DNase I sensitivity of the chromatin of the yeast SUC2 gene for invertase

Pérez‐Ortín, José E.; Estruch, Francisco; Matallana, Emilia; Franco, Luís

doi:10.1007/bf00338077

Cited by 18 publications

(7 citation statements)

References 33 publications

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“…Ladders of fuzzy bands both upstream and downstream of the hypersensitive site were visible, especially in the repressed state. This kind of DNase I bands has been previously found in yeast and interpreted as the result of a somewhat preferential attack to linker DNA (Perez-Ortin et al, 1986a, 1987Szent-Giorgyi et al, 1987). Identical results were obtained with the genomic copy of FBPI when the experiments were carried out with untransformed CJM88 cells (not shown).…”

Section: A) Promoter (Probe Eh)supporting

confidence: 66%

“…At any rate, it is remarkable that hypersensitive sites close to the 3' end have been found in many yeast genes, e.g. SUC2 (Perez-Ortin et al, 1986a), HSP82 (Szent-Giorgyi et al, 1987), TRPl (Thoma et al, 1984), CZN2 (Lee and Garrard, 1991), URA3 (Thoma, 1986). In all these cases the hypersensitive sites are flanked by positioned nucleosomes and in some instances it has been shown that positioning results from a boundary effect due to the structure of the hypersensitive site (Matallana et al, in preparation;Thoma, 1986).…”

Section: Chromatin Structure Of the 3'jlankmentioning

confidence: 99%

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Chromatin structure of the yeast FBP1 gene: Transcription‐dependent changes in the regulatory and coding regions

Olmo

Sogo²,

Franco

et al. 1993

Yeast

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We have studied the chromatin structure of the Saccharomyces cerevisiae FBP1 gene, which codes for fructose‐1,6‐bisphosphatase. A strong, constitutive, DNase I, micrococcal nuclease and S1 nuclease hypersensitive site is present close to the 3′ end of the coding region. In the repressed state, positioned nucleosomes exist around this site, and subtle changes occur in this nucleosomal organization upon derepression. A DNase I hypersensitive region is located within the promoter between positions −540 and −400 and it extends towards the gene in the derepressed state, leading to an alteration of nucleosomal positioning. Psoralen crosslinking of chromatin, which is used for the first time to study the mobility of restriction fragments from an RNA polymerase II gene, revealed that part of the promoter is nucleosome‐free, in accordance with the results of DNase I digestion. A model is presented that, based on the chromatin structure, puts forward the hypothesis that the promoter UAS is located between − 540 and − 340. Finally, psoralen crosslinking, as well as digestions with micrococcal nuclease or restriction endonucleases suggests that most if not all of the copies of the active FBP1 gene are covered by nucleosomes.

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Section: A) Promoter (Probe Eh)supporting

confidence: 66%

Section: Chromatin Structure Of the 3'jlankmentioning

confidence: 99%

Chromatin structure of the yeast FBP1 gene: Transcription‐dependent changes in the regulatory and coding regions

Olmo

Sogo²,

Franco

et al. 1993

Yeast

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“…Another interesting feature of the promoter structure is the fact that the hypersensitive site becomes MNase resistant upon activation (compare for example in Figure 3, CHA4 −Ser and +Ser), although it maintains its accessibility to DNase I (compare for example Figure 1, +Ser with Figure 3, CHA4 +Ser). This peculiar change has been observed in other genes, namely in the UAS of the GAL1‐10 genes (Lohr and Hopper, 1985) and in the regulatory region of the SUC2 gene (Perez‐Ortin et al ., 1986, 1987) under derepressed conditions. In the CHA1 promoter, this change is specifically dependent on the transcriptional state of the gene, that is, even under derepressed conditions this MNase‐specific protection is not seen unless the gene is actively being transcribed.…”

Section: Discussionmentioning

confidence: 69%

Nucleosome structure of the yeast CHA1 promoter: analysis of activation-dependent chromatin remodeling of an RNA-polymerase-II-transcribed gene in TBP and RNA pol II mutants defective invivo in response to acidic activators

Moreira

Holmberg

1998

The EMBO Journal

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The Saccharomyces cerevisiae CHA1 gene encodes the catabolic L-serine (L-threonine) dehydratase. We have previously shown that the transcriptional activator protein Cha4p mediates serine/threonine induction of CHA1 expression. We used accessibility to micrococcal nuclease and DNase I to determine the in vivo chromatin structure of the CHA1 chromosomal locus, both in the non-induced state and upon induction. Upon activation, a precisely positioned nucleosome (nuc-1) occluding the TATA box and the transcription start site is removed. A strain devoid of Cha4p showed no chromatin alteration under inducing conditions. Five yeast TBP mutants defective in different steps in activated transcription abolished CHA1 expression, but failed to affect induction-dependent chromatin rearrangement of the promoter region. Progressive truncations of the RNA polymerase II C-terminal domain caused a progressive reduction in CHA1 transcription, but no difference in chromatin remodeling. Analysis of swi1, swi3, snf5 and snf6, as well as gcn5, ada2 and ada3 mutants, suggested that neither the SWI/SNF complex nor the ADA/GCN5 complex is involved in efficient activation and/or remodeling of the CHA1 promoter. Interestingly, in a sir4 deletion strain, repression of CHA1 is partly lost and activatorindependent remodeling of nuc-1 is observed. We propose a model for CHA1 activation based on promoter remodeling through interactions of Cha4p with chromatin components other than basal factors and associated proteins.

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“…This basal acetylation is high around the upstream activating sequence (Fig. 2), where a DNase I hypersensitive site exists (1). A relatively high, transcription-independent, basal level of histone acetylation is common in yeast (48), but the mechanisms for maintaining this nontargeted level of acetylation are not clear.…”

Section: Discussionmentioning

confidence: 99%

A Short-range Gradient of Histone H3 Acetylation and Tup1p Redistribution at the Promoter of the Saccharomyces cerevisiae SUC2 Gene

Boukaba

Georgieva

Myers³

et al. 2004

Journal of Biological Chemistry

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Chromatin immunoprecipitation assays are used to map H3 and H4 acetylation over the promoter nucleosomes and the coding region of the Saccharomyces cerevisiae SUC2 gene, under repressed and derepressed conditions, using wild type and mutant strains. In wild type cells, a high level of H3 acetylation at the distal end of the promoter drops sharply toward the proximal nucleosome that covers the TATA box, a gradient that become even steeper on derepression. In contrast, substantial H4 acetylation shows no such gradient and extends into the coding region. Overall levels of both H3 and H4 acetylation rise on derepression. Mutation of GCN5 or SNF2 lead to substantially reduced SUC2 expression; in gnc5 there is no reduction in basal H3 acetylation, but large reductions occur on derepression. SNF2 mutation has little effect on H3 acetylation, so SAGA and SWI/SNF recruitment seem to be independent events. H4 acetylation is little affected by either GCN5 or SNF2 mutation. In a double snf2/gcn5 mutant (very low SUC2 expression), H3 acetylation is at the minimal level, but H4 acetylation remains largely unaffected. Transcription is thus linked to H3 but not H4 acetylation. Chromatin immunoprecipitation assays show that Tup1p is evenly distributed over the four promoter nucleosomes in repressed wild type cells but redistributes upstream on derepression, a movement probably linked to its conversion from a repressor to an activator.The Saccharomyces cerevisiae SUC2 gene codes for invertase, an enzyme that catalyzes the hydrolysis of sucrose and raffinose to provide the cell with glucose in the absence of this essential fuel. It has been widely used to study the mechanisms underlying glucose regulation in yeast. Because these mechanisms result in changes in chromatin structure, this has been a long-lasting field of research. We first analyzed the DNase I sensitivity of the SUC2 gene (1) as well as nucleosome positioning under repressing and derepressing conditions, in both wild type cells (2) and in regulatory mutants (3). These initial data, obtained by indirect end labeling, showed that four nucleosomes are positioned on the promoter in such a way that certain crucial elements, including the TATA box, are occluded, whereas other regulatory sequences are nucleosome-free (2). These results were refined by other workers (4, 5) who mapped the four nucleosomes at high resolution by primer extension analysis.The SUC2 gene is repressed in the presence of glucose by the Ssn6-Tup1 corepressor complex (6, 7), which is tethered to the promoter by Mig1p (8). Tup1-mediated repression of SUC2 results in deacetylation of histone H3 at the promoter, as shown by an increase in H3 acetylation in tup1 mutants, but a lack of Tup1p does not change the acetylation level of H4 (9). This result contrasts with findings for other Tup1-regulated genes in which the repression also results in deacetylation of H4 (9).The SUC2 gene is effectively derepressed by lowering the concentration of glucose (10), and several genes required for derepression were ide...

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DNase I sensitivity of the chromatin of the yeast SUC2 gene for invertase

Cited by 18 publications

References 33 publications

Chromatin structure of the yeast FBP1 gene: Transcription‐dependent changes in the regulatory and coding regions

Chromatin structure of the yeast FBP1 gene: Transcription‐dependent changes in the regulatory and coding regions

Nucleosome structure of the yeast CHA1 promoter: analysis of activation-dependent chromatin remodeling of an RNA-polymerase-II-transcribed gene in TBP and RNA pol II mutants defective invivo in response to acidic activators

A Short-range Gradient of Histone H3 Acetylation and Tup1p Redistribution at the Promoter of the Saccharomyces cerevisiae SUC2 Gene

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