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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

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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

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

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

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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.

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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

Murine hippocampal proteome - Phosphoproteome Profiling Reveals Circadian Clock Regulation of Posttranslational Modifications in the Murine Hippocampus

Project description:The circadian clock is an endogenous oscillator that drives daily rhythms in physiology, behavior and gene expression. The underlying mechanisms of circadian timekeeping are cell-autonomous and involve interconnecting transcription-translation feedback loops. The hippocampus plays an important role in spatial memory and the conversion of short-term to long-term memory. Several studies have reported the presence of a peripheral oscillator in the hippocampus, and have highlighted the importance of circadian regulation in memory formation. In this study we performed global quantitative proteome and phosphoproteome analyses of the murine hippocampus across the circadian cycle, applying spiked-in labeled reference and high accuracy mass spectrometry.

2017-04-11 | PXD005668 | Pride

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