Expression data from Saccharomyces cerevisiae with Rnase H overexpression
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae Schizosaccharomyces pombe
PROVIDER: GSE46652 | GEO | 2013/09/01
SECONDARY ACCESSION(S): PRJNA201411
REPOSITORIES: GEO
Similar Datasets
Project description:Transcripts up- or down-regulated comparing a strain where Rnase H is ectopically overexpressed versus wild type (empty vector); assessing the effect of DNA:RNA hybrid degradation on the transcriptome. Strains harboring the RNase H1 over-expression plasmid (p425-GPD-RNase H1) or control plasmid (p425-GPD) were grown in SC-Leucine at 30M-BM-0C. For both sets of microarray experiments, duplicate cultures were analyzed. Total RNA was isolated from 1 unit of A600 mid-log phase cells using a RiboPure Yeast kit (A&B Applied Biosystems), amplified, labeled and fragmented using a Message Apm III RNA Amplification Kit (A&B Applied Biosystems) and hybridized to a GeneChIP Yeast Genome 2.0 array using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix). Arrays were scanned by the Gene Chip Scanner 3000 7G and expression data was extracted using Expression ConsoleM-bM-^DM-" Software (Affymetrix) with the MAS5.0 statistical algorithm.
2013-09-01 | E-GEOD-46652 | biostudies-arrayexpress
Project description:Analysis of the transcriptional effects of pGAL1-MKS1, pGAL1-NNK1, and pGAL1-FMP48 overexpression. BY4700 gal1::NAT ura3delta0 S. cerevisiae cells carrying a [pGAL1-MKS1-HA, URA3, CEN], [pGAL1-NNK1-HA, URA3, CEN], or [pGAL1-FMP48-HA, URA3, CEN] plasmid, or empty vector BG1805, were grown to early log phase, induced with 0.2% galactose, and harvested after 1.5 h and 6 h. RNA from a strain overexpressing MKS1, NNK1, or FMP48 was competitively hybridized with RNA from an identically treated strain carrying empty vector.<br><br>FMP48 = YGR052W. MKS1 = YNL076W. NNK1 = YKL171W.
2010-05-25 | E-MEXP-2171 | biostudies-arrayexpress
Project description:To investigate the possible range of additional RNase P substrates in vivo a strand-specific, high-density microarray was used to analyze what RNA accumulates with a mutation in the catalytic RNA subunit of nuclear RNase P in Saccharomyces cerevisiae. A wide variety of noncoding RNAs were shown to accumulate, suggesting nuclear RNase P participates in the turnover of normally unstable nuclear RNAs. In some cases, the accumulated noncoding RNAs were shown to be antisense to transcripts that commensurately decreased in abundance. Pre-mRNAs containing introns also accumulated broadly, consistent with either compromised splicing or failure to efficiently turnover pre-mRNAs that do not enter the splicing pathway. Taken together with the high complexity of the nuclear RNase P holoenzyme and its relatively non-specific capacity to bind and cleave mixed sequence RNAs, these data suggest nuclear RNase P facilitates turnover of nuclear RNAs in addition to its role in pre-tRNA biogenesis.
2011-08-29 | E-MEXP-3140 | biostudies-arrayexpress
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
Project description:Genome-wide alterations in yeast strains lacking RNase H1, RNase H2, or both RNase H1 and RNase H2
| PRJNA296698 | ENA
Project description:Transcription analysis of M. tuberculosis H37Ra devR overexpressing strain (LIX48) versus empty vector control strain (LIX47); H37Rv devR overexpressing strain t (LIX50) versus empty vector control strain (LIX49) to study the effect of DevR overexpression
2018-08-31 | GSE103551 | GEO
Project description:Male sterility is an important trait in hybrid crop breeding. Thermo-sensitive genic male sterility (TGMS) lines, which are male-sterile at restrictive (high) temperatures but convert to male-fertile at permissive (low) temperatures, have been widely utilized in two-line hybrid rice breeding3. However, the molecular mechanism underlying TGMS remains unclear. Here we show that the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene 5 (tms5) locus, which in 2010 was present in cultivars occupying more than 70% (2.4 million hectares) of two-line hybrid rice-growing land in China, confers the TGMS trait through a loss-of-function mutation of RNase ZS1, resulting in failure to mediate mRNA decay of three temperature-responsive ubiquitin fusion ribosomal protein L40 genes (UbL40). TMS5 encodes an evolutionarily conserved endonuclease, RNase ZS1. RNase ZS1 can process tRNAs in vitro, but does not do so in vivo due to its localization in the cytoplasm. Defective RNase ZS1 in tms5 plants leads to over-accumulation of UbL401, UbL402 and UbL404 mRNAs at restrictive but not permissive temperatures. Furthermore, over-expression of UbL401 and UbL404 in wild-type plants causes male sterility, while knockdown of UbL401 and UbL404 in tms5 partially restores its fertility. Our results uncover a novel mechanism of RNase ZS1-mediated UbL40 mRNA decay which controls TGMS in rice and has potential applications in hybrid breeding not only of rice but also of other crops.
2014-09-11 | GSE42314 | GEO
Project description:Flowers stage 15: Comparison of miR159a overexpressers to empty-vector control. Keywords: parallel sample
2005-02-01 | GSE2078 | GEO
Project description:Male sterility is an important trait in hybrid crop breeding. Thermo-sensitive genic male sterility (TGMS) lines, which are male-sterile at restrictive (high) temperatures but convert to male-fertile at permissive (low) temperatures, have been widely utilized in two-line hybrid rice breeding3. However, the molecular mechanism underlying TGMS remains unclear. Here we show that the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene 5 (tms5) locus, which in 2010 was present in cultivars occupying more than 70% (2.4 million hectares) of two-line hybrid rice-growing land in China, confers the TGMS trait through a loss-of-function mutation of RNase ZS1, resulting in failure to mediate mRNA decay of three temperature-responsive ubiquitin fusion ribosomal protein L40 genes (UbL40). TMS5 encodes an evolutionarily conserved endonuclease, RNase ZS1. RNase ZS1 can process tRNAs in vitro, but does not do so in vivo due to its localization in the cytoplasm. Defective RNase ZS1 in tms5 plants leads to over-accumulation of UbL401, UbL402 and UbL404 mRNAs at restrictive but not permissive temperatures. Furthermore, over-expression of UbL401 and UbL404 in wild-type plants causes male sterility, while knockdown of UbL401 and UbL404 in tms5 partially restores its fertility. Our results uncover a novel mechanism of RNase ZS1-mediated UbL40 mRNA decay which controls TGMS in rice and has potential applications in hybrid breeding not only of rice but also of other crops. Examination of differences in mRNA accumulation between 93-11, NIL5 and NIL8.
2014-09-11 | E-GEOD-42314 | biostudies-arrayexpress
Project description: Not available
| S-EPMC3535280 | biostudies-literature