Abf1 and Rap1 effect on nucleosome occupancy in yeast
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE22514 | GEO | 2010/10/15
SECONDARY ACCESSION(S): PRJNA128473
REPOSITORIES: GEO
Similar Datasets
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
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
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. Keywords: Genetic modification (ts mutant versus wild type)
2006-10-24 | GSE6073 | GEO
Project description:Pioneer transcription factors (pTFs) bind to target sites within compact chromatin initiating chromatin remodeling and controlling the recruitment of downstream factors. The mechanisms by which pTFs overcome the chromatin barrier are not well understood. Here we reveal, using single-molecule fluorescence, how the yeast transcription factor Rap1 invades and remodels chromatin. Using a reconstituted chromatin system replicating yeast promoter architecture we demonstrate that Rap1 can bind nucleosomal DNA within a chromatin fiber, but with shortened dwell times compared to naked DNA. Moreover, we show that Rap1 binding opens chromatin fiber structure by inhibiting inter-nucleosome contacts. Finally, we reveal that Rap1 collaborates with the chromatin remodeler RSC to displace promoter nucleosomes, paving the way to form long-lived bound states on now exposed DNA. Together, our results provide a mechanistic view of how Rap1 gains access and opens chromatin, thereby establishing an active promoter architecture and controlling gene expression.
2019-11-21 | GSE134143 | GEO
Project description:We constructed the inducible H3-depleted and FLAG-tag of the repressor activator protein 1 (Rap1) yeasts to investigate the depleted effect of nucleosomal H3 on DNA-binding profiles of Rap1 and resulting transcriptional changes. The H3 inducible shut-off strain (named “DGS200.1” or “H3i” strain) was prepared from the wildtype YEF473A strain by knocking out the HHT1 gene (encoding H3), and replacing the native promoter of the HHT2 gene (the other H3-encoding gene) with an inducible Gal1 promoter. Conditional depletion of H3 was induced by culturing the H3i strain in the YPGal liquid medium (1% yeast extract, 2% peptone, 2% galactose) and transferring to the YPD medium (1% yeast extract, 2% peptone, 2% dextrose) for three hours. WT yeast were also cultured and switched the growth media in the same way as controls. DNA-binding profiles of H3 and Rap1 were determined using chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq), and the changes in transcriptional levels were investigated using RNA-seq.
2023-10-31 | GSE232682 | GEO
Project description:We constructed the inducible H3-depleted and FLAG-tag of the repressor activator protein 1 (Rap1) yeasts to investigate the depleted effect of nucleosomal H3 on DNA-binding profiles of Rap1 and resulting transcriptional changes. The H3 inducible shut-off strain (named “DGS200.1” or “H3i” strain) was prepared from the wildtype YEF473A strain by knocking out the HHT1 gene (encoding H3), and replacing the native promoter of the HHT2 gene (the other H3-encoding gene) with an inducible Gal1 promoter. Conditional depletion of H3 was induced by culturing the H3i strain in the YPGal liquid medium (1% yeast extract, 2% peptone, 2% galactose) and transferring to the YPD medium (1% yeast extract, 2% peptone, 2% dextrose) for three hours. WT yeast were also cultured and switched the growth media in the same way as controls. DNA-binding profiles of H3 and Rap1 were determined using chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq), and the changes in transcriptional levels were investigated using RNA-seq.
2023-10-31 | GSE232681 | GEO
Project description:We constructed the inducible H3-depleted and FLAG-tag of the repressor activator protein 1 (Rap1) yeasts to investigate the depleted effect of nucleosomal H3 on DNA-binding profiles of Rap1 and resulting transcriptional changes. The H3 inducible shut-off strain (named “DGS200.1” or “H3i” strain) was prepared from the wildtype YEF473A strain by knocking out the HHT1 gene (encoding H3), and replacing the native promoter of the HHT2 gene (the other H3-encoding gene) with an inducible Gal1 promoter. Conditional depletion of H3 was induced by culturing the H3i strain in the YPGal liquid medium (1% yeast extract, 2% peptone, 2% galactose) and transferring to the YPD medium (1% yeast extract, 2% peptone, 2% dextrose) for three hours. WT yeast were also cultured and switched the growth media in the same way as controls. DNA-binding profiles of H3 and Rap1 were determined using chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq), and the changes in transcriptional levels were investigated using RNA-seq.
2023-10-31 | GSE237515 | GEO
Project description:We constructed the inducible H3-depleted and FLAG-tag of the repressor activator protein 1 (Rap1) yeasts to investigate the depleted effect of nucleosomal H3 on DNA-binding profiles of Rap1 and resulting transcriptional changes. The H3 inducible shut-off strain (named “DGS200.1” or “H3i” strain) was prepared from the wildtype YEF473A strain by knocking out the HHT1 gene (encoding H3), and replacing the native promoter of the HHT2 gene (the other H3-encoding gene) with an inducible Gal1 promoter. Conditional depletion of H3 was induced by culturing the H3i strain in the YPGal liquid medium (1% yeast extract, 2% peptone, 2% galactose) and transferring to the YPD medium (1% yeast extract, 2% peptone, 2% dextrose) for three hours. WT yeast were also cultured and switched the growth media in the same way as controls. DNA-binding profiles of H3 and Rap1 were determined using chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq), and the changes in transcriptional levels were investigated using RNA-seq.
2023-10-31 | GSE232684 | GEO
Project description:Seven temperature sensitive Saccharomyces cerevisiae BY4741 mutants (rsc3-1, abf1-101, reb1-212, rap1-1, mcm1, tbf1 and cep3-1) were grown at restrictive temperatures until a difference in OD600 was observed relative to a wild-type control. Nucleosomal DNA, whole genomic DNA and total RNA were isolated and hybridized onto yeast whole-genome tiling arrays.<br>
2009-01-15 | E-MEXP-1754 | biostudies-arrayexpress
Project description:Nucleosomal DNA was prepared using Simple ChIP Enzymatic Chromatin IP Kit according to manufacturer’s instruction. Briefly, Nuclei were isolated from purified Ter119 negative or in vitro cultured erythroblasts. Cross-linked native chromatin was then digested with MNase into mononucleosomal DNA. Sequencing libraries were generated from nucleosomal DNA, and sequencing was carried out using the Illumina system according to the manufacturer’s specification.
2014-10-01 | GSE55825 | GEO