Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Context dependent function of transcriptional regulator Rap1 in gene silencing and activation [ChIP-seq II]

ABSTRACT: As part of a study on the function of Rap1 at HML and MAT in Saccharomyces cerevisiae, we performed ChIP-seq on myc-tagged Sir3 in cells with and without a Rap1 binding site mutation at the promoter.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE227759 | GEO | 2023/05/09

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Context dependent function of transcriptional regulator Rap1 in gene silencing and activation [ChIPseq I]

Project description:As part of a study on the role of Rap1 at the promoters of HML and MAT in S cerevisiae, we endogenously tagged Rap1 with a 3xV5 tag and performed ChIPseq in a variety of genetic backgrounds including: silenced (SIR); unsilenced (sir1∆/sir3∆/sir4∆); in strains witha wild type alpha2 promoter (wtpromoter); or with a point mutation at the promoter (mutpromoter).

2023-05-09 | GSE227757 | GEO

Context dependent function of transcriptional regulator Rap1 in gene silencing and activation [ChIP-seq timecourse]

Project description:As part of a study on the function of Rap1 at HML and MAT in Saccharomyces cerevisiae, we performed an Anchor Away experiment on Rap1, inducibly depleting it from the nucleus upon addition of Rapamycin, followed by a ChIP-seq time-course. This was done in a strain that had SNPs introduced to HMLalpha to make it distinguishable from MATalpha. Samples were spiked with a constant amount (5% by OD) of a S.paradoxus strain that also expressed 2xV5-Rap1. Reads from the S.paradoxus sample served as the normalization factor. Peaks were then fit to a non-linear regression model to extract the k(off) and apparent residence time in vivo.

2023-05-09 | GSE227761 | GEO

Context dependent function of transcriptional regulator Rap1 in gene silencing and activation [ChIP-seq III]

Project description:As part of a study on the mechanism of Sir-based silencing at HML in S.cerevisiae, and the contribution of Rap1 to transcription of the locus, we performed ChIP-seq of multiple components of RNA Pol II machinery in different genetic backgrounds including: sir4∆, SIR+, and with or without a mutation that abbrogated Rap1 binding at the alpha promoter.

2023-05-09 | GSE227760 | GEO

Rap1, Sir2, Sir3, Sir4 immunoprecipitations

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

Rap1, Sir2, Sir3, Sir4 immunoprecipitations

2005-09-24 | GSE3360 | GEO

S-phase independent silencing establishment in Saccharomyces cerevisiae

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

Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae [I]

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

Distinguishing between recruitment and spread of silent chromatin structures in Saccharomyces cerevisiae [II]

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. We mapped sites of Sir3-chromatin interactions genome-wide using long-read Nanopore sequencing to detect adenines methylated by the fusion protein. We also used a temperature-sensitive allele of SIR3 (sir3-8) fused to M.ECOGII to induce m6A methylation over time. Time courses involved a switch from restrictive temperature (37°C) to permissive temperature (25°C).

2022-01-17 | GSE190136 | GEO

Roles of mammalian Rap1 in TERT recruitment to chromatin, subtelomeric gene silencing and transcriptional regulation

Project description:Repressor-activator protein 1 (scRap1) is the major binding activity at Saccharomyces cerevisiae telomeres, with roles in telomere length regulation and establishment of subtelomeric silencing by recruiting the Sir proteins. scRap1 also acts as a transcription factor controlling the expression of ribosomal proteins and glycolytic enzymes. A homolog of scRap1 exist in mammals, Rap1 (also known as Terf2ip), however, its roles in telomere biology and transcriptional regulation are largely unknown. We have employed microarrays to obtain gene expression signatures related to Rap1-deleted mice when compared to the wild-type.

2010-07-10 | GSE19011 | GEO

Analysis of a novel existence region of Sir3p in S. cerevisiae

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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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