Dataset Information

Extracellular phosphate alters cementoblast gene expression.

ABSTRACT: Genetic data from humans and mice reveal that the formation of cementum is sensitive to intra- and extracellular phosphate/pyrophosphate distribution. The intracellular molecular pathways whereby altered levels of extracellular phosphate concentration may affect cementum formation have not been elucidated. To initiate inquiry, we have studied the temporal effects of extracellular phosphate on global patterns of gene expression in a line of immortalized mouse cementoblasts. Total RNA from cultured cementoblasts treated with 5 mM inorganic phosphate over a designated time period, from 1-48 hrs, was analyzed for global patterns of gene expression by means of DNA microarrays representing the complete mouse genome. Analyses of significant hybridization signals indicated that 5 mM extracellular phosphate alters the expression of genes comprising several gene ontology (GO) groups, including transcription factor activity and Wnt signaling.

SUBMITTER: Rutherford RB

PROVIDER: S-EPMC2266827 | biostudies-literature | 2006 Jun

REPOSITORIES: biostudies-literature

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Extracellular phosphate alters cementoblast gene expression.

Rutherford R B RB Foster B L BL Bammler T T Beyer R P RP Sato S S Somerman M J MJ

Journal of dental research 20060601 6

Genetic data from humans and mice reveal that the formation of cementum is sensitive to intra- and extracellular phosphate/pyrophosphate distribution. The intracellular molecular pathways whereby altered levels of extracellular phosphate concentration may affect cementum formation have not been elucidated. To initiate inquiry, we have studied the temporal effects of extracellular phosphate on global patterns of gene expression in a line of immortalized mouse cementoblasts. Total RNA from culture ...[more]

PMID: 16723645

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Project description:Purpose:This study was aimed to profile the transcriptome changes of Toxoplasma after loss of phosphate transporters. For this purpose, phosphate transporter TgPiT and TgPT2 mutants were constructed by using direct knockout or conditional knockdown methods in RH or TATi parasite strain, respectively. The transcriptome changes were captured by RNA-seq analyses. Methods: Transcriptomic profiles of mutants (Δpit and iKD-PT2+ATc, respectively) and controls (RH and iKD-PT2-ATc,respectively) were generated by deep sequencing, in triplicate, using Illumina HiSeq xten. The sequence reads that passed quality filters were analyzed at the transcript level with TopHat (v2.1.1) followed by RSEM (v1.3.3). The differential expression genes were identified by DESeq2 (v1.24.0) analyses (mutant samples versus control samples). Results: Using an optimized data analysis workflow, More than 30 million paired-end reads were generated for each sample and about 90% of the clean reads were mapped to GT1 reference genome. RNA-seq data indicated deletion of TgPiT caused modest transcriptome changes in Toxoplasma. Within the 61 DEGs, several genes are typically increased during transition from tachyzoites to bradyzoites, were upregulated in the Δpit mutant, thus suggest stress response in Toxoplasma due to inactivation of TgPiT. While more than 900 genes (fold change ≥2 and adjusted p value <0.05) were significantly regulated in TgPT2 knockdown mutant. Enrichment of the differentially expressed genes using cluster of orthologous group indicate that these DEGs were enriched in pathways like genetic information processing (such as protein translation, transcription, RNA processing and modification, DNA replication and repair, chromatin structure regulation), nutrient transport and metabolism, signal transduction, intracellular trafficking, protein secretion and vesicular transport etc. 24 of 61 DEGs in Δpit strain were also found in DEGs of TgPT2 deficient parasites. The similar gene expression changes caused by inactivation of TgPiT and TgPT2 suggest that the two proteins have overlapping functions. Conclusions: Our study revealed the transcriptome changes in Toxoplasma due to phosphate transporters deficiency with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here provide the overall transcripts changes in TgPiT and TgPT2 defect strains, respectively. The results showed the unique and overlapping impacts of TgPiT and TgPT2 on Toxoplasma. These widen our understanding of phosphate requirements and potential transport pathway in Toxoplasma.

Dataset Information

Extracellular phosphate alters cementoblast gene expression.

Publications

Extracellular phosphate alters cementoblast gene expression.

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