Elements involved in S-adenosylmethionine-mediated regulation of the Saccharomyces cerevisiae MET25 gene

In Saccharomyces cerevisiae, the MET25 gene encodes O-acetylhomoserine sulfhydrylase. Synthesis of this enzyme is repressed by the presence of S-adenosylmethionine (AdoMet) in the growth medium. We identified cis elements required for MET25 expression by analyzing small deletions in the MET25 promoter region. The results revealed a regulatory region, acting as an upstream activation site, that activated transcription of MET25 in the absence of methionine or AdoMet. We found that, for the most part, repression of MET25 expression was due to a lack of activation at this site, reinforced by an independent repression mechanism. The activation region contained a repeated dyad sequence that is also found in the promoter regions of other unlinked but coordinately regulated genes (MET3, MET2, and SAM2). We show that the presence of the two dyads is necessary for maximal gene expression. Moreover, we demonstrate that in addition to this transcriptional regulation, a posttranscriptional regulation, probably targeted at the 5' region of mRNA, is involved in MET25 expression.

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Bidirectional titration of yeast gene expression using a pooled CRISPR guide RNA approach

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2007413117 ◽

2020 ◽

Vol 117 (31) ◽

pp. 18424-18430 ◽

Cited By ~ 2

Author(s):

Emily K. Bowman ◽

Matthew Deaner ◽

Jan-Fang Cheng ◽

Robert Evans ◽

Ernst Oberortner ◽

...

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Essential Genes ◽

Yeast Gene ◽

Promoter Regions ◽

Guide Rna ◽

Metabolic Genes ◽

Complementary Approach ◽

Modulation Of Gene Expression ◽

Generation Sequencing

Most classic genetic approaches utilize binary modifications that preclude the identification of key knockdowns for essential genes or other targets that only require moderate modulation. As a complementary approach to these classic genetic methods, we describe a plasmid-based library methodology that affords bidirectional, graded modulation of gene expression enabled by tiling the promoter regions of all 969 genes that comprise the ito977 model ofSaccharomyces cerevisiae’s metabolic network. When coupled with a CRISPR-dCas9–based modulation and next-generation sequencing, this method affords a library-based, bidirection titration of gene expression across all major metabolic genes. We utilized this approach in two case studies: growth enrichment on alternative sugars, glycerol and galactose, and chemical overproduction of betaxanthins, leading to the identification of unique gene targets. In particular, we identify essential genes and other targets that were missed by classic genetic approaches.

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Targeted modification of promoters

Genome editing for precision crop breeding - Burleigh Dodds Series in Agricultural Science ◽

10.19103/as.2020.0082.29 ◽

2021 ◽

pp. 247-278

Author(s):

Andika Gunadi ◽

◽

Ning Zhang ◽

John J. Finer ◽

◽

...

Keyword(s):

Gene Expression ◽

Genome Editing ◽

Promoter Region ◽

Regulatory Region ◽

Regulatory Elements ◽

Upstream Regulatory Region ◽

Precise Control ◽

Coding Regions ◽

Gene Coding ◽

Altered Regulation

Although most genome editing efforts focus on modifications to gene coding regions, this chapter emphasizes genome editing of the upstream regulatory regions. Thoughtful editing of the promoter region will ultimately lead to improved plants, modified for more precise control of the intensity and specificity of native gene expression. In this chapter, we present an overview of the promoter or upstream regulatory region of a gene, and describe how this sequence is defined and studied. We then describe how the composition and arrangements of cis-regulatory elements within the promoter and the leading intron associated with the promoter region have been studied using classical transgenic approaches to reveal what regulatory components might be suitable for genome editing approaches. Finally, we offer some suggestions for pursuit of promoter editing and gene expression modulation, which will eventually lead to modified plants with an altered regulation of native gene expression.

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Altered Promoter and G-Box Binding Factor for 1-Deoxy-d-Xylulose-5-Phosphate Synthase Gene Grown from Poa pratensis Seeds after Spaceflight

International Journal of Molecular Sciences ◽

10.3390/ijms20061398 ◽

2019 ◽

Vol 20 (6) ◽

pp. 1398

Author(s):

Lu Gan ◽

Yuehui Chao ◽

Haotian Su ◽

Yujing Ren ◽

Shuxia Yin ◽

...

Keyword(s):

Gene Expression ◽

Promoter Region ◽

Poa Pratensis ◽

Regulatory Region ◽

Space Environment ◽

Luciferase Assay ◽

Dwarf Mutant ◽

Transcript Accumulation ◽

Binding Factor ◽

Phosphate Synthase

In plant cells, the nucleus DNA is considered the primary site of injury by the space environment, which could generate genetic alteration. As the part of genomic mutation, genetic variation in the promoter region could regulate gene expression. In the study, it is observed that there is a deletion in the upstream regulatory region of the 1-deoxy-d-xylulose-5-phosphate synthase 1 gene (PpDXS1) of Poa pratensis dwarf mutant and the PpDXS1 transcript abundance is lower in the dwarf mutant. It is indicated that the deletion in the promoter region between wild type and dwarf mutant could be responsible for the regulation of PpDXS1 gene expression. The PpDXS1 promoter of dwarf mutant shows a lower activity as determined by dual luciferase assay in Poa pratensis protoplast, as well as the GUS activity is lower in transgenic Poa pratensis plant. To further investigate the effect of the deletion in the promoter region on PpDXS1 transcript accumulation, the transient assay and yeast one-hybrid experiment demonstrate that the deletion comprises a motif which is a target of G-box binding factor (GBF1), and the motif correlates with an increase in transactivation by GBF1 protein. Taken together, these results indicate that the deletion in the promoter of PpDXS1 isolated from dwarf mutant is sufficient to account for the decrease in PpDXS1 transcript level and GBF1 can regulate the PpDXS1 gene expression, and subsequently affect accumulation of various isoprenoids throughout the plant.

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Bioinformatics Analysis of SNPs in IL-6 Gene Promoter of Jinghai Yellow Chickens

Genes ◽

10.3390/genes9090446 ◽

2018 ◽

Vol 9 (9) ◽

pp. 446 ◽

Cited By ~ 3

Author(s):

Shijie Xin ◽

Xiaohui Wang ◽

Guojun Dai ◽

Jingjing Zhang ◽

Tingting An ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Binding Sites ◽

Promoter Region ◽

Bioinformatics Analysis ◽

Cpg Islands ◽

Regulatory Region ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Factor Binding

The proinflammatory cytokine, interleukin-6 (IL-6), plays a critical role in many chronic inflammatory diseases, particularly inflammatory bowel disease. To investigate the regulation of IL-6 gene expression at the molecular level, genomic DNA sequencing of Jinghai yellow chickens (Gallus gallus) was performed to detect single-nucleotide polymorphisms (SNPs) in the region −2200 base pairs (bp) upstream to 500 bp downstream of IL-6. Transcription factor binding sites and CpG islands in the IL-6 promoter region were predicted using bioinformatics software. Twenty-eight SNP sites were identified in IL-6. Four of these 28 SNPs, three [−357 (G > A), −447 (C > G), and −663 (A > G)] in the 5′ regulatory region and one in the 3′ non-coding region [3177 (C > T)] are not labelled in GenBank. Bioinformatics analysis revealed 11 SNPs within the promoter region that altered putative transcription factor binding sites. Furthermore, the C-939G mutation in the promoter region may change the number of CpG islands, and SNPs in the 5′ regulatory region may influence IL-6 gene expression by altering transcription factor binding or CpG methylation status. Genetic diversity analysis revealed that the newly discovered A-663G site significantly deviated from Hardy-Weinberg equilibrium. These results provide a basis for further exploration of the promoter function of the IL-6 gene and the relationships of these SNPs to intestinal inflammation resistance in chickens.

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Genome-Wide Relationships between TAF1 and Histone Acetyltransferases in Saccharomyces cerevisiae

Molecular and Cellular Biology ◽

10.1128/mcb.26.7.2791-2802.2006 ◽

2006 ◽

Vol 26 (7) ◽

pp. 2791-2802 ◽

Cited By ~ 36

Author(s):

Melissa Durant ◽

B. Franklin Pugh

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Histone Acetylation ◽

Rna Polymerase Ii ◽

Histone Acetyltransferases ◽

Histone H4 ◽

Promoter Regions ◽

Genome Wide ◽

Acetylated Histone H4

ABSTRACT Histone acetylation regulates gene expression, yet the functional contributions of the numerous histone acetyltransferases (HATs) to gene expression and their relationships with each other remain largely unexplored. The central role of the putative HAT-containing TAF1 subunit of TFIID in gene expression raises the fundamental question as to what extent, if any, TAF1 contributes to acetylation in vivo and to what extent it is redundant with other HATs. Our findings herein do not support the basic tenet that TAF1 is a major HAT in Saccharomyces cerevisiae, nor do we find that TAF1 is functionally redundant with other HATs, including Gcn5, Elp3, Hat1, Hpa2, Sas3, and Esa1, which is in contrast to previous conclusions regarding Gcn5. Our findings do reveal that of these HATs, only Gcn5 and Esa1 contribute substantially to gene expression genome wide. Interestingly, histone acetylation at promoter regions throughout the genome does not require TAF1 or RNA polymerase II, indicating that most acetylation is likely to precede transcription and not depend upon it. TAF1 function has been linked to Bdf1, which binds TFIID and acetylated histone H4 tails, but no linkage between TAF1 and the H4 HAT Esa1 has been established. Here, we present evidence for such a linkage through Bdf1.

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Control of Sporulation Gene Expression in Bacillus subtilis by the Chromosome Partitioning Proteins Soj (ParA) and Spo0J (ParB)

Journal of Bacteriology ◽

10.1128/jb.182.12.3446-3451.2000 ◽

2000 ◽

Vol 182 (12) ◽

pp. 3446-3451 ◽

Cited By ~ 62

Author(s):

John D. Quisel ◽

Alan D. Grossman

Keyword(s):

Gene Expression ◽

Bacillus Subtilis ◽

Promoter Region ◽

Null Mutant ◽

Promoter Regions ◽

Heterologous Promoter ◽

Phosphorylated Form ◽

Chromosome Partitioning ◽

Inhibit Gene Expression

ABSTRACT Two chromosome partitioning proteins, Soj (ParA) and Spo0J (ParB), regulate the initiation of sporulation in Bacillus subtilis. In a spo0J null mutant, sporulation is inhibited by the action of Soj. Soj negatively regulates expression of several sporulation genes by binding to the promoter regions and inhibiting transcription. All of the genes known to be inhibited by Soj are also activated by the phosphorylated form of the transcription factor Spo0A (Spo0A∼P). We found that, in a spo0J null mutant, Soj affected sporulation, in part, by decreasing the level of Spo0A protein. Soj negatively regulated transcription ofspo0A and associated with the spo0A promoter region in vivo. Expression of spo0A from a heterologous promoter in a spo0J null mutant restored Spo0A levels and partly bypassed the sporulation and gene expression defects. Soj did not appear to significantly affect phosphorylation of Spo0A. Thus, in the absence of Spo0J, Soj inhibits sporulation and sporulation gene expression by inhibiting accumulation of the activator protein Spo0A and by acting downstream of Spo0A to inhibit gene expression directly.

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Structure and distribution of specific cis-elements for transcriptional regulation of PH084 in Saccharomyces cerevisiae

MGG Molecular & General Genetics ◽

10.1007/bf00287102 ◽

1995 ◽

Vol 249 (4) ◽

pp. 406-416 ◽

Cited By ~ 26

Author(s):

Nobuo Ogawa ◽

Hiroyuki Saitoh ◽

Kenji Miura ◽

Jose Paolo Vinco Magbanua ◽

Masanori Bun-ya ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Transcriptional Regulation ◽

Cis Elements

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Transcriptional regulation of a sterol-biosynthetic enzyme by sterol levels in Saccharomyces cerevisiae.

Molecular and Cellular Biology ◽

10.1128/mcb.16.8.3981 ◽

1996 ◽

Vol 16 (8) ◽

pp. 3981-3989 ◽

Cited By ~ 46

Author(s):

D Dimster-Denk ◽

J Rine

Keyword(s):

Saccharomyces Cerevisiae ◽

Transcriptional Regulation ◽

Feedback Control ◽

Dna Sequences ◽

Promoter Region ◽

Mevalonate Pathway ◽

Transcriptional Level ◽

Biosynthetic Enzyme ◽

Animal Cells ◽

Regulatory Response

Sterols and all nonsterol isoprenoids are derived from the highly conserved mevalonate pathway. In animal cells, this pathway is regulated in part at the transcriptional level through the action of sterol response element-binding proteins acting at specific DNA sequences near promoters. Here we extend at least part of this regulatory paradigm to the ERG10 gene, which encodes a sterol-biosynthetic enzyme of Saccharomyces cerevisiae. Specifically, the discovery of sterol-mediated feedback control of ERG10 transcription is reported. Deletion analysis of the ERG10 promoter region identified sequences involved in the expression of ERG10. This regulatory axis appeared to involve sterol levels, as a late block in the pathway that depletes sterol, but not nonsterol isoprenoids, was able to elicit the regulatory response.

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Functional analysis of haplotypes and promoter activity at the 5' region of the DRD2 gene and associations with schizophrenia.

10.21203/rs.3.rs-15812/v1 ◽

2020 ◽

Author(s):

Xicen Zhang ◽

Mei Ding ◽

Yi Liu ◽

Yongping Liu ◽

Jiaxin Xing ◽

...

Keyword(s):

Gene Expression ◽

Cell Lines ◽

Promoter Region ◽

Regulatory Region ◽

Gene Promoter ◽

Luciferase Reporter ◽

Drd2 Gene ◽

Functional Regions

Abstract Background: In previous studies, we researched the association of the DRD2 gene promoter region SNP loci rs7116768, rs1047479195, rs1799732, rs1799978 and schizophrenia using Sanger sequencing. rs7116768 and rs1799978 were found to be slightly associated with schizophrenia. This study investigated the effects of haplotypes consisted of the four SNPs on protein expression level in vitro and identified the functional sequence in the 5’ regulatory region of DRD2 gene which has a potential link with schizophrenia.Methods: Recombinant plasmids with haplotypes, SNPs and 13 recombinant vectors containing deletion fragments from the DRD2 gene 5' regulatory region were transfected into HEK293 and SK-N-SH cell lines. Relative luciferase activity of the haplotypes, SNPs and different sequences was compared using a dual luciferase reporter assay system.Results: Haplotype H4(G-C-InsC-G) could significantly increase the gene expression in SK-N-SH cell lines. Allele C of rs7116768, allele A of rs1047479195 and allele del C of rs1799732 could up-regulate the gene expression. There were 5~7 functional regions in the promoter region of DRD2 gene that could affect the level of gene expression.Conclusion: We cannot rule out the possibility that different haplotypes may influence DRD2 gene expression in vivo. We observed that allele C of rs7116768, allele A of rs1047479195 and allele del C of rs1799732 could up-regulate gene expression. The truncation results confirmed the existence of functional regions in the promoter region of DRD2 gene that could affect the level of gene expression.

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