LOW IN VIVO LEVELS OF HUMAN ANX7 (ANNEXIN VII) GENE EXPRESSION ARE DUE TO ENDOGENOUS INHIBITORY PROMOTER SEQUENCES

2000 ◽  
Vol 24 (7) ◽  
pp. 475-481 ◽  
Author(s):  
M Srivastava
Keyword(s):  
Gene Expression ◽  
Promoter Sequences

scholarly journals Control of differentiation-induced calbindin-D9k gene expression in Caco-2 cells by cdx-2 and HNF-1α

2004 ◽  
Vol 287 (5) ◽  
pp. G943-G953 ◽  
Author(s):  
Liyong Wang ◽  
Anna Klopot ◽  
Jean-Noel Freund ◽  
Lauren N. Dowling ◽  
Stephen D. Krasinski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Calcium Absorption ◽  
Hepatocyte Nuclear Factor ◽  
Promoter Sequences ◽  
Physiological Importance ◽  
Calbindin D9k ◽  
Enhancer Binding Protein ◽  
Promoter Construct ◽  
Calbindin D

Calbindin D9k (CaBP) is critical for intestinal calcium absorption; its in vivo expression is restricted to differentiated enterocytes of the small intestine. Our goal was to identify factors controlling the transcriptional regulation of this gene in the human intestine. Both the natural gene and a 4600-bp promoter construct were strongly regulated by differentiation (>100-fold) but not by treatment with 1,25(OH)2 vitamin D (<2-fold) in the Caco-2 clone TC7. Deletion-mutation studies revealed that conserved promoter sequences for cdx-2 (at −3158 bp) and hepatocyte nuclear factor (HNF)-1 (at −3131 and at −98 bp) combined to control CaBP expression during differentiation. Other putative response elements were not important for CaBP regulation in TC7 cells (CCAAT enhancer binding protein, pancreatic duodenal homebox-1 (pdx-1), a proximal cdx-2 element). Mutation of the distal HNF-1 site had the greatest impact on CaBP gene expression through disruption of HNF-1α binding; both basal and differentiation-mediated CaBP expression was reduced by 80%. In contrast, mutation of the distal cdx-2 element reduced only basal CaBP expression. Whereas a 60% reduction of CaBP mRNA in the duodenum of HNF-1α null mice confirmed the physiological importance of HNF-1α for CaBP gene regulation, additional studies showed that maximal CaBP expression requires the presence of both HNF-1α and cdx-2. Our data suggest that cdx-2 is a permissive factor that influences basal CaBP expression in enterocytes and that HNF-1α modulates CaBP gene expression during cellular differentiation.

scholarly journals Normative models of enhancer function

2020 ◽  
Author(s):  
Rok Grah ◽  
Benjamin Zoller ◽  
Gašper Tkačik
Keyword(s):  
Gene Expression ◽  
High Specificity ◽  
Equilibrium Models ◽  
Gene Expression Noise ◽  
Promoter Sequences ◽  
Physical Measurements ◽  
Enhancer Function ◽  
Non Equilibrium

In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology.

scholarly journals Quadruplex structures of muscle gene promoter sequences enhance in vivo MyoD-dependent gene expression

2010 ◽  
Vol 38 (7) ◽  
pp. 2369-2377 ◽  
Author(s):  
Jeny Shklover ◽  
Pnina Weisman-Shomer ◽  
Anat Yafe ◽  
Michael Fry
Keyword(s):  
Gene Expression ◽  
Gene Promoter ◽  
Promoter Sequences ◽  
Muscle Gene

scholarly journals Nonequilibrium models of optimal enhancer function

2020 ◽  
Vol 117 (50) ◽  
pp. 31614-31622
Author(s):  
Rok Grah ◽  
Benjamin Zoller ◽  
Gašper Tkačik
Keyword(s):  
Gene Expression ◽  
High Specificity ◽  
Eukaryotic Transcription ◽  
Gene Expression Noise ◽  
Promoter Sequences ◽  
Enhancer Function ◽  
Near Future ◽  
Nonequilibrium Models

In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene-expression levels that is compatible with in vivo and in vitro biophysical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In nonequilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal nonequilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity, and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate,” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in nonequilibrium models is in a trade-off with gene-expression noise, predicting bursty dynamics—an experimentally observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space of nonequilibrium enhancer models to a much smaller subspace that optimally realizes biological function, we deliver a rich class of models that could be tractably inferred from data in the near future.

scholarly journals Systematic tools for reprogramming plant gene expression in a simple model, Marchantia polymorpha

2020 ◽  
Author(s):  
Susanna Sauret-Güeto ◽  
Eftychios Frangedakis ◽  
Linda Silvestri ◽  
Marius Rebmann ◽  
Marta Tomaselli ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chloroplast Transformation ◽  
Cellular Growth ◽  
Marchantia Polymorpha ◽  
Promoter Sequences ◽  
Vector Systems ◽  
Gene Redundancy ◽  
Dna Elements ◽  
Living Tissues

ABSTRACTWe present the OpenPlant toolkit, a set of interlinked resources and techniques to develop Marchantia as testbed for bioengineering in plants. Marchantia is a liverwort, a simple plant with an open form of development that allows direct visualization of gene expression and dynamics of cellular growth in living tissues. We describe new techniques for simple and efficient axenic propagation and maintenance of Marchantia lines with no requirement for glasshouse facilities. Marchantia plants spontaneously produce clonal propagules within a few weeks of regeneration, and lines can be amplified million-fold in a single generation by induction of the sexual phase of growth, crossing and harvesting of progeny spores. The plant has a simple morphology and genome with reduced gene redundancy, and the dominant phase of its life cycle is haploid, making genetic analysis easier. We have built robust Loop assembly vector systems for nuclear and chloroplast transformation and genome editing. These have provided the basis for building and testing a modular library of standardized DNA elements with highly desirable properties. We have screened transcriptomic data to identify a range of candidate genes, extracted putative promoter sequences, and tested them in vivo to identify new constitutive promoter elements. The resources have been combined into a toolkit for plant bioengineering that is accessible for laboratories without access to traditional facilities for plant biology research. The toolkit is being made available under the terms of the OpenMTA and will facilitate the establishment of common standards and the use of this simple plant as testbed for synthetic biology.

Effect of X-irradiation on gene expression of rat liver chemokines: in vivo and in vitro studies

2008 ◽  
Vol 46 (01) ◽  
Author(s):  
F Moriconi ◽  
H Christiansen ◽  
H Christiansen ◽  
N Sheikh ◽  
J Dudas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rat Liver ◽  
In Vitro Studies ◽  
X Irradiation

Vibrio harveyi virulence gene expression in vitro and in vivo during infection in black tiger shrimp Penaeus monodon

2020 ◽  
Vol 139 ◽  
pp. 153-160
Author(s):  
S Peeralil ◽  
TC Joseph ◽  
V Murugadas ◽  
PG Akhilnath ◽  
VN Sreejith ◽  
...  
Keyword(s):  
Gene Expression ◽  
Virulence Genes ◽  
Vibrio Harveyi ◽  
Penaeus Monodon ◽  
Challenge Test ◽  
Virulence Gene ◽  
Economic Losses ◽  
Virulence Gene Expression

Luminescent Vibrio harveyi is common in sea and estuarine waters. It produces several virulence factors and negatively affects larval penaeid shrimp in hatcheries, resulting in severe economic losses to shrimp aquaculture. Although V. harveyi is an important pathogen of shrimp, its pathogenicity mechanisms have yet to be completely elucidated. In the present study, isolates of V. harveyi were isolated and characterized from diseased Penaeus monodon postlarvae from hatcheries in Kerala, India, from September to December 2016. All 23 tested isolates were positive for lipase, phospholipase, caseinase, gelatinase and chitinase activity, and 3 of the isolates (MFB32, MFB71 and MFB68) showed potential for significant biofilm formation. Based on the presence of virulence genes, the isolates of V. harveyi were grouped into 6 genotypes, predominated by vhpA+ flaB+ ser+ vhh1- luxR+ vopD- vcrD+ vscN-. One isolate from each genotype was randomly selected for in vivo virulence experiments, and the LD50 ranged from 1.7 ± 0.5 × 103 to 4.1 ± 0.1 × 105 CFU ml-1. The expression of genes during the infection in postlarvae was high in 2 of the isolates (MFB12 and MFB32), consistent with the result of the challenge test. However, in MFB19, even though all genes tested were present, their expression level was very low and likely contributed to its lack of virulence. Because of the significant variation in gene expression, the presence of virulence genes alone cannot be used as a marker for pathogenicity of V. harveyi.

Evidence that gene expression of ovarian follicular tight junction proteins is regulated in vivo and in vitro in cattle

2017 ◽  
Vol 95 (3) ◽  
pp. 1313 ◽  
Author(s):  
L. Zhang ◽  
L. F. Schütz ◽  
C. L. Robinson ◽  
M. L. Totty ◽  
L. J. Spicer
Keyword(s):  
Gene Expression ◽  
Tight Junction ◽  
Tight Junction Proteins ◽  
Junction Proteins
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