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RIME against PBX1 protein in P19.6 mouse embryonal carcinoma cells treated for 48 hours with all-trans retinoic acid

ABSTRACT: Identification of PBX1 interactors in P19.6 mouse embryonal carcinoma cells treated for 48 hours with all-trans retinoic acid.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Cell Culture, Early Embryonic Cell

SUBMITTER: Aurelien Serandour

LAB HEAD: Gilles Salbert

PROVIDER: PXD006158 | Pride | 2017-04-03

REPOSITORIES: Pride

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			Action	DRS
	PR314_AUS_140413_JP536-01.mzid.gz	Mzid
	PR314_AUS_140413_JP536-01.mzid_PR314_AUS_140413_JP536-01.MGF	Mzid
	PR314_AUS_140413_JP536-01.mzid_PR314_AUS_140413_JP536-01.pride.mgf.gz	Mzid
	PR314_AUS_140413_JP536-01.pride.mztab.gz	Mztab
	PR314_AUS_140413_JP536_PBX1_P19-cells_rep1.raw	Raw

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Publications

Cytosine modifications modulate the chromatin architecture of transcriptional enhancers.

Mahé Elise A EA Madigou Thierry T Sérandour Aurélien A AA Bizot Maud M Avner Stéphane S Chalmel Frédéric F Palierne Gaëlle G Métivier Raphaël R Salbert Gilles G

Genome research 20170410 6

Epigenetic mechanisms are believed to play key roles in the establishment of cell-specific transcription programs. Accordingly, the modified bases 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) have been observed in DNA of genomic regulatory regions such as enhancers, and oxidation of 5mC into 5hmC by Ten-eleven translocation (TET) proteins correlates with enhancer activation. However, the functional relationship between cytosine modifications and the chromatin architecture of enhance ...[more]

PMID: 28396520

Similar Datasets

Whole-genome gene expression level changes in P19.6 mouse embryonal carcinoma cells compared to P19.6 cells treated for 48 hours with all-trans retinoic acid

Project description:Enhancers are developmentally-controlled transcriptional regulatory regions whose activities are modulated through histone modifications or histone variant deposition. Here, we show by genome-wide mapping that the newly discovered DNA modification 5-hydroxymethylcytosine (5hmC) is dynamically associated with transcription factor binding to distal regulatory sites during neural differentiation of mouse P19 cells as well as during adipocyte differentiation of mouse 3T3-L1 cells. Functional annotation reveals that regions gaining 5hmC are associated with genes expressed either in neural tissues when P19 cells undergo neural differentiation or in adipose tissue when 3T3-L1 cells undergo adipocyte differentiation. Furthermore, distal regions gaining 5hmC together with H3K4me2 and H3K27ac in P19 cells behave as differentiation-dependent transcriptional enhancers. Identified regions are enriched in motifs for transcription factors regulating specific cell fates like Meis1 in P19 cells and PPARgamma in 3T3-L1 cells. Accordingly, a fraction of hydroxymethylated Meis1 sites were associated with a dynamic engagement of the 5mC hydroxylase Tet1. In addition, kinetic studies of cytosine hydroxymethylation of selected enhancers indicated that DNA hydroxymethylation is an early event of enhancer activation. Hence, acquisition of 5hmC in cell-specific distal regulatory regions may represent a major event of enhancer progression toward an active state and participate in selective activation of tissue-specific genes A 6-chip study aiming to characterize regulated genes in P19.6 mouse embryonal carcinoma cells following 48 hours treatment with 1M-BM-5M all-trans retinoic acid. RNAs were prepared from three independent triplicate experiments.

2012-06-03 | E-GEOD-27334 | biostudies-arrayexpress

Whole-genome mapping of MEIS1, TET1, H3K4me2 and H3K27ac in P19.6 mouse embryonal carcinoma cells and P19.6 cells treated for 48 hours with all-trans retinoic acid

Project description:Enhancers are developmentally-controlled transcriptional regulatory regions whose activities are modulated through histone modifications or histone variant deposition. Here, we show by genome-wide mapping that the newly discovered DNA modification 5-hydroxymethylcytosine (5hmC) is dynamically associated with transcription factor binding to distal regulatory sites during neural differentiation of mouse P19 cells as well as during adipocyte differentiation of mouse 3T3-L1 cells. Functional annotation reveals that regions gaining 5hmC are associated with genes expressed either in neural tissues when P19 cells undergo neural differentiation or in adipose tissue when 3T3-L1 cells undergo adipocyte differentiation. Furthermore, distal regions gaining 5hmC together with H3K4me2 and H3K27ac in P19 cells behave as differentiation-dependent transcriptional enhancers. Identified regions are enriched in motifs for transcription factors regulating specific cell fates like Meis1 in P19 cells and PPARgamma in 3T3-L1 cells. Accordingly, a fraction of hydroxymethylated Meis1 sites were associated with a dynamic engagement of the 5mC hydroxylase Tet1. In addition, kinetic studies of cytosine hydroxymethylation of selected enhancers indicated that DNA hydroxymethylation is an early event of enhancer activation. Hence, acquisition of 5hmC in cell-specific distal regulatory regions may represent a major event of enhancer progression toward an active state and participate in selective activation of tissue-specific genes MEIS1 and H3K27ac genome-wide distributions were determined using ChIP-seq. Cells used in this study are P19.6 mouse embryonal carnicoma cells and P19.6 cells treated for 48 hours with 1M-BM-5M all-trans retinoic acid (RA). ChIP samples were done by SM-CM-)randour A.A. Libraries were prepared and sequenced by the IGBMC sequencing facility (Strasbourg, France) by an Illumina Genome Analyzer II.

2012-06-04 | E-GEOD-33067 | biostudies-arrayexpress

Clinical Trial of All-trans-retinoic Acid, Bevacizumab and Atezolizumab in Colorectal Cancer

Project description:The main purpose of this clinical trial is to learn about the good and the bad effects of all trans retinoic acid (ATRA), atezolizumab and bevacizumab as a possible treatment for advanced colorectal patients. Participants will be treated with the following combination of these drugs: 1. ATRA will be given in a pill form to be taken twice a day at home for 7 days starting on day 1 of a cycle. 2. Atezolizumab will be given through a vein in arm or through mediport over 60-90 minutes every 2 weeks in the outpatient chemotherapy infusion centers at UTSW. 3. Bevacizumab will be given through a vein in arm or through mediport over 20-40 minutes every 2 weeks in the outpatient chemotherapy infusion centers at UTSW.

| 70824 | ecrin-mdr-crc

Short-term in vitro culture of rat fetal testes with all-trans retinoic acid

Project description:Analysis of gene expression and alternate splicing effects of retinoic acid treatment on gestational day 15 rat fetal testes in whole testis culture Retinoic acid exposure in cultured fetal testis has previously been demonstrated to have significant effects on the histology of the fetal testis in multiple species, as well as to alter the meiotic states of germ cells. However, previous experiments have not analyzed the mechanisms by which retinoic acid exposure leads to altered tubulogenesis and loss of seminiferous cord structure. This experiment demonstrated that retinoic acid exposure activated signaling pathways that promote the ovary development program and oppose normal testis development in mid-gestational rat fetal testes.

2017-09-26 | GSE101634 | GEO

Gene expression changes in mouse neuroepithelial organoids in response to all-trans retinoic acid.

Project description:We describe the transcriptomic changes in neuroepithelial organoids in response to all-trans retinoic acid.

2022-10-01 | GSE214368 | GEO

All-Trans-Retinoic Acid Treatment of IDH Mutant Astrocytes

Project description:All-Trans-Retinoic Acid Treatment of IDH Mutant Astrocytes

| PRJNA1061109 | ENA

All-Trans-Retinoic Acid Treatment of IDH Mutant Astrocytes

Project description:All-Trans-Retinoic Acid Treatment of IDH Mutant Astrocytes

| PRJNA721930 | ENA

Hepatic gene expression data from mice injected with all-trans-retinoic acid

Project description:Mice were given an intraperitoneal injection of a pharmacologic dose of all-trans-retinoic acid or vehicle control and liver tissue was collected 4 hours post-injection. RNA was extracted from liver samples and used in microarray analysis.

2020-10-06 | E-MTAB-9396 | biostudies-arrayexpress

All-trans retinoic acid effect on the squamous cell carcinoma cell line ME180: time course

Project description:All-trans retinoic acid (ATRA) has been shown to have anti-proliferative effects, particularly in the context of cancer. However, the effects of ATRA on gene and microRNA expression in solid tumors have not been investigated. In this study, we performed gene expression and microRNA analysis of the squamous cell carcinoma cell line, ME180, following treatment with 10 micromolar all-trans retinoic acid (ATRA) for 1, 3, and 6 hours. Results provide insight into the temporal regulation of genes and microRNAs by retinoids.

2014-08-01 | GSE54464 | GEO

Transcription profiling of human promyelocytic NB4 cells treated with all-trans retinoic acid

Project description:Gene expression profiles of promyelocytic NB4 cells treated with all-trans retinoic acid (ATRA, 1 microM) during short periods of time (1h30 and 3h) were performed and compared to untreated cells (vehicule control, 0,02% ethanol).

2009-02-04 | E-BASE-7 | biostudies-arrayexpress

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