutathione-S-transferases, sulfotransferases and UDP-glucuronosyl transferases) and phase III (transporters). We have generated a comprehensive catalog of XME hepatic gene changes through the life stages of the mouse that can be used to predict chemicals and chemical classes different life stages are more sensitive to. Some CEL files used in this study have been submitted through GSE21224. Keywords: gene expression/microarray
2010-10-01 | GSE21716 | GEO
Project description:Regeneration of skeletal muscle depends on a population of adult stem cells (satellite cells) that remain quiescent throughout life. Satellite cell regenerative functions decline with aging and in progeric conditions. Here we report that geriatric satellite cells, compared to old cells, are incapable of maintaining their normal quiescent state in muscle homeostatic conditions, and this irreversibly affects their intrinsic regenerative and self-renewal capacities. We analyzed the global changes in gene expression occurring within muscle stem cells (satellite cells) in homeostatic conditions during physiological aging and progeria. Pure satellite cell populations from dissociated skeletal muscle from Young (2-3 months), Old (22-24 months), Geriatric (28-30 months), SAMR1 and SAMP8 mice were isolated using a well-established flow cytometry protocol gating on integrin a7(+)/CD34(+) (positive selection) and Lin- (CD31, CD45, CD11b, Sca1) (negative selection).
2013-12-31 | E-GEOD-53725 | biostudies-arrayexpress
Project description:The small intestinal epithelium mediates vital functions of nutrient absorption and host defense. The spatial organization of the epithelial cells along the crypt-villus axis segregates them into regions of specialized function. However, many of the mechanisms governing intestinal epithelial cell migration and the coordination of interactions with adjacent cells and the extracellular matrix are not fully understood. We have evaluated in vivo gene expression patterns of ileal epithelial cells in healthy human subjects, isolated by laser capture microdissection from either the villus epithelial or crypt cell regions of the small intestinal mucosa. Expression profiles in villus epithelium and Paneth cell lineages were determined by quantitative real-time PCR, DNA microarray, and immunohistochemistry based methods. Relative expression levels of selected epithelial biomarkers were compared between the ileum, jejunum, duodenum, colon, stomach, and esophagus. Previously established biomarkers as well as a novel and distinct set of genes believed to be linked to epithelial cell motility, adhesion, and differentiation were found to be enriched in each of the two corresponding cell populations. Additionally, high baseline expression levels of innate antimicrobials, alpha defensin 5 (HD5) and regenerating islet-derived 3 alpha (Reg3A), were detected exclusively within the small bowel, most notably in the ileum, in comparison to other sites along the gastrointestinal tract. Our findings provide new and important insights regarding the molecular machinery employed by small intestinal epithelial cells to mediate their function and spatial organization in vivo. Keywords: analysis of epithelial cells from crypt or upper villus regions
2008-02-28 | GSE10629 | GEO