Ontology highlight
ABSTRACT:
PROVIDER: PRJNA945378 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We report DNA content of yeast strains that are growing asynchronously or treated with hydroxyurea (HU). We selected two strains from our Epi-Decoder library, that are wild-type but have BAR1 or RPO21 TAP-tagged. This reveals that HU-treated samples have peaks in DNA content representing stalled replication forks.
2018-07-16 | GSE114290 | GEO
Project description:Transcription of transfer-RNA genes (tDNAs) by RNA Polymerase III (RNAPIII) is tightly regulated upon nutrient and stress signaling. However, identical tDNAs across the genome are differentially regulated, suggesting regulation at the chromatin-level plays a crucial role. This study aimed to identify such mechanisms by decoding the chromatin proteome of a native tDNA locus in yeast using Epi-Decoder. The tDNA proteome showed dynamic binding of both known and unknown factors upon nutrient stress, including Ykr011c (Fpt1), a protein of unknown function. Decoding the tDNA proteome in the absence of Fpt1 revealed a role in the eviction of RNAPIII during repressed transcription. Fpt1 exclusively occupied RNAPIII-regulated genes, but cells without Fpt1 also showed impaired shutdown of RNAPII-transcribed ribosome biogenesis genes in changing nutrient conditions. These findings provide support for a novel chromatin-associated regulator required for proper RNAPIII assembly that also tunes an integrated physiological response to changing metabolic conditions.
2023-11-21 | GSE228556 | GEO
Project description:To identify yeast proteins associated with Ty1 integrase (IN) that could regulate Ty1 replication, we co-purified IN partners using the tandem chromatin affinity purification procedure after in vivo cross-link (TChAP), which we developed previously (Nguyen et al. 2014). We first identified RNA Pol I and Pol III complexes and also a small subset of additional evolutionary conserved complexes, including PAF1 (Polymerase-Associated Factor 1),FACT (FAcilitates Chromatin Transcription), the proteasome and the CK2 kinase. We next confirmed that CK2 interacts with Ty1 integrase in vivo and repress Ty1 retromobility. We showed that Ty1 IN is a substrate of CK2 in vitro and identified 12 phosphorylated residues. In vivo approaches showed that only part of the protein was phosphorylated in the cells and did not demonstrate any direct evidence between Ty1 IN phosphorylation and retromobility inhibition.
2022-11-17 | PXD027420 | Pride
Project description:Analysis of the genome-wide distribution of the histone H2A, using TY1-H2A as a Proxy
2020-02-21 | GSE145625 | GEO
Project description:We tested the ability of trans siRNAs to establish a silent allele of endogenous ade6+ or an ade6+ transgene inserted within euchromatic loci. We found that a silent ade6-OFF epi-allele that grows red on low adenine medium could be established in several mutant backgrounds (mlo3∆, leo1∆) in the presence of ectopic siRNAs. Furthermore, we found that the silent ade6-OFF epi-allele could be meiotically inherited to wildtype progeny lacking the establishing mutation or ectopic siRNAs. Here, we sequenced genome-wide DNA associated with conserved heterochromatin markers and found that silencing of the endogenous ade6 locus correlates with increased spreading of H3K9me2 and H3K9me3. Additionally, heterochromatin domains established with cen::ade6 as the ectopic siRNA-producing locus were associated with significantly more spreading of H3K9me2 and H3K9me3 than those established using an ade6 hairpin as the driver siRNA-producing locus.
2018-04-26 | GSE111851 | GEO
Project description:Chromatin immunoprecipitation of genomic loci in Trypanosoma brucei where Scc1 is deposited. This was achieved by deletion of one Scc1 allele and N-terminal tagging of the second Scc1 allele with a Ty1-tag. During the ChIP experiment, the DNA was crosslinked and cells were permeabilized with digitonin. DNA was fragmented by sonication with a Covaris instrument. DNA bound to Ty1-Scc1 was pulled down by using a BB2 anti-Ty1 antibody. Cross links are reversed and the DNA was purified and prepared for Illumina sequencing.
2018-11-06 | GSE119071 | GEO
Project description:Analysis of the genome-wide distribution of RNA Pol II subunit RPB9, endogenously tagged with 2 x TY1, following depletion of HAT1 or HAT2 over a time period up to 48 h and in WT cells
2020-02-22 | GSE145707 | GEO
Project description:We tested the ability of trans siRNAs to establish a silent allele of endogenous ade6+ or an ade6+ transgene inserted within euchromatic loci. We found that a silent ade6-OFF epi-allele that grows red on low adenine medium could be established in several mutant backgrounds (mlo3∆, leo1∆) in the presence of ectopic siRNAs. Furthermore, we found that the silent ade6-OFF epi-allele could be meiotically inherited to wildtype progeny lacking the establishing mutation or ectopic siRNAs. Here, we sequenced genome-wide small RNAs and found widespread generation of secondary siRNAs at genes surrounding the ade6-OFF locus in cells expressing the ectopic siRNAs source cen::ade6. In wildtype meiotic progeny lacking the driver cen::ade6 siRNAs, we observed establishment of a local siRNA producing locus at genes adjacent to the endogenous ade6-OFF or at a kanMX-ade6-OFF transgene inserted within euchromatic loci. In contrast, spreading of secondary siRNAs was limited or nonexistent in ade6-ON cells. Finally, we found that spreading of secondary siRNAs at the endogenous ade6 locus was limited when an ade6 hairpin construct served as the ectopic siRNA driver locus instead of cen::ade6.
2018-04-26 | GSE111858 | GEO