scholarly journals Role of the Saccharomyces cerevisiae general regulatory factor CP1 in methionine biosynthetic gene transcription.

1995 ◽  
Vol 15 (4) ◽  
pp. 1879-1888 ◽  
Author(s):  
K F O'Connell ◽  
Y Surdin-Kerjan ◽  
R E Baker
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Gene Transcription ◽  
Chromatin Structure ◽  
Micrococcal Nuclease ◽  
Regulatory Factor ◽  
Lacz Reporter ◽  
Endogenous Gene ◽  
Cis Acting ◽  
Nuclease Digestion

Saccharomyces cerevisiae general regulatory factor CP1 (encoded by the gene CEP1) is required for optimal chromosome segregation and methionine prototrophy. MET16-CYC1-lacZ reporter constructs were used to show that MET16 5'-flanking DNA contains a CP1-dependent upstream activation sequence (UAS). Activity of the UAS required an intact CP1-binding site, and the effects of cis-acting mutations on CP1 binding and UAS activity correlated. In most respects, MET16-CYC1-lacZ reporter gene expression mirrored that of chromosomal MET16; however, the endogenous gene was found to be activated in response to amino acid starvation (general control). The latter mechanism was both GCN4 and CP1 dependent. MET25 was also found to be activated by GCN4, albeit weakly. More importantly, MET25 transcription was strongly CP1 dependent in gcn4 backgrounds. The modulation of MET gene expression by GCN4 can explain discrepancies in the literature regarding CP1 dependence of MET gene transcription. Lastly, micrococcal nuclease digestion and indirect end labeling were used to analyze the chromatin structure of the MET16 locus in wild-type and cep1 cells. The results indicated that CP1 plays no major role in configuring chromatin structure in this region, although localized CP1-specific differences in nuclease sensitivity were detected.

scholarly journals The chromatin structure at the promoter of a glyceraldehyde phosphate dehydrogenase gene from Saccharomyces cerevisiae reflects its functional state.

1988 ◽  
Vol 8 (12) ◽  
pp. 5513-5520 ◽  
Author(s):  
B Pavlović ◽  
W Hörz
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromatin Structure ◽  
Carbon Sources ◽  
Initiation Site ◽  
Wild Type ◽  
Cis Acting ◽  
Genes Encoding ◽  
Nuclease Digestion ◽  
Dna Elements ◽  
Regulatory Dna

The chromatin structure of TDH3, one of three genes encoding glyceraldehyde phosphate dehydrogenases in Saccharomyces cerevisiae, was analyzed by nuclease digestion. A large hypersensitive region was found at the TDH3 promoter extending from the RNA initiation site at position -40 to position -560. This hypersensitive domain is nucleosome free and includes all putative cis-acting regulatory DNA elements. It is equally present in cells grown on fermentable as well as nonfermentable carbon sources. In a mutant which lacks the trans-activating protein GCR1 and which as a consequence expresses TDH3 at less than 5% of the wild-type level, the chromatin structure is different. Hypersensitivity between -40 and -370 is lost, due to the deposition of nucleosomes on a stretch that is nucleosome free in wild-type cells. Hypersensitivity is retained, however, further upstream (from -370 to -560). A similarly altered chromatin structure, as in a ger1 mutant, is found in wild-type cells when they approach stationary phase. This is the first evidence for a growth-dependent regulation of the TDH3 promoter.

The chromatin structure at the promoter of a glyceraldehyde phosphate dehydrogenase gene from Saccharomyces cerevisiae reflects its functional state

1988 ◽  
Vol 8 (12) ◽  
pp. 5513-5520
Author(s):  
B Pavlović ◽  
W Hörz
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromatin Structure ◽  
Carbon Sources ◽  
Initiation Site ◽  
Wild Type ◽  
Cis Acting ◽  
Genes Encoding ◽  
Nuclease Digestion ◽  
Dna Elements ◽  
Regulatory Dna

The chromatin structure of TDH3, one of three genes encoding glyceraldehyde phosphate dehydrogenases in Saccharomyces cerevisiae, was analyzed by nuclease digestion. A large hypersensitive region was found at the TDH3 promoter extending from the RNA initiation site at position -40 to position -560. This hypersensitive domain is nucleosome free and includes all putative cis-acting regulatory DNA elements. It is equally present in cells grown on fermentable as well as nonfermentable carbon sources. In a mutant which lacks the trans-activating protein GCR1 and which as a consequence expresses TDH3 at less than 5% of the wild-type level, the chromatin structure is different. Hypersensitivity between -40 and -370 is lost, due to the deposition of nucleosomes on a stretch that is nucleosome free in wild-type cells. Hypersensitivity is retained, however, further upstream (from -370 to -560). A similarly altered chromatin structure, as in a ger1 mutant, is found in wild-type cells when they approach stationary phase. This is the first evidence for a growth-dependent regulation of the TDH3 promoter.

Proximal cis-acting elements cooperate to set Hoxb-7 (Hox-2.3) expression boundaries in transgenic mice

Development ◽  
1993 ◽  
Vol 118 (1) ◽  
pp. 71-82 ◽  
Author(s):  
R. Vogels ◽  
J. Charite ◽  
W. de Graaff ◽  
J. Deschamps
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Hox Genes ◽  
Gene Clustering ◽  
Lacz Gene ◽  
Dependent Manner ◽  
Endogenous Gene ◽  
Cis Acting ◽  
Gene Map ◽  
Partial Overlap

The Hox genes have been proved to be instrumental in establishing the positional identity of cells along the embryonic anteroposterior (A-P) axis. Studying the regulation of these genes is a first step toward elucidating the molecular basis of regionalization during embryogenesis. We report here on the identification of cis-acting elements controlling the expression of Hoxb-7 (Hox-2.3). We show that elements driving A-P restricted gene expression are located within the 3.5 kb proximal upstream sequences of the Hoxb-7 gene. A deletion analysis provides evidence for at least three cis-acting control elements upstream from Hoxb-7, and for cooperative interactions between some of these elements in generating the A-P restricted transgenic pattern. One element, conferring by itself Hox-like expression boundaries to the transgene, has been studied in more detail and found to act in an orientation-and promoter-dependent manner. Together the 3.5 kb sequences proximal to Hoxb-7 mediate A-P restricted Hoxb-7/lacZ gene expression in a domain showing rostral boundaries more posterior than those of Hoxb-7. The evolution throughout embryogenesis of the expression pattern of a transgene carrying these sequences has been analysed and shown to mimick that of the endogenous gene, except for a slight delay in the initial expression. We conclude that the transgenes that we tested, spanning a total of 27 kb genomic sequences, do not reproduce all the features of the Hoxb-7 expression pattern. The differences in expression between Hoxb-7 and the transgenes may reveal an aspect of the Hox regulation for which either remote cis-acting control elements and/or gene clustering is required. Additional features that may have favoured maintenance of clustered organisation during evolution are partial overlap of transcription units with the regulatory regions of the neighbouring genes, and cis-regulatory interactions between multiple Hox genes: not only do cis-acting control elements of the Hoxb-7 gene map in the 3′ untranslated sequences of the Hoxb-8 (Hox-2.4) gene, but our experiments suggest that Hoxb-7 control sequences modulate expression of the Hoxb-8 gene as well.

scholarly journals Determination of the Global Pattern of Gene Expression in Yeast Cells by Intracellular Levels of Guanine Nucleotides

mBio ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Andy Hesketh ◽  
Marta Vergnano ◽  
Stephen G. Oliver
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Carbon Source ◽  
Gene Transcription ◽  
Adenine Nucleotide ◽  
High Energy ◽  
Yeast Cells ◽  
Purine Nucleotides ◽  
Global Pattern ◽  
Content Type

ABSTRACT Correlations between gene transcription and the abundance of high-energy purine nucleotides in Saccharomyces cerevisiae have often been noted. However, there has been no systematic investigation of this phenomenon in the absence of confounding factors such as nutrient status and growth rate, and there is little hard evidence for a causal relationship. Whether transcription is fundamentally responsive to prevailing cellular energetic conditions via sensing of intracellular purine nucleotides, independently of specific nutrition, remains an important question. The controlled nutritional environment of chemostat culture revealed a strong correlation between ATP and GTP abundance and the transcription of genes required for growth. Short pathways for the inducible and futile consumption of ATP or GTP were engineered into S. cerevisiae, permitting analysis of the transcriptional effect of an increased demand for these nucleotides. During steady-state growth using the fermentable carbon source glucose, the futile consumption of ATP led to a decrease in intracellular ATP concentration but an increase in GTP and the guanylate energy charge (GEC). Expression of transcripts encoding proteins involved in ribosome biogenesis, and those controlled by promoters subject to SWI/SNF-dependent chromatin remodelling, was correlated with these nucleotide pool changes. Similar nucleotide abundance changes were observed using a nonfermentable carbon source, but an effect on the growth-associated transcriptional programme was absent. Induction of the GTP-cycling pathway had only marginal effects on nucleotide abundance and gene transcription. The transcriptional response of respiring cells to glucose was dampened in chemostats induced for ATP cycling, but not GTP cycling, and this was primarily associated with altered adenine nucleotide levels. IMPORTANCE This paper investigates whether, independently of the supply of any specific nutrient, gene transcription responds to the energy status of the cell by monitoring ATP and GTP levels. Short pathways for the inducible and futile consumption of ATP or GTP were engineered into the yeast Saccharomyces cerevisiae, and the effect of an increased demand for these purine nucleotides on gene transcription was analyzed. The resulting changes in transcription were most consistently associated with changes in GTP and GEC levels, although the reprogramming in gene expression during glucose repression is sensitive to adenine nucleotide levels. The results show that GTP levels play a central role in determining how genes act to respond to changes in energy supply and that any comprehensive understanding of the control of eukaryotic gene expression requires the elucidation of how changes in guanine nucleotide abundance are sensed and transduced to alter the global pattern of transcription.

scholarly journals CHD8 Is an ATP-Dependent Chromatin Remodeling Factor That Regulates β-Catenin Target Genes

2008 ◽  
Vol 28 (12) ◽  
pp. 3894-3904 ◽  
Author(s):  
Brandi A. Thompson ◽  
Véronique Tremblay ◽  
Grace Lin ◽  
Daniel A. Bochar
Keyword(s):  
Gene Expression ◽  
Rna Interference ◽  
Chromatin Remodeling ◽  
Gene Transcription ◽  
Chromatin Structure ◽  
Target Genes ◽  
Promoter Regions ◽  
Hairpin Rna ◽  
Short Hairpin ◽  
Targeted Gene Expression

ABSTRACT ATP-dependent chromatin remodeling by the CHD family of proteins plays an important role in the regulation of gene transcription. Here we report that full-length CHD8 interacts directly with β-catenin and that CHD8 is also recruited specifically to the promoter regions of several β-catenin-responsive genes. Our results indicate that CHD8 negatively regulates β-catenin-targeted gene expression, since short hairpin RNA against CHD8 results in the activation of several β-catenin target genes. This regulation is also conserved through evolution; RNA interference against kismet, the apparent Drosophila ortholog of CHD8, results in a similar activation of β-catenin target genes. We also report the first demonstration of chromatin remodeling activity for a member of the CHD6-9 family of proteins, suggesting that CHD8 functions in transcription through the ATP-dependent modulation of chromatin structure.

scholarly journals cis-Dominant mutations which dramatically enhance DUR1,2 gene expression without affecting its normal regulation.

1984 ◽  
Vol 4 (5) ◽  
pp. 947-955 ◽  
Author(s):  
G Chisholm ◽  
T Cooper
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Control System ◽  
Normal Control ◽  
Chromatin Structure ◽  
Catabolite Repression ◽  
Mutant Phenotype ◽  
Nitrogen Catabolite Repression ◽  
Upstream Control ◽  
Affect Gene Expression

We have isolated three cis-dominant mutations which dramatically enhance DUR1 ,2 gene expression in Saccharomyces cerevisiae. The mutant phenotype, which is expressed both in haploid and MATa/MAT alpha diploid strains, does not appear to be an alteration of the normal control system for this gene because its expression remained fully inducible and sensitive to nitrogen catabolite repression. Instead, we found much higher levels of DUR1 ,2-specific RNA under both uninduced and induced conditions, i.e., the overproduction trait was superimposed on normal regulation of the gene. The mutations seemed to affect gene expression in a unidirectional manner or to be specific for DUR1 ,2 gene expression, because other genes in proximity to the mutations were not affected. We feel that these mutations may alter the chromatin structure in the vicinity of the DUR1 ,2 upstream control sequences or, alternatively, may be Ty insertions which no longer possess the ROAM characteristics reported by others and ourselves.

scholarly journals Requirement of Multiple cis-Acting Elements in the Human Cytomegalovirus Major Immediate-Early Distal Enhancer for Viral Gene Expression and Replication

2002 ◽  
Vol 76 (1) ◽  
pp. 313-326 ◽  
Author(s):  
Jeffery L. Meier ◽  
Michael J. Keller ◽  
James J. McCoy
Keyword(s):  
Gene Expression ◽  
Viral Replication ◽  
Gene Transcription ◽  
Human Cytomegalovirus ◽  
Viral Gene Expression ◽  
Immediate Early ◽  
Viral Gene ◽  
Distal Enhancer ◽  
Cis Acting ◽  
Hcmv Replication

ABSTRACT We have shown previously that the human cytomegalovirus (HCMV) major immediate-early (MIE) distal enhancer is needed for MIE promoter-dependent transcription and viral replication at low multiplicities of infection (MOI). To understand how this region works, we constructed and analyzed a series of HCMVs with various distal enhancer mutations. We show that the distal enhancer is composed of at least two parts that function independently to coordinately activate MIE promoter-dependent transcription and viral replication. One such part is contained in a 47-bp segment that has consensus binding sites for CREB/ATF, SP1, and YY1. At low MOI, these working parts likely function in cis to directly activate MIE gene expression, thus allowing viral replication to ensue. Three findings support the view that these working parts are likely cis-acting elements. (i) Deletion of either part of a bisegmented distal enhancer only slightly alters MIE gene transcription and viral replication. (ii) Reversing the distal enhancer’s orientation largely preserves MIE gene transcription and viral replication. (iii) Placement of stop codons at −300 or −345 in all reading frames does not impair MIE gene transcription and viral replication. Lastly, we show that these working parts are dispensable at high MOI, partly because of compensatory stimulation of MIE promoter activity and viral replication that is induced by a virion-associated component(s) present at a high viral particle/cell ratio. We conclude that the distal enhancer is a complex multicomponent cis-acting region that is required to augment both MIE promoter-dependent transcription and HCMV replication.

Regulation of gene expression by insulin

1996 ◽  
Vol 76 (4) ◽  
pp. 1109-1161 ◽  
Author(s):  
R. M. O'Brien ◽  
D. K. Granner
Keyword(s):  
Gene Expression ◽  
Gene Transcription ◽  
Regulation Of Gene Expression ◽  
Insulin Dependent Diabetes Mellitus ◽  
Dependent Diabetes Mellitus ◽  
Intracellular Location ◽  
Cis Acting ◽  
Transactivation Potential ◽  
Insulin Dependent ◽  
Intracellular Metabolism

While insulin has long been known to modulate intracellular metabolism by altering the activity or intracellular location of various enzymes, it is only in the past 10 years that the regulation of gene expression by insulin has been recognized as a major action of this hormone. This review principally focuses on the regulation of gene transcription by insulin, although recent progress in the understanding of insulin-regulated mRNA stability and translation is also summarized. The identification of cis-acting elements and associated trans-acting factors through which insulin either increases or decreases the transcription of specific genes is reviewed in detail. Recent advances in the understanding of the mechanisms of insulin signaling are discussed in the context of insulin-regulated gene transcription, and emphasis is placed on the gaps that remain between the upstream signaling molecules and the downstream trans-acting factors whose binding/transactivation potential is ultimately regulated. Finally, potential gene expression defects that may contribute to the pathophysiology of non-insulin-dependent diabetes mellitus and hypertriglyceridemia are considered.

scholarly journals Chromatin remodelling of the cardiac β-myosin heavy chain gene

1998 ◽  
Vol 330 (2) ◽  
pp. 871-876 ◽  
Author(s):  
Weei-Yuarn HUANG ◽  
Choong-Chin LIEW
Keyword(s):  
Gene Expression ◽  
Chromatin Structure ◽  
Dnase I ◽  
Micrococcal Nuclease ◽  
Proximal Promoter ◽  
Chain Gene ◽  
Cardiac Gene Expression ◽  
Cardiac Gene ◽  
Hamster Heart ◽  
Adult Hamster

To investigate the role of chromatin structure in cardiac gene expression, we used the DNase I and micrococcal nuclease to probe the chromatin structure of the hamster cardiac β-MyHC gene. Two cardiac-specific DNase I hypersensitive sites (DHS) were identified, one of which was mapped to the -2.3 kb (β-2.3 kb) region and the other to the proximal promoter region of the β-MyHC gene. The two sites were readily detectable using nuclei from neonatal hamster heart; however, the proximal promoter site disappeared when adult hamster heart nuclei were used, and the -2.3 kb site decreased in intensity. We were able to demonstrate the gradual disappearance of this proximal promoter DHS by comparing heart nuclei isolated from animals at late-gestation and 1-day-old stages. Furthermore, injecting thyroid hormone caused the disappearance of the proximal promoter DHS in late gestational fetal ventricular nuclei. Digestion of nuclei from various tissues by micrococcal nuclease revealed that the β-MyHC gene proximal promoter exists in an array of three specifically-positioned nucleosomes only in fetal heart chromatin. The β-MyHC gene proximal promoter is DNase I hypersensitive within one of the nucleosomal particles. Our data suggest that chromatin structure may participate actively in cardiac gene expression.

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