U.S. flag

An official website of the United States government

Search results

Items: 1 to 20 of 103134

1.

Sir2 and Fun30 regulate ribosomal DNA replication timing via MCM helicase positioning and nucleosome occupancy

(Submitter supplied) The association between late replication timing and low transcription rates in eukaryotic heterochromatin is well-known, yet the specific mechanisms underlying this link remain uncertain. In Saccharomyces cerevisiae, the histone deacetylase Sir2 is required for both transcriptional silencing and late replication at the repetitive ribosomal DNA arrays (rDNA). We have previously reported that in the absence of SIR2, a derepressed RNA PolII repositions MCM replicative helicases from their loading site at the ribosomal origin, where they abut well-positioned, high-occupancy nucleosomes, to an adjacent region with lower nucleosome occupancy. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL17342
168 Samples
Download data: BEDGRAPH
Series
Accession:
GSE285768
ID:
200285768
2.

Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression [MeDIP]

(Submitter supplied) Some transcription factors (TFs) can form liquid-liquid phase separated (LLPS) condensates. However, the function of these TF condensates in 3D genome organization and gene regulation remains elusive. In response to methionine (met) starvation in budding yeast, Met4 and a few sequence-specific co-activators, including Met32, induce a set of genes involved in met biosynthesis. Here, we show that the endogenous Met4 and Met32 form puncta-like structures that significantly overlap in yeast nuclei upon met depletion. more...
Organism:
Saccharomyces cerevisiae
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL31112
40 Samples
Download data: BIGWIG, TXT, XLSX
Series
Accession:
GSE252985
ID:
200252985
3.

Characterizing the regulatory effects of H2A.Z and SWR1 on gene expression during hydroxyurea exposure in Saccharomyces cerevisiae

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19756
60 Samples
Download data: BW
Series
Accession:
GSE261121
ID:
200261121
4.

Characterizing the regulatory effects of H2A.Z and SWR1 on gene expression during hydroxyurea exposure in Saccharomyces cerevisiae [ChIP-seq]

(Submitter supplied) Chromatin structure and DNA accessibility are partly modulated by the incorporation of histone variants. H2A.Z, encoded by the non-essential HTZ1 gene in S. cerevisiae, is an evolutionarily conserved H2A histone variant that is predominantly incorporated at transcription start sites by the SWR1-complex (SWR1-C). While H2A.Z has often been implicated in transcription regulation, htz1Δ mutants exhibit minimal changes in gene expression compared to wild-type. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL19756
12 Samples
Download data: BW
Series
Accession:
GSE261120
ID:
200261120
5.

Characterizing the regulatory effects of H2A.Z and SWR1 on gene expression during hydroxyurea exposure in Saccharomyces cerevisiae [RNA-Seq]

(Submitter supplied) Chromatin structure and DNA accessibility are partly modulated by the incorporation of histone variants. H2A.Z, encoded by the non-essential HTZ1 gene in S. cerevisiae, is an evolutionarily conserved H2A histone variant that is predominantly incorporated at transcription start sites by the SWR1-complex (SWR1-C). While H2A.Z has often been implicated in transcription regulation, htz1Δ mutants exhibit minimal changes in gene expression compared to wild-type. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19756
48 Samples
Download data: XLSX
Series
Accession:
GSE254648
ID:
200254648
6.

Serine mistranslation induces the integrated stress response through the P1 stalk

(Submitter supplied) Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that support robust and accurate protein synthesis. A rapidly expanding number of studies show that mutations in aaRSs lead to multiple human diseases, including neurological disorders and cancer. Much remains unknown about how aaRS mutations impact human health. In particular, how aminoacylation errors affect stress responses and fitness in eukaryotic cells remains poorly understood. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23014
6 Samples
Download data: XLSX
Series
Accession:
GSE284986
ID:
200284986
7.

Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes

(Submitter supplied) The multiprotein bridging factor 1 (Mbf1) proteins are a family of conserved eukaryotic proteins thought to mediate the activity of stress-induced transcription factors. In yeast, Mbf1 has been proposed to function in the integrated stress response (ISR) by mediating an interaction between the basal transcription machinery and the process’s key effector Gcn4. Curiously, mounting recent evidence has strongly suggested that the factor and its human homologue to be recruited to collided ribosomes, the very signal newly recognized to activate the ISR. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27812
24 Samples
Download data: SF, XLSX
Series
Accession:
GSE255383
ID:
200255383
8.

Transcriptome reshaping of the evolved thermotolerant Saccharomyces cerevisiae strain compared with the parental strain by RNA-Seq

(Submitter supplied) Elevated thermotolerance is an important desired property of Saccharomyces cerevisiae for its industrial applications. Here, adaptive laboratory evolution experiments were employed to further improve the thermotolerance of an industrial strain ScY. The resulting evolved strain showing enhanced thermotolerance was named ScY01. We sequenced mRNA from the cultures of the evolved strain ScY01 and the parental strain ScY grown on YP medium containing 200 g/l glucose at 40ºC at 200 rpm for 14 h ~ 16 h to the early-log phase. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13272
2 Samples
Download data: XLSX
Series
Accession:
GSE96829
ID:
200096829
9.

High-Resolution Genome-Wide Maps Reveal Widespread Presence of Torsional Insulation

(Submitter supplied) Torsional stress in chromatin plays a fundamental role in cellular functions, influencing key processes such as transcription, replication, and chromatin organization. Transcription and other processes may generate and be regulated by torsional stress. In the genome, the interplay of these processes creates complicated patterns of both positive (+) and negative (-) torsion. However, a challenge in generating an accurate torsion map is determining the zero-torsion baseline signal, which is conflated with chromatin accessibility. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL31112
20 Samples
Download data: BW
Series
Accession:
GSE284352
ID:
200284352
10.

Formylation occurrence on translation in s. cerevisiae

(Submitter supplied) This study elucidates the processes of transcription and translation in Saccharomyces cerevisiae following MTF (Mitochondrial Transcription Factor) expression. We identifed the functional significance of MTF in the translation process through a comprehensive analysis of multi-omics data.
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing; Other
Platforms:
GPL27812 GPL32505
20 Samples
Download data: RESULTS
Series
Accession:
GSE246349
ID:
200246349
11.

Hi-C Calibration by Chemically Induced Chromosomal Interactions

(Submitter supplied) The genome-wide chromosome conformation capture method, Hi-C, has greatly advanced our understanding of genome organization. However, its quantitative properties, including sensitivity, bias, and linearity, remain challenging to assess. Measuring these properties in vivo is difficult due to the heterogenous and dynamic nature of chromosomal interactions. Here, using Chemically Induced Chromosomal Interaction (CICI) method, we create stable intra- and inter-chromosomal interactions in G1-phase budding yeast across a broad range of contact frequencies. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL31112
20 Samples
Download data: COOL
Series
Accession:
GSE283767
ID:
200283767
12.

RNA primer removal at lagging telomere by RNase H2 recapitulates end replication problem

(Submitter supplied) The end replication problem refers to the incomplete replication of parental DNA at telomeres, a process whose molecular depiction is hampered by the complex nature of telomere ends. Here we recapitulate this process using a synthetic de novo telomere in yeast and delineate distinct molecular fates of telomere ends in vivo. We show that the lagging strand telomere carries a ~10 nt 3’ overhang, while the leading strand telomere has a Yku-protected blunt end, which is prevalent on native telomeres. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL33987
4 Samples
Download data: BW
Series
Accession:
GSE283459
ID:
200283459
13.

Cell integrity limits ploidy in budding yeast

(Submitter supplied) Evidence suggests that increases in ploidy have occurred frequently in the evolutionary history of organisms, and can serve adaptive functions to specialized, somatic cells in multicellular organisms (Edgar & Orr-Weaver, 2001; Orr-Weaver, 2015; Van De Peer et al., 2017). However, the sudden multiplication of all chromosome content may present physiological challenges to the cells in which it occurs. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL27812
72 Samples
Download data: TXT
Series
Accession:
GSE275298
ID:
200275298
14.

H3K56 acetylation regulates chromatin maturation following DNA replication

(Submitter supplied) Following DNA replication, the newly reassembled chromatin is disorganized and must mature to its steady state to maintain both genome and epigenome integrity. However, the regulatory mechanisms governing this critical process remain poorly understood. Here, we show that histone H3K56 acetylation (H3K56ac), a mark on newly-synthesized H3, facilitates the remodeling of disorganized nucleosomes in nascent chromatin, and its removal at the subsequent G2/M phase of the cell cycle marks the completion of chromatin maturation. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL27812 GPL19756
116 Samples
Download data: BW
Series
Accession:
GSE269558
ID:
200269558
15.

Osmotic disruption of chromatin induces Topoisomerase 2 activity at sites of transcriptional stress [RNA-Seq]

(Submitter supplied) Transcription generates superhelical stress in DNA that poses problems for genome stability, but determining when and where such stress arises within chromosomes is challenging. Here, using G1-arrested S. cerevisiae cells, and employing rapid fixation and ultra-sensitive enrichment, we utilise the physiological activity of endogenous topoisomerase 2 (Top2) as a probe of transcription-induced superhelicity. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19756
10 Samples
Download data: TXT
Series
Accession:
GSE280157
ID:
200280157
16.

Osmotic disruption of chromatin induces Topoisomerase 2 activity at sites of transcriptional stress [Mnase-Seq]

(Submitter supplied) Transcription generates superhelical stress in DNA that poses problems for genome stability, but determining when and where such stress arises within chromosomes is challenging. Here, using G1-arrested S. cerevisiae cells, and employing rapid fixation and ultra-sensitive enrichment, we utilise the physiological activity of endogenous topoisomerase 2 (Top2) as a probe of transcription-induced superhelicity. more...
Organism:
Saccharomyces cerevisiae
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL32505
16 Samples
Download data: TXT
Series
Accession:
GSE280155
ID:
200280155
17.

Osmotic disruption of chromatin induces Topoisomerase 2 activity at sites of transcriptional stress [CC-seq-v2]

(Submitter supplied) Transcription generates superhelical stress in DNA that poses problems for genome stability, but determining when and where such stress arises within chromosomes is challenging. Here, using G1-arrested S. cerevisiae cells, and employing rapid fixation and ultra-sensitive enrichment, we utilise the physiological activity of endogenous topoisomerase 2 (Top2) as a probe of transcription-induced superhelicity. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platforms:
GPL32505 GPL19756
56 Samples
Download data: TXT
Series
Accession:
GSE280153
ID:
200280153
18.

Yeast Thigmotropism Controlled by a Cell-Surface Mucin and a MAP-Kinase Pathway

(Submitter supplied) Budding yeast can switch from growth as ovoid cells to growth in an adhesive and invasive filamentous form. Limiting availability of reduced nitrogen is thought to be the signal that induces filamentous growth. In contrast, we find that filamentation is a thigmotropic response. In the absence of repressive agents, growth on a surface is necessary and sufficient to induce filamentation, whereas nitrogen limitation is neither sufficient nor necessary. more...
Organism:
Saccharomyces cerevisiae; Schizosaccharomyces pombe
Type:
Expression profiling by array
Platform:
GPL2529
90 Samples
Download data: CEL
Series
Accession:
GSE17295
ID:
200017295
19.

QTL mapping reveals novel genes and mechanisms underlying variations in H2S production during alcoholic fermentation in Saccharomyces cerevisiae

(Submitter supplied) Saccharomyces cerevisiae’s requirement of reduced sulfur to synthesise methionine and cysteine during alcoholic fermentation, is mainly fulfilled through the sulfur assimilation pathway. S. cerevisiae reduces sulfate into sulfur dioxide (SO2) and sulfide (H2S), whose overproduction is a major issue in winemaking, due to its negative impact on wine aroma. The amount of H2S produced is highly strain-specific and depends as well on the SO2 concentration, often added to the grape must. more...
Organism:
Saccharomyces cerevisiae
Type:
Expression profiling by array
Platform:
GPL17690
24 Samples
Download data: GPR, TXT
Series
Accession:
GSE246311
ID:
200246311
20.

Yeast elongation factor homolog New1 protects a subset of mRNAs from degradation by no-go decay

(Submitter supplied) New1 is a homolog of fungal translation elongation factor 3 (eEF3) inSaccharomyces cerevisiae. Its absence has previously been described to lead to cold sensitivity, ribosome biogenesis defects, and ribosomal queues upstream of Stop codons on selected mRNAs. Here, we find that, especially in cold conditions, lack of New1 induces no-go decay (NGD) on specificmRNAs, leading, as a consequence, to decreased mRNA and protein levels of such genes.The effect correlates with the presence of specific Lysine and Arginine codons just upstream of the Stop codon. more...
Organism:
Saccharomyces cerevisiae
Type:
Other
Platform:
GPL22715
16 Samples
Download data: TXT
Series
Accession:
GSE275093
ID:
200275093

Supplemental Content

db=gds|term=txid4932[Organism:noexp]|query=2|qty=174|blobid=MCID_6781702a7eb86f557f7d99d1|ismultiple=true|min_list=5|max_list=20|def_tree=20|def_list=|def_view=|url=/Taxonomy/backend/subset.cgi?|trace_url=/stat?
   Taxonomic Groups  [List]
Tree placeholder
    Top Organisms  [Tree]

Find related data

Search details

See more...

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
Support Center
External link. Please review our privacy policy.