Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Rap1 and Abf1 DNA-binding ts mutants and wild type after 1 hr at 37 C

ABSTRACT: Abf1 and Rap1 are General Regulatory Factors that contribute to transcriptional activation of a large number of genes, as well as to replication, silencing, and telomere structure in yeast. In spite of their widespread roles in transcription, the scope of their functional targets genome-wide has not been previously determined. We have used microarrays to examine the contribution of these essential GRFs to transcription genome-wide, by using ts mutants that dissociate from their binding sites at 37 C. We combined this data with published ChIP-chip studies and motif analysis to identify probable direct targets for Abf1 and Rap1. We also identified a substantial number of genes likely to bind Rap1 or Abf1, but not affected by loss of GRF binding. Interestingly, the results strongly suggest that Rap1 can contribute to gene activation from farther upstream than can Abf1. Also, consistent with previous work, more genes that bind Abf1 are unaffected by loss of binding than those that bind Rap1. Finally, we showed for several such genes that the Abf1 C-terminal region, which contains the putative activation domain, is not needed to confer this peculiar "memory effect" that allows continued transcription after loss of Abf1 binding. Keywords: Genetic modification (ts mutant versus wild type)

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE6073 | GEO | 2006/10/24

SECONDARY ACCESSION(S): PRJNA97845

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of yeast Rap1 and Abf1 DNA-binding temperature sensitive mutants and wild type controls

Project description:Abf1 and Rap1 are General Regulatory Factors that contribute to transcriptional activation of a large number of genes, as well as to replication, silencing, and telomere structure in yeast. In spite of their widespread roles in transcription, the scope of their functional targets genome-wide has not been previously determined. We have used microarrays to examine the contribution of these essential GRFs to transcription genome-wide, by using ts mutants that dissociate from their binding sites at 37 C. We combined this data with published ChIP-chip studies and motif analysis to identify probable direct targets for Abf1 and Rap1. We also identified a substantial number of genes likely to bind Rap1 or Abf1, but not affected by loss of GRF binding. Interestingly, the results strongly suggest that Rap1 can contribute to gene activation from farther upstream than can Abf1. Also, consistent with previous work, more genes that bind Abf1 are unaffected by loss of binding than those that bind Rap1. Finally, we showed for several such genes that the Abf1 C-terminal region, which contains the putative activation domain, is not needed to confer this peculiar "memory effect" that allows continued transcription after loss of Abf1 binding. Experiment Overall Design: Three replicates each of rap1 ts and abf1 ts yeast were grown at 25 C and shifted to 37 C, along with matched wild type controls, prior to RNA isolation. The ts mutants lose DNA binding at 37 C.

2009-04-24 | E-GEOD-6073 | biostudies-arrayexpress

Abf1 and Rap1 effect on nucleosome occupancy in yeast

Project description:We grew wild type and corresponding mutant abf1 and rap1 temperature sensitive yeast at 25 C, then for one hour after shifting to 37 C. We then prepared nucleosomal (mostly mononucleosomal) DNA and hybridized to tiling arrays. Three abf1 ts mutant and corresponding wild type, and three rap1 ts mutant and corresponding wild type (note not the same wild type; BY4741 for Rap1, but TMY86 for Abf1)

2010-10-15 | E-GEOD-22514 | biostudies-arrayexpress

Transcription profiling of yeast Rap1 and Abf1 DNA-binding temperature sensitive mutants and wild type controls

2014-10-10 | E-GEOD-6073 | ExpressionAtlas

Saccharomyces cerevisiae

Project description:Rap1 and Abf1 DNA-binding ts mutants and wild type after 1 hr at 37 C

| PRJNA97845 | ENA

Expression data from rGRF3, 35S:GIF1 and rGRF3x35S:GIF1 plants

Project description:The Growth Regulating Factors (GRFs) are plant specific transcription factors. They form complexes with GRF Interacting Factors (GIFs), a small family of transcriptional co-activators. In Arabidopsis thaliana, seven out of the nine GRFs are regulated by microRNA miR396. A detailed analysis of GRF3 revealed that a modified transgene, insensitive to the regulation of miR396, causes a strong increase in the number of cells in leaves, while an additional increase of GIF1 expression further enhances the number of cells synergistically. Genome-wide transcript profiling revealed that simultaneous increase of GRF3 and GIF1 levels causes additional effects in gene expression compared to either of the transgenes alone. We observed that GIF1 interacts in vivo with GRF3, as well as chromatin remodeling complexes, providing a mechanistic explanation for the additional activities of a GRF3-GIF1 complex. Interestingly, we found that the GRF system also regulates leaf longevity. Genetic and molecular analysis revealed that the functions of GRFs in leaf size and senescence can be uncoupled, demonstrating that the GRFs control different stages of leaf development. The results provide new insights into the functions of a complex regulatory network composed of microRNAs, transcription factors, and co-transcription factors. We used microarrays to obtain the transcription profile of plants overexpressing GRF3, GIF1 or both genes toghether. We compared the transcriptome of 35S:GIF1, rGRF3 and rGRF3x35S:GIF1 plants vs wild-type plants (Col-0 accession), using ATH1 Affymetrics microarrays. For these experiments we collected vegetative apices together with the leaf primordia from plants of 20 days growth in short-day. For each genotype (Col-0, rGRF3, 35S:GIF1 and rGRF3x35S:GIF1) we collected two samples.

2014-06-17 | E-GEOD-53438 | biostudies-arrayexpress

Expression data from rGRF3, 35S:GIF1 and rGRF3x35S:GIF1 plants

2014-06-17 | GSE53438 | GEO

Post-replicative nick translation occurs on the lagging strand during prolonged depletion of DNA ligase I in Saccharomyces cerevisiae

Project description:During lagging-strand synthesis, strand-displacement synthesis by DNA polymerase delta (Pol ∂), coupled to nucleolytic cleavage of DNA flap structures, combine to produce a nick translation reaction that replaces the DNA at the 5’ end of the preceding Okazaki fragment. Previous work following depletion of DNA ligase I in Saccharomyces cerevisae suggests that DNA-bound proteins, principally nucleosomes and the transcription factors Abf1/Rap1/Reb1, pose a barrier to Pol ∂ synthesis and thereby limit the extent of nick translation in vivo. However, the extended ligase depletion required for these experiments could lead to ongoing, non-physiological nick translation. Here, we investigate nick translation by analyzing Okazaki fragments purified after transient nuclear depletion of DNA ligase I in synchronized or asynchronous S. cerevisiae cultures. We observe that, even with a short ligase depletion, Okazaki fragment termini are enriched around nucleosomes and Abf1/Reb1/Rap1 binding sites. However protracted ligase depletion leads to a global change in the location of these termini, moving them towards nucleosome dyads from a more upstream location and further enriching termini at Abf1/Reb1/Rap1 binding sites. Additionally, we observe an under-representation of DNA derived from DNA polymerase alpha – the polymerase that initiates Okazaki fragment synthesis – around the sites of Okazaki termini obtained from transient ligase depletion. Our data suggest that, while nucleosomes and transcription factors do limit strand-displacement synthesis by Pol ∂ in vivo, post-replicative nick translation can occur at unligated Okazaki fragment termini such that previous analyses represent an overestimate of the extent of nick translation occurring during normal lagging-strand synthesis.

2021-04-22 | GSE173065 | GEO

Abf1 and Rap1 effect on nucleosome occupancy in yeast

2010-10-15 | GSE22514 | GEO

ChIP-seq of Abf1, TATA-binding protein, and RNA Polymerase II in wild type and abf1 temperature sensitive mutant yeast (Saccharomyces cerevisiae)

Project description:ChIP was performed in wild type and abf1-101 ts yeast after 60 minutes at 37 C

2015-02-01 | E-MTAB-3208 | biostudies-arrayexpress

Defining the genomic occupancy of the general regulatory factor Abf1 in budding yeast

Project description:Abf1 has been defined as a general regulatory factor involved in determining chromatin structure in the yeast Saccharomyces cerevisiae. As such, it plays a major role in a range of functions including DNA replication, transcriptional activation and gene silencing, as well as DNA repair. Previous studies have identified an Abf1 DNA consensus binding sequence and Abf1 binding at up to several hundred locations throughout the genome. Depletion of Abf1 in the cell, however, results in altered nucleosome structure at many thousands of sites throughout the yeast genome, suggesting a far greater role for Abf1 in chromatin structure and dynamics. Here, we examine genome-wide Abf1 binding using ChIP-Chip to measure its chromatin occupancy. Using a novel software package, Sandcastle, we detect 3,821 genomic positions at which Abf1 binds. We conducted a detailed bioinformatic analysis of these novel Abf1 binding sites, defining variations in the current consensus sequence and identifying many more genomic locations at which Abf1 can be found. These observations define the sites at which Abf1 occupancy determines chromatin structure, providing a framework for understanding how processes such as replication, transcription and DNA repair are organised within the genome.

2017-12-31 | E-MTAB-3890 | biostudies-arrayexpress

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