scholarly journals Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences

2004 ◽  
Vol 32 (15) ◽  
pp. 4512-4523 ◽  
Author(s):  
Y. V. Sun ◽  
D. R. Boverhof ◽  
L. D. Burgoon ◽  
M. R. Fielden ◽  
T. R. Zacharewski
Keyword(s):  
Gene Expression ◽  
Transcriptional Start Site ◽  
Genomic Sequences ◽  
Mouse Tissue ◽  
Start Site ◽  
Orthologous Genes ◽  
Multiple Sequence ◽  
Response Elements

Abstract Comparative approaches were used to identify human, mouse and rat dioxin response elements (DREs) in genomic sequences unambiguously assigned to a nucleotide RefSeq accession number. A total of 13 bona fide DREs, all including the substitution intolerant core sequence (GCGTG) and adjacent variable sequences, were used to establish a position weight matrix and a matrix similarity (MS) score threshold to rank identified DREs. DREs with MS scores above the threshold were disproportionately distributed in close proximity to the transcription start site in all three species. Gene expression assays in hepatic mouse tissue confirmed the responsiveness of 192 genes possessing a putative DRE. Previously identified functional DREs in well-characterized AhR-regulated genes including Cyp1a1 and Cyp1b1 were corroborated. Putative DREs were identified in 48 out of 2437 human–mouse–rat orthologous genes between −1500 and the transcriptional start site, of which 19 of these genes possessed positionally conserved DREs as determined by multiple sequence alignment. Seven of these nineteen genes exhibited 2,3,7,8-tetrachlorodibenzo- p -dioxin-mediated regulation, although there were significant discrepancies between in vivo and in vitro results. Interestingly, of the mouse–rat orthologous genes with a DRE between −1500 and +1500, only 37% had an equivalent human ortholog. These results suggest that AhR-mediated gene expression may not be well conserved across species, which could have significant implications in human risk assessment.

scholarly journals In vitro analysis of the pea chloroplast 16S rRNA gene promoter.

1989 ◽  
Vol 9 (12) ◽  
pp. 5650-5659 ◽  
Author(s):  
E Sun ◽  
B W Wu ◽  
K K Tewari
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Topoisomerase I ◽  
Transcriptional Start Site ◽  
Gene Promoter ◽  
In Vitro Transcription ◽  
Rrna Gene ◽  
Start Site

A cloned pea chloroplast 16S rRNA gene promoter has been characterized in detail by use of a homologous in vitro transcription system that contains a highly purified chloroplast RNA polymerase. The in vivo and in vitro 16S rRNA transcriptional start site has been identified to be a T on the plus strand, 158 bases upstream of the mature 5' end of the gene. BAL 31 deletions of the 16S rRNA leader region demonstrated that the bases between -66 to +30 relative to the transcriptional start site (+1) are necessary for specific 16S transcription. Disruption of canonical TTGACA or TATAAT elements within this region caused complete transcriptional inactivation and prevented protein binding. The topological requirement for 16S transcription was examined by using a construct that synthesized a transcript from the 16S promoter and released it from a pea plastid putative terminator sequence. This minigene was relaxed in vitro with a topoisomerase I from pea chloroplast. It was shown that the 16S promoter was most active when the minigene plasmid was supercoiled.

scholarly journals Versatile in vivo regulation of tumor phenotypes by dCas9-mediated transcriptional perturbation

2016 ◽  
Vol 113 (27) ◽  
pp. E3892-E3900 ◽  
Author(s):  
Christian J. Braun ◽  
Peter M. Bruno ◽  
Max A. Horlbeck ◽  
Luke A. Gilbert ◽  
Jonathan S. Weissman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Transcription Start Site ◽  
Gene Activation ◽  
Start Site ◽  
Transcription Start ◽  
High Coverage ◽  
Tumor Phenotypes

Targeted transcriptional regulation is a powerful tool to study genetic mediators of cellular behavior. Here, we show that catalytically dead Cas9 (dCas9) targeted to genomic regions upstream or downstream of the transcription start site allows for specific and sustainable gene-expression level alterations in tumor cells in vitro and in syngeneic immune-competent mouse models. We used this approach for a high-coverage pooled gene-activation screen in vivo and discovered previously unidentified modulators of tumor growth and therapeutic response. Moreover, by using dCas9 linked to an activation domain, we can either enhance or suppress target gene expression simply by changing the genetic location of dCas9 binding relative to the transcription start site. We demonstrate that these directed changes in gene-transcription levels occur with minimal off-target effects. Our findings highlight the use of dCas9-mediated transcriptional regulation as a versatile tool to reproducibly interrogate tumor phenotypes in vivo.

scholarly journals In vivo manipulation of foreign gene expression by steroid administration in the oviduct of laying hens

1999 ◽  
Vol 163 (2) ◽  
pp. 173-179 ◽  
Author(s):  
HM Park ◽  
T Muramatsu
Keyword(s):  
Gene Expression ◽  
Laying Hens ◽  
Foreign Gene ◽  
Foreign Gene Expression ◽  
Response Elements ◽  
Steroid Administration ◽  
Steroid Response ◽  
In Vivo Induction

The experiments described herein were conducted to examine whether or not steroid administration allows in vivo induction of foreign gene expression in the oviduct of laying hens. The chloramphenicol acetyltransferase reporter gene driven by several viral and cellular promoters with or without steroid response elements was transfected by in vivo electroporation. The results indicated that in vivo, as observed in vitro, steroid administration induced transcriptional activities of the promoters with steroid response elements but it did not do so without steroid response elements. Our data implicate, therefore, that in vivo induction of foreign gene expression is possible in the oviduct of laying hens, and that the present in vivo gene transfer approach would serve as a useful tool to elucidate the mechanism of tissue-specific and steroid-induced transcription of chicken egg white genes.

In vitro analysis of the pea chloroplast 16S rRNA gene promoter

1989 ◽  
Vol 9 (12) ◽  
pp. 5650-5659
Author(s):  
E Sun ◽  
B W Wu ◽  
K K Tewari
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Topoisomerase I ◽  
Transcriptional Start Site ◽  
Gene Promoter ◽  
In Vitro Transcription ◽  
Rrna Gene ◽  
Start Site

A cloned pea chloroplast 16S rRNA gene promoter has been characterized in detail by use of a homologous in vitro transcription system that contains a highly purified chloroplast RNA polymerase. The in vivo and in vitro 16S rRNA transcriptional start site has been identified to be a T on the plus strand, 158 bases upstream of the mature 5' end of the gene. BAL 31 deletions of the 16S rRNA leader region demonstrated that the bases between -66 to +30 relative to the transcriptional start site (+1) are necessary for specific 16S transcription. Disruption of canonical TTGACA or TATAAT elements within this region caused complete transcriptional inactivation and prevented protein binding. The topological requirement for 16S transcription was examined by using a construct that synthesized a transcript from the 16S promoter and released it from a pea plastid putative terminator sequence. This minigene was relaxed in vitro with a topoisomerase I from pea chloroplast. It was shown that the 16S promoter was most active when the minigene plasmid was supercoiled.

Promoter characterization and role of CRE in the basal transcription of the rat SNAT2 gene

2011 ◽  
Vol 300 (6) ◽  
pp. E1092-E1102 ◽  
Author(s):  
Victor Ortiz ◽  
Gabriela Alemán ◽  
Martín Escamilla-Del-Arenal ◽  
Félix Recillas-Targa ◽  
Nimbe Torres ◽  
...  
Keyword(s):  
Gene Expression ◽  
Amino Acid ◽  
Transcriptional Start Site ◽  
Mrna Level ◽  
Regulatory Region ◽  
Amino Acid Transporter ◽  
Start Codon ◽  
Acid Transporter

Small neutral amino acid transporter 2 (SNAT2) is the most abundant and ubiquitous transporter for zwitterionic short-chain amino acids. The activity of this amino acid transporter is stimulated in vivo or in vitro by glucagon or cAMP analogs. However, it is not known whether the increase in activity at the protein level is due to an increase in SNAT2 gene transcription. Thus, the aim of the present work was to study whether cAMP was able to stimulate SNAT2 gene expression and to localize and characterize the presence of cAMP response elements (CRE) in the promoter that controls the expression of the rat SNAT2 gene. We found that consumption of a high-protein diet that increased serum glucagon concentration or the administration of glucagon or incubation of hepatocytes with forskolin increased the SNAT2 mRNA level. We then isolated the 5′ regulatory region of the SNAT2 gene and determined that the transcriptional start site was located 970 bp upstream of the translation start codon. We identified two potential CRE sites located at −354 and −48 bp. Our results, using deletion analysis of the 5′ regulatory region of the SNAT2 gene, revealed that the CRE site located at −48 bp was fully responsible for SNAT2 regulation by cAMP. This evidence was strongly supported by mutation of the CRE site and EMSA and ChIP analysis. Alignment of rat, mouse, and human sequences revealed that this CRE site is highly conserved among species, indicating its essential role in the regulation of SNAT2 gene expression.

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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