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Publication Record


Differential role of an NF-κB transcriptional response element in endothelial versus intimal cell VCAM-1 expression.
Milstone DS, Ilyama M, Chen M, O'Donnell P, Davis VM, Plutzky J, Brown JD, Haldar SM, Siu A, Lau AC, Zhu SN, Basheer MF, Collins T, Jongstra-Bilen J, Cybulsky MI
(2015) Circ Res 117: 166-77
MeSH Terms: 5' Untranslated Regions, Animals, Atherosclerosis, Carotid Artery Injuries, Cells, Cultured, Chemotaxis, Leukocyte, Cholesterol, Dietary, E-Selectin, Endothelial Cells, Endothelium, Vascular, Humans, Mice, Mice, Inbred C57BL, Mice, Knockout, Promoter Regions, Genetic, Protein Interaction Mapping, RNA Polymerase II, Receptors, LDL, Response Elements, Transcription Factor RelA, Transcription, Genetic, Tunica Intima, Vascular Cell Adhesion Molecule-1
Show Abstract · Added September 6, 2016
RATIONALE - Human and murine Vcam1 promoters contain 2 adjacent nuclear factor-κB (NF-κB)-binding elements. Both are essential for cytokine-induced transcription of transiently transfected promoter-reporter constructs. However, the relevance of these insights to regulation of the endogenous Vcam1 gene and to pathophysiological processes in vivo remained unknown.
OBJECTIVE - Determine the role of the 5' NF-κB-binding element in expression of the endogenous Vcam1 gene.
METHODS AND RESULTS - Homologous recombination in embryonic stem cells was used to inactivate the 5' NF-κB element in the Vcam1 promoter and alter 3 nucleotides in the 5' untranslated region to allow direct comparison of wild-type versus mutant allele RNA expression and chromatin configuration in heterozygous mice. Systemic treatment with inflammatory cytokines or endotoxin (lipopolysaccharide) induced lower expression of the mutant allele relative to wild-type by endothelial cells in the aorta, heart, and lungs. The mutant allele also showed lower endothelial expression in 2-week atherosclerotic lesions in Vcam1 heterozygous/low-density lipoprotein receptor-deficient mice fed a cholesterol-rich diet. In vivo chromatin immunoprecipitation assays of heart showed diminished lipopolysaccharide-induced association of RNA polymerase 2 and NF-κB p65 with the mutant promoter. In contrast, expression of mutant and wild-type alleles was comparable in intimal cells of wire-injured carotid artery and 4- to 12-week atherosclerotic lesions.
CONCLUSIONS - This study highlights differences between in vivo and in vitro promoter analyses, and reveals a differential role for a NF-κB transcriptional response element in endothelial vascular cell adhesion molecule-1 expression induced by inflammatory cytokines or a cholesterol-rich diet versus intimal cell expression in atherosclerotic lesions and injured arteries.
© 2015 American Heart Association, Inc.
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23 MeSH Terms
Evaluating the potential for undesired genomic effects of the piggyBac transposon system in human cells.
Saha S, Woodard LE, Charron EM, Welch RC, Rooney CM, Wilson MH
(2015) Nucleic Acids Res 43: 1770-82
MeSH Terms: 5' Untranslated Regions, Chromosomes, Artificial, Bacterial, DNA Damage, DNA Transposable Elements, Genome, Human, Green Fluorescent Proteins, HEK293 Cells, Humans, Plasmids, Polymerase Chain Reaction, Transgenes, Transposases
Show Abstract · Added January 30, 2015
Non-viral transposons have been used successfully for genetic modification of clinically relevant cells including embryonic stem, induced pluripotent stem, hematopoietic stem and primary human T cell types. However, there has been limited evaluation of undesired genomic effects when using transposons for human genome modification. The prevalence of piggyBac(PB)-like terminal repeat (TR) elements in the human genome raises concerns. We evaluated if there were undesired genomic effects of the PB transposon system to modify human cells. Expression of the transposase alone revealed no mobilization of endogenous PB-like sequences in the human genome and no increase in DNA double-strand breaks. The use of PB in a plasmid containing both transposase and transposon greatly increased the probability of transposase integration; however, using transposon and transposase from separate vectors circumvented this. Placing a eGFP transgene within transposon vector backbone allowed isolation of cells free from vector backbone DNA. We confirmed observable directional promoter activity within the 5'TR element of PB but found no significant enhancer effects from the transposon DNA sequence. Long-term culture of primary human cells modified with eGFP-transposons revealed no selective growth advantage of transposon-harboring cells. PB represents a promising vector system for genetic modification of human cells with limited undesired genomic effects.
Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.
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12 MeSH Terms
Upstream open reading frame in 5'-untranslated region reduces titin mRNA translational efficiency.
Cadar AG, Zhong L, Lin A, Valenzuela MO, Lim CC
(2014) Biochem Biophys Res Commun 453: 185-91
MeSH Terms: 5' Untranslated Regions, Animals, Base Sequence, Cell Line, Connectin, Doxorubicin, Gene Expression Regulation, HEK293 Cells, Half-Life, Humans, Mice, Molecular Sequence Data, Myocytes, Cardiac, Open Reading Frames, Polymorphism, Single Nucleotide, Protein Kinases, RNA Stability, RNA, Messenger, Rats, Sarcomeres, Sequence Homology, Nucleic Acid
Show Abstract · Added February 19, 2015
Titin is the largest known protein and a critical determinant of myofibril elasticity and sarcomere structure in striated muscle. Accumulating evidence that mRNA transcripts are post-transcriptionally regulated by specific motifs located in the flanking untranslated regions (UTRs) led us to consider the role of titin 5'-UTR in regulating its translational efficiency. Titin 5'-UTR is highly homologous between human, mouse, and rat, and sequence analysis revealed the presence of a stem-loop and two upstream AUG codons (uAUGs) converging on a shared in frame stop codon. We generated a mouse titin 5'-UTR luciferase reporter construct and targeted the stem-loop and each uAUG for mutation. The wild-type and mutated constructs were transfected into the cardiac HL-1 cell line and primary neonatal rat ventricular myocytes (NRVM). SV40 driven 5'-UTR luciferase activity was significantly suppressed by wild-type titin 5'-UTR (∼ 70% in HL-1 cells and ∼ 60% in NRVM). Mutating both uAUGs was found to alleviate titin 5'-UTR suppression, while eliminating the stem-loop had no effect. Treatment with various growth stimuli: pacing, PMA or neuregulin had no effect on titin 5'-UTR luciferase activity. Doxorubicin stress stimuli reduced titin 5'-UTR suppression, while H2O2 had no effect. A reported single nucleotide polymorphism (SNP) rs13422986 at position -4 of the uAUG2 was introduced and found to further repress titin 5'-UTR luciferase activity. We conclude that the uAUG motifs in titin 5'-UTR serve as translational repressors in the control of titin gene expression, and that mutations/SNPs of the uAUGs or doxorubicin stress could alter titin translational efficiency.
Copyright © 2014 Elsevier Inc. All rights reserved.
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21 MeSH Terms
A predicted hairpin cluster correlates with barriers to PCR, sequencing and possibly BAC recombineering.
Nelms BL, Labosky PA
(2011) Sci Rep 1: 106
MeSH Terms: 5' Untranslated Regions, Animals, Base Sequence, Chromosomes, Artificial, Bacterial, Cluster Analysis, DNA Primers, Forkhead Transcription Factors, Humans, Polymerase Chain Reaction, Recombination, Genetic, Sequence Analysis, DNA
Show Abstract · Added March 14, 2012
Formation of higher-order structure of nucleic acids (hairpins or loops, for example) may impact not only gene regulation, but also molecular biology techniques and approaches critical for design and production of vectors needed for genetic engineering approaches. In the course of designing vectors aimed to modify the murine Foxd3 locus through homologous recombination in embryonic stem cells, we discovered a 370 nucleotide segment of DNA resistant to polymerase read-through. In addition to sequencing and PCR disruptions, we were unable to use BAC recombineering strategies to exchange sequences within the Foxd3 locus. This segment corresponds to a putative DNA hairpin region just upstream of the 5' untranslated region of Foxd3. This region is also highly conserved across vertebrate species, suggesting possible functional significance. Our findings provide a cautionary note for researchers experiencing technical challenges with BAC recombineering or other molecular biology methods requiring recombination or polymerase activity.
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11 MeSH Terms
Saccharomyces cerevisiae Gis2 interacts with the translation machinery and is orthogonal to myotonic dystrophy type 2 protein ZNF9.
Sammons MA, Samir P, Link AJ
(2011) Biochem Biophys Res Commun 406: 13-9
MeSH Terms: 5' Untranslated Regions, Amino Acid Sequence, Conserved Sequence, Evolution, Molecular, HEK293 Cells, Humans, Molecular Sequence Data, Myotonic Disorders, Myotonic Dystrophy, Phylogeny, Polyribosomes, Protein Biosynthesis, RNA-Binding Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins
Show Abstract · Added April 18, 2013
The myotonic dystrophy type 2 protein ZNF9/CNBP is a small nucleic acid binding protein proposed to act as a regulator of transcription and translation. The precise functions and activity of this protein are poorly understood. Previous studies suggested that ZNF9 regulates translation and facilitates the process of cap-independent translation through interactions with mRNA and the translating ribosome. To help determine the role played by ZNF9 in the activation of translation initiation, we combined genetic and biochemical analysis of the putative ZNF9 ortholog GIS2, in the budding yeast Saccharomyces cerevisiae. Purification of the Gis2p protein followed by mass spectrometry based-proteomic analysis identified a large number of co-purifying ribosomal subunits and translation factors, strongly suggesting that Gis2p interacts with the protein translation machinery. Polysome profiling and ribosome isolation experiments confirm that Gis2p physically interacts with the translating ribosome. Interestingly, expression of yeast Gis2p in HEK293T cells activates cap-independent translation driven by the 5'UTR of the ODC gene. These data suggest that Gis2 is functionally orthologous to ZNF9 and acts as a cap-independent translation factor.
Copyright © 2011 Elsevier Inc. All rights reserved.
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15 MeSH Terms
miR-33 links SREBP-2 induction to repression of sterol transporters.
Marquart TJ, Allen RM, Ory DS, Baldán A
(2010) Proc Natl Acad Sci U S A 107: 12228-32
MeSH Terms: 5' Untranslated Regions, ATP Binding Cassette Transporter 1, ATP Binding Cassette Transporter, Subfamily G, Member 1, ATP-Binding Cassette Transporters, Animals, Base Sequence, Cell Line, Cholesterol, Cholesterol, HDL, Gene Expression Regulation, Humans, Lipoproteins, LDL, Male, Mice, Mice, Inbred C57BL, MicroRNAs, Molecular Sequence Data, RNA, Messenger, Receptors, LDL, Response Elements, Reverse Transcriptase Polymerase Chain Reaction, Sterol Regulatory Element Binding Protein 2, Transcriptional Activation, Transfection
Show Abstract · Added February 12, 2016
The sterol regulatory element binding protein 2 (SREBP-2) and the liver X receptor (LXR) control antagonistic transcriptional programs that stimulate cellular cholesterol uptake and synthesis, and cholesterol efflux, respectively. The clinical importance of SREBP-2 is revealed in patients with hypercholesterolemia treated with statins, which reduce low-density lipoprotein (LDL) cholesterol levels by increasing hepatic expression of SREBP-2 and its target, the LDL receptor. Here we show that miR-33 is encoded within SREBP-2 and that both mRNAs are coexpressed. We also identify sequences in the 3' UTR of ABCA1 and ABCG1, sterol transporter genes both previously shown to be regulated by LXR, as targets for miR-33-mediated silencing. Our data show that LXR-dependent cholesterol efflux to both ApoAI and serum is ameliorated by miR-33 overexpression and, conversely, stimulated by miR-33 silencing. Finally, we show that ABCA1 mRNA and protein and plasma HDL levels decline after hepatic overexpression of miR-33, whereas they increase after hepatic miR-33 silencing. These results suggest novel ways to manage hypercholesterolemic patients.
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24 MeSH Terms
Cell cycle-dependent regulation of the bi-directional overlapping promoter of human BRCA2/ZAR2 genes in breast cancer cells.
Misra S, Sharma S, Agarwal A, Khedkar SV, Tripathi MK, Mittal MK, Chaudhuri G
(2010) Mol Cancer 9: 50
MeSH Terms: 5' Untranslated Regions, Animals, BRCA2 Protein, Breast Neoplasms, Cell Cycle, Cell Line, Tumor, Cell Nucleus, Codon, Conserved Sequence, Cytosol, Exons, Female, G1 Phase, Gene Expression Regulation, Neoplastic, Gene Knockdown Techniques, Gene Rearrangement, Humans, Introns, Promoter Regions, Genetic, Protein Transport, RNA, Messenger, Resting Phase, Cell Cycle, Sequence Homology, Amino Acid, Transcription Factors, Vertebrates
Show Abstract · Added June 14, 2013
BACKGROUND - BRCA2 gene expression is tightly regulated during the cell cycle in human breast cells. The expression of BRCA2 gene is silenced at the G0/G1 phase of cell growth and is de-silenced at the S/G2 phase. While studying the activity of BRCA2 gene promoter in breast cancer cells, we discovered that this promoter has bi-directional activity and the product of the reverse activity (a ZAR1-like protein, we named ZAR2) silences the forward promoter at the G0/G1 phase of the cell. Standard techniques like cell synchronization by serum starvation, flow cytometry, N-terminal or C-terminal FLAG epitope-tagged protein expression, immunofluorescence confocal microscopy, dual luciferase assay for promoter evaluation, and chromatin immunoprecipitation assay were employed during this study.
RESULTS - Human BRCA2 gene promoter is active in both the forward and the reverse orientations. This promoter is 8-20 fold more active in the reverse orientation than in the forward orientation when the cells are in the non-dividing stage (G0/G1). When the cells are in the dividing state (S/G2), the forward activity of the promoter is 5-8 folds higher than the reverse activity. The reverse activity transcribes the ZAR2 mRNA with 966 nt coding sequence which codes for a 321 amino acid protein. ZAR2 has two C4 type zinc fingers at the carboxyl terminus. In the G0/G1 growth phase ZAR2 is predominantly located inside the nucleus of the breast cells, binds to the BRCA2 promoter and inhibits the expression of BRCA2. In the dividing cells, ZAR2 is trapped in the cytoplasm.
CONCLUSIONS - BRCA2 gene promoter has bi-directional activity, expressing BRCA2 and a novel C4-type zinc finger containing transcription factor ZAR2. Subcellular location of ZAR2 and its expression from the reverse promoter of the BRCA2 gene are stringently regulated in a cell cycle dependent manner. ZAR2 binds to BRCA2/ZAR2 bi-directional promoter in vivo and is responsible, at least in part, for the silencing of BRCA2 gene expression in the G0/G1 phase in human breast cells.
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25 MeSH Terms
ZNF9 activation of IRES-mediated translation of the human ODC mRNA is decreased in myotonic dystrophy type 2.
Sammons MA, Antons AK, Bendjennat M, Udd B, Krahe R, Link AJ
(2010) PLoS One 5: e9301
MeSH Terms: 5' Untranslated Regions, Binding Sites, Blotting, Western, Cell Line, Cells, Cultured, HeLa Cells, Humans, Myoblasts, Myotonic Dystrophy, Ornithine Decarboxylase, Protein Binding, Protein Biosynthesis, RNA Caps, RNA Interference, RNA, Messenger, RNA-Binding Proteins, Reverse Transcriptase Polymerase Chain Reaction, Ribosomes
Show Abstract · Added April 18, 2013
Myotonic dystrophy types 1 and 2 (DM1 and DM2) are forms of muscular dystrophy that share similar clinical and molecular manifestations, such as myotonia, muscle weakness, cardiac anomalies, cataracts, and the presence of defined RNA-containing foci in muscle nuclei. DM2 is caused by an expansion of the tetranucleotide CCTG repeat within the first intron of ZNF9, although the mechanism by which the expanded nucleotide repeat causes the debilitating symptoms of DM2 is unclear. Conflicting studies have led to two models for the mechanisms leading to the problems associated with DM2. First, a gain-of-function disease model hypothesizes that the repeat expansions in the transcribed RNA do not directly affect ZNF9 function. Instead repeat-containing RNAs are thought to sequester proteins in the nucleus, causing misregulation of normal cellular processes. In the alternative model, the repeat expansions impair ZNF9 function and lead to a decrease in the level of translation. Here we examine the normal in vivo function of ZNF9. We report that ZNF9 associates with actively translating ribosomes and functions as an activator of cap-independent translation of the human ODC mRNA. This activity is mediated by direct binding of ZNF9 to the internal ribosome entry site sequence (IRES) within the 5'UTR of ODC mRNA. ZNF9 can activate IRES-mediated translation of ODC within primary human myoblasts, and this activity is reduced in myoblasts derived from a DM2 patient. These data identify ZNF9 as a regulator of cap-independent translation and indicate that ZNF9 activity may contribute mechanistically to the myotonic dystrophy type 2 phenotype.
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18 MeSH Terms
Population-based case-control study of VEGF gene polymorphisms and breast cancer risk among Chinese women.
Kataoka N, Cai Q, Wen W, Shu XO, Jin F, Gao YT, Zheng W
(2006) Cancer Epidemiol Biomarkers Prev 15: 1148-52
MeSH Terms: 3' Untranslated Regions, 5' Untranslated Regions, Alleles, Breast, Breast Neoplasms, Case-Control Studies, China, Disease-Free Survival, Female, Genetic Predisposition to Disease, Genotype, Haplotypes, Humans, Menopause, Middle Aged, Neoplasm Staging, Polymorphism, Genetic, Promoter Regions, Genetic, Survival Rate, Vascular Endothelial Growth Factor A
Show Abstract · Added December 10, 2013
Vascular endothelial growth factor (VEGF) is a major angiogenic factor involved in a number of pathologic processes, including neovascularization, a crucial step in the development of solid malignancies. Using data and specimens collected in the Shanghai Breast Cancer Study, a population-based case-control study conducted in urban Shanghai, China from 1996 to 1998, we evaluated the association of VEGF gene polymorphisms with breast cancer risk. Included in this study were 1,093 cases and 1,184 age-matched controls who had completed an in-person interview and donated a blood sample to the study. Polymorphisms in the promoter region (T -460C), 5' untranslated region (C +405G), and 3'untranslated region (C936T) were genotyped using the Taqman allelic discrimination assay. No statistically significant case-control difference was found for the C +405G and T -460C polymorphisms. However, the C936T polymorphism was associated with a reduced risk of breast cancer. Compared with CC genotype carriers, women who had the TT genotype showed a decreased risk [odds ratio (OR), 0.65; 95% confidence interval (95% CI) 0.41-1.02], and the inverse association was restricted to premenopausal women (OR, 0.45; 95% CI, 0.25-0.79). Six common haplotypes were identified. Compared with the most common haplotype (-460T/405C/936C), the -460T/405G/936T haplotype was associated with a reduced risk of breast cancer (OR, 0.67; 95% CI, 0.43-1.04), particularly in premenopausal women (OR, 0.47; 95% CI, 0.27-0.81). Our study suggests that the VEGF C936T polymorphism might be a susceptibility factor for breast cancer among Chinese women.
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3 Members
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20 MeSH Terms
Influence of an insertion variant in the 5'UTR of the endothelin-1 gene on orthostatic intolerance.
Winker R, Garland EM, Rüdiger HW, Diedrich A, Biaggioni I, Ponocny I, Cascorbi I, Robertson D
(2005) Am J Med Sci 330: 166-71
MeSH Terms: 5' Untranslated Regions, Adult, Alleles, Endothelin-1, Female, Genetic Variation, Genotype, Humans, Hypotension, Orthostatic, Male
Show Abstract · Added December 10, 2013
BACKGROUND - Orthostatic intolerance is a multifactorial disease in which the genetic contribution is probably the result of a number of genes acting in combination. Recent work has shown that orthostatic intolerance is influenced by endothelial nitric oxide synthase gene polymorphisms. Since endothelin-1 (ET-1) is one of the most important vasoconstrictor peptides, a frequent adenine insertion polymorphism within the 5'-untranslated region (5'UTR), which is of functional importance for ET-1 expression, could influence orthostatic intolerance. The aim of this study was therefore to ascertain whether this frequent variant of the endothelin-1 gene influences the risk for orthostatic intolerance.
METHODS - We studied 257 white patients (120 cases with orthostatic intolerance and 137 controls) for genotyping of the 5'UTR I variant. From this cohort, 111 patients and 99 control subjects underwent a tilt-table test or an upright posture study, including monitoring of blood pressure, heart rate, and plasma catecholamines, in the supine position and during 30 minutes of standing. Genotyping was performed in all participants. Chi tests of independence were used to test for associations between orthostatic intolerance and genotype. In addition, an association of the insertion polymorphism with hemodynamic variables (heart rate, supine and upright blood pressure) was ascertained using one-way analysis of variance.
RESULTS - The 5'UTR I variant was significantly less common in patients with orthostatic intolerance (allele frequency 0.36 and 0.28, in controls and cases, respectively). Additionally, we found a significant decrease in the risk of orthostatic intolerance among people who were homozygous for the 5'UTR variant (I/I) compared with the wild-type variant (D/D) (odds ratio, 0.41; 95% confidence interval, 0.17 to 0.97; P = 0.04). No association between the 5'UTR variant and heart rate or blood pressure regardless of diagnosis was found.
CONCLUSIONS - Our current results suggest that the hereditary adenine insertion variant in the 5'-UTR of the endothelin-1 gene is protective for orthostatic intolerance. The increased ET-1 protein expression that has been linked with the I variant might be associated with a more efficient hemodynamic response to standing. This is likely one of several common genetic loci that may represent modifiers of orthostatic intolerance phenotypes.
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10 MeSH Terms