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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Drosophila PTB regulates dorso-ventral patterning genes in embryos

ABSTRACT: Drosophila PTB (Polypyrimidine Tract-binding protein dmPTB) regulates dorso-ventral patterning genes in embryos Comparison of wild type (yw genotype) and PTB mutant (heph03429) drosophila embryos

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Joseph Heimiller

PROVIDER: E-GEOD-57517 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Drosophila polypyrimidine tract-binding protein (DmPTB) regulates dorso-ventral patterning genes in embryos.

Heimiller Joseph J Sridharan Vinod V Huntley Jim J Wesley Cedric S CS Singh Ravinder R

PloS one 20140711 7

The Drosophila polypyrimidine tract-binding protein (dmPTB or hephaestus) plays an important role during embryogenesis. A loss of function mutation, heph(03429), results in varied defects in embryonic developmental processes, leading to embryonic lethality. However, the suite of molecular functions that are disrupted in the mutant remains unknown. We have used an unbiased high throughput sequencing approach to identify transcripts that are misregulated in this mutant. Misregulated transcripts sh ...[more]

PMID: 25014769

Similar Datasets

Drosophila PTB regulates dorso-ventral patterning genes in embryos

Project description:Drosophila PTB (Polypyrimidine Tract-binding protein dmPTB) regulates dorso-ventral patterning genes in embryos

2014-05-10 | GSE57517 | GEO

PTB CLIP-seq

2009-12-24 | GSE19323 | GEO

PTB CLIP-seq

Project description:Recent transcriptome analysis indicates that >90% of human genes undergoes alternative splicing, underscoring the contribution of differential RNA processing to diverse proteomes in higher eukaryotic cells. The polypyrimidine tract binding protein PTB is a well-characterized splicing repressor, but PTB knockdown causes both exon inclusion and skipping. Genome-wide mapping of PTB-RNA interactions and construction of a functional RNA map now revealed that dominant PTB binding near a competing constitutive splice site generally induces exon inclusion whereas prevalent binding close to an alternative site often causes exon skipping. This positional effect was further demonstrated by disrupting or creating a PTB binding site on minigene constructs and testing their responses to PTB knockdown or overexpression. These findings suggest a mechanism for PTB to modulate splice site competition to produce opposite functional consequences, which may be generally applicable to RNA binding splicing factors to positively or negatively regulate alternative splicing in mammalian cells. Examination of PTB-RNA binding in Hela cells using CLIP-seq (Cross-Linking ImmunoPrecipitation coupled with high-throughput sequencing) method. Peaks: The four alignment files (linked as supplementary files on Sample records) were combined together for peak finding, as we found that most of the monomeric and dimeric tags are similarly distributed in the genome with high pearson correlation coefficient. The method to detect the peaks above gene-specific randomized background was similar to (Yeo et al., 2009) and described in the paper (Xue et al., 2009).

2009-12-24 | E-GEOD-19323 | biostudies-arrayexpress

Transcriptome analysis of Drosophila neural stem cells reveals a transcriptional network for self-renewal.

Project description:Drosophila neuroblasts have emerged as a model for stem cell biology that is ideal for genetic analysis but is limited by the lack of cell-type specific gene expression data. Here, we describe a methodology to isolate large numbers of pure neuroblasts and differentiating neurons that retain both cell cycle and lineage characteristics. We determine transcriptional profiles by mRNA sequencing and identify 28 predicted neuroblast specific transcription factors, which can be arranged in a network containing hubs for Notch signaling, growth control and chromatin regulation. Overexpression and RNAi for these factors identify Klumpfuss as a regulator of self-renewal. We show that loss of Klu function causes premature differentiation while overexpression results in the formation of transplantable brain tumors. Our data represent a valuable resource for Drosophila developmental neurobiology and we describes methodology that can be applied to other invertebrate stem cell lineages as well. comparison of transcriptomes of Drosophila melanogaster larval neuroblasts and their differentiated daughter cells (neurons)

2012-08-21 | E-GEOD-38764 | biostudies-arrayexpress

Ecdysone and Mediator trigger a metabolic switch uncoupling cell cycle from cell growth to end proliferation in Drosophila neural stem cells

Project description:Stem cells are highly abundant and proliferate rapidly during early development but become a rare population in most adult organs. The molecular mechanisms causing stem cells to exit proliferation at a specific time are not well understood. Here, we show that changes in energy metabolism induced by the steroid hormone Ecdysone initiate an irreversible cascade of events leading to cell cycle exit in Drosophila neural stem cells. We show that the timely induction of oxidative phosphorylation and the mitochondrial respiratory chain are required in neuroblasts to uncouple cell cycle progression from cell growth. This results in a progressive reduction in neuroblast cell size and ultimately in terminal differentiation. Neuroblasts isolated from brain tumors fail to undergo this shrinkage process and this may explain why they are immortalized. Our findings show that cell size control can be modified by systemic hormonal signaling and reveal a unique connection between metabolism and proliferation control in stem cells. Comparison of transcriptomes of Drosophila melanogaster central brain NBs from wild-type larval NBs, wild type pupal NBs and med27 RNAi pupal NBs.

2014-08-14 | E-GEOD-53265 | biostudies-arrayexpress

The SWI/SNF Complex Regulates the PRDM Protein Hamlet to Ensure Lineage Directionality in Drosophila Neural Stem Cells

Project description:Members of the SWI/SNF chromatin-remodeling complex are among the most frequently mutated genes in human cancer. SWI/SNF complex controls self-renewal and differentiation in stem cell lineages but how this function relates to tumorigenesis is currently unclear. Here, we use Drosophila neuroblasts to demonstrate that the SWI/SNF component Osa (ARID1) prevents tumorigenesis in stem cell lineages by ensuring correct unidirectional lineage progression. Our transcriptome anaysis identifies Ham as a key Osa target gene. comparison of transcriptomes of wild type Drosophila melanogaster larval type II NB lineages (excluding neurons) and osa RNAi type II lineages containing mainly NB-like cells and INPs

2014-03-13 | E-GEOD-48242 | biostudies-arrayexpress

Identification of PTB ΔNLS-GFP interacting proteins precipitated by magnetic beads against GFP

Project description:The purpose of the study was to determine proteins that specially interact cytoplasmic PTB. PTB is an RNA binding protein that shuttles between the nucleus and cytoplasm. To identified proteins interacting with cytoplasmic PTB, nucleus localization signal was deleted (PTB ΔNLS-GFP) and overexpressed followed by IP and MS.

2022-02-17 | PXD026837 | Pride

Gene regulation in LPS-induced PTB in E15.5 C57BL/6 mice

Project description:Multiple molecular pathways affected in LPS-triggered PTB with IL-beta major node

2013-08-15 | GSE49895 | GEO

Gene regulation in LPS-induced PTB in E15.5 C57BL/6 mice

Project description:Multiple molecular pathways affected in LPS-triggered PTB with IL-beta major node

2013-08-15 | GSE49895 | GEO

Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (HJAY)

Project description:To gain global insights into the role of the well-known repressive splicing regulator PTB we analyzed the consequences of PTB knockdown in HeLa cells using high-density oliogonucleotide splice-sensitive microarrays. The major class of identified PTB-regulated splicing event was PTB-repressed cassette exons, but there was also a substantial number of PTB-activated splicing events. PTB repressed and activated exons showed a distinct arrangement of motifs with pyrimidine-rich motif enrichment within and upstream of repressed exons, but downstream of activated exons. The N-terminal half of PTB was sufficient to activate splicing when recruited downstream of a PTB-activated exon. Moreover, insertion of an upstream pyrimidine tract was sufficient to convert a PTBactivated to a PTB-repressed exon. Our results demonstrate that PTB, an archetypal splicing repressor, has variable splicing activity that predictably depends upon its binding location with respect to target exons. Target was prepared from 3 biological replicates of PTB/nPTB knockdown and 3 control mock knockdowns from HeLa S3 cell line and hybridized to a custom Affymetrix array containing exon and exon-junction probes for more than 30,000 human genes

2010-09-01 | E-GEOD-23513 | biostudies-arrayexpress

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