scholarly journals Expression of the woodchuck N-myc2 retroposon in brain and in liver tumors is driven by a cryptic N-myc promoter.

1992 ◽  
Vol 12 (12) ◽  
pp. 5336-5344 ◽  
Author(s):  
G Fourel ◽  
C Transy ◽  
B C Tennant ◽  
M A Buendia
Keyword(s):  
Binding Sites ◽  
Liver Tumors ◽  
Cpg Island ◽  
Evolutionary Conservation ◽  
Transient Transfection ◽  
Tata Box ◽  
Potential Binding ◽  
Myc Gene ◽  
Low Levels ◽  
Different Tissues

The woodchuck intronless proto-oncogene N-myc2 was initially discovered as a frequent target site for hepadnavirus integration in hepatocellular carcinoma. N-myc2 possesses characteristics of a functional retroposon derived from the woodchuck N-myc gene. We have investigated the regulatory signals governing N-myc2 expression and found that a short promoter, including a variant TATA box and potential binding sites for several transcription factors, is localized in the N-myc2 sequences homologous to the 5' untranslated region of the second N-myc exon. The corresponding region in the intron-containing woodchuck N-myc gene also exhibited promoter activity in transient transfection assays. The high evolutionary conservation of these sequences in mammalian N-myc genes suggests that they contain a cryptic N-myc promoter which may be unmasked in the particular context provided by the N-myc2 retroposon. Although N-myc2, like the woodchuck N-myc gene, contributes to an extended CpG island and was found constitutively hypomethylated, it presents a highly restricted expression pattern in adult animals. Whereas the intron-containing N-myc gene is expressed at low levels in different tissues, N-myc2 mRNA was detected only in brain tissue, raising questions about the functional significance of the maintenance of a second N-myc gene in the woodchuck genome.

scholarly journals Expression of the woodchuck N-myc2 retroposon in brain and in liver tumors is driven by a cryptic N-myc promoter

1992 ◽  
Vol 12 (12) ◽  
pp. 5336-5344
Author(s):  
G Fourel ◽  
C Transy ◽  
B C Tennant ◽  
M A Buendia
Keyword(s):  
Binding Sites ◽  
Liver Tumors ◽  
Cpg Island ◽  
Evolutionary Conservation ◽  
Transient Transfection ◽  
Tata Box ◽  
Potential Binding ◽  
Myc Gene ◽  
Low Levels ◽  
Different Tissues

The woodchuck intronless proto-oncogene N-myc2 was initially discovered as a frequent target site for hepadnavirus integration in hepatocellular carcinoma. N-myc2 possesses characteristics of a functional retroposon derived from the woodchuck N-myc gene. We have investigated the regulatory signals governing N-myc2 expression and found that a short promoter, including a variant TATA box and potential binding sites for several transcription factors, is localized in the N-myc2 sequences homologous to the 5' untranslated region of the second N-myc exon. The corresponding region in the intron-containing woodchuck N-myc gene also exhibited promoter activity in transient transfection assays. The high evolutionary conservation of these sequences in mammalian N-myc genes suggests that they contain a cryptic N-myc promoter which may be unmasked in the particular context provided by the N-myc2 retroposon. Although N-myc2, like the woodchuck N-myc gene, contributes to an extended CpG island and was found constitutively hypomethylated, it presents a highly restricted expression pattern in adult animals. Whereas the intron-containing N-myc gene is expressed at low levels in different tissues, N-myc2 mRNA was detected only in brain tissue, raising questions about the functional significance of the maintenance of a second N-myc gene in the woodchuck genome.

The rat albumin promoter: cooperation with upstream elements is required when binding of APF/HNF1 to the proximal element is partially impaired by mutation or bacterial methylation

1989 ◽  
Vol 9 (11) ◽  
pp. 4759-4766
Author(s):  
F Tronche ◽  
A Rollier ◽  
I Bach ◽  
M C Weiss ◽  
M Yaniv
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Transcriptional Activity ◽  
Transient Transfection ◽  
Tata Box ◽  
Specific Factor ◽  
Target Sequence ◽  
Functional Interaction ◽  
Dna Methylase ◽  
Ccaat Box

We have characterized in the accompanying paper (P. Herbomel, A. Rollier, F. Tronche, M.-O. Ott, M. Yaniv, and M. C. Weiss, Mol. Cell. Biol. 9:4750-4758, 1989) six different elements in the albumin promoter. One of them, the proximal element (PE), is the binding site for a strictly liver specific factor, APF/HNF1. This binding site contains a bacterial DAM DNA methylase methylation target sequence which, when methylated, decreases the affinity of the protein for this element. When the different albumin promoter constructions were prepared in an Escherichia coli deoxyadenosine methylase-negative strain, the respective contributions of the elements to the overall promoter activity were strikingly different. An intact proximal element plus the TATA box gave almost full transcriptional activity in transient transfection experiments and only in differentiated hepatoma cells of line H4II, whereas the distal elements (distal element III [DEIII], the NF1-binding site DEII, and the E/CBP-binding site DEI) had become essentially dispensable. Mutations affecting the CCAAT box showed only a two- to threefold decrease. When PE was methylated, mutated, or replaced by the homologous element from the alpha-fetoprotein gene, activity in the context of the short promoter (PE plus the TATA box) was abolished. However, activity was restored in the presence of the upstream elements, showing that cooperation with factors binding to the CCAAT box and distal elements favors the functional interaction of the liver-specific APF/HNF1 factor with lower-affinity binding sites.

scholarly journals The rat albumin promoter: cooperation with upstream elements is required when binding of APF/HNF1 to the proximal element is partially impaired by mutation or bacterial methylation.

1989 ◽  
Vol 9 (11) ◽  
pp. 4759-4766 ◽  
Author(s):  
F Tronche ◽  
A Rollier ◽  
I Bach ◽  
M C Weiss ◽  
M Yaniv
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Transcriptional Activity ◽  
Transient Transfection ◽  
Tata Box ◽  
Specific Factor ◽  
Target Sequence ◽  
Functional Interaction ◽  
Dna Methylase ◽  
Ccaat Box

We have characterized in the accompanying paper (P. Herbomel, A. Rollier, F. Tronche, M.-O. Ott, M. Yaniv, and M. C. Weiss, Mol. Cell. Biol. 9:4750-4758, 1989) six different elements in the albumin promoter. One of them, the proximal element (PE), is the binding site for a strictly liver specific factor, APF/HNF1. This binding site contains a bacterial DAM DNA methylase methylation target sequence which, when methylated, decreases the affinity of the protein for this element. When the different albumin promoter constructions were prepared in an Escherichia coli deoxyadenosine methylase-negative strain, the respective contributions of the elements to the overall promoter activity were strikingly different. An intact proximal element plus the TATA box gave almost full transcriptional activity in transient transfection experiments and only in differentiated hepatoma cells of line H4II, whereas the distal elements (distal element III [DEIII], the NF1-binding site DEII, and the E/CBP-binding site DEI) had become essentially dispensable. Mutations affecting the CCAAT box showed only a two- to threefold decrease. When PE was methylated, mutated, or replaced by the homologous element from the alpha-fetoprotein gene, activity in the context of the short promoter (PE plus the TATA box) was abolished. However, activity was restored in the presence of the upstream elements, showing that cooperation with factors binding to the CCAAT box and distal elements favors the functional interaction of the liver-specific APF/HNF1 factor with lower-affinity binding sites.

scholarly journals Connecting Structure with Kinetics of Single-Stranded DNA Fluctuations that Provide Potential Binding Sites for Replication Proteins

2021 ◽  
Vol 120 (3) ◽  
pp. 219a
Author(s):  
Claire Albrecht ◽  
Brett A. Israels ◽  
Chloe Chvatal ◽  
Peter H. von Hippel ◽  
Andrew H. Marcus
Keyword(s):  
Binding Sites ◽  
Replication Proteins ◽  
Single Stranded Dna ◽  
Potential Binding ◽  
Kinetics Of

scholarly journals An In-Silico Study of Stable and Environment-Friendly Oryza sativa Urease

2020 ◽  
Vol 11 (3) ◽  
pp. 10238-10247
Keyword(s):  
Oryza Sativa ◽  
Binding Sites ◽  
3D Structure ◽  
Crop Productivity ◽  
Environment Friendly ◽  
Potential Binding ◽  
Urease Enzyme ◽  
In Silico Study ◽  
Stable Mutant ◽  
Detrimental Impact

Urea is one of the most extensively used fertilizers in agriculture but has a detrimental impact on the environment. One of the strategies to reduce this impact can be engineering modified plants containing urease enzyme with a considerably higher affinity for urea so that the urea applied in the fields can be significantly reduced. In this study, we have selected Oryza sativa Urease and generated stable mutants having a high affinity for urea. We modeled the 3D structure of the enzyme and identified the potential binding sites by analyzing the binding sites of similar proteins, i.e., 48 urea binding proteins. We found that mutation of Arg578 with Cys near the substrate-binding site of Oryza sativa Urease leads to a stable mutant protein that has a higher binding affinity for urea. This study will lead to a generation of environment-friendly, stable, genetically modified rice crop that consumes lesser urea, without compromising with crop productivity.

scholarly journals INSILICO STUDIES OF OXIME PRODRUG OF GLICLAZIDE AGAINST SULPHONYLUREA RECEPTORS (SUR 1)

2017 ◽  
Vol 9 (4) ◽  
pp. 100
Author(s):  
Surendran Vijayaraj ◽  
Kannekanti Chaithanya Veena
Keyword(s):  
Binding Sites ◽  
Pancreatic Beta Cells ◽  
Molecular Targets ◽  
Docking Studies ◽  
Docking Analysis ◽  
Potential Binding ◽  
In Silico Study ◽  
Molecular Docking Analysis ◽  
Autodock 4.2

Objective: Objective of the study is to perform a molecular docking analysis of novel oxime prodrug of gliclazide against SUR1 receptor.Methods: Sulfonylurea receptors (SUR) are membrane proteins which are the molecular targets of the sulfonylurea class of anti-diabetic drugs whose mechanism of action is to promote insulin release from pancreatic beta cells. Oxime prodrug of gliclazide a better soluble derivative of gliclazide is used for enhancement of bioavailability of gliclazide. Autodock 4.2 software was used for docking studies. Ligand 2D structures were drawn using ChemDraw Ultra 7.0. Binding sites, docking poses and interactions of the ligand with SUR1 receptors were studied by pymol software.Results: The docking studies suggest that potential binding sites of oxime prodrug of gliclazide exhibiting all the major interactions such as hydrogen bonding, hydrophobic interaction and electrostatic interaction with GLU43, LEU11, LEU 40, ILE17 GLU 68, GLN72 residues of SUR1. The binding energy of complexes are also found to be minimal forming stable complexes.Conclusion: In silico study of oxime prodrug of gliclazide conforms, the binding of oxime prodrug of glicalzide with SUR1 receptors which effectively controls the release insulin to regulate plasma glucose concentrations. Hence, the oxime prodrug of gliclazide could be a potent anti-diabetic target molecule which may be worth for further in vitro and in vivostudies. 

scholarly journals The -175T----C mutation increases promoter strength in erythroid cells: correlation with evolutionary conservation of binding sites for two trans-acting factors

Blood ◽  
1990 ◽  
Vol 75 (3) ◽  
pp. 756-761 ◽  
Author(s):  
DL Gumucio ◽  
WK Lockwood ◽  
JL Weber ◽  
AM Saulino ◽  
K Delgrosso ◽  
...  
Keyword(s):  
Binding Site ◽  
Point Mutation ◽  
Binding Sites ◽  
Globin Gene ◽  
Evolutionary Conservation ◽  
Single Point Mutation ◽  
Promoter Strength ◽  
Globin Genes ◽  
Gamma Globin ◽  
Specific Distribution

Abstract A point mutation at position -175 has been detected in Agamma as well as Ggamma globin genes in individuals with hereditary persistence of fetal hemoglobin (HPFH). To prove that this single point mutation results in increased promoter strength, we transfected erythroid and nonerythroid cell lines with constructs containing normal and mutant promoters linked to the bacterial chloramphenicol acetyl transferase (CAT) gene. Differences in transfection efficiency were controlled by cotransfection of pRSVgpt. In K562 erythroleukemia cells, the -175 HPFH promoter directed three- to fourfold more CAT activity than its wild type counterpart. However, in HeLa cells the two promoters were similar in strength. The -195 to -165 region of the gamma-globin promoter contains binding sites for two proteins: a ubiquitously distributed octamer binding protein, OBP, and the erythroid-specific protein, GF-1. We find that while the GF-1 binding site is highly conserved among related primate gamma-globin genes, the octamer binding site is not. The evolutionary conservation of GF-1 as well as its erythroid-specific distribution suggest that this protein is important in gamma-globin gene expression. A role for OBP in the regulation of gamma-globin, if any, must have arisen recently in primate evolution.

Rat intestinal and hepatic ferritin subunit expression during development and after dietary iron feeding

1996 ◽  
Vol 270 (3) ◽  
pp. G498-G505 ◽  
Author(s):  
K. Y. Yeh ◽  
X. Alvarez-Hernandez ◽  
J. Glass ◽  
M. Yeh
Keyword(s):  
Early Life ◽  
Translational Repression ◽  
Milk Formula ◽  
Mrna Levels ◽  
Dietary Iron ◽  
Subsequent Increase ◽  
Iron Depletion ◽  
Subunit Expression ◽  
Low Levels ◽  
Different Tissues

Ferritin consists of 24 heavy (H) and light (L) subunits in varying proportions in different tissues and plays a significant role in iron metabolism. We studied rat ferritin subunit expression in the duodenum and liver during early life, when a cycle of iron depletion and repletion occurs. In both tissues, ferritin contents decreased to low levels from day 3 to day 12. The ferritin on day 3 had an H/L mRNA ration of 0.9 and an H/L subunit ratio of 0.6. The decrease of tissue ferritin levels, but not mRNA, on day 12 suggests translational repression consistent with iron depletion. In the duodenum, a twofold increase in both H and mRNA and subunit protein occurred on day 18. The subsequent increase of H mRNA was accompanied by a 50% decrease in L mRNA, resulting in the increase of H/L mRNA and subunit ratios to 7.9 and 9, respectively, by day 32. In contrast, liver H/L mRNA and subunit ratios were similar throughout development. The possibility that dietary iron regulates duodenal ferritin subunit expression was investigated. When day 12 rats were fed 6 ml of a milk formula containing 56 microgram/ml iron for 18 h, dietary iron increased the duodenal levels of L mRNA but not H mRNA. In contrast, hepatic H and L mRNA levels did not change. Dietary iron promoted greater increases in ferritin protein than mRNA in both tissues. Thus a shift from L-rich to H-rich ferritin isoforms occurs in the duodenum but not in the liver during neonatal development. This change is regulated at the pretranslational level and is independent of dietary iron.

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