Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq analysis of Foxa2 binding sites in midbrain dopaminergic progenitors

ABSTRACT: Embryonic stem (ES) cells were differentiated in culture to midbrain dopaminergic (mDA) progenitors and subjected to ChIP-seq analysis to resolve genome-wide binding sites of forkhead box protein A2 (Foxa2). Foxa2 was found to directly regulate multiple lineage pathways to specify midbrain dopaminergic and floor plate progenitor identity.

ORGANISM(S): Mus musculus

SUBMITTER: Paul Bertone

PROVIDER: E-MTAB-1137 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Genome-wide characterization of Foxa2 targets reveals upregulation of floor plate genes and repression of ventrolateral genes in midbrain dopaminergic progenitors.

Metzakopian Emmanouil E Lin Wei W Salmon-Divon Mali M Dvinge Heidi H Andersson Elisabet E Ericson Johan J Perlmann Thomas T Whitsett Jeffrey A JA Bertone Paul P Ang Siew-Lan SL

Development (Cambridge, England) 20120613 14

The transcription factors Foxa1 and Foxa2 promote the specification of midbrain dopaminergic (mDA) neurons and the floor plate. Whether their role is direct has remained unclear as they also regulate the expression of Shh, which has similar roles. We characterized the Foxa2 cis-regulatory network by chromatin immunoprecipitation followed by high-throughput sequencing of mDA progenitors. This identified 9160 high-quality Foxa2 binding sites associated with 5409 genes, providing mechanistic insigh ...[more]

PMID: 22696295

Similar Datasets

Microarray analysis of Nurr1 and Foxa2 synergisitic effect for DA neuron induction

Project description:Analysis of dopaminergic neuronal gene expression changes by Nurr1 and/or Foxa2 overexpression. Result provides that Foxa2 potentiates Nurr1-induced DA neuronal phenotype gene expression. To identify the syergism of Nurr1 and Foxa2 for developing DA neural precursors, neural precusor cells (NPCs) isolated from embryonic brain were treated control, Nurr1, Foxa2 and Nurr1-Foxa2 retrovirus. After treatment of retroviruses, NPCs were cultrued in N2 media withdrawn mitogen (bFGF, EGF) for differetiation of DA neuron. Total RNA was obtained from NPCs in differentiation day 2.

2014-01-16 | E-GEOD-54086 | biostudies-arrayexpress

Isolation of human iPSC and ESC-derived mesDA progenitor cells by immunomagnetic cells sorting (MACS)

Project description:Human embryonic and induced pluripotent stem cells are a promising cell source for the future treatment of Parkinson´s disease. It has been shown that mesencephalic dopaminergic (mesDA) neurons arise from the midbrain floor plate in which FOXA2 acts as a key transcription factor. We identified IAP which is specifically co-expressed with FOXA2 positive cells and is suitable to isolate mesDA progenitors utilizing MACS Technolog.The sorted iPSCs were viable, enriched for midbrain specific markers, lacked expression of pluripotency markers, and differentiated into mature dopaminergic neurons in vitro. IAP might be used as a tool to purify mesDA progenitor cells for regenerative therapy in PD patients

2017-09-25 | GSE74991 | GEO

Identification of candidate FOXA2-regulated genes in the adult mouse uterus

Project description:To identify candidate genes regulated by forkhead transcription factor box A2 (FOXA2) in the uterus, control and Foxa2-deleted uteri were collected at day of pseudopregnancy (DOPP) 3.5 (DOPP 0.5= vaginal plug). Microarray analysis identified differentially expressed genes in the Foxa2-deleted as compared to control uteri that are candidiate FOXA2-regulated genes in the uterus. Whole uteri (control wild type n=4; Foxa2-deleted n=4) were analyzed for differences in their transcriptome using a mouse microarray.

2013-12-01 | E-GEOD-48339 | biostudies-arrayexpress

High throughput sequencing of human HepG2 DNA immunoprecipitated with FOXA2, HNF4a and NRF2/GABP

Project description:In each cell type the expression of genes is regulated by the action of a large number of transcription factors, but so far we have only a rudimentary knowledge of the location of the gene regulatory elements where they bind. This can now be addressed with genome-wide ChIP experiments. In a previous ChIP-chip study of USF1 and USF2 we found evidence also of binding of GABP, FOXA2 and HNF4a within the enriched regions. Here we have applied ChIP-seq for these transcription factors and identified 3064 peaks of enrichment for GABP, 7266 for FOXA2 and 18783 for HNF4a. HNF4a and FOXA2 binding was found in at least half of the regions previously identified as bound by USF2 but not USF1, showing that they frequently bind the same regulatory elements. GABP peaks were found at transcription start sites whereas 94 % of FOXA2 and 90 % of HNF4a peaks were located at other positions. We developed a method based on the high resolution achieved by ChIP-seq to accurately define TFBS within peaks, and found the predicted sites to have an elevated conservation level compared to peak centers; however the majority of bindings were not evolutionary conserved. An unexpected interaction between HNF4a and GABP was seen at TSS, with as many as 1/3 of the HNF4a positive promoters being bound also by GABP, and co-immunoprecipitations show that these factors are in the same complex in the nucleus.

2009-06-09 | E-MTAB-115 | biostudies-arrayexpress

Analysis of FoxA2 occupancy in mouse liver with endoderm ChIP-chip array

Project description:Understanding how silent genes can be competent for activation provides insight into development as well as cellular reprogramming and pathogenesis. We performed genomic location analysis of the pioneer transcription factor FoxA in the adult liver and found that about one-third of the FoxA bound sites are near silent genes, including genes without detectable RNA polymerase II. Virtually all of the FoxA-bound silent sites are within extended conserved sequences, suggesting possible function. Such sequences are enriched in motifs for transcriptional repressors, including for Rfx1. We found one such target site containing functional FoxA and Rfx1 sites is a cryptic enhancer 7 kb downstream of the Cdx2 gene, the latter being an effector of esophageal metaplasia. Indeed, Rfx1 sites restrict transcriptional activation by FoxA at the +7 kb Cdx2 element. Furthermore, Rfx1 expression in the esophageal epithelium becomes extinguished during its metaplastic progression to carcinoma. We propose that motif analysis of other transcription factors bound to silent genes can reveal unanticipated regulatory networks that provide insights into reprogramming and oncogenic progression. We analyzed FOXA2 occupancy in a mouse liver sample. We ran three competitive hybridizations: (i) FOXA2 vs IgG, (ii) FOXA2 vs input, and (iii) IgG vs input.

2011-07-18 | E-GEOD-23551 | biostudies-arrayexpress

ChIP-seq analysis of Foxa2 binding sites in midbrain dopaminergic progenitors

Project description:ChIP-seq analysis of Foxa2 binding sites in midbrain dopaminergic progenitors

| PRJEB3033 | ENA

FOXA2 regulates a network of genes involved in critical functions of intestinal epithelia

Project description:Background and Aims: The forkhead box A (FOXA) family of pioneer transcription factors is critical for the development of many endoderm-derived tissues including the lung and the liver. Here we investigate the role of FOXA2 in regulating intestinal epithelial cell function. Methods: ChIP-seq was used to identify FOXA2 binding sites genome-wide. Targets of FOXA2 were validated using ChIP-qPCR and siRNA-mediated depletion of FOXA1/2 followed by RT-qPCR. A luciferase-based assay was used to measure intracellular cAMP after FOXA1/2 modulation.Results: Peaks of FOXA2 occupancy were frequent at loci contributing to gene ontology pathways of regulation of cell migration, cell motion, and plasma membrane function. Depletion of both FOXA1 and FOXA2 led to a significant reduction in the expression of multiple transmembrane proteins including ion transporters. One of the targets was the adenosine A2B receptor, and reduced receptor mRNA levels were associated with a functional decrease in intracellular cAMP. We also observed that 30% of FOXA2 binding sites contained a GATA motif and that FOXA1/A2 depletion reduced GATA-4, but not GATA-6 protein levels. Conclusions: These data show that FOXA2 plays a critical role in regulating intestinal epithelial cell function. FOXA2 depletion affects the expression of ion transporters and other transmembrane proteins, which form a network essential for maintaining normal ion and solute transport. Moreover, we show that the FOXA and GATA families of transcription factors may work cooperatively to regulate gene expression genome-wide. To determine the role of FOXA2 in regulating gene expression in intestinal epithelial cells, ChIP-seq was performed for FOXA2 in Caco2 (colorectal adenocarcinoma) cells.

2015-08-06 | E-GEOD-66218 | biostudies-arrayexpress

RNA-SEQ profiling of mouse whole midbrain and dopaminergic neurons from the mouse mid-brain

Project description:RNA-SEQ profiling of mouse whole midbrain and dopaminergic neurons from the mouse mid-brain Murine whole midbrain and murine midbrain dopaminergic neurons

2015-07-27 | E-GEOD-64526 | biostudies-arrayexpress

Siah2-dependent concerted activity of HIF and FoxA2 regulates formation of neuroendocrine prostate tumors

Project description:Neuroendocrine (NE) carcinoma and NE differentiation (NED) of human prostate tumor are hallmarks of aggressive human prostate cancer. Here we reveal that HIF-1a cooperation with FoxA2, a transcription factor expressed in NE tissue, is required for determining NE phenotype. Reduced HIF-1a expression, as seen in the E3 ubiquitin ligase Siah2 mutant mice, converted NE tumors to atypical hyperplasia when crossed with the TRAMPTg mice. Significantly, HIF-1a cooperation with FoxA2 enables the trans-activation of select HRE-regulated genes such as Hes6, Plod2 and Jmjd1a, whose expression is notably higher in metastatic prostate adenocarcinomas. Our findings disclose the requirement for spatial and timely regulation of FoxA2 and HIF-1a for NE/NED in prostate tumors. 12 prostate tumor samples were analyzed during normoxia and hypoxia, with different FOX/HIF genotypes. The pivotal samples are represented as duplicates.

2010-07-13 | E-GEOD-18478 | biostudies-arrayexpress

ChIPmentation of FOXA2 in Fh1-WT and Fh1-KO cells

Project description:To identify the genomic location of FOXA2 in Fh1-WT and Fh1-KO cells.

2022-09-01 | E-MTAB-11785 | biostudies-arrayexpress