Saccharomyces cerevisiae
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ABSTRACT:
PROVIDER: PRJNA93487 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In the budding yeast, HMR, HML, telomere and rDNA domain are known as a silencing region. Sir2 need to make it at rDNA and, HMR, HML and the telomere need to Sir2, Sir3, Sir4 complex to control internal gene repression. In this report, we found a newly Sir3 binding domain, CN domain (Chromosome New region) 1~14, by the ChIP on chip analysis on S.cerevisiae chromosome. In addition, we also performed ChIP on chip analysis with anti-Sir3 antibody using G1 phase synchronized cell to find Sir3 distribution difference of stage of cell cycle and we found CN15~CN25 which was G1 phase specific Sir3 binding region. Furthermore, we analyzed difference of gene expression at CN region in sir3 strain, and some regions did not change level of gene expression. In the conventional report, Sir3 had recruited by Sir2 and Sir4 on chromosome, but recruit of Sir3 was independent on Sir2 and Sir4 at some CN regions. These data suggested that we found a newly Sir3 function and Sir3 recruited system on chromosome.
2015-11-18 | GSE75075 | GEO
Project description:All Rap1, Sir2, Sir3, Sir4, and mock immunoprecipitation experiments associated with Lieb et al. Nature Genetics, August 2001, Volume 28, Issue 4 Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-09-24 | GSE3360 | GEO
Project description:All Rap1, Sir2, Sir3, Sir4, and mock immunoprecipitation experiments associated with Lieb et al. Nature Genetics, August 2001, Volume 28, Issue 4 Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
2005-09-24 | E-GEOD-3360 | biostudies-arrayexpress
Project description:Gene silencing at the mating type loci in budding yeast depends on the Sir proteins. Sir2, Sir3 and Sir4 are indispensable for silencing, whereas Sir1 has a more limited role. The Sir proteins are also involved in repression at telomeres and ribosomal DNA (rDNA) repeats. Proposed mechanisms for Sir-mediated silencing include limiting access to silenced DNA and inhibition of transcript initiation and/or elongation. Using an inducible M.SssI DNA methyltransferase expression system, we showed previously that the silenced mating type loci are methylated at a much slower rate than the rest of the genome in vivo. Here, we show that, in the absence of Sir2, Sir3 or Sir4, the silenced loci and the telomeric X elements are methylated at a similar rate to the rest of the genome, indicating that these Sir proteins impede access, but do not prevent it. Loss of Sir1 has a minor effect. The rDNA repeats are methylated faster in the absence of Sir2 and, to a lesser extent, of Sir3, but not of Sir4. Our data indicate that steric occlusion is unlikely to be the primary mechanism of silencing, since silenced DNA is accessible in vivo, albeit at a slower rate than elsewhere in the genome.
2026-03-12 | GSE311530 | GEO
Project description:Chip-chip of Sir3 and of Sir2, and ChAP-chip of AAR from budding yeast cells
| PRJNA274692 | ENA
Project description:O-acetyl-ADP-ribose (AAR) is a small metabolic molecule that is generated during NAD-dependent deacetylation by Sir2. Sir2 regulates gene expression, DNA repair, and genome stability. chromatin affinity-precipitation (ChAP) method was used to detect the chromatin fragments at which small molecules interact with binding partners. Chromatin immunoprecipitation of Sir3 and of Sir2, respectively, applied with tilling array chip (ChIP on chip of Sir3 and of Sir2, respectively) and Chromatin affinity-precipitation of AAR applied with tilling array chip (ChAP on chip of AAR ) analysis demonstrated that an extended spreading of Sir3 and of AAR, but not Sir2 in Saccharomyces cerevisiae Ysa1 deleted cells compared with those in wild type cells Comparison the distributions of Sir3, of Sir2 and of AAR on silent heterochromatin of Ysa1 deletion cells vs those of wild type cells
2015-12-31 | E-GEOD-65672 | biostudies-arrayexpress
Project description:O-acetyl-ADP-ribose (AAR) is a small metabolic molecule that is generated during NAD-dependent deacetylation by Sir2. Sir2 regulates gene expression, DNA repair, and genome stability. chromatin affinity-precipitation (ChAP) method was used to detect the chromatin fragments at which small molecules interact with binding partners. Chromatin immunoprecipitation of Sir3 and of Sir2, respectively, applied with tilling array chip (ChIP on chip of Sir3 and of Sir2, respectively) and Chromatin affinity-precipitation of AAR applied with tilling array chip (ChAP on chip of AAR ) analysis demonstrated that an extended spreading of Sir3 and of AAR, but not Sir2 in Saccharomyces cerevisiae Ysa1 deleted cells compared with those in wild type cells
2015-12-31 | GSE65672 | GEO
Project description:Analysis of gene expression changes following deletion of SIR genes at subtelomeric region. A total of 4 samples were analyzed : Wild type (BY4742) strain, SIR2 deletion strain, SIR3 deletion strain, SIR4 deletion strain.
2023-12-28 | GSE230739 | GEO
Project description:As part of a study of establishment of silencing in Saccharomyces cerevisiae, we performed ChIP-seq on myc-tagged Sir4 in several conditions. Included in those conditions are wild-type cycling cells, cycling sir3∆ cells, and various experiments during which silencing establishment was controlled using the inducible SIR3-EBD allele. Silencing establishment experiments were performed in both wild-type and dot1∆ cells.
2020-05-19 | GSE150737 | GEO
Project description:The formation of heterochromatin at HML, HMR, and telomeres in Saccharomyces cerevisiae involves two main steps: Recruitment of Sir proteins to silencers and their spread throughout the silenced domain. For the following datasets, we created a fusion protein between the heterochromatin protein Sir3 and the non-site-specific bacterial adenine methyltransferase M.EcoGII, with or without a 3xV5 epitope at the C-terminus. We performed ChIP-seq experiments (immunoprecipitated Sir3-M.EcoGII-3xV5) and MeDIP-seq experiments (immunoprecipitated m6A methylated DNA). We also used a temperature-sensitive allele of SIR3 (sir3-8) fused to M.ECOGII to induce m6A methylation for MeDIP-seq.
2021-11-24 | GSE189038 | GEO