Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ribonucleotides in DNA

ABSTRACT: We report here the consequences of loss of Saccharomyces cerevisiae RNase H2 by comparing mRNA expression profiles in wild type yeast versus a strain lacking the RNH201 gene, encoding the catalytic subunit. Deleting RHN201 alters mRNA expression for hundreds of genes. Expression changes were based on seven biological replicates (3 from one batch and 4 from another batch) and are seen for many genes involved in stress responses and genome maintenance, consistent with a role of RNase H2 in removing ribonucleotides incorporated into DNA during replication. Differentially expressed genes include, those involved in ribosomal RNA processing and biogenesis and in tRNA modification, supports a role for RNase H2 in resolving R-loops formed during transcription of rRNA and tRNA. Other differentially expresses genes include putative or known helicases and nucleases maintenance of dsRNA viruses, which could be relevant to how mammalian RNase H2 dysfunction elicits an innate immune response leading to neurodegeneration.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE34668 | GEO | 2012/12/20

SECONDARY ACCESSION(S): PRJNA151217

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Ribonucleotides in DNA

Project description:We report here the consequences of loss of Saccharomyces cerevisiae RNase H2 by comparing mRNA expression profiles in wild type yeast versus a strain lacking the RNH201 gene, encoding the catalytic subunit. Deleting RHN201 alters mRNA expression for hundreds of genes. Expression changes were based on seven biological replicates (3 from one batch and 4 from another batch) and are seen for many genes involved in stress responses and genome maintenance, consistent with a role of RNase H2 in removing ribonucleotides incorporated into DNA during replication. Differentially expressed genes include, those involved in ribosomal RNA processing and biogenesis and in tRNA modification, supports a role for RNase H2 in resolving R-loops formed during transcription of rRNA and tRNA. Other differentially expresses genes include putative or known helicases and nucleases maintenance of dsRNA viruses, which could be relevant to how mammalian RNase H2 dysfunction elicits an innate immune response leading to neurodegeneration. We examine the consequences of loss of Saccharomyces cerevisiae RNase H2 by comparing mRNA expression profiles in wild type yeast versus a strain lacking the RNH201 gene encoding the catalytic subunit. Expression changes were based on seven biological replicates (3 from one batch and 4 from another batch). For strain reference please see S.A. Nick McElhinny, et al, Genome instability due to ribonucleotide incorporation into DNA, Nat Chem Bio 6, 774-781 (2010).

2012-12-20 | E-GEOD-34668 | biostudies-arrayexpress

Ribodysgenesis: sudden genome instability in the yeast Saccharomyces cerevisiae arising from RNase H2 cleavage at genomic-embedded ribonucleotides

Project description:Yeast Saccharomyces cerevisiae has been widely used as a model system for studying genome instability. Here, heterozygous S. cerevisiae zygotes were generated to determine the genomic alterations induced by sudden introduction of active RNase H2. In combination of a custom SNP microarray, the patterns of chromosomal instability could be explored at a whole genome level. Ribonucleotides can be incorporated into DNA during replication by the replicative DNA polymerases. These aberrant DNA subunits are efficiently recognized and removed by Ribonucleotide Excision Repair, which is initiated by the heterotrimeric enzyme RNase H2. While RNase H2 is essential in higher eukaryotes, the yeast Saccharomyces cerevisiae can survive without RNase H2 enzyme, although the genome undergoes mutation, recombination and other genome instability events at an increased rate. Although RNase H2 can be considered as a protector of the genome from the deleterious events that can ensue from recognition and removal of embedded ribonucleotides, under conditions of high ribonucleotide incorporation and retention in the genome in a RNase H2-negative strain, sudden introduction of active RNase H2 causes massive DNA breaks and genome instability in a condition which we term “ribodysgenesis”. The DNA breaks and genome instability arise solely from RNase H2 cleavage directed to the ribonucleotide-containing genome. Survivors of ribodysgenesis have massive loss of heterozygosity events stemming from recombinogenic lesions on the ribonucleotide-containing DNA, with increases of over 1000X from wild-type. DNA breaks are produced over one to two divisions and subsequently cells adapt to RNase H2 and ribonucleotides in the genome and grow with normal levels of genome instability.

2022-03-26 | GSE199262 | GEO

Global mapping of ribonucleotides embedded in DNA

Project description:Capture and massively parallel DNA sequencing of ribonucleotides embedded in S. cerevisiae genomic DNA We developed a new method to map the positions of ribonucleotides embedded in DNA using the unique specificity of A. thaliana tRNA ligase. Ribonucleotides were generated in budding yeasts of different genetic backgrounds and mapped to single nucleotide resolution using the new method.

2015-01-15 | E-GEOD-61464 | biostudies-arrayexpress

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

Ribodysgenesis: sudden genome instability in the yeast Saccharomyces cerevisiae arising from RNase H2 cleavage at genomic-embedded ribonucleotides

Project description:Ribodysgenesis: sudden genome instability in the yeast Saccharomyces cerevisiae arising from RNase H2 cleavage at genomic-embedded ribonucleotides

| PRJNA819077 | ENA

Genome wide maps of replicative polymerase contributions to the fully replicated yeast genome

Project description:We report the application of high through-put tag sequencing to measure the location and strand of DNA embedded ribonucleotides in the yeast genome. Mutations in the catalytic subunits of the polymerases (pol1-L868M, pol2-M644G and pol3-L612M) lead to the increased incorporation of ribonucleotides during DNA replication, providing an in vivo label with which to track the contribution of each polymerase to the fully replicated genome. Yeast strains used in this study are deleted for rnh201, encoding the catalytic subunit of the RNase H2 gene so that embedded ribonucleotides are not rapidly removed by ribonucleotide excision repair following DNA replication. Analysis of this data demonstrates that polymerase alpha contributes to the fully replicated genome. Sequencing of DNA embedded ribonucleotides in S. cerevisiae strains to map the contribution of replicative polymerases to the fully replicated genome.

2015-01-26 | E-GEOD-64521 | biostudies-arrayexpress

Genome wide maps of replicative polymerase contributions to the fully replicated yeast genome

2015-01-26 | GSE64521 | GEO

Ribonucleotide excision repair is essential to prevent skin cancer [CD45+ CD49f- epidermal cells]

Project description:Large numbers of ribonucleotides are incorporated into the eukaryotic nuclear genome during S-phase due to imperfect discrimination against ribonucleoside triphosphates by the replicative DNA polymerases. Ribonucleotides, by far the most common DNA lesion in replicating cells, destabilize the DNA, and an evolutionarily conserved DNA repair machinery, ribonucleotide excision repair (RER), ensures ribonucleotide removal. Complete lack of RER is embryonically lethal. Partial loss-of-function mutations in the genes encoding subunits of RNase H2, the enzyme essential for initiation of RER, cause the SLE-related type I interferonopathy Aicardi-Goutières syndrome. Here we establish that selective inactivation of RER in mouse epidermis results in spontaneous DNA damage, epidermal hyperproliferation associated with loss of hair follicle stem cells and hair follicle function. The animals develop keratinocyte intraepithelial neoplasia and invasive squamous cell carcinoma with complete penetrance, despite potent type I interferon production and skin inflammation. Compromised RER-mediated genome maintenance might represent an important tumor-promoting principle in human cancer.

2019-05-29 | GSE115004 | GEO

Ribonucleotide excision repair is essential to prevent skin cancer [CD49f+ epidermal cells]

2019-05-29 | GSE115003 | GEO

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

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