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Effects of purine de novo synthesis knockdown on gene expression in Drosophila melanogaster S2 tissue culture cells

ABSTRACT: The effect of inhibiting expression of the ade2 gene by RNA interference in Drosophila S2 tissue culture cells was examined.

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE24123 | GEO | 2010/12/01

SECONDARY ACCESSION(S): PRJNA130063

REPOSITORIES: GEO

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Effects of purine de novo synthesis knockdown on gene expression in Drosophila melanogaster S2 tissue culture cells

Project description:The effect of inhibiting expression of the ade2 gene by RNA interference in Drosophila S2 tissue culture cells was examined. S2 cells underwnt three different dsRNA treatments. Two were for non-overlapping sequences of ade2 transcripts and the third was for a non-specific Chlamydomonas reinhardtii lhcb sequence. 3 samples from ade2 dsRNA-1 treated cells, 2 samples from ade2 dsRNA-2, and 3 samples from lhcb dsRNA treated cells were used on two 4x44K format slides (G2519F).

2010-12-01 | E-GEOD-24123 | biostudies-arrayexpress

Pathway engineered enzymatic de novo purine nucleotide synthesis.

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De Novo Purine Synthesis Mediates Circadian Control of Cell Cycle in Zebrafish

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-10-01 | E-GEOD-51279 | biostudies-arrayexpress

Human de novo purine biosynthesis.

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De Novo Purine Synthesis Mediates Circadian Control of Cell Cycle in Zebrafish (HTS)

Project description:Inosine 5'-phosphate dehydrogenase (impdh) has been well known as a key enzyme in GTP biosynthesis pathway. We found that three isoforms of impdh in zebrafish, namely impdh1a, impdh1b and impdh2, all show robust circadian expression.To examine the molecular functions of three impdh isoforms in zebrafish on the genome scale, we measured the global expression changes of impdh1a, impdh1b and impdh2 morpholino injected larvae (morphants) respectively using RNA-seq. Wild type (WT), control and three impdh morphants were collected at 32 hpf. In our RNA-seq result, we identified 468, 331 and 1166 significant genes affected by impdh1a, impdh1b and impdh2 morpholino (MO) knock-down respectively. Among them, there are limited overlaps between genes affected by different MOs and only 36 genes in common among all three MOs. This indicates that the three impdh isoforms have distinct molecular functions. To knock down the target genes, three impdh MOs and control MO were pressure-injected into 1- to 2-cell stage embryos. WT, control and three impdh morphants were raised at 28Â°C under 14h: 10h light/dark cycle from birth and sampled simultaneously at 32 hpf. Each group has at least 40 embryos.

2013-10-01 | E-GEOD-51278 | biostudies-arrayexpress

De Novo Purine Synthesis Mediates Circadian Control of Cell Cycle in Zebrafish (array)

Project description:Cell cycle and metabolism are two major outputs controlled by circadian rhythm in many organisms. Here we show that the three processes were linked through inosine 5'-phosphate dehydrogenase (impdh), a rate-limiting enzyme in de novo purine synthesis. We using adult zebrafish as a model system,we applied a genome-wide transcriptome approach that allowed us to investigate circadian gene expression. The whole-genome transcriptome profiles of adult brain in time-series were assayed on Agilent zebrafish microarrays. We used a similar statistical method to identify zebrafish circadian genes (ZCOG) as our previous study in larval zebrafish. Three isoforms of impdh show strong circadian oscillations in different tissues of zebrafish. impdh1a contributes to the ocular development and pigment synthesis, impdh2 promotes and impdh1b delays the development. By limiting the GTP required by DNA synthesis, impdh2 contributes to the daily rhythm of S phase in cell cycle. Multiple enzymes in the de novo purine synthesis pathway show the same circadian oscillations with peaks similar to impdh2. The circadian expression of this pathway is conserved in mouse liver. In summary, we show that the circadian regulation of de novo purine synthesis that supplies crucial building blocks for DNA replication is critical for gating cell cycle in circadian rhythm. Adult zebrafish were sacrificed and dissected at 4h intervals starting at CT0 in both LD and DD conditions for 12 time points. Total RNA of individual zebrafish brain was extracted using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturerM-bM-^@M-^Ys instruction. Microarrays were manufactured by Agilent Technologies (Agilent Technologies, Palo Alto, CA), containing 43,603 probes for zebrafish whole-genome transcriptional profiling.

2013-10-01 | E-GEOD-51277 | biostudies-arrayexpress

De Novo Purine Synthesis Mediates Circadian Control of Cell Cycle in Zebrafish

Project description:This SuperSeries is composed of the SubSeries listed below.

2013-10-01 | GSE51279 | GEO

Folate depletion induces erythroid differentiation through perturbation of de novo purine synthesis

Project description:Folate, an essential vitamin, is a one-carbon acceptor and donor in key metabolic reactions. Erythroid cells harbor a unique sensitivity to folate deprivation, as revealed by the primary pathological manifestation of nutritional folate deprivation: megaloblastic anemia. To study this metabolic sensitivity, we applied mild folate depletion to human and mouse erythroid cell lines, and primary murine erythroid progenitors. We show that folate depletion induces early blockade of purine synthesis and accumulation of the purine synthesis intermediate and signaling molecule, AICAR, followed by enhanced heme metabolism, hemoglobin synthesis, and erythroid differentiation. This is phenocopied by inhibition of folate metabolism using the SHMT1/2 inhibitor - SHIN1, and by AICAR supplementation. Mechanistically, the metabolically-driven differentiation is independent of nucleotide sensing through mTORC1 and AMPK, and is instead mediated by protein kinase C (PKC). Our findings suggest that folate deprivation-induced premature differentiation of erythroid progenitor cells is a molecular etiology to folate-deficiency induced anemia.

2024-02-07 | GSE245011 | GEO

The Drosophila melanogaster ade5 gene encodes a bifunctional enzyme for two steps in the de novo purine synthesis pathway.

Project description: Not available

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The distribution of Brahma in the genome of Drosophila melanogaster S2 cells and the roles of Brahma in transcription and pre-mRNA processing

Project description:We have carried out ChIP-seq to study the distribution of Brahma in the genome of S2 cells and to identify the Brahma-bound genes. We have also knocked down Brahma by RNA interference and we have carried out RNA-seq to determine the changes induced by Brahma depletion in the transcriptome of S2 cells. Furthermore, we have carried out RNA-seq experiments to profile S2 cells in which we first deplete Brahma by RNA interference and then express recombinant Brahma (either wild-type or ATPase mutant). These datasets are being used in several projects aimed at gaining understanding on the roles of Brahma in transcription regulation and pre-mRNA processing.

2018-05-11 | GSE95236 | GEO

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