ChIP-seq of Abf1, TATA-binding protein, and RNA Polymerase II in wild type and abf1 temperature sensitive mutant yeast (Saccharomyces cerevisiae)
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Similar Datasets
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
Project description:The aim of this study is to define the groups of genes which are de-regulated in temperature-sensitive abf1-1 cells when grown at the restricitve temperature of 37 degrees C as compared to wild-type cells grown under same conditions. Control samples also include RNA extracted from mutant and wild-type cells grown at the permissive temperature of 25°C. Furthermore, de-regulation was measured not only under mitotic growth conditions (YPD and YPA) but also at two time-points during sporulation (at 6h and 10h).
2008-03-18 | E-TABM-291 | biostudies-arrayexpress
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: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.
2010-10-15 | GSE22514 | GEO
Project description:Gould2011 - Temperature Sensitive Circadian
Clock
This model is a temperature sensitive
version of Pokhilko
et al. 2010 (PMID:
20865009),
which is
BIOMD0000000273
in BioModels.
This model is described in the article:
Network balance via CRY
signalling controls the Arabidopsis circadian clock over
ambient temperatures.
Gould PD, Ugarte N, Domijan M, Costa
M, Foreman J, Macgregor D, Rose K, Griffiths J, Millar AJ,
Finkenstädt B, Penfield S, Rand DA, Halliday KJ, Hall
AJ.
Mol. Syst. Biol. 2013; 9: 650
Abstract:
Circadian clocks exhibit 'temperature compensation', meaning
that they show only small changes in period over a broad
temperature range. Several clock genes have been implicated in
the temperature-dependent control of period in Arabidopsis. We
show that blue light is essential for this, suggesting that the
effects of light and temperature interact or converge upon
common targets in the circadian clock. Our data demonstrate
that two cryptochrome photoreceptors differentially control
circadian period and sustain rhythmicity across the
physiological temperature range. In order to test the
hypothesis that the targets of light regulation are sufficient
to mediate temperature compensation, we constructed a
temperature-compensated clock model by adding passive
temperature effects into only the light-sensitive processes in
the model. Remarkably, this model was not only capable of full
temperature compensation and consistent with mRNA profiles
across a temperature range, but also predicted the
temperature-dependent change in the level of LATE ELONGATED
HYPOCOTYL, a key clock protein. Our analysis provides a
systems-level understanding of period control in the plant
circadian oscillator.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000564.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2010-10-21 | BIOMD0000000564 | BioModels
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:To identify conditional alleles which disrupt the splicing pathway, we screened a collection of ~2000 chemically mutagenized temperature-sensitive fission yeast isolates for intron accumulation in three introns, including a naturally occurring U2-dependent AT-AC intron. We identified 54 strains which accumulate unspliced message at the non-permissive temperature. A combination of mutation effect prediction and genetic mapping techniques revealed missense mutations in core splicing genes which function at various steps of spliceosome assembly and activation including: prp10, prp28, sap61, ntr1, spp42, sap114, cwf22, and prp22. Interrogation of structural data and genome-wide analysis of the splicing defects in these mutations revealed intron-specific defects which suggest the biochemical basis for these mutations’ effects on splicing.
2020-11-13 | GSE161333 | GEO
Project description:We obtained RNA polymerase II occupancy profiles across the genome of S.cerevisiae strains: Abf1 anchor-away cells after addition of rapamycin for different time points (including no addition of rapamycin) and Rap1-AID auxin-degron cells after addition of auxin for different time points (including no addition of auxin) . This allowed us to compare polymerase occupancy profiles when these proteins are depleted from the nucleus or degraded.
2018-12-20 | GSE114589 | GEO
Project description:Despite being one of the first eukaryotic transcriptional regulatory elements identified, the sequence of a native TATA box and its significance remain elusive. Applying criteria associated with TATA boxes we queried several Saccharomyces genomes and arrived at the consensus TATA(A/T)A(A/T)(A/G). Approximately 20% of yeast genes contain a TATA box. Strikingly, TATA box-containing genes are associated with responses to stress, are highly regulated, and preferentially utilize SAGA rather than TFIID when compared to TATA-less promoters. Transcriptional regulation in yeast appears to be mechanistically bipolar, possibly reflecting a need to balance inducible stress-related responses with constitutive housekeeping functions. A strain containing amino terminal HA-tagged TBP and its parental untagged counterpart BY4741 (Resgen) were grown at 23?C in CSM to OD600 = 0.8-1.0. Cultures were shifted to 37?C for 5 minutes (to mimic heat treatments used elsewhere (Huisinga and Pugh, 2004)), then crosslinked at 23?C with 1% formaldehyde. ChIP was performed as described previously (Strahl-Bolsinger et al., 1997) with the some modification. Following cell disruption with glass beads, the chromatin was partially purified by centrifugation (Kurdistani and Grunstein, 2003). HA-TBP was immunopurified with 12CA5 antibody. After elution and reversal of the crosslinks, samples were subjected to non-specific amplification, labeling, and array hybridization as described (Bohlander et al., 1992; Chitikila et al., 2002). The amplification procedure was modified as follows. Following 15 round B amplification cycles, DNA was purified via QIAquick PCR Purification kit. Ten cycles were used in round C. Intergenic microarrays were generated by PCR amplification of entire intergenic regions of all yeast genes, then spotted onto glass slides. Spot intensities were filtered to remove any signal that was less then one standard deviation above local background. Three replicates were performed and their log2 ratios (enriched/input) were averaged. Keywords = Chromatin Immunoprecipitation Keywords = genome-wide binding Keywords: other
2004-03-05 | GSE886 | GEO