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The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae.

McKnight JN, Tsukiyama T - Genom Data (2015)

Bottom Line: Quiescence is a ubiquitous cell cycle stage conserved from microbes through humans and is essential to normal cellular function and response to changing environmental conditions.We recently reported a massive repressive event associated with quiescence in Saccharomyces cerevisiae, where Rpd3 establishes repressive chromatin structure that drives transcriptional shutoff [6].Our results provide a bona fide molecular event driven by widespread changes in chromatin structure through action of Rpd3 that distinguishes quiescence as a unique cell cycle stage in S. cerevisiae.

View Article: PubMed Central - PubMed

Affiliation: Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

ABSTRACT
Quiescence is a ubiquitous cell cycle stage conserved from microbes through humans and is essential to normal cellular function and response to changing environmental conditions. We recently reported a massive repressive event associated with quiescence in Saccharomyces cerevisiae, where Rpd3 establishes repressive chromatin structure that drives transcriptional shutoff [6]. Here, we describe in detail the experimental procedures, data collection, and data analysis related to our characterization of transcriptional quiescence in budding yeast (GEO: GSE67151). Our results provide a bona fide molecular event driven by widespread changes in chromatin structure through action of Rpd3 that distinguishes quiescence as a unique cell cycle stage in S. cerevisiae.

No MeSH data available.


Related in: MedlinePlus

Transcription factor binding site analysisIndividual profiles for ChIP-seq (log2 H4ac/Input is shown) or MNase-seq data were determined for logarithmically growing (log) cells or purified quiescent (Q) cells within 500 base pairs of intergenic instances of transcription factor binding motifs normalized to the number of motif instances (left). Differences in profiles were determined and ranked for 166 transcription factor motifs from the JASPAR database (right). These analyses were used to implicate transcription factors whose binding is likely regulated during the transition to quiescence in S. cerevisiae.
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f0005: Transcription factor binding site analysisIndividual profiles for ChIP-seq (log2 H4ac/Input is shown) or MNase-seq data were determined for logarithmically growing (log) cells or purified quiescent (Q) cells within 500 base pairs of intergenic instances of transcription factor binding motifs normalized to the number of motif instances (left). Differences in profiles were determined and ranked for 166 transcription factor motifs from the JASPAR database (right). These analyses were used to implicate transcription factors whose binding is likely regulated during the transition to quiescence in S. cerevisiae.

Mentions: For analyzing features at predicted transcription factor (TF) binding sites, we obtained TF consensus sequences from the JASPAR CORE fungi database [5] (http://jaspar.genereg.net/). Instances of intergenic motifs (excluding the rDNA locus and mitochondrial genome) were obtained using the pattern matching tool from SGD (http://www.yeastgenome.org/cgi-bin/PATMATCH/nph-patmatch). Normalized coverage file data were binned within 500 bp of individual motifs and normalized to the number of instances for each motif to give the average signal (nucleosome dyads or ChIP) at a given motif. Motifs were then ranked based on difference between log and Q cells in within the 500 bp window (Fig. 1). Correlations between transcriptional shutoff, histone density, histone acetylation, and Rpd3 binding at transcription start sites were determined as follows: average acetylation ChIP signal or Rpd3 ChIP signal from (TSS − 300) to (TSS + 400) was calculated or average H3 ChIP signal from (TSS − 300) to (TSS + 200) was calculated for each TSS. Difference in transcription, H3, acetylation, or Rpd3 binding was determined for different growth conditions and Pearson correlations between relevant variables were determined using R software.


The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae.

McKnight JN, Tsukiyama T - Genom Data (2015)

Transcription factor binding site analysisIndividual profiles for ChIP-seq (log2 H4ac/Input is shown) or MNase-seq data were determined for logarithmically growing (log) cells or purified quiescent (Q) cells within 500 base pairs of intergenic instances of transcription factor binding motifs normalized to the number of motif instances (left). Differences in profiles were determined and ranked for 166 transcription factor motifs from the JASPAR database (right). These analyses were used to implicate transcription factors whose binding is likely regulated during the transition to quiescence in S. cerevisiae.
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664762&req=5

f0005: Transcription factor binding site analysisIndividual profiles for ChIP-seq (log2 H4ac/Input is shown) or MNase-seq data were determined for logarithmically growing (log) cells or purified quiescent (Q) cells within 500 base pairs of intergenic instances of transcription factor binding motifs normalized to the number of motif instances (left). Differences in profiles were determined and ranked for 166 transcription factor motifs from the JASPAR database (right). These analyses were used to implicate transcription factors whose binding is likely regulated during the transition to quiescence in S. cerevisiae.
Mentions: For analyzing features at predicted transcription factor (TF) binding sites, we obtained TF consensus sequences from the JASPAR CORE fungi database [5] (http://jaspar.genereg.net/). Instances of intergenic motifs (excluding the rDNA locus and mitochondrial genome) were obtained using the pattern matching tool from SGD (http://www.yeastgenome.org/cgi-bin/PATMATCH/nph-patmatch). Normalized coverage file data were binned within 500 bp of individual motifs and normalized to the number of instances for each motif to give the average signal (nucleosome dyads or ChIP) at a given motif. Motifs were then ranked based on difference between log and Q cells in within the 500 bp window (Fig. 1). Correlations between transcriptional shutoff, histone density, histone acetylation, and Rpd3 binding at transcription start sites were determined as follows: average acetylation ChIP signal or Rpd3 ChIP signal from (TSS − 300) to (TSS + 400) was calculated or average H3 ChIP signal from (TSS − 300) to (TSS + 200) was calculated for each TSS. Difference in transcription, H3, acetylation, or Rpd3 binding was determined for different growth conditions and Pearson correlations between relevant variables were determined using R software.

Bottom Line: Quiescence is a ubiquitous cell cycle stage conserved from microbes through humans and is essential to normal cellular function and response to changing environmental conditions.We recently reported a massive repressive event associated with quiescence in Saccharomyces cerevisiae, where Rpd3 establishes repressive chromatin structure that drives transcriptional shutoff [6].Our results provide a bona fide molecular event driven by widespread changes in chromatin structure through action of Rpd3 that distinguishes quiescence as a unique cell cycle stage in S. cerevisiae.

View Article: PubMed Central - PubMed

Affiliation: Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

ABSTRACT
Quiescence is a ubiquitous cell cycle stage conserved from microbes through humans and is essential to normal cellular function and response to changing environmental conditions. We recently reported a massive repressive event associated with quiescence in Saccharomyces cerevisiae, where Rpd3 establishes repressive chromatin structure that drives transcriptional shutoff [6]. Here, we describe in detail the experimental procedures, data collection, and data analysis related to our characterization of transcriptional quiescence in budding yeast (GEO: GSE67151). Our results provide a bona fide molecular event driven by widespread changes in chromatin structure through action of Rpd3 that distinguishes quiescence as a unique cell cycle stage in S. cerevisiae.

No MeSH data available.


Related in: MedlinePlus