Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ATAC-Seq analysis in vasopressin-responsive mouse renal collecting duct mpkCCD cells

ABSTRACT: Vasopressin, a peptide hormone, controls renal water excretion, largely through regulation of water channel aquaporin-2 (AQP2) in the renal collecting duct. There are two regulatory mechanisms of AQP2: 1) short-term regulation by membrane trafficking of AQP2; and 2) long-term regulation involving vasopressin-induced changes of protein abundance of AQP2 through regulation of gene transcription and protein half-life. Vasopressin binds a G protein-coupled receptor (V2R) activating several downstream signaling pathways. At downstream of V2R activation, many of transcription factors involve gene transcription process associated with status of chromatin structure. ATAC-Seq (Assay for Transpoase-Accessible Chromatin using Sequencing) is a recent technique to study chromatin accessibility (Buenrostro et al. Nat Methods 2013). We carried out ATAC-Seq following standard an ATAC-Seq protocol in mpkCCD cells treated with vehicle or dDAVP for 30 minutes.

ORGANISM(S): Mus musculus

PROVIDER: GSE108786 | GEO | 2018/03/26

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

ChIP-Seq analysis of transcription factors CREB and C/EBP beta in vasopressin-responsive mouse renal collecting duct mpkCCD cells

Project description:Vasopressin, a peptide hormone, controls renal water excretion, largely through regulation of water channel aquaporin-2 (AQP2) in the renal collecting duct. There are two regulatory mechanisms of AQP2: 1) short-term regulation by membrane trafficking of AQP2; and 2) long-term regulation involving vasopressin-induced changes of protein abundance of AQP2 through regulation of gene transcription and protein half-life. Vasopressin binds a G protein-coupled receptor (V2R) activating a cyclic AMP/protein kinase A (PKA) signaling pathway. Sequentially, after activation of cAMP/PKA signaling, many of transcription factors involve gene transcription process. cAMP-response element binding protein (CREB) and cAMP-responsive transcription factor C/EBP beta are potential candidates for vaopressin-mediated regulation of Aqp2 gene transcription proviously reported. In the present study, genome-wide binding sites for two b-ZIP transcription factors CREB and C/EBP beta were identified in vasopressin-responsive mouse collecting duct mpkCCD cells using ChIP-Seq.

2018-03-26 | GSE98076 | GEO

Expression data from mouse collecting duct cell, mpkCCD, in response to a peptide hormone vasopressin analog, dDAVP

Project description:Vasopressin is the major hormone that regulates renal water excretion. It does so by binding to a receptor in renal collecting duct cells, triggering signaling pathways that ultimately regulate the abundance, location, and activity of the water channel protein aquaporin 2. We took an advantage of quantitative large scale proteomic technologies and oligonucleotide microarrays to quantify steady state changes in protein and transcript abundances in response to vasopressin in a collecting duct cell line, mpkCCD clone 11 (Yu et al. PNAS 2009, 106:2441-2446). This cell line originally developed by Alan Vandewalle’s group recapitulates vasopressin-mediated AQP2 expression and phosphorylation as seen in native colleting duct cells. The mpkCCD cells were grown on membrane supports to permit polarization. Once transepithelial resistance reached 5kohm per centimeter square and higher, the cells were exposed to the vasopressin V2 receptor analog, dDAVP, at a physiological concentration, 0.1nM, for 5 days. Control experiments were done with cells exposed to vehicle alone. Total RNA was harvested and processed for transcript expression analysis using Affymetrix GeneChip Mouse Genome 430 2.0 Arrays. Each experimental treatment, vehicle and dDAVP, was repeated 3 times.

2010-12-09 | E-GEOD-19938 | biostudies-arrayexpress

PKA-Independent Vasopressin Signaling in Renal Collecting Duct

Project description:Vasopressin regulates renal water excretion by binding to the Gs-coupled vasopressin receptor (V2R) in collecting duct cells, resulting in cyclic AMP-dependent increases in epithelial water permeability through regulation of the aquaporin-2 (AQP2) water channel. Our prior studies showed that CRISPR-mediated deletion of protein kinase A (PKA) in cultured mpkCCD cells largely eliminates these regulatory events. These PKA-null cells provide a means of identifying PKA-independent signaling downstream from the V2 receptor. We carried out large-scale quantitative protein mass spectrometry (SILAC) to identify PKA-independent phosphorylation changes in response to V2R-selective vasopressin analog, dDAVP. The results show that V2R-mediated vasopressin signaling is predominantly, but not entirely, PKA-dependent. Target motif analysis of the phosphopeptides increased in response to dDAVP in PKA-null cells indicates that the vasopressin activates of one or more members of the AMPK/SNF1 subfamily of basophilic protein kinases. Among the upregulated phosphorylation sites were three known targets of SNF1-subfamily kinases, namely Lipe (S559), Crtc1 (S151) and Arhgef2 (S151). One of the phosphorylation sites that increased in occupancy in PKA-null cells was Ser256 of AQP2, a site critical for vasopressin-mediated trafficking of AQP2 to the cell surface. Beyond this, PKA-independent active site phosphorylation changes were also seen for protein kinases Stk39 (SPAK) and Prkci (Protein kinase C iota). Cyclic AMP levels were ~10-fold higher in PKA-null than in PKA-intact cells in the presence of phosphodiesterase inhibitor IBMX, consistent with a marked acceleration of cAMP production in PKA-null cells. The findings are indicative of substantial PKA-independent signaling downstream from the Gs-coupled V2 receptor.

2020-03-05 | PXD015719 | Pride

ChIP-Seq analysis of Histone H3 acetylation (K27) changes in response to vasopressin in mouse renal collecting duct mpkCCD cells

Project description:In mammals, the peptide hormone vasopressin controls renal water excretion, largely through regulation of the molecular water channel aquaporin-2 (AQP2) in the renal collecting duct. Regulatory mechanisms of AQP2 show: 1) short-term regulation by membrane trafficking; and 2) long-term regulation involving vasopressin-induced changes in the abundance of the aquaporin-2 protein. Vasopressin activates a G protein-coupled receptor (V2R) increasing cyclic AMP and activating protein kinase PKA. Crebbp and Ep300 are known targets of PKA. They are histone acetyltransferases that acetylate histone H3 lysine-27, a histone mark associated with open chromatin and increased transcription (Tie F et al. Development 2009). The translocation of CREBBP and Ep300 into the nucleus in response to vasopressin in the collecting duct cells, predicts that vasopressin, working through PKA, may increase histone H3K27 acetylation of some genes. We tested this by performing ChIP-Seq for this modification.

2018-01-02 | GSE95007 | GEO

Expression data from mouse collecting duct cell, mpkCCD, in response to a peptide hormone vasopressin analog, dDAVP

2010-12-09 | GSE19938 | GEO

Time-course transcriptome profiling in vasopressin-treated mouse kidney collecting duct mpkCCD

Project description:Purpose: The goal of this study is to identify vasopressin-regulated genes in mouse kidney collecting duct cell line mpkCCD. To explore dynamic regulation of vasoressin-mediated transcriptional regulation, transcriptome of vasopressin-treated cells at four different time points (3h, 6h, 12h, and 24h) were profiled and analyzed. Methods: Total RNAs were isolated from vasopressin-treated mpkCCD cells at different time points (3h, 6h, 12h, and 24h). Three replicates for vehicle- or vasopressin-treated group were generated at each tested time point. cDNA libraries were prepared using a Nextera DNA library preparation protocol. The sequence reads from Illumina HiSeq3000 platform were qualified and quantified at the transcript level using Salmon (0.14.1). Differential expression analysis were performed using edgeR. Results: mRNA profiles of mouse kidney collecting duct mpkCCD cells treated with vasopressin analog (dDAVP) for four different time potins (3h, 6h, 12h, and 24h) were generated using an optimized RNA-Seq workflow. Transcript level quantification using a pseudo-alignment quantification method (Salmon) was performed to calculate transcript abundance in each sample. Then differential expression analysis identified the differentially expressed genes including Aqp2 gene at each time point comparison (dDAVP vs vehicle, FDR < 0.05). In addition, several new vasopressin-responsive genes that have not been elucidated before were identified. Conclusions: This study revealed dynamic changes of vasopressin-responsive gene expression within 24 hours in mouse kidney collecting duct cells. The results from time-course transcriptome profiling identified the known vasopressin-responsive genes and several novel gene that are regulated temporally.

2021-07-22 | GSE163566 | GEO

Transcriptome changes in response to dDAVP stimulation in CRISPR/Cas9 mediated Camk2d knock-out mpkCCD cells

Project description:The Ca2+/CaM-dependent protein kinase 2-delta (CAMK2D) has been proposed to be involved in vasopressin signaling in the renal collecting duct, which controls water and salt excretion by the kidney. RNA sequancing and quantitative proteomics analyses identified the expression of multiple CAMK2 isoforms, with CAMK2D being the most abundant in collecting duct cells. To investigate the role of CAMK2D in regulating RNA expression in response to vasopressin signaling, the transcriptome of CRISPR/Cas9-mediated Camk2d knock-out mpkCCD cells was profiled using RNA-Seq in the presence of vasopressin analogue dDAVP.

2023-06-01 | GSE228762 | GEO

Vasopressin V2 Receptor, Tolvaptan, and ERK1/2 Phosphorylation in the Renal Collecting Duct II

Project description:Activation of ERK1 and ERK2 is essential in regulation of a wide variety of cellular and physiological processes. In native inner medullary collecting ducts, vasopressin (AVP) working through the V2 subtype vasopressin receptor (V2R)-mediated activation of Gαs, inhibits ERK1 and ERK2 activity. However, it has been reported that V2R can signal independently of Gαs through the activation of β-arrestin, which activates ERK1 and ERK2. Vaptans, V2R antagonists that function as so-called “inverse agonists”, have the potential of promoting cell proliferation via β-arrestin-dependent ERK activation. Here we use the mpkCCD cell line which natively expresses V2R to investigate the effects of AVP, the V2-selective analog dDAVP, and tolvaptan on ERK1 and ERK2 phosphorylation and activation. We demonstrated that ERK1 and ERK2 phosphorylation in mpkCCD cells was significantly reduced by either AVP or dDAVP, in contrast to the increases seen in non-collecting duct cells overexpressing V2R. We also found that tolvaptan has a strong effect to increase ERK1 and ERK2 phosphorylation in the presence of dDAVP and that the tolvaptan effect to increase ERK1 and ERK2 phosphorylation is absent in PKA-null mpkCCD cells. Thus, it appears that the tolvaptan effect to increase ERK activation is PKA-dependent and, therefore, not mediated by the β-arrestin pathway. Overall, the studies show that AVP decreases and that tolvaptan increases ERK1 and ERK2 activation in cells expressing V2R at endogenous levels, and provide no evidence for a role for β-arrestin in the regulation of ERK1 and ERK2 activity.

2023-11-17 | GSE243773 | GEO

Transcription profiling of mpkCCDc14 cells cloned into colonies with varying aquaporin 2 (AQP2) expression levels in the presence of vasopressin analogy dDAVP to identify transcripts responsible for cell-specific expression of AQP2

Project description:This series of microarray data contain transcript intensity of mpkCCD cells. Experiment Overall Design: The mpkCCDc14 cells were cloned into colonies with varying aquaporin 2 (AQP2) expression levels in the presence of vasopressin analogy dDAVP. Transcript profiling was done for the original cells and cell clones 2, 3, 9, 10, and 11. By studying transcripts that correlate with AQP2 mRNA levels among cell clones, the objective was to identify transcripts responsible for cell-specific expression of AQP2.

2009-01-31 | E-GEOD-13667 | biostudies-arrayexpress

Vasopressin (AVP) and the V2R specific agonist dDAVP 7 day infusion into Aquaporin 1 knockout animals

Project description:Vasopressin, the antidiuretic hormone, acts on the renal collecting duct. In this experiment both vasopressin (AVP) and the V2R specific agonist dDAVP were infused into Aquaporin 1 knockout animals for 7 days. The aim of the experiment was to identify genes increased by vasopressin receptors in the renal medullary collecting ducts, in the absence of an increase in renal medullary osmolarity (the AQP1 knockouts are concentrating mechanism knockouts). All experiments used inner medulla tissue for the RNA isolation. Hybridizations were performed that compared kidney inner medulla total RNA from three control mice against kidney medulla total RNA from 3 mice infused with either arginine vasopressin (AVP) or des-amino-D-arginine vasopressin (dDAVP).

2007-10-06 | E-GEOD-5953 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data