Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The Saccharomyces cerevisiae genome is highly connected by inter- and intra- chromosomal interactions

ABSTRACT: Nuclear and mitochondrial organelles must maintain a communication system. Loci on the mitochondrial genome were recently reported to interact with nuclear loci. To determine whether this is part of a DNA based communication system we used genome conformation capture to map the global network of DNA-DNA interactions between the mitochondrial and nuclear genomes (Mito-nDNA) in Saccharomyces cerevisiae cells grown under three different metabolic conditions. The interactions that form between mitochondrial and nuclear loci are dependent on the metabolic state of the yeast. Moreover, the frequency of specific mitochondrial - nuclear interactions (i.e. COX1-MSY1 and Q0182-RSM7) showed significant reductions in the absence of mitochondrial encoded reverse transcriptase machinery. Furthermore, these reductions correlated with increases in the transcript levels of the nuclear loci (MSY1 and RSM7). We propose that these interactions represent an inter-organelle DNA mediated communication system and that reverse transcription of mitochondrial RNA plays a role in this process.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE33073 | GEO | 2013/01/17

SECONDARY ACCESSION(S): PRJNA156573

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Mitochondrial-nuclear DNA interactions contribute to the regulation of nuclear transcript levels as part of the inter-organelle communication system

Project description:Nuclear and mitochondrial organelles must maintain a communication system. Loci on the mitochondrial genome were recently reported to interact with nuclear loci. To determine whether this is part of a DNA based communication system we used genome conformation capture to map the global network of DNA-DNA interactions between the mitochondrial and nuclear genomes (Mito-nDNA) in Saccharomyces cerevisiae cells grown under three different metabolic conditions. The interactions that form between mitochondrial and nuclear loci are dependent on the metabolic state of the yeast. Moreover, the frequency of specific mitochondrial - nuclear interactions (i.e. COX1-MSY1 and Q0182-RSM7) showed significant reductions in the absence of mitochondrial encoded reverse transcriptase machinery. Furthermore, these reductions correlated with increases in the transcript levels of the nuclear loci (MSY1 and RSM7). We propose that these interactions represent an inter-organelle DNA mediated communication system and that reverse transcription of mitochondrial RNA plays a role in this process. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series.

2013-01-17 | E-GEOD-34132 | biostudies-arrayexpress

The Saccharomyces cerevisiae genome is highly connected by inter- and intra- chromosomal interactions

Project description:Nuclear and mitochondrial organelles must maintain a communication system. Loci on the mitochondrial genome were recently reported to interact with nuclear loci. To determine whether this is part of a DNA based communication system we used genome conformation capture to map the global network of DNA-DNA interactions between the mitochondrial and nuclear genomes (Mito-nDNA) in Saccharomyces cerevisiae cells grown under three different metabolic conditions. The interactions that form between mitochondrial and nuclear loci are dependent on the metabolic state of the yeast. Moreover, the frequency of specific mitochondrial - nuclear interactions (i.e. COX1-MSY1 and Q0182-RSM7) showed significant reductions in the absence of mitochondrial encoded reverse transcriptase machinery. Furthermore, these reductions correlated with increases in the transcript levels of the nuclear loci (MSY1 and RSM7). We propose that these interactions represent an inter-organelle DNA mediated communication system and that reverse transcription of mitochondrial RNA plays a role in this process. Genome Conformation Capture (GCC) has been performed on exponentially growing Saccharomyces cerevisiae cultures in glucose containing media. Paired end sequencing on an Illumina Genome Analyser was performed before the sequences were analysed by the propieatry software Topography 1.19. Inter- and intra- chromosomal interactions were mapped onto the S. cerevisiae S288 genome scaffold.

2013-01-17 | E-GEOD-33073 | biostudies-arrayexpress

Inter- and intra- chromosomal interactions change on a global scale according to the metabolic regime employed by Saccharomyces cerevisiae

Project description:Nuclear and mitochondrial organelles must maintain a communication system. Loci on the mitochondrial genome were recently reported to interact with nuclear loci. To determine whether this is part of a DNA based communication system we used genome conformation capture to map the global network of DNA-DNA interactions between the mitochondrial and nuclear genomes (Mito-nDNA) in Saccharomyces cerevisiae cells grown under three different metabolic conditions. The interactions that form between mitochondrial and nuclear loci are dependent on the metabolic state of the yeast. Moreover, the frequency of specific mitochondrial - nuclear interactions (i.e. COX1-MSY1 and Q0182-RSM7) showed significant reductions in the absence of mitochondrial encoded reverse transcriptase machinery. Furthermore, these reductions correlated with increases in the transcript levels of the nuclear loci (MSY1 and RSM7). We propose that these interactions represent an inter-organelle DNA mediated communication system and that reverse transcription of mitochondrial RNA plays a role in this process. Genome Conformation Capture (GCC) has been performed on exponentially growing Saccharomyces cerevisiae cultures in glycerol lactate or galactose media. Paired end sequencing on an Illumina Genome Analyser was performed before the sequences were analysed by the propieatry software Topography 1.19. Inter- and intra- chromosomal interactions were mapped onto the S. cerevisiae S288 genome scaffold.

2013-01-17 | E-GEOD-33074 | biostudies-arrayexpress

Inter- and intra- chromosomal interactions change on a global scale according to the metabolic regime employed by Saccharomyces cerevisiae

2013-01-17 | GSE33074 | GEO

Mitochondrial-nuclear DNA interactions contribute to the regulation of nuclear transcript levels as part of the inter-organelle communication system

2013-01-17 | GSE34132 | GEO

Interactions between mitochondrial and nuclear DNA in mammalian cells are non-random

Project description:There is evidence for the on-going recurrent transfer of mitochondrial DNA (mtDNA) into the nucleus in both germ line and somatic cells. However, the outcomes associated with the transfer of mtDNA into somatic cell nuclei are poorly understood. High-resolution Chromosome Conformation Capture (HiC) techniques, which are used to identify global patterns of chromatin interactions, regularly capture physical interactions between mitochondrial and nuclear DNA (i.e. mito-nDNA interactions) in mammalian cells. These mito-nDNA interactions are routinely considered a consequence of nonspecific ligation events during chromatin library preparation. Here, we have evaluated mito-nDNA interactions captured by HiC in six human cell lines, and by Circular Chromosome Conformation Capture (4C) in mouse cortical astrocytes. We show that mito-nDNA interactions are statistically significant and shared between biological and technical replicates in the HiC and 4C experiments. The most frequent interactions between mtDNA and nuclear loci in the HiC and 4C data occur with repetitive DNA sequences including the centromeric regions in the six human cell lines and 18S rDNA in mouse cortical astrocytes. Such findings confirm previous observations of mtDNA forming interactions with rDNA genes in budding yeast and centomeres in rat bone marrow cells. Finally the mitochondrial D-loop tends to be enriched in the captured mito-nDNA interactions. Collectively our results imply a degree of selective regulation in the identity of the interacting mitochondrial partners confirming that mito-nDNA interactions in mammalian cells are not random.

2017-11-21 | GSE77610 | GEO

Mitochondrial-nuclear DNA interactions contribute to the regulation of nuclear transcript levels as part of the inter-organelle communication system

Project description:Mitochondrial-nuclear DNA interactions contribute to the regulation of nuclear transcript levels as part of the inter-organelle communication system

| PRJNA149849 | ENA

Transcription profiling of human cells to the absence of mitochondrial DNA

Project description:Mitochondrial biogenesis is under the control of two different genetic systems: the nuclear genome (nDNA) and the mitochondrial genome (mtDNA). mtDNA is a circular genome of 16.6 kb encoding 13 of the approximately 90 subunits that form the respiratory chain, the remaining ones being encoded by the nuclear genome (nDNA). Eukaryotic cells are able to monitor and respond to changes in mitochondrial function through alterations in nuclear gene expression, a phenomenon first defined in yeast and known as retrograde regulation. With this experiment we aimed to identify the set of nuclear genes that significantly change their expression level in response to depletion of mtDNA. Experiment Overall Design: We used Affymetrix HG-U133A GeneChips to study the transcriptome of two human cell lines, 143BTK- and A549, which had been entirely depleted of mtDNA (rho0 cells), and compared it with the corresponding undepleted parental cells (rho+ cells). Three independent biological replicates were analyzed for each cell line and treatment group.

2009-05-11 | E-GEOD-14900 | biostudies-arrayexpress

Transcriptional response of human cells to the absence of mitochondrial DNA

2009-05-01 | GSE14900 | GEO

Targeted down regulation of core mitochondrial genes during SARS-CoV-2 infection

Project description:SARS-CoV-2 polypeptides bind mitochondrial proteins, and the virus inhibits oxidative phosphorylation (OXPHOS) nuclear DNA (nDNA) gene transcription by blocking coordinately expressed genes of modular components of the OXPHOS holoenzymes. While initial nasopharyngeal infection is associated with the down regulation of OXPHOS genes, at death lung OXPHOS is up regulated. By contrast, heart, kidney, and liver nDNA gene expression remains suppressed, likely contributing to mortality. The virus also induces miR-2392 which inhibits mitochondrial DNA (mtDNA) transcription and the translation of mitochondrial cytosolic mRNAs. This concerted inhibition of OXPHOS activates HIF-1α inducing a pseudo-hypoxic state favoring viral biogenesis. We interrogated the effects of SARS-CoV-2 infection by infecting BALB/c and C57BL/6 mice with the mouse-adapted SARS-CoV-2 MA10 virus and analyzed their lung transcripts at day 4 post infection.

2022-12-27 | GSE221510 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data