Glucose regulates transcription in yeast through a network of signaling pathways

Zaman, Shadia; Lippman, Soyeon I.; Schneper, Lisa; Slonim, Noam; Broach, James R.

doi:10.1038/msb.2009.20

Cited by 59 publications

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“…From a 2-liter culture of strain Y2864 (Zaman et al, 2009) grown at 30°in SC ϩ 3% glycerol to 2-3 ϫ 10 6 cells/ml (A 660 ϭ 0.2-0.3), we removed and cross-linked (see below) 650 ml of culture as the zero time point and added glucose to 2% to the remaining culture. We then removed 650 ml of culture after 20 and 60 min and crosslinked cells by addition of formaldehyde to a concentration of 4% and incubation at room temperature for 30 min with gentle shaking; we found that spheroplasts from glycerol-grown cells are extremely fragile, necessitating increased cross-linking relative to previously published protocols.…”

Section: Nucleosomal Dna Isolationmentioning

confidence: 99%

“…This carbon source upshift significantly alters expression of more than half of all yeast genes (Wang et al, 2004;Zaman et al, 2009) and thereby provides numerous individual examples to examine the relationship between nucleosome positioning and gene expression. To perform this analysis, samples of glycerol grown cells were collected and formaldehyde cross-linked both before glucose addition and 20 and 60 min after addition.…”

Section: Genome-wide Positions Of Nucleosomes In Saccharomycesmentioning

confidence: 99%

“…We previously applied a mutual information based algorithm, FIRE (Elemento et al, 2007), to identify promoterlocalized sequence motifs that mediate glucose-induced changes in gene expression, many of which corresponded to binding sites for transcription factors known to be involved in the glucose response, such as Msn2/4 and Hap4 (Zaman et al, 2009). Limiting our analysis to promoters, we measured differences in nucleosome occupancy in response to glucose addition directly over all instances of these individual motifs and observed little change in their nucleosome occupancy upon glucose addition (data not shown).…”

Section: Functional Transcription Factor Binding Motifs Reside In Regmentioning

confidence: 99%

“…For example, Leu3 sites to which Leu3 is not bound in vivo tend to lie under well positioned nucleosomes (Liu et al, 2006). Thus, as Morse has proposed, chromatin may be "instructive" for transcription factor binding (Morse, 2007).To We determined nucleosome occupancy before and after addition of glucose to cells grown in a poor carbon source, a nutrient upshift in which more than half of all yeast genes significantly change expression (Wang et al, 2004;Zaman et al, 2009). Accordingly, we have been able to correlate changes in nucleosome occupancy to changes in transcriptional activity in a large number of genes and relate those changes to the presence of previously predicted transcription factor binding motifs.…”

mentioning

confidence: 99%

“…The microarray data are available for download from http://puma.princeton.edu/publications.html. Yeast mRNA expression data have been published previously (Zaman et al, 2009). …”

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Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae

Zawadzki

Morozov

Broach

2009

MBoC

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Several well-studied promoters in yeast lose nucleosomes upon transcriptional activation and gain them upon repression, an observation that has prompted the model that transcriptional activation and repression requires nucleosome remodeling of regulated promoters. We have examined global nucleosome positioning before and after glucose-induced transcriptional reprogramming, a condition under which more than half of all yeast genes significantly change expression. The majority of induced and repressed genes exhibit no change in promoter nucleosome arrangement, although promoters that do undergo nucleosome remodeling tend to contain a TATA box. Rather, we found multiple examples where the pre-existing accessibility of putative transcription factor binding sites before glucose addition determined whether the corresponding gene would change expression in response to glucose addition. These results suggest that selection of appropriate transcription factor binding sites may be dictated to a large extent by nucleosome prepositioning but that regulation of expression through these sites is dictated not by nucleosome repositioning but by changes in transcription factor activity. INTRODUCTIONChromatin, whose basic unit is a nucleosome that consists of 147 base pairs of DNA wrapped twice around a histone octamer, plays a central role in the regulation of genes. Several experiments in yeast have shown that nucleosome depletion causes derepression of PHO5, GAL1, CUP1, SUC2, and HIS3 in the absence of their transcriptional activators Durrin et al., 1992;Hirschhorn et al., 1992). These observations suggested that nucleosomes in promoters can function as nonspecific repressors, consistent with the concept that DNA sequences incorporated into nucleosomes are less accessible to DNA binding proteins such as transcription factors (Morse, 2003(Morse, , 2007. Subsequent observations have demonstrated that chromatin structure can participate actively in gene regulation through repositioning of nucleosomes so as to block access of a transcription factor to its cognate binding sites or to remove a barrier to such access. Consistent with this notion, several examples have been reported in which gene induction involves recruitment to a promoter of chromatin remodeling factors and histone modifying activities designed to remove or reposition a nucleosome to allow access to an otherwise masked transcription factor binding site (Li et al., 2007;Williams and Tyler, 2007). For example, remodeling factors act at the above-mentioned promoters for PHO5, GAL1, CUP1, and SUC2 to facilitate nucleosome loss on transcriptional activation and conversely to assemble or stabilize nucleosomes on the gene promoter during transcriptional repression (Almer et al., 1986;Fedor and Kornberg, 1989;Shen et al., 2001;Kim et al., 2006).Chromatin can also play a more passive role in gene regulation by simply controlling which transcription factor binding sites are available for participation in gene regulation. Recent genome-wide studies of nucleosome positioning fo...

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Section: Nucleosomal Dna Isolationmentioning

confidence: 99%

Section: Genome-wide Positions Of Nucleosomes In Saccharomycesmentioning

confidence: 99%

Section: Functional Transcription Factor Binding Motifs Reside In Regmentioning

confidence: 99%

mentioning

confidence: 99%

“…The microarray data are available for download from http://puma.princeton.edu/publications.html. Yeast mRNA expression data have been published previously (Zaman et al, 2009). …”

mentioning

confidence: 99%

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Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae

Zawadzki

Morozov

Broach

2009

MBoC

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Cancer Metabolism

Pavlova

Thompson

2016

Holland‐Frei Cancer Medicine

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Overview Successful cell proliferation is dependent on a profound remodeling of cellular metabolism, required to support the biosynthetic needs of a growing cell. Constitutive signaling through aberrantly activated oncogenes activates pro‐growth metabolic circuits that can lock cancer cells into net macromolecular synthesis and resistance to cell death. Oncogenic signaling can induce cellular uptake of metabolic substrates, such as glucose and glutamine, as well as utilization of unconventional nutrient sources. In contrast to nonproliferating tissues, which preferentially oxidize acquired metabolic substrates in mitochondria to fuel the oxidative phosphorylation and energy production, cancer cells prioritize the use of acquired metabolic substrates in anabolic processes, including fatty acid, cholesterol, nonessential amino acid, and nucleotide biosynthesis. The accumulation of these precursors supports the synthesis of the macromolecules necessary to sustain cell growth. Oncogene‐directed increases in levels of select metabolites can also influence cellular processes beyond metabolic circuits, resulting in changes to the cellular epigenetic state as well as long‐ranging effects on cells within the tumor microenvironment. Recent studies suggest these alterations in tumor cell metabolism can be exploited to improve the diagnosis and treatment of a wide variety of cancers.

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mRNA Degradation and Decay

Fromont‐Racine

Saveanu

2014

Fungal RNA Biology

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International audienceWhy is it important to understand mRNA degradation in a cell? First,RNA degradation has a clearing function and removes RNAs arising from tran-scription, splicing, export, or translation “accidents” to ensure robust geneexpression (see Chap. 8). Second, while regulation of gene expression has a veryimportant transcription component, mRNAs must be turned over rapidly for fastchanges in transcriptome composition. Coordinated destabilization of an entireclass of mRNAs can promote major physiological changes in a cell. Third, specificmechanisms of mRNA decay can serve to regulate gene expression throughfeedback control. Research on these topics has been frequently done first withyeasts and led to a better understanding of gene expression in eukaryotes. We startwith an overview of the methods for measuring mRNA decay on a large scale withan emphasis on how technical issues affect the current picture of global mRNAdecay in yeast. Next, we describe the importance of nuclear degradation in shapingthe stable transcriptome. Once in the cytoplasm, mRNAs are exposed to translationand we provide an overview of the complexes and individual enzymes that ensureprogressive deadenylation, mRNA decapping, and 5 ́ to 3 ́ or 3 ́ to 5 ́ exonucle-olytic RNA degradation. Finally, how organelle transcripts are degraded inmitochondria is briefly exposed

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Glucose regulates transcription in yeast through a network of signaling pathways

Abstract: Correction to: Molecular Systems Biology 5 :245. doi:10.1038/msb.2009.2; published online 17 February 2009

Cited by 59 publications

References 0 publications

Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae

Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae

Cancer Metabolism

mRNA Degradation and Decay

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