Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Gene Targeting”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,045 records · Page 58Linked to original sources
PubMed2002

DNA damage-dependent acetylation of p73 dictates the selective activation of apoptotic target genes.

The tumor suppressor p53 and its close relative p73 are activated in response to DNA damage resulting in either cell cycle arrest or apoptosis. Here, we show that DNA damage induces the acetylation of p73 by the acetyltransferase p300. Inhibiting the enzymatic activity of p300 hampers apoptosis in a p53(-/-) background. Furthermore, a nonacetylatable p73 is defective in activating transcription of the proapoptotic p53AIP1 gene but retains an intact ability to regulate other targets such as p21. Finally, p300-mediated acetylation of p73 requires the protooncogene c-abl. Our results suggest that DNA damage-induced acetylation potentiates the apoptotic function of p73 by enhancing the ability of p73 to selectively activate the transcription of proapoptotic target genes.

Acetylation↗
PubMed2002

Gene targeting of tissue factor, factor X, and factor VII in mice: their involvement in embryonic development.

Inactivation of specific genes in mammals by gene targeting has accelerated our ability to determine gene function. Nearly all genes involved in the blood coagulation system have been knocked out in mice. Tissue factor (TF) is the main initiator of the coagulation system and functions as a cell surface receptor for coagulation factor VII (FVII). Knockout studies have shown that TF deficiency results in lethality around embryonic day (E) 8.5-10.5. The results suggest a role for TF in embryonic blood vessel development and maintenance of vascular integrity in the yolk sac. In addition, TF may be involved in the maintenance of the placental labyrinth. Factor X (FX) deficiency causes partial embryonic lethality between E11.5-12.5. FX-/- mice that were born died from fatal neonatal bleeding. In contrast, FVII deficiency is not embryonic lethal, but FVII-/- neonates died from hemorrhage within the first days after birth. The various lethal phenotypes of deficiencies of the different coagulation factors suggest involvement in processes beyond hemostasis. Both TF/FVIIa and FXa can trigger intracellular signaling events in certain cell types. Signaling by coagulation proteases and protease-activated receptors (PARs) may have important roles in embryonic development.

Animals↗
PubMed1996

Gene targeting reveals a hierarchy of transcription factors regulating specification of lymphoid cell fates.

Specification of B- and T-lymphoid cell fates appears to involve the expression of a shared set of genes encoding recombination proteins and of genes encoding lineage-specific components of antigen receptors. Recent studies using gene targeting have identified transcription factors that are required for the proper specification of lymphoid cell fates. On the basis of these data, a regulatory gene hierarchy which orchestrates the development of lymphoid progenitors from hematopoietic stem cells can be proposed.

Animals↗
PubMed2002

brachyury Target genes in the early sea urchin embryo isolated by differential macroarray screening.

Brachyury is a transcription factor that functions in gastrulation and endoderm development throughout the Bilateria. Here, we identify genes that are expressed downstream of brachyury during gastrulation of the sea urchin embryo. Screens with two different complex probes generated by subtractive hybridization were carried out on high-density arrays of embryonic cDNA libraries. An mRNA sequence population from embryos expressing brachyury at its peak stage of expression was subtracted with message sequence from embryos in which Brachyury function had been "knocked-out" by injection of a morpholine-substituted antisense oligonucleotide to generate a differential probe for brachyury target genes. Another probe was made by using an mRNA population from embryos that mis-express brachyury at a stage just prior to the normal onset of expression, subtracted with message sequence taken from normal embryos at this stage. Screens carried out with these probes target overlapping but distinct sets of downstream genes. After partial sequence characterization, promising genes were independently analyzed by quantitative real-time PCR and by in situ hybridization. Two major classes of genes emerge in this study: genes expressed in the subset of the secondary mesenchyme cells (SMC) that will become pigment cells, and genes that are expressed in portions of the endoderm coincident with brachyury expression. The latter genes are candidates for direct transcriptional targets of Brachyury. Some of the endodermal genes that respond to Brachyury are cytoskeletal modulators that may play a role in gut morphogenesis. This finding is consistent with the block in gastrulation induced by interfering with Brachyury function in sea urchins, and with known or suggested Brachyury function in other species. Other endodermal target genes are expressed in the archenteron and might be terminal differentiation enzymes of the gut. Brachyury expression patterns for Strongylocentrotus purpuratus reported in this paper are entirely consistent with data from other echinoderm species. Brachyury expression in the vegetal plate is confined to the presumptive endodermal cells. Therefore, the SMC genes are likely to be indirect targets of Brachyury-induced signaling from the surrounding endoderm to the central mesoderm, or the effects on these genes may be indirect consequences of gross disruption of the vegetal plate. These results and other data suggest that the brachyury gene transduces information about the state of endodermal specification to genes that modulate morphogenesis and genes that perform terminal functions in the gut.

Animals↗
PubMed2001

[Construction of a Flp "exchange cassette" contained vector and gene targeting in mouse ES cell].

Using the HPRT genomic DNA fragment and synthesized oligonucliotides, pSP-HPRT-F-Neo-F3 was designed and constructed as a replacement gene targeting vector by usual molecular cloning techniques. Structure of pSP-HPRT-F-Neo-F3 was identified by restrictive digestion analysis and partly sequencing. Then linearized pSP-HPRT-F-Neo-F3 DNA was electroporated into ES cells, and transfected cells were screened by being cultured in medium containing 200 micrograms/mL G418 and 2 micrograms/mL 6-GT. Twenty-four double drug resistant clones were picked up and analyzed, among them, two clones were proved to have taken place the required recombination by PCR and southern blotting analysis.

Animals↗
PubMed2001

Identification of novel oestrogen receptor target genes in human ZR75-1 breast cancer cells by expression profiling.

Oligonucleotide microarrays were used to analyse gene expression profiles in human ZR75-1 breast cancer cells in the presence of 17beta-oestradiol and oestrogen antagonists. Differential gene expression of a number of genes was confirmed by quantitative RNA analysis. In addition to known oestrogen-responsive genes, an appreciable number of novel targets were identified, including growth factors and components of the cell cycle, adhesion molecules, enzymes, signalling molecules and transcription factors. The most pronounced oestrogen-sensitive gene was that for the cytochrome P450-IIB enzyme, involved in metabolising steroids and xenobiotics, which was increased 100-fold over a 24 h period. It is a direct target gene for oestrogens, because its expression was increased in the presence of cyclohexamide. In contrast, expression of cytochrome P450-IIB was not detected in human MCF7 breast cancer cells. Expressions of the cationic amino acid transporter E16, gap junction protein and insulin-like growth factor binding protein 4 were also markedly increased by oestrogens, but the kinetics of induction varied according to the target gene. With the exception of the cationic amino acid transporter E16 and the insulin-like growth factor binding protein 4, the expression of the majority of the genes was unaffected by antioestrogen treatment. Further analysis of this set of markers will provide alternative approaches to the investigation of the mitogenicity of oestrogens in breast cancer cells.

Breast Neoplasms↗
PubMed2004

Expression and amplification of therapeutic target genes in retinoblastoma.

PURPOSE: We set out to evaluate alterations of the therapeutic target genes KIT (CD 117), EGFR, and HER-2 in human retinoblastoma. METHODS: Ninety-five formalin-fixed, paraffin-embedded retinoblastomas were brought into a tissue microarray (TMA) format. Immunohistochemistry was performed to analyze the expression of CD117, EGFR, and HER-2. Fluorescence in situ hybridization (FISH) was utilized for detection of EGFR amplifications. Three tumors with strong CD117 positivity were sequenced for KIT exon 11 mutations. RESULTS: Detectable CD117 expression was seen in 19% of all interpretable cases. Sequence analysis of the three tumors with the strongest CD117 expression revealed no mutations. EGFR was positive in 14% of all cases. No EGFR amplification was observed by FISH, however. All tumors were negative for HER-2 expression. CONCLUSIONS: Our data suggest that selected cases of retinoblastoma may be candidates for anti-EGFR and imatinib mesylate (STI571) therapy.

Adolescent↗
PubMed2005

JCat: a novel tool to adapt codon usage of a target gene to its potential expression host.

A novel method for the adaptation of target gene codon usage to most sequenced prokaryotes and selected eukaryotic gene expression hosts was developed to improve heterologous protein production. In contrast to existing tools, JCat (Java Codon Adaptation Tool) does not require the manual definition of highly expressed genes and is, therefore, a very rapid and easy method. Further options of JCat for codon adaptation include the avoidance of unwanted cleavage sites for restriction enzymes and Rho-independent transcription terminators. The output of JCat is both graphically and as Codon Adaptation Index (CAI) values given for the pasted sequence and the newly adapted sequence. Additionally, a list of genes in FASTA-format can be uploaded to calculate CAI values. In one example, all genes of the genome of Caenorhabditis elegans were adapted to Escherichia coli codon usage and further optimized to avoid commonly used restriction sites. In a second example, the Pseudomonas aeruginosa exbD gene codon usage was adapted to E.coli codon usage with parallel avoidance of the same restriction sites. For both, the degree of introduced changes was documented and evaluated. JCat is integrated into the PRODORIC database that hosts all required information on the various organisms to fulfill the requested calculations. JCat is freely accessible at http://www.prodoric.de/JCat.

Algorithms↗
PubMed2005

Gene targeting using peptide nucleic acid.

A brief overview of the properties of the deoxyribonucleic acid mimic peptide nucleic acid (PNA) is given, and the recent progress in cellular delivery of PNA and of using PNA oligomers for antisense and antigene gene targeting is presented.

Amino Acid Sequence↗
PubMed2002

Somatic gene targeting in the developing and adult mouse retina.

Retinogenesis is a developmental process that is tightly regulated both temporally and spatially and is therefore an excellent model system for studying the molecular and cellular mechanisms of neurogenesis in the central nervous system. Understanding of these events in vivo is greatly facilitated by the availability of mouse mutant models, including those with natural or targeted mutations and those with conditional knockout or forced expression of genes. This article reviews these genetic modifications and their contribution to the study of retinogenesis in mammals, with special emphasis on conditional gene targeting approaches.

Age Factors↗
PubMed1996

Transcriptional activation of hedgehog target genes in Drosophila is mediated directly by the cubitus interruptus protein, a member of the GLI family of zinc finger DNA-binding proteins.

Members of the Hedgehog (Hh) family of secreted proteins have been identified recently as key signaling molecules that regulate a variety of inductive interactions central to the development of both Drosophila and vertebrates. Despite their widespread importance, the way in which Hh signals are transduced inside the cell remains poorly understood. The best candidate for a transcription factor that mediates Hh signaling in Drosophila is the product of the cubitus interruptus (ci) gene, a zinc finger protein that exhibits significant homology to protein products of the vertebrate GLI gene family. Here, we show that elevated levels of Ci are sufficient to activate patched (ptc) and other hh target genes, even in the absence of hh activity. We also show that Ci can function as a transcriptional activator in yeast and demonstrate that the zinc finger domain of the protein is sufficient for its target specificity. Finally, we identify sequences in the promoter region of the ptc gene, a primary target of Hh signaling, that are identical to the consensus-binding sequence of the GLI protein and are required for reporter gene expression in response to Hh activity. Taken together, our results strongly support the role for Ci as the transcriptional activator that mediates hh signaling.

Animals↗
PubMed2003

Targeted gene disruption by homologous recombination in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.

In contrast to the high accumulation in sequence data for hyperthermophilic archaea, methodology for genetically manipulating these strains is still at an early stage. This study aimed to develop a gene disruption system for the hyperthermophilic euryarchaeon Thermococcus kodakaraensis KOD1. Uracil-auxotrophic mutants with mutations in the orotidine-5'-monophosphate decarboxylase gene (pyrF) were isolated by positive selection using 5-fluoroorotic acid (5-FOA) and used as hosts for further transformation experiments. We then attempted targeted disruption of the trpE locus in the host strain by homologous recombination, as disruption of trpE was expected to result in tryptophan auxotrophy, an easily detectable phenotype. A disruption vector harboring the pyrF marker within trpE was constructed for double-crossover recombination. The host cells were transformed with the exogenous DNA using the CaCl(2) method, and several transformants could be selected based on genetic complementation. Genotypic and phenotypic analyses of a transformant revealed the unique occurrence of targeted disruption, as well as a phenotypic change of auxotrophy from uracil to tryptophan caused by integration of the wild-type pyrF into the host chromosome at trpE. As with the circular plasmid, gene disruption with linear DNA was also possible when the homologous regions were relatively long. Shortening these regions led to predominant recombination between the pyrF marker in the exogenous DNA and the mutated allele on the host chromosome. In contrast, we could not obtain trpE disruptants by insertional inactivation using a vector designed for single-crossover recombination. The gene targeting system developed in this study provides a long-needed tool in the research on hyperthermophilic archaea and will open the way to a systematic, genetic approach for the elucidation of unknown gene function in these organisms.

Base Sequence↗
PubMed1996

Liver and intestinal fatty acid binding proteins in control and TGF beta 1 gene targeted deficient mice.

The effect of transforming growth factor beta-1 (TGF beta 1) expression on fatty acid binding proteins was examined in control and two strains of gene targeted TGF beta 1-deficient mice. Homozygous TGF beta 1-deficient 129 x CF-1, expressing multifocal inflammatory syndrome, had 25% less liver fatty acid binding protein (L-FABP) when compared to control mice. The decrease in L-FABP expression was not due to multifocal inflammatory syndrome since homozygous TGF beta 1-deficient/immunodeficient C3H mice on a SCID background had 36% lower liver L-FABP than controls. This effect was developmentally related and specific to liver, but not the proximal intestine, where L-FABP is also expressed. Finally, the proximal intestine also expresses intestinal-FABP (I-FABP) which decreased 3-fold in the TGF beta 1-deficient/immunodeficient C3H mice only. Thus, TGF beta 1 appears to regulate the expression of L-FABP and I-FABP in the liver and the proximal intestine, respectively.

Animals↗
PubMed1999

Thrombopoietin and the c-Mpl receptor: insights from gene targeting.

The availability of thrombopoietin (TPO) in recombinant form has revolutionized the study of megakaryocytopoiesis and provided an exciting new reagent for clinical evaluation. Through the application of gene targeting technology, the production of mice lacking TPO or its receptor c-Mpl has provided valuable insights into the physiological roles of TPO signalling. The near identical phenotype of c-mpl-/- and TPO-/- mice provides strong biological evidence that TPO is the sole c-Mpl ligand and uses no other additional receptor itself. TPO-/- and mpl-/- mice are severely thrombocytopenic indicating that TPO is the primary physiological regulator of platelet production in vivo. The physiological basis for this platelet deficiency has been further defined by analysis of megakaryocytes and committed progenitor cells, the numbers of which are also reduced in these mutants. The platelets that are produced in the absence of TPO signalling are morphologically and functionally normal and residual production is sufficient to prevent bleeding and allow a normal lifespan. Thus, TPO-/- and mpl-/- mice also reveal that important TPO-independent mechanisms exist that control platelet production in vivo, and these mice are ideal models to explore the nature of these alternative regulators. The mechanisms regulating the circulating levels of TPO have also been elucidated in these mice, highlighting the central role of c-Mpl mediated internalisation and degradation. The unexpected observation that progenitor cells of all hemopoietic lineages are produced in reduced numbers in TPO-/- and mpl-/- mice has also led to studies that uncovered a central role for TPO signalling in hemopoietic stem cell regulation.

Animals↗
PubMed1996

Characterization of a putative p53 binding site in the promoter of the mouse tissue inhibitor of metalloproteinases-3 (TIMP-3) gene: TIMP-3 is not a p53 target gene.

We have recently cloned the promoter of the mouse tissue inhibitor of metalloproteinases-3 (TIMP-3) gene and have identified a putative p53 binding site (5'-GGGCTTGCTT GACGTCCA GAACAGGGTC-3'), which contains two p53 consensus binding motifs (bold) with two nucleotide mismatches (underlined) in the second motif and an 8 bp spacer in between. Since both p53 and TIMP-3 are involved in cell cycle progression, we tested the hypothesis that TIMP-3 is a p53 downstream effector gene, mediating p53 activity. A good correlation between p53 protein levels and TIMP-3 expression was found among mouse liver cell lines. However, when TIMP-3 promoter driven luciferase constructs were tested for p53 responsiveness in these cells, the construct containing the putative p53 binding site did not show significant difference from the one having the p53 site deleted. The gel retardation assay showed that the oligo (T3) made from the putative p53 binding site in the mouse TIMP-3 promoter did not bind to p53 protein, nor did an oligo (T3W) with a correction for the two mismatched nucleotides in the second motif. When the 8 bp spacer was removed, however, the oligo T3WSF (same as the T3W with spacer free) but not T3SF (T3 without spacer) binds to p53, indicating that both the spacer between two motifs and consensus binding sites determined the p53 binding. It is worth noting that under a less stringent assay condition (0.2 microg instead of 1.0 microg of dI/dC), T3SF did weakly bind to p53. Lastly, the compounds that induce p53 transactivation activity did not induce TIMP-3 expression. We concluded from this study that TIMP-3 is not a p53 downstream effector gene.

Animals↗
PubMed2001

DNA microarrays identification of primary and secondary target genes regulated by p53.

The transcriptional program regulated by the tumor suppressor p53 was analysed using oligonucleotide microarrays. A human lung cancer cell line that expresses the temperature sensitive murine p53 was utilized to quantitate mRNA levels of various genes at different time points after shifting the temperature to 32 degrees C. Inhibition of protein synthesis by cycloheximide (CHX) was used to distinguish between primary and secondary target genes regulated by p53. In the absence of CHX, 259 and 125 genes were up or down-regulated respectively; only 38 and 24 of these genes were up and down-regulated by p53 also in the presence of CHX and are considered primary targets in this cell line. Cluster analysis of these data using the super paramagnetic clustering (SPC) algorithm demonstrate that the primary genes can be distinguished as a single cluster among a large pool of p53 regulated genes. This procedure identified additional genes that co-cluster with the primary targets and can also be classified as such genes. In addition to cell cycle (e.g. p21, TGF-beta, Cyclin E) and apoptosis (e.g. Fas, Bak, IAP) related genes, the primary targets of p53 include genes involved in many aspects of cell function, including cell adhesion (e.g. Thymosin, Smoothelin), signaling (e.g. H-Ras, Diacylglycerol kinase), transcription (e.g. ATF3, LISCH7), neuronal growth (e.g. Ninjurin, NSCL2) and DNA repair (e.g. BTG2, DDB2). The results suggest that p53 activates concerted opposing signals and exerts its effect through a diverse network of transcriptional changes that collectively alter the cell phenotype in response to stress.

Animals↗
PubMed2003

Identification of target genes of the p16INK4A-pRB-E2F pathway.

Deregulation of the retinoblastoma protein (pRB) pathway is a hallmark of human cancer. The core members of this pathway include the tumor suppressor protein, pRB, which through binding to a number of cellular proteins, most notably members of the E2F transcription factor family, regulates progression through the cell division cycle. With the aim of identifying transcriptional changes provoked by deregulation of the pRB pathway, we have used cell lines that conditionally express a constitutively active phosphorylation site mutant of pRB (pRBDeltaCDK) or p16INK4A (p16). The expression of pRBDeltaCDK and p16 resulted in significant repression and activation of a large number of genes as measured by high density oligonucleotide array analysis. Transcriptional changes were found in genes that are essential for DNA replication and cell proliferation. In agreement with previous results, we found a high degree of overlap between genes regulated by p16 and pRB. Data we have obtained previously for E2F family members showed that 74 of the genes repressed by pRB and p16 were induced by the E2Fs and 23 genes that were induced by pRB and p16 were repressed by the E2Fs. Thus, we have identified 97 genes as physiological targets of the pRB pathway, and the further characterization of these genes should provide insights into how this pathway controls proliferation. We show that Gibbs sampling detects enrichment of several sequence motifs, including E2F consensus binding sites, in the upstream regions of these genes and use this enrichment in an in silico filtering process to refine microarray derived gene lists.

Amino Acid Motifs↗
PubMed2002

Novel Sxr(a) ES cell line offers hope for Y chromosome gene-targeted mice.

A mouse targeted for a Y Chromosome gene has not been reported. Because the Y Chromosome is present in only one copy, and most of its genes are critical for germ cell development, such a mouse would likely be infertile. Thus, we describe a new reproductive strategy to enable transmission of targeted Y Chromosome genes to subsequent generations. The strategy uses two segregating copies of Y Chromosome genes to mimic the autosomal condition. To achieve this, we developed a new embryonic stem cell line from the XYSxr(a) mouse, which carries a duplication of the gene-rich Y Chromosome short arm. Importantly, we demonstrate germ line transmission of the YSxr(a) chromosome and describe this significant new tool as a practical solution to enable reproduction in mice targeted for Y Chromosome genes.

Animals↗