Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Characterization of peroxisome-associated transcriptome

ABSTRACT: This is a pioneer genome-wide study of localization of mRNAs to peroxisomes. The findings suggest that translation of a subset of peroxiomal proteins and other cellular metabolic enzymes may be spatially regulated by directing their encoding mRNAs to the surface of peroxisomes. The study provides foundation for more detailed dissection of mechanisms of RNA targeting to subcellular compartments. In this study we performed the genome-wide transcriptome analysis of peroxisome preparations from the mouse liver using microarrays. We demonstrate that RNA is absent inside peroxisomes, however it is associated at their exterior via the noncovalent contacts with the membrane proteins. We detect enrichment of specific sets of transcripts in two preparations of peroxisomes, purified with different degrees of stringency. Importantly, among these were mRNAs encoding bona fide peroxisomal proteins, such as peroxins and peroxisomal matrix enzymes involved in beta-oxidation of fatty acids and bile acid biosynthesis. Two subcellular fractions were obtained from the mouse liver by centrifugation in iodixanol density gradient: 1) Peroxisomal (PX), 2) Mitochondrial/Lysosomal (ML). The membrane-enclosed peroxisomal fraction (PX-IP) was obtained by immuno-precispitation of the PX fraction with the PMP70-specific antibodies. RNA was extracted from each fraction. Additionally, the total cellular RNA was obtained from the whole cell extracts (T). Thus, four RNA sample types were obtained for gene expression analysis: T, ML, PX, PI. Three technical replicates of each sample ware analyzed with Illumina microarrays.

ORGANISM(S): Mus musculus

SUBMITTER: Arsen Batagov

PROVIDER: E-GEOD-84972 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:FOXO transcription factors control cellular formation of reactive oxygen species (ROS), which critically contribute to cell survival and cell death in neuroblastoma. Here, we report that C10orf10, also named M-bM-^@M-^\Decidual Protein induced by Progesterone (DEPP)M-bM-^@M-^], is a direct transcriptional target of FOXO3 in human neuroblastoma. As FOXO3-mediated apoptosis involves a biphasic ROS accumulation, we analyzed cellular ROS levels in DEPP-knockdown cells by live-cell imaging. Knockdown of DEPP prevented the primary and secondary ROS accumulation during FOXO3 activation and attenuates FOXO3-induced apoptosis, whereas its overexpression raises cellular ROS levels and sensitizes to cell death. In neuronal cells, cellular steady state ROS are mainly detoxified in peroxisomes by the enzyme CAT/catalase. As DEPP contains a peroxisomal-targeting-signal-type-2 (PTS2) sequence at its N-terminus that enables protein import into peroxisomes, we analyzed the effect of DEPP on peroxisomal function by measuring the catalase enzyme activity. Catalase activity was reduced by conditional DEPP overexpression and significantly increased in DEPP-knockdown cells. Using live cell imaging and fluorescent peroxisomal and mitochondrial probes we demonstrate that DEPP localizes to peroxisomes and mitochondria in neuroblastoma cells. The combined data indicate that DEPP reduces peroxisomal activity and thereby impairs the cellular ROS detoxification capacity and contributes to death sensitization. SH-EP, NB15 neuroblastoma cells and CCRF-CEM-C7H2 acute lymphoblastic leukemia cells were infected with the retrovirus plasmid pLIB-FOXO3(A3)-Ertm-iresNeo. Gene expression measures of samples with activated FOXO3 transcription factor (3h OHT treated) have been compared to untreated samples (0h time point). To rule out gene regulations by estrogen samples treated for 3 hours with tamoxifen have been compared to the untreated samples. Only genes that were more than two-fold regulated in the first, but not in the second comparison were defined to be FOXO3 regulated.

Dataset Information

Characterization of peroxisome-associated transcriptome

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure