Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Sexual differentiation controlled by RNA polymerase II CTD phosphorylation on serine 2

ABSTRACT: The switch from cellular proliferation to differentiation occurs to a large extend through specific programs of gene expression. In fission yeast, the high-mobility-group transcription factor Ste11 is the master regulator of sexual differentiation. ste11 is induced by environmental conditions, mostly nitrogen starvation, leading to mating and meiosis 1. We have used ChIP-chip and gene expression profiling to show that CDK-dependent phosphorylation of serine 2 in the C-terminal domain (CTD) of the largest subunit of the RNA polymerase II (PolII) holoenzyme plays a critical role in the induction of ste11 transcription during sexual differentiation while it has a minor impact on gene expression during vegetative growth. Moreover, we demonstrate that both the recruitment of the CTD serine 2 kinase and the phosphorylation event initiate at the promoter region of ste11 in contrast to the classical case where serine 2 phosphorylation occurs across the coding region 2. In the absence of CTD serine 2 phosphorylation, both PolII occupancy at the ste11 locus, and ste11 expression are impaired. This results in sterility that is rescued when ste11 is expressed from the canonical adh promoter. We conclude that a modification of the RNA polymerase II holoenzyme plays a specific and pivotal role in the sexual differentiation. For the ChIP-chip experiments, 3-4 biological replicates were performed for each tagged protein of interest. For the expression experiments, two biological samples were hybridized for each mutant strain (replicates 1 and 2), with two dye-swap technical replicates per sample (replicates 3 and 4).

ORGANISM(S): Schizosaccharomyces pombe

SUBMITTER: Harm Bakel

PROVIDER: E-GEOD-16498 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:This study was designed to investigate the modulation of GBE on cellular cholesterol metabolism which has been suggested in recent studies. To explore the molecular mechanisms gain insights into the molecular network, we used microarray to high-throughput measurement of genes concerning both spatial and temporal levels to understand the complexity and dynamics of cells in response to GBE and Lovastatin, the genes expression pattern were similar between GBE and Lovastatin treatment in HepG2 cells, the major changed genes were involved in biosynthesis of steroids and cell cycle. Cholesterol metabolism related genes were further examined by RT-PCR and western blot, showing that the cholesterogenic genes were upregulated in response to the reduction of cholesterol and were consistent with the microarray findings. Keywords: time course HepG2 cells were maintained in Minimum Essential Medium supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37°C. For experiments, cells were seeded in 6-well plates at a density of 4×105 cells per well, when the cells were grown into a 70 % confluence, the medium was replaced with 2%FBS medium for later drug treatment, cells were incubated with 200μg/mL of GBE or 0.5μM Lovastatin for various time periods (2, 6, 12, 24hours). The control groups were treated with 0.1% DMSO that contained in drug as vehicle at most time point. The cells were collected and RNA were used for transcript profiling analysis. Label protocol:Total RNA were primed with T7 Promoter Primer (from the Agilent Low RNA Input Linear Amplification Kit PLUS, Two-Color) at 65 ℃ for 10 min, then reversed transcribed at 40℃ for 2 h in the presence of 1ul MMLV-RT (Agilent), and 10 mM dNTP, and RNase OUT (Agilent) and labeled with either Cy3-dCTP or Cy5-dCTP. Equal amounts of the RNA from control sample were mixed, and the mixture was labeled with Cy5, while the RNA from each GBE treated HepG2 cells was labeled with Cy3. Hybridization protocol: After mixed with hybridization buffer(GE healthcare), samples were applied to microarray slide, cover the slip with care. Place the slide in a wet box.Incubate in a hybridization chamber at 42℃ for 16-18 hours, avoid light exposure. After hybridization, slides were washed sequentially with 1 SSC/0.2 SDS(50°C), 0.1 SSC/0.2%SDS(50°C) and 0.1 SSC(room temperature) before scanning. Scan protocol: Axon GenePix 4000B Description: Total RNA was prepared by using TRIzol reagent (Life Technologies, USA), further purified with an RNEasy column (Qiagen, Germany), and quantified by using gel electrophoresis and spectrophotometer followed by reverse transcription labeling. Each RNA sample was reverse-transcribed into cDNA primed with oligo(dT) and labeled with either Cy3-dCTP or Cy5-dCTP by using Superscript II reverse transcriptase (Life Technologies, USA). After hybridization under a standard protocol, data acquisition was performed by using a laser scanner (Agilent, USA), and the image data were analyzed using ImaGene 4.2 (Biodiscovery, Santa Monica, CA, USA). Data processing: LOWESS normalized, background subtracted VALUE data obtained from log of processed Red signal/processed Green signal.

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Sexual differentiation controlled by RNA polymerase II CTD phosphorylation on serine 2

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