Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Functional genomic analysis of the periodic transcriptome in the developing Drosophila wing [Affymetrix]

ABSTRACT: The eukaryotic cell cycle, driven by both transcriptional and post-translational mechanisms, is the central molecular oscillator underlying tissue growth throughout animals. While genome-wide studies have investigated cell cycle-associated transcription in unicellular systems, global patterns of periodic transcription in multicellular tissues remain largely unexplored. Here we define the cell cycle-associated transcriptome of the developing Drosophila wing epithelium and compare it with that of cultured Drosophila S2 cells, revealing a core set of periodic genes as well as a surprising degree of context-specificity in periodic transcription. We further employ RNAi-mediated phenotypic profiling to define functional requirements for over 300 periodic genes, with a focus on those required for cell proliferation in vivo. Finally, we investigate the role of novel genes required for interkinetic nuclear migration. Combined, these findings provide a global perspective on cell cycle control in vivo, and highlight a critical need to understand the context-specific regulation of cell proliferation.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE54926 | GEO | 2014/03/15

SECONDARY ACCESSION(S): PRJNA238061

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Functional genomic analysis of the periodic transcriptome in the developing Drosophila wing [Affymetrix]

Project description:The eukaryotic cell cycle, driven by both transcriptional and post-translational mechanisms, is the central molecular oscillator underlying tissue growth throughout animals. While genome-wide studies have investigated cell cycle-associated transcription in unicellular systems, global patterns of periodic transcription in multicellular tissues remain largely unexplored. Here we define the cell cycle-associated transcriptome of the developing Drosophila wing epithelium and compare it with that of cultured Drosophila S2 cells, revealing a core set of periodic genes as well as a surprising degree of context-specificity in periodic transcription. We further employ RNAi-mediated phenotypic profiling to define functional requirements for over 300 periodic genes, with a focus on those required for cell proliferation in vivo. Finally, we investigate the role of novel genes required for interkinetic nuclear migration. Combined, these findings provide a global perspective on cell cycle control in vivo, and highlight a critical need to understand the context-specific regulation of cell proliferation. Cells from developing Drosophila wing epithelium, and cultured S2 cells are FACS sorted into G1 and G2 populations based on DNA content and compared in triplicate on Affymetrix microarrays to identify differences in the transcriptional program of the cell cycle by cell type.

2014-03-15 | E-GEOD-54926 | biostudies-arrayexpress

Transcriptional profiling of Drosophila wing pouch following CR32027 RNAi

Project description:The eukaryotic cell cycle, driven by both transcriptional and post-translational mechanisms, is the central molecular oscillator underlying tissue growth throughout animals. While genome-wide studies have investigated cell cycle-associated transcription in unicellular systems, global patterns of periodic transcription in multicellular tissues remain largely unexplored. Here we define the cell cycle-associated transcriptome of the developing Drosophila wing epithelium and compare it with that of cultured Drosophila S2 cells, revealing a core set of periodic genes as well as a surprising degree of context-specificity in periodic transcription. We further employ RNAi-mediated phenotypic profiling to define functional requirements for over 300 periodic genes, with a focus on those required for cell proliferation in vivo. Finally, we investigate the role of novel genes required for interkinetic nuclear migration. Combined, these findings provide a global perspective on cell cycle control in vivo, and highlight a critical need to understand the context-specific regulation of cell proliferation. Two RNAi lines of CR32027, a non-coding RNA gene identified in this study, are examined for transcriptional changes relative to wt. Transcriptional profiles of two RNAi knockdowns, CR32027-IR1 and CR32027-IR2, are examined in Drosophila wing pouch relative to OreR wt in triplicate by RNA Seq.

2014-03-15 | E-GEOD-54927 | biostudies-arrayexpress

Transcriptional profiling of Drosophila wing pouch following CR32027 RNAi

Project description:The eukaryotic cell cycle, driven by both transcriptional and post-translational mechanisms, is the central molecular oscillator underlying tissue growth throughout animals. While genome-wide studies have investigated cell cycle-associated transcription in unicellular systems, global patterns of periodic transcription in multicellular tissues remain largely unexplored. Here we define the cell cycle-associated transcriptome of the developing Drosophila wing epithelium and compare it with that of cultured Drosophila S2 cells, revealing a core set of periodic genes as well as a surprising degree of context-specificity in periodic transcription. We further employ RNAi-mediated phenotypic profiling to define functional requirements for over 300 periodic genes, with a focus on those required for cell proliferation in vivo. Finally, we investigate the role of novel genes required for interkinetic nuclear migration. Combined, these findings provide a global perspective on cell cycle control in vivo, and highlight a critical need to understand the context-specific regulation of cell proliferation. Two RNAi lines of CR32027, a non-coding RNA gene identified in this study, are examined for transcriptional changes relative to wt.

2014-03-15 | GSE54927 | GEO

An extensive program of periodic alternative splicing linked to cell cycle progression

Project description:Progression through the mitotic cell cycle requires periodic regulation of gene function at the levels of transcription, translation, protein-protein interactions, post-translational modification and degradation. However, the role of alternative splicing (AS) in the temporal control of cell cycle is not well understood. By sequencing the human transcriptome through two continuous cell cycles, we identify ~1,300 genes with cell cycle-dependent AS changes. These genes are significantly enriched in functions linked to cell cycle control, yet they do not significantly overlap genes subject to periodic changes in steady-state transcript levels. Many of the periodically spliced genes are controlled by the SR protein kinase CLK1, whose level undergoes cell cycle-dependent fluctuations via an auto-inhibitory circuit. Disruption of CLK1 causes pleiotropic cell cycle defects and loss of proliferation, whereas CLK1 over-expression is associated with various cancers. These results thus reveal a large program of CLK1-regulated periodic AS intimately associated with cell cycle control.

2016-05-19 | GSE81485 | GEO

Cdk1 activity levels drive periodic transcription independently of cell cycle progression

Project description:Cdk1 activity levels drive periodic transcription independently of cell cycle progression

| PRJNA289441 | ENA

Saccharomyces cerevisiae

Project description:Checkpoints Couple Transcription Network Oscillator Dynamics to Cell-Cycle Progression

| PRJNA214609 | ENA

Cbf11 Regulates Periodic Expression of Genes Required to Prevent Catastrophic Mitosis in the Fission Yeast Cell Cycle

Project description:The expression of a large proportion of the fission yeast genome changes periodically with the cell cycle. Several key transcription factors have been identified that regulate these oscillating and interdependent waves of gene expression. However, for a significant number of cell cycle-regulated genes the regulator(s) driving these oscillations remain unknown. Cbf11 and Cbf12, the fission yeast CSL transcription factors, have been implicated in the regulation of cell cycle progression, yet the details of their functioning are poorly understood. Using a combination of transcriptome profiling and genome-wide mapping of CSL-DNA interactions we have identified a comprehensive set of CSL-regulated genes. Our data indicate that Cbf11 and Cbf12 contribute directly and indirectly to the regulation of periodically expressed genes in fission yeast. We show that during S phase/cytokinesis Cbf11 directly activates the transcription of several periodic genes required in the cell to prevent catastrophic mitosis. In agreement with these findings, multiple aspects of cell cycle progression are perturbed when CSL cellular levels are genetically manipulated. We have identified Cbf11 as a novel cell cycle phase-specific activator of genes required for proper coordination of cell and nuclear division, and prevention of catastrophic mitosis in fission yeast.

2015-09-18 | E-MTAB-2724 | biostudies-arrayexpress

Cyclical macrophage plasticity provides periodic inflammatory and regenerative gene expression programs in cell cycle.

Project description:Cyclical macrophage plasticity provides periodic inflammatory and regenerative gene expression programs in cell cycle.

| PRJNA739496 | ENA

Cell cycle expression profiles in HeLa cells

Project description:Periodic expression of cell cycle genes highlights the importance of precise temporal control of transcription in regulating cell cycle events. We used HeLa cells enriched for different phases of the cell cycle to identify genes that are expressed in a periodic fashion in specific cell cycle phases. These data were generated for comparison with ChIP-Sequencing data obtained for two subunits of the B-Myb-MuvB complex, B-Myb and LIN9, in HeLa cells.

2012-01-25 | GSE26922 | GEO

Cyclical macrophage plasticity provides periodic inflammatory and regenerative gene expression programs in cell cycle [RNA-seq]

Project description:Cyclical macrophage plasticity provides periodic inflammatory and regenerative gene expression programs in cell cycle [RNA-seq]

| PRJNA739499 | ENA

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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