Transcriptome analyses based on genetic screens for Pax3 myogenic targets in the mouse embryo
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: mounia lagha
PROVIDER: E-GEOD-22041 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:We used microarrays to identify Pax3 targets during myogenesis in the mouse embryo Mouse embryos were genotyped Pax3GFP/+ or Pax3PAX3-FKHR/GFP and dissected at E9.5 under a fluorescent binocular. Somites were dissected from the interlimb region and the more hypaxial domain separated from the neural tube and the epaxial extremity of the somites. GFP positive cells were then sorted by flow cytometry before RNA extraction and hybridization on Affymetrix microarrays. We also sorted GFP negative cells.
2010-12-01 | E-GEOD-22040 | biostudies-arrayexpress
Project description:We used microarrays to identify Pax3 targets during myogenesis in the mouse embryo Mouse embryos were genotyped Pax3GFP/+ or Pax3PAX3-FKHR/GFP and dissected at E10.5 under a fluorescent binocular. The forelimb buds were dissected and dissociated and GFP positive cells were then sorted by flow cytometry before RNA extraction and hybridization on Affymetrix microarrays. We also sorted GFP negative cells.
2010-12-01 | E-GEOD-22039 | biostudies-arrayexpress
Project description:The skeletal myogenic lineage in developing embryos is specified within the somites and requires members of the Paired box (Pax) family of transcription factors. In particular, Pax3 is the first member of this family expressed in the central region of the dermomyotome and it is necessary for specification, migration and survival of the myogenic progenitors that will form the muscles of the limbs, diaphragm and tongue. To investigate Pax3 molecular functions in the developing mesoderm, we generated doxycycline-inducible mouse embryonic stem (ES) cells expressing untagged and HaFlag-tagged-Pax3. These cell lines were used to unbiasedly identify its interacting partners by tandem affinity purification followed by mass spectrometry.
2019-04-18 | PXD012693 | Pride
Project description:BackgroundPax3 is a key upstream regulator of the onset of myogenesis, controlling progenitor cell survival and behaviour as well as entry into the myogenic programme. It functions in the dermomyotome of the somite from which skeletal muscle derives and in progenitor cell populations that migrate from the somite such as those of the limbs. Few Pax3 target genes have been identified. Identifying genes that lie genetically downstream of Pax3 is therefore an important endeavour in elucidating the myogenic gene regulatory network.ResultsWe have undertaken a screen in the mouse embryo which employs a Pax3GFP allele that permits isolation of Pax3 expressing cells by flow cytometry and a Pax3PAX3-FKHR allele that encodes PAX3-FKHR in which the DNA binding domain of Pax3 is fused to the strong transcriptional activation domain of FKHR. This constitutes a gain of function allele that rescues the Pax3 mutant phenotype. Microarray comparisons were carried out between Pax3GFP/+ and Pax3GFP/PAX3-FKHR preparations from the hypaxial dermomyotome of somites at E9.5 and forelimb buds at E10.5. A further transcriptome comparison between Pax3-GFP positive and negative cells identified sequences specific to myogenic progenitors in the forelimb buds. Potential Pax3 targets, based on changes in transcript levels on the gain of function genetic background, were validated by analysis on loss or partial loss of function Pax3 mutant backgrounds. Sequences that are up- or down-regulated in the presence of PAX3-FKHR are classified as somite only, somite and limb or limb only. The latter should not contain sequences from Pax3 positive neural crest cells which do not invade the limbs. Verification by whole mount in situ hybridisation distinguishes myogenic markers. Presentation of potential Pax3 target genes focuses on signalling pathways and on transcriptional regulation.ConclusionsPax3 orchestrates many of the signalling pathways implicated in the activation or repression of myogenesis by regulating effectors and also, notably, inhibitors of these pathways. Important transcriptional regulators of myogenesis are candidate Pax3 targets. Myogenic determination genes, such as Myf5 are controlled positively, whereas the effect of Pax3 on genes encoding inhibitors of myogenesis provides a potential brake on differentiation. In the progenitor cell population, Pax7 and also Hdac5 which is a potential repressor of Foxc2, are subject to positive control by Pax3.
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Project description:Determing the gene network regulated by Pitx2 in during forelimb muscle development of mouse embryos at E12.5. Lbx1 is coexpressed in Pitx2+ cells during forelimb development, thus Pitx2-LacZ and Lbx1-EGFP+ mice were cross bred to allow us to purify Lbx1-EGFP+|Pitx2 -wild type, het, or null cells by flow sorting We used microarray analysis to determine the genes misregulated in Pitx2 null mice compared to Pitx2 wild type and heterozygotes. Lbx1-EGFP+|Pitx2(+/+, LacZ/+, or LacZ/LacZ) cells were flow sorted, RNA extracted, labelled cDNA was hybridized to Affymetrix mouse genome 430 2.0 arrays
2013-06-11 | E-GEOD-31945 | biostudies-arrayexpress
Project description:As the only truly flying mammals, bats use their unique wing formed from elongated digits connected by membranes to power their flight. The forelimb of bats consists of four elongated digits (digits II-V) and one shorter digit (digit I) that is morphologically similar to the hindlimb digits. Elongation of bat forelimb digits is thought to results from changes in the temporal and spatial expression of a number of developmental genes. As a result, comparing gene expression profiles between short and elongated digit morphologies of the fore- and hindlimbs may elucidate the molecular mechanisms underlying digit elongation in bats. Here, we performed a large-scale analysis of gene expression of forelimb digit I, forelimb digits II-V, and all five hindlimb digits in Myotis ricketti using digital gene expression tag profiling approach. Results of this study not only implicate several developmental genes as robust candidates underlying digit elongation in bats, but also provide a better understanding of the genes involved in autopodial development in general. A large-scale analysis of gene expression of 3 different parts of autopods in Myotis ricketti using digital gene expression tag profiling approach.
2010-12-06 | E-GEOD-20038 | biostudies-arrayexpress
Project description:PAX3-FOXO1 is a fusion transcription factor that is the main driver of tumorigenesis leading to the development of alveolar rhabdomyosarcoma (aRMS). Since aRMS cells are addicted to PAX3-FOXO1 activity, the fusion protein also represents a major target for therapeutic interference, which is however challenging as transcription factors usually cannot be inhibited directly by small molecules. Hence, characterization of the biology of PAX3-FOXO1 might lead to the discovery of new possibilities for an indirect inhibition of its activity. Here, our goal was to characterize the proteomic neighborhood of PAX3-FOXO1 and to find candidates potentially affecting its activity and tumor cell viability. Towards this aim, we expressed BirA fused versions of PAX3-FOXO1 (N- and C-terminal) in HEK293T cells under presence of biotin. In the control setup, we expressed the BirA enzyme alone. After Streptavidin purification of biotinylated proteins, we performed mass spectrometry and quantified relative abundances compared to control conditions. This enabled us to determine PAX3-FOXO1 proximal proteins, which we investigated further in orthogonal endogenous systems.
2021-09-16 | PXD022187 | Pride
Project description:Polycomb group (PcG) proteins play a pivotal role in epigenetically silencing development-related genes, restricting their expression to appropriate tissues. However, in some instances PcG target genes must also be dynamically regulated in response to developmental signals encountered during morphogenesis. Here we examine the role of PcG factors in early forelimb bud patterning, a process that relies on various morphogenetic signals. Depletion of Ring1 proteins, which are essential components of Polycomb repressive complex-1 (PRC1), led to dramatic deficiencies in forelimb formation and proximal-distal regionalization. Gene expression analysis identified Meis2 and Meis1 as critical PRC1 targets genes in early distal specification, with PcG proteins counteracting retinoic acid (RA) signaling to control their expression. Importantly, in this system, PcG factors appear to function by adjusting the threshold for RA signaling, revealing an unexpected role of polycomb proteins in dynamic gene regulation during development. [Affymetrix] Mouse E10.5 forelimb buds of Ring1A-KO, Ring1A/B-dKO and RA-treated wild type were used for RNA extraction and hybridization on Affymetrix microarrays. [Agilent] ChIP analysis of mouse E10.5 whole forelimb buds against anti-H3K27me3 antibody.
2015-05-27 | E-GEOD-57990 | biostudies-arrayexpress
Project description:This data set contains 3 replicates each for a Pax7 overexpression, Pax3 overexpression and an empty vector Control Measurement of expression levels in Pax3, Pax3 overepxression and empty vector control
2012-05-22 | E-GEOD-32266 | biostudies-arrayexpress
Project description:Exposure to environmental teratogenic pollutant leads to severe birth defects. However, the biological events underlying these developmental abnormalities remain undefined. Here we report a molecular link between an environmental stress response pathway and key developmental genes during craniofacial development. In our study, we focused on the development of the facial prominences at E11.5. To do so, we compared the transcriptomes of mutant embryos (*Pax3Pax3-ERD/GFP *called DM in the microarray samples) to the one of control embryos (*Pax3GFP/+ *called GFP in the sample names). These are knock-in genetic models described in Bajard et al., 2006 and Relaix et al., 2005. In both of them a cassette coding for the GFP is replacing one allele of the Pax3 gene. The Pax3-ERD allele is a conditional one that drives the expression of the dominant negative form of Pax3 (Pax3-ERD) composed of the Pax3 DNA binding domain fused to the engrailed repressor domain (ERD) upon activation of a Cre recombinase. In this study, the Cre was driven by the zygote specific PGK enhancer. Strikingly, mutant mice with impaired Pax3/7 function display severe craniofacial defects. We show these are associated with an up-regulation of the signaling pathway mediated by the Aryl hydrocarbon Receptor (AhR), the receptor to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), revealing a genetic interaction between Pax3 and AhR signaling. Activation of AhR signaling in Pax3-deficient embryos drives facial mesenchymal cells out of the cell cycle through the up-regulation of p21 expression. Accordingly, inhibiting AhR activity rescues the cycling status of these cells and the facial closure of Pax3/7 mutants. Together, our findings demonstrate that the regulation of AhR signaling by Pax3/7 is required to protect against TCDD/AhR-mediated teratogenesis during craniofacial development.
2015-04-06 | E-MTAB-3238 | biostudies-arrayexpress