Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nucleotide pools dictate the identity and frequency of ribonucleotide incorporation in mitochondrial DNA

ABSTRACT: Previous work has demonstrated the presence of ribonucleotides in human mitochondrial DNA (mtDNA) and in the present study we use a genome-wide approach to precisely map the location of these. We find that ribonucleotides are distributed evenly between the heavy- and light-strand of mtDNA. The relative levels of incorporated ribonucleotides reflect that DNA polymerase γ discriminates the four ribonucleotides differentially during DNA synthesis. The observed pattern is also dependent on the mitochondrial deoxyribonucleotide (dNTP) pools and disease-causing mutations that change these pools alter both the absolute and relative levels of incorporated ribonucleotides. Our analyses strongly suggest that DNA polymerase γ-dependent incorporation is the main source of ribonucleotides in mtDNA and argues against the existence of a mitochondrial ribonucleotide excision repair pathway in human cells. Furthermore, we clearly demonstrate that when dNTP pools are limiting, ribonucleotides serve as a source of building blocks to maintain DNA replication and genome stability. Increased levels of embedded ribonucleotides in patient cells with disturbed nucleotide pools may constitute to a pathogenic mechanism that affects mtDNA stability and impair new rounds of mtDNA replication

ORGANISM(S): Homo sapiens

PROVIDER: GSE90054 | GEO | 2017/02/13

SECONDARY ACCESSION(S): PRJNA354396

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Ribonucleotides incorporated by the yeast mitochondrial DNA polymerase are not repaired

Project description:Misincorporation of ribonucleotides into DNA during genome replication has recently become recognized as a significant source of genomic instability. The frequency of ribonucleotides in the genome is determined by dNTP/rNTP ratios, the ability of the DNA polymerases to discriminate against ribonucleotides, and by the capacity of repair mechanisms to remove misincorporated ribonucleotides. To simultaneously compare how the nuclear and mitochondrial genomes incorporate and remove ribonucleotides, we challenged these processes by imbalancing cellular dNTP pools. Using a collection of yeast strains with altered dNTP pools, we discovered an inverse relationship between the concentration of individual dNTPs and the amount of the corresponding ribonucleotides incorporated in mitochondrial DNA, while in nuclear DNA the ribonucleotide pattern was only altered in the absence of ribonucleotide excision repair. Our analysis uncovers major differences in ribonucleotide repair between the two genomes and provides concrete evidence that yeast mitochondria lack mechanisms for repair of misincorporated ribonucleotides.

2017-11-07 | GSE100352 | GEO

Elimination of rNMPs from mitochondrial DNA has no effect on its stability

Project description:Ribonucleotides (rNMPs) incorporated in the nuclear genome are a well-established threat to genome stability and can result in DNA strand breaks when not removed in a timely manner. However, the presence of a certain level of rNMPs is tolerated in mitochondrial DNA (mtDNA), although aberrant mtDNA rNMP content has been identified in disease models. We investigated the effect of incorporated rNMPs on mtDNA stability over the mouse lifespan and found that the mtDNA rNMP content increased during early life. The rNMP content of mtDNA varied greatly across different tissues and was defined by the rNTP/dNTP ratio of the tissue. Accordingly, mtDNA rNMPs were nearly absent in SAMHD1−/− mice that have increased dNTP pools. The near absence of rNMPs did not, however, appreciably affect mtDNA copy number or the levels of mtDNA molecules with deletions or strand breaks in aged animals near the end of their lifespan. The physiological rNMP load therefore does not contribute to the progressive loss of mtDNA quality that occurs as mice age.

2020-05-25 | GSE133584 | GEO

Stably incorporated ribonucleotides in murine tissues: quantitation, base identity and distribution in nuclear and mitochondrial DNA

Project description:Ribonucleotides are estimated to be the most common non-canonical nucleotides transiently incorporated in DNA. Their presence or failure of their removal can affect genome stability and mutations in factors involved in dNTP pool maintenance or ribonucleotide removal can cause Aicardi-Goutières syndrome or promote certain human cancers. Here, we have mapped and quantitated ribonucleotides genome-wide, in nine tissues of wild-type mice. We observed tissue-specific variation in number and base identity of incorporated ribonucleotides and present evidence that a number of genomic features, such as tRNA genes, transcription start sites and G-quadruplexes, can increase the frequency of stably incorporated ribonucleotides in their proximity. Moreover, we present the non-random distribution of incorporated ribonucleotides in mtDNA and identified ribonucleotide hotpots. The study presents a framework to understand the physiological role of ribonucleotides in mammalian DNA.

2024-09-01 | GSE183589 | GEO

Aberrant ribonucleotide incorporation and multiple deletions in mitochondrial DNA of the murine MPV17 disease model [EmRibo-seq]

Project description:All DNA polymerases misincorporate ribonucleotides despite their preference for deoxyribonucleotides, and analysis of cultured cells indicates that mammalian mitochondrial DNA (mtDNA) tolerates such replication errors. However, it is not clear to what extent ribonucleotides are incorporated into the mtDNA of solid tissues, or whether they might play a role in human pathologies. Here, we show the DNA in mitochondria of solid tissues contains many more embedded ribonucleotides than that of cultured cells, consistent with the former’s high ratio of ribonucleotide to deoxynucleotide triphosphates and that rAMPs are the predominant ribosubstitution events. This pattern changes in a mouse model of Mpv17 deficiency, as rGMPs are the major embedded ribonucleotides of mtDNA. However, while mitochondrial dGTP is reduced in the liver of the KO mice, the brain shows no change in the overall dGTP pool, leading us to infer that Mpv17 determines the local concentration or quality of dGTP. Embedded rGMPs are expected to impede DNA replication more than other rNMPs, and elevated rGMP incorporation is associated with early-onset mtDNA depletion in liver and late-onset multiple deletions in brain of the Mpv17 ablated mice. These findings suggest that aberrant ribonucleotide incorporation is a primary mtDNA abnormality that can result in pathology.

2017-10-23 | GSE103429 | GEO

Disruption of deoxynucleotide biosynthesis leads to RASproto-oncogene activation and perturbation of mitochondrial metabolism [DNA-seq]

Project description:Perturbation of the deoxyribonucleotide triphosphate (dNTP) pool is recognized for contributing to the mutagenic processes involved in oncogenesis. The RAS gene family encodes well characterized oncoproteins whose structure and function are among the most frequently altered in several cancers. In this work, we show that fluctuation of the dNTP pool induces CG->TA mutations across the whole genome, including RAS gene at codons for glycine 12 and 13, known hotspots in cancers. Cell culture addition of the ribonucleotide reductase inhibitor thymidine increases the mutation frequency in nuclear DNA and leads to disruption of mitochondrial metabolism. Interestingly, this effect is counteracted by the addition of deoxycytidine. Finally, screening for the loss of hydrogen bonds detecting CG->TA transition in RAS gene of 135 patients with colorectal cancer confirmed the clinical relevance of this process. All together, these data demonstrate that fluctuation of intracellular dNTP pool alters the nuclear DNA and mitochondrial metabolism.

2024-10-02 | GSE261896 | GEO

Disruption of deoxynucleotide biosynthesis leads to RASproto-oncogene activation and perturbation of mitochondrial metabolism [RNA-seq]

2024-10-02 | GSE261895 | GEO

Saccharomyces cerevisiae

Project description:Ribonucleotides incorporated by the yeast mitochondrial DNA polymerase are not repaired

| PRJNA391428 | ENA

Genome-wide tracking of DNA polymerase III in E. coli

Project description:We used steric gate variants of DNA polymerase III that allows increased amounts of ribonucleotides to be incorporated. Ribonucleotides incorporated into genomic is hydrolyzed by alkali. The generated 5-ends are subsequently mapped.

2023-01-09 | GSE141315 | GEO

Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation

Project description:Multiple DNA polymerases are needed to replicate genetic information. Here we describe the use of ribonucleotide incorporation as a biomarker of replication enzymology in vivo. We find that ribonucleotides are incorporated into the yeast nuclear genome in replicase specific and strand-specific patterns that identify replication origins and where polymerase switching occurs. Ribonucleotide density varies across the genome as a function of the replicase, base, local sequence and proximity to nucleosomes and transcription start sites. Ribonucleotides are present in one strand at high densityat mitochondrial replication origins, implying unidirectional replication of a circular genome. The evolutionary conservation of the enzymes that incorporate and process ribonucleotides in DNA suggests that the use of ribonucleotides as biomarkers of DNA synthesis in cells will have widespread applicability. Mapping genomic ribonucleotides in 14 Saccharomyces cerevisiae strains (seven DNA polymerase backgrounds, with or without RNH201), via HydEn-seq (end sequencing of genomic fragments generated by alkaline hydrolysis).

2015-01-26 | E-GEOD-62181 | biostudies-arrayexpress

YME1L1 KnockOut MEF Cells Whole Proteomics

Project description:Cytosolic mitochondrial DNA (mtDNA) elicits a type I interferon response, but signals triggering the release of mtDNA from mitochondria remained enigmatic. We found that mtDNA-dependent immune signaling via the cGAS-STING pathway is under metabolic control and induced by cellular nucleotide deficiency. The mitochondrial protease YME1L preserves nucleotide pools by supporting de novo nucleotide synthesis and by proteolysis of the pyrimidine nucleotide carrier SLC25A33, limiting mitochondrial nucleotide import and accumulation of mtDNA. Deficiency of YME1L or the mitochondrial transcription factor A (TFAM) drives an mtDNA-dependent inflammatory response, which depends on SLC25A33 and is suppressed upon replenishment of cellular nucleotide pools. Metabolic insults that deplete cytosolic nucleotides trigger mtDNA-dependent immune responses. Our results thus identify mtDNA release and innate immune signaling as a metabolic response, offering new therapeutic opportunities in disease.

2021-04-27 | PXD018097 | Pride

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