No Factors Except for the Hap Complex increase the Taka-amylase A Gene Expression by Binding to the CCAAT Sequence in the Promoter Region

2001 ◽  
Vol 65 (10) ◽  
pp. 2340-2342 ◽  
Author(s):  
Masashi KATO ◽  
Fumiko NARUSE ◽  
Tetsuo KOBAYASHI ◽  
Norihiro TSUKAGOSHI
Keyword(s):  
Gene Expression ◽  
Promoter Region ◽  
Hap Complex ◽  
Complex Increase ◽  
Ccaat Sequence

scholarly journals Assessing the Genome-Wide Effect of Promoter Region Tandem Repeat Natural Variation on Gene Expression

2012 ◽  
Vol 2 (12) ◽  
pp. 1643-1649 ◽  
Author(s):  
Martha H. Elmore ◽  
John G. Gibbons ◽  
Antonis Rokas
Keyword(s):  
Gene Expression ◽  
Tandem Repeat ◽  
Promoter Region ◽  
Natural Variation ◽  
Genome Wide

AVP-induced VIT32 gene expression in collecting duct cells occurs via trans-activation of a CRE in the 5′-flanking region of the VIT32 gene

2004 ◽  
Vol 287 (3) ◽  
pp. F460-F468 ◽  
Author(s):  
Christie P. Thomas ◽  
Randy W. Loftus ◽  
Kang Z. Liu
Keyword(s):  
Gene Expression ◽  
Promoter Region ◽  
Collecting Duct ◽  
Airway Epithelial Cells ◽  
Proximal Promoter ◽  
Xenopus Laevis Oocytes ◽  
Proximal Promoter Region ◽  
Duct Cells ◽  
Collecting Duct Cells ◽  
Flanking Region

VIT32, a vasopressin-induced transcript, inhibits Na+ transport when coexpressed with the epithelial sodium channel in Xenopus laevis oocytes ( EMBO J 21: 5109–5117, 2002). To understand the mechanism of VIT32 gene regulation, we examined the effect of DDAVP and cAMP stimulation on VIT32 expression in M-1 mouse collecting duct cells and in H441 human airway epithelial cells. Elevation of cAMP with forskolin and IBMX increased VIT32 gene expression with a peak effect at 2 h. The increase in gene expression was abolished by H89 and by actinomycin D, suggesting that cAMP stimulates VIT32 mRNA expression by a PKA-mediated increase in gene transcription. An ∼1.5-kb fragment of the 5′-flanking region of VIT32 was cloned and was able to confer cAMP-stimulated reporter gene activity when transfected into M-1 and H441 cells. By deletion analysis and site-directed mutagenesis, a cAMP response element (CRE) was identified within the proximal promoter region that was sufficient to account for the increase in VIT32 gene expression seen with DDAVP and elevation of cAMP. Furthermore, DDAVP-stimulated VIT32 promoter-reporter activity was inhibited by H89 and by a dominant negative CREB construct. Finally, we were able to identify CREB as a nuclear protein that bound to the VIT32 CRE in gel mobility shift assays. In summary, DDAVP stimulates transcription of VIT32 via a CRE within the proximal promoter region of the VIT32 gene.

scholarly journals Unraveling the functional role of DNA methylation using targeted DNA demethylation by steric blockage of DNA methyltransferase with CRISPR/dCas9

2020 ◽  
Author(s):  
Daniel M. Sapozhnikov ◽  
Moshe Szyf
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Promoter Region ◽  
Dna Methyltransferase ◽  
Dna Demethylation ◽  
New Method ◽  
Inducible Promoters ◽  
Specific Targeting ◽  
Main Effect

AbstractAlthough associations between DNA methylation and gene expression were established four decades ago, the causal role of DNA methylation in gene expression remains unresolved. Different strategies to address this question were developed; however, all are confounded and fail to disentangle cause and effect. We developed here a highly effective new method using only deltaCas9(dCas9):gRNA site-specific targeting to physically block DNA methylation at specific targets in the absence of a confounding flexibly-tethered enzymatic activity, enabling examination of the role of DNA methylation per se in living cells. We show that the extensive induction of gene expression achieved by TET/dCas9-based targeting vectors is confounded by DNA methylation-independent activities, inflating the role of DNA methylation in the promoter region. Using our new method, we show that in several inducible promoters, the main effect of DNA methylation is silencing basal promoter activity. Thus, the effect of demethylation of the promoter region in these genes is small, while induction of gene expression by different inducers is large and DNA methylation independent. In contrast, targeting demethylation to the pathologically silenced FMR1 gene targets robust induction of gene expression. We also found that standard CRISPR/Cas9 knockout generates a broad unmethylated region around the deletion, which might confound interpretation of CRISPR/Cas9 gene depletion studies. In summary, this new method could be used to reveal the true extent, nature, and diverse contribution to gene regulation of DNA methylation at different regions.

The snail repressor establishes a muscle/notochord boundary in the Ciona embryo

Development ◽  
1998 ◽  
Vol 125 (13) ◽  
pp. 2511-2520 ◽  
Author(s):  
S. Fujiwara ◽  
J.C. Corbo ◽  
M. Levine
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Binding Sites ◽  
Promoter Region ◽  
Muscle Cells ◽  
Specific Pattern ◽  
Binding Assays ◽  
Heterologous Promoter ◽  
Present Evidence ◽  
Tail Muscle

Previous studies have identified a minimal 434 bp enhancer from the promoter region of the Ciona Brachyury gene (Ci-Bra), which is sufficient to direct a notochord-specific pattern of gene expression. Here we present evidence that a Ciona homolog of snail (Ci-sna) encodes a repressor of the Ci-Bra enhancer in the tail muscles. DNA-binding assays identified four Ci-Sna-binding sites in the Ci-Bra enhancer, and mutations in these sites cause otherwise normal Ci-Bra/lacZ transgenes to be misexpressed in ectopic tissues, particularly the tail muscles. Selective misexpression of Ci-sna using a heterologous promoter results in the repression of Ci-Bra/lacZ transgenes in the notochord. Moreover, the conversion of the Ci-Sna repressor into an activator results in the ectopic induction of Ci-Bra/lacZ transgenes in the muscles, and also causes an intermixing of notochord and muscle cells during tail morphogenesis. These results suggest that Ci-Sna functions as a boundary repressor, which subdivides the mesoderm into separate notochord and tail muscle lineages.

Targeted modification of promoters

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.

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

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.

Candidatecis-elements for humanrenin gene expression in the promoter region

2004 ◽  
Vol 93 (2) ◽  
pp. 327-336 ◽  
Author(s):  
Tadashi Konoshita ◽  
Yasukazu Makino ◽  
Shigeyuki Wakahara ◽  
Kanako Ido ◽  
Masahiro Yoshida ◽  
...  
Keyword(s):  
Gene Expression ◽  
Promoter Region

Evaluation of DNMT1 gene expression profile and methylation of its promoter region in patients with ankylosing spondylitis

2016 ◽  
Vol 35 (11) ◽  
pp. 2723-2731 ◽  
Author(s):  
Saeed Aslani ◽  
Mahdi Mahmoudi ◽  
Masoud Garshasbi ◽  
Ahmad Reza Jamshidi ◽  
Jafar Karami ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ankylosing Spondylitis ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Promoter Region
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