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Results for “regulatory element transcripts”

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PubMed1999

Swinepox virus as a vaccine vector for swine pathogens.

Several small and large viruses (e.g., adenovirus, poxvirus, and herpesviruses) have been investigated as vaccine vectors. Each viral system has its advantages and disadvantages. One major advantage for viral vector vaccines is their ability to elicit a protective cell-mediated immunity as well as a humoral response to the antigen delivered by the vector. One major problem to using recombinant viruses as vaccines is the pathogenic potential of the parent virus. Therefore, it is important that along with the optimal expression of the foreign genes and ability to provide protection, the pathogenicity of the vector virus must be reduced during genetic manipulation without affecting its multiplication. The requirements to develop a viral vector, for example, swinepox virus, are a cell culture system that will support the growth of the virus, a suitable nonessential region(s) in the virus genome for insertion of foreign DNA so that virus replication is not affected, a foreign gene(s) that encodes for an immunogenic protein of a swine pathogen, strong transcriptional regulatory elements (promoters) necessary for optimal expression of the foreign genes, a procedure for delivering the foreign gene(s) into the nonessential locus, and a convenient method of distinguishing the recombinant viruses from the parent wild-type virus. Using this methodology, recombinant swinepox virus vaccines expressing pseudorabies virus antigens have been developed and shown to provide protection against challenge. These studies and evidence of local infection of the oral tract by swinepox virus indicate its potential as a recombinant vector for providing immunity against various swine pathogens including those that infect the respiratory and gastrointestinal tracts.

Animals↗

PubMed2003

Structure, genomic organization, and phylogenetic implications of six new VH families in the channel catfish.

To define members of previously unknown VH gene families, a channel catfish immunoglobulin heavy chain cDNA library was constructed and screened with probes specific for the seven known catfish VH families. Reiterative screening and sequence studies defined six new VH families, designated VH8-VH13, which brings the total number of VH families in the catfish to 13. This is the highest number of VH families presently defined in a lower vertebrate. Sequence comparisons indicate there is extensive diversity between members of different families with the greatest variability encoded within the complementarity determining regions. Genomic libraries were screened, and germline VH segments representing each of these new families were identified. The VH segments are closely linked and interspersed with members of different VH families. Each of these germline gene segments shared characteristic structural features: an upstream region that contained transcriptional regulatory elements, a leader sequence split by a short intron, an open reading frame encoding readily identified framework and complementarity determining regions, and a terminal recombination signal sequence consisting of a consensus heptamer, a 22-24 bp spacer with conserved 5'- and 3'-ends, and a consensus A-rich nonamer. Southern blot analyses estimate the number of members within these new families ranges from small (2-7 members in VH9, VH10, and VH12) to medium (9-13 members in VH8, VH11, and VH13). Thus, there are between 165 and 200 germline VH segments represented by these combined 13 families with present analyses indicating that perhaps one-half of these are pseudogenes. Phylogenetic comparisons indicate that members of these different catfish VH families cluster within Groups C and D of vertebrate VH genes. These analyses also indicate that Group D is represented by two different branches and both branches include VH families from different lineages of bony fish that diverged early in vertebrate phylogeny.

Amino Acid Sequence↗

PubMed2002

Structural gene organization and evolutionary aspects of the V-ATPase accessory subunit Ac45.

The vacuolar H+-ATPase (V-ATPase) is a multisubunit enzyme that couples ATP hydrolysis to proton pumping across membranes. The intracellular targeting and activity of the V-ATPase may be regulated via proteins that interact with the pump such as the accessory subunit Ac45. Here we report the isolation and characterization of the gene encoding Ac45. This single-copy gene is located in a gene-dense region of chromosome Xq and consists of 10 exons spanning approximately 8 kb in the mouse and human genomes. The gene structure is poorly conserved in that its invertebrate orthologs of Caenorhabditis elegans and Drosophila melanogaster encompass only six and four exons extending over 4.1 and 2.1 kb, respectively. Furthermore, the overall degree of amino acid sequence identity between the mammalian and invertebrate Ac45 proteins is very low (<18%), except for a surprisingly highly conserved putative targeting motif in the carboxy-terminal region. Primer extension analysis revealed that the mouse Ac45 gene contains two major transcription initiation sites. The start sites are not preceded by a clear CAAT-box and are located in a CpG island. The most downstream start site contains a TATA-box and transcriptional regulatory elements such as PEA-3, F2F, Maz and Sp1. The limited number of regulatory DNA elements common in the genes encoding Ac45 and V-ATPase subunits suggests a differential regulation of these genes. Together with the finding that Ac45 appears to occur only in multicellular organisms, these results indicate that this accessory subunit directs the V-ATPase to specialized and complex vacuolar systems.

Amino Acid Sequence↗

PubMed2001

Cloning and characterization of the 5'-flanking region of human cytokeratin 19 gene in human cholangiocarcinoma cell line.

BACKGROUND/AIMS: The regulatory mechanism of cell-specific gene expression in cholangiocytes has not been sufficiently evaluated. In this study, we characterized the 5'-flanking region of the cytokeratin 19 gene expressed specifically in cholangiocytes. METHODS: We cloned a 2952-bp fragment in the 5'-flanking region of cytokeratin 19 and evaluated the regulatory mechanism of gene expression in this region by assaying transient expression of reporter gene and DNA footprinting. RESULTS: This segment of the 5'-flanking region of the human cytokeratin 19 gene shows an intense transcriptional activity in the cholangioma cell line KMBC, which was about 10 times its activity in the osteosarcoma cell line Saos-2, which does not express cytokeratin 19. From the results of reporter assays, important transcription regulatory elements are considered to be located in the segments from -2249 to -2050 bp and from -732 bp to the first ATG, and six protein-binding sites were detected in the segment from -732 bp to the first ATG by the DNA footprinting technique. CONCLUSIONS: Sp1 site, CCAAT box, and TATA box were present in the segment from -374 to the first ATG, and they are considered to constitute a cholangiocyte-specific promoter.

Base Sequence↗

PubMed1992

The 5' ends of LINE1 repeats in rabbit DNA define subfamilies and reveal a short sequence conserved between rabbits and humans.

The 5' ends of five full-length LINE1 (L1) repeats from the rabbit genome (L1Oc) were mapped and their nucleotide sequences determined. Computer-generated alignments showed that these five L1Oc repeats can be divided into subfamilies, each of which has a characteristic sequence upstream of the first open reading frame (ORF1). These five L1Ocs range in size from 6.5 to 7.3 kb, with 5' ends located 76 to 1125 bp upstream of ORF1. Two of these subfamilies appear to have diverged from a common ancestor at least 66 million years ago. Comparisons of the 5' ends of L1s from rabbit, human, mouse, and rat show no common sequence 5' to ORF1, except for a 22-bp sequence that is found near the beginning of all characterized full-length L1s from rabbit and human. A statistical analysis indicates that this 22-bp aligned block is highly significant. Part of this 22-bp sequence matches the microE1 binding site in immunoglobulin gene enhancers. This strong conservation suggests that the microE1 binding site may be part of a transcriptional regulatory element at the 5' ends of rabbit and human L1 repeats.

Animals↗

PubMedDate not supplied

Localization of protein kinase C to UV-sensitive photoreceptors in the mouse retina.

The present study has identified a population of cone photoreceptors in the murine retina that are uniquely immunoreactive for protein kinase C (PKC). Wavelength-sensitive cone subtypes are segregated along the dorso-ventral axis in the mouse retina with ventral retina occupied exclusively by ultraviolet wavelength-sensitive (UVWS) cones, and dorsal retina dominated by middle wavelength-sensitive cones. PKC-positive cones are found primarily in the ventral retina, and double-label immunocytochemistry using a short wavelength-sensitive opsin antibody confirms that they specifically correspond to the UVWS cone subtype. The PKC antibody, as documented in other mammals, also identifies rod bipolar cells in the mouse retina. UVWS cones and bipolar cells have previously been shown to share transcriptional regulatory elements, as observed in transgenic mice encoding a portion of the human SWS-opsin promoter controlling the lacZ reporter gene. In such mice, the transgene product, beta-galactosidase, is expressed in populations of both cones and bipolar cells. The present study confirms that lacZ-expressing photoreceptors are indeed PKC-positive photoreceptors, but that the lacZ-expressing bipolar cells are not the PKC-positive rod bipolar cells. These cells must correspond to a type of cone bipolar cell.

Animals↗

PubMed2003

Expression and regulation of nuclear retinoic acid receptors in human lymphoid cells.

Retinoids are known to play an important role in cellular growth and differentiation and more recently in the immune response. Our laboratory has previously shown that all-trans-retinoic acid (atRA) augments immunoglobulin synthesis of cord blood mononuclear cells by enhancing the synthesis of certain cytokines. Transcriptional regulatory elements, the retinoic acid nuclear receptors (RAR), could mediate the RA-induced regulation of genes, e.g., cytokines whose products are involved in the pathways of immunoglobulin synthesis. Although much is known about RAR in various animal species and tissues, little is known about the expression of RAR and its isotypes in human lymphoid cells. In this study, we examined the RAR isotypes (RAR-alpha, RAR-beta, RAR-gamma) and their respective isoforms in T- and B-lymphoid cells using a quantitative RT-PCR assay. RAR-alpha1 and -gamma1 were both constitutively expressed and did not change with the addition of atRA to human T- and B-cell lines or adenoidal T and B lymphocytes. In contrast, RAR-beta2 was not detected. The addition of atRA to cell culture produced a marked increase in the amounts of RAR-beta2 mRNA (2.2- to 41-fold). As with the RAR-beta2 isoform, the addition of atRA increased RAR-alpha2 mRNA levels (3.4- to 17-fold), but only in EBV-transformed B cells and adenoidal B lymphocytes. The RAR-beta1 and -beta3 isoforms were undetectable in lymphoid cells and not inducible with atRA. RAR-gamma2 was expressed at very low levels and was not inducible with atRA. Our results suggest that the expressions of the RAR-alpha2 and -beta2 isoforms in lymphoid cells are highly controlled by atRA. Differences in the regulation of RAR isoforms by atRA in human lymphoid cells may be an important factor in the modulation of cytokine production and the augmentation in Ig synthesis by atRA.

Animals↗

PubMed2003

Targeting exogenous genes to tumor angiogenesis by transplantation of genetically modified hematopoietic stem cells.

Angiogenic tumor vessels are promising targets for the activity and the selective delivery of cancer therapeutics. The bone marrow contributes different cell types to the tumor stroma, including hematopoietic cells and, as recently suggested, vascular endothelial cells (ECs). Thus, transplantation of genetically modified bone marrow progenitors may represent a vehicle for the transport of gene therapy to tumors. We transduced bone marrow progenitors with lentiviral vectors expressing genes from transcription-regulatory elements of Tie2/Tek gene. When tumors were grown in the transplanted mice, the new vector marked a distinct hematopoietic population that 'homed' to the tumor and closely interacted with vascular ECs at the tumor periphery. These Tie2-expressing mononuclear (TEM) cells had a distinguishable phenotype and were present selectively at angiogenic sites. Unexpectedly, we did not find bone marrow-derived ECs in tumor vessels when we transplanted bone marrow progenitors constitutively expressing a marker gene from the Tie2 or ubiquitously active promoters. By delivering a 'suicide' gene, we selectively eliminated the TEM cells and achieved substantial inhibition of angiogenesis and slower tumor growth without systemic toxicity. Thus, TEM cells may account for the proangiogenic activity of bone marrow-derived cells in tumors, may represent a new target for drug development and may provide the means for selective gene delivery and targeted inhibition of tumor angiogenesis.

Animals↗

PubMed2026

Regulatory mechanisms of maternal imprinting at the murine Dlk1-Dio3 domain.

Genomic imprinting is an epigenetic process causing parent-of-origin specific gene expression. The Dlk1-Dio3 domain is one of the largest imprinted clusters. While DNA methylation at an intergenic CpG-island (IG-CGI) within the imprinting control region (ICR) controls expression from the paternal chromosome, mechanisms regulating the unmethylated maternal chromosome remain unknown. Within the transcriptional regulatory element (IG-TRE) of the ICR, deletions identified a minimal region in vitro exhibiting both silencing and enhancing activity, with SOX2 and ZFP281 contributing to enhancer function on the maternal chromosome. In vivo, however, this deletion did not affect maternal expression in mouse embryos; instead it activated Dlk1 on both parental chromosomes. Combining deletion of this IG-TRE with the lethal IG-CGI deletion rescued lethality in mice by balancing Dlk1 expression, despite persistent maternal gene upregulation. These results demonstrate that loss of expression at this domain is more detrimental than gain, highlighting the importance of in vivo analysis. Identification of active regulatory factors on the unmethylated maternal chromosome challenges the prevailing view that imprinting is primarily a methylation-driven phenomenon, further revealing the sophisticated hierarchical mechanisms governing imprinting control.

Animals↗

PubMed1999

Tissue-selective expression of dominant-negative proteins for the regulation of vascular smooth muscle cell proliferation.

The transcription factors c-myb and c-myc are essential for vascular smooth muscle cell (VSMC) replication and are rapidly induced following mitogenic stimulation of quiescent VSMCs in vitro and in vivo following balloon catheter injury. Consequently, interference with c-myb and c-myc function provides a possible avenue for the prevention of VSMC proliferation associated with intimal hyperplasia. We have carried out studies focused on the inhibition of VSMC proliferation using dominant-negative gene constructs incorporating the DNA-binding domains of the c-myb or c-myc genes fused to the repressor domain of the Drosophila engrailed gene. Transient transfection of rat, rabbit and human vascular SMCs results in a dramatic inhibition of proliferation for at least 72 h after transfection. Furthermore, this inhibition of cellular proliferation was found to be due, at least in part, to the induction of apoptosis. Coupling expression of the chimeric dominant-negative proteins to transcriptional regulatory elements of the human vascular smooth muscle alpha-actin gene allows specific targeting of vascular smooth muscle cells.

Actins↗

PubMed1999

Gene therapy expression vectors based on the clotting Factor IX promoter.

The liver is one of the prime targets for gene therapy, and the correction of defects in a variety of clotting factor genes is one of the main goals of liver-directed therapies. The use of transcriptional regulatory elements derived from these genes may provide for the optimal expression of transduced genes. We have applied our knowledge of the promoter structure of the clotting Factor IX gene to design optimized expression vectors for use in gene therapy. The activity of the proximal promoter has been augmented by the introduction of a multimerized upstream site which we have previously shown to be a prime regulator of the pro- moter. Introduction of this element increases promoter activity at least 20-fold over the proximal promoter alone when assayed in the human liver cell line Hep G2. This optimized promoter is significantly more active than the SV40 enhancer/early promoter. The expression of the optimized Factor IX promoter is also more persistent in the short term. The inclusion of a liver-specific locus control region, derived from the apolipoprotein E/C locus, did not further augment expression levels. These Factor IX vectors also exhibit a high degree of tissue specificity, as measured by transfection into breast and muscle cell lines.

Cell Line↗

PubMed2004

Adeno-associated viral glutamate decarboxylase expression in the lateral nucleus of the rat hypothalamus reduces feeding behavior.

In vivo gene transfer of glutamate decarboxylase (GAD) has been explored as a means of inducing or increasing the production of the inhibitory amino-acid neurotransmitter, GABA. This strategy has been applied to neuroprotection, seizure prevention, and neuromodulation. In the present experiment, AAV2 was used to transfer the genes for green fluorescence protein (GFP) and GAD65 into the lateral nucleus of the rat hypothalamus. Microinjection of 500 nl of AAV2 resulted in transduction of a 0.25+/-0.04 mm(3) with targeting errors of X=0.48 mm, Y=0.18 mm, Z=0.37 mm using standard stereotactic technique. Pre- and postinjection food and water consumption, urine and feces production, and weight were recorded. In comparison with rAAVCAGGFP- and PBS-injected animals, rats treated with rAAVCAGGAD65 demonstrated reduced weight gain (P<0.014) and transiently reduced daily food consumption (P<0.007) during the postoperative period. No changes in water consumption or waste production were recorded. Effective GAD65 gene transfer was confirmed with in situ hybridization using a probe to the woodchuck post-transcriptional regulatory element sequence included in the vector. These findings suggest that increased GABA production in lateral nucleus of the hypothalamus induced by GAD65 gene transfer may reduce weight gain through reduced feeding.

Adenoviridae↗

PubMed2006

The CD20/alphaCD20 'suicide' system: novel vectors with improved safety and expression profiles and efficient elimination of CD20-transgenic T cells.

Adoptive transfer of T lymphocytes is an attractive strategy for many experimental treatment strategies for cancer. Unfortunately, manipulated T cells could be responsible for serious adverse events. Retroviral CD20-transduced T cells may be able to control these unwanted effects. CD20-positive cells are sensitive to rituximab (RTX), a monoclonal antibody specific for CD20. This permits their selective elimination in vivo in case of adverse events. To this end, a system is required that permits efficient and safe transduction of donor T cells and effective elimination of CD20-positive T cells. We constructed different CD20-encoding retroviral vectors and investigated the impact of inclusion of the woodchuck post-transcriptional regulatory element (WPRE) and the chicken hypersensitivity site 4 insulator elements on the levels, homogeneity and stability of CD20 expression. Importantly, inclusion of either WPRE or insulator elements in the retroviral vector resulted in a dramatic improvement in the stability of CD20 expression. The insulator element also led to a much more homogeneous level of CD20 expression. We also show the efficient elimination of the CD20-transgenic T cells via RTX by different effector mechanisms. In conclusion, we have constructed CD20-encoding retroviral vectors with improved efficiency and safety profiles, which can be used as a suicide strategy.

Adoptive Transfer↗

PubMed1998

Cloning and chromosomal mapping of the murine norepinephrine transporter.

The norepinephrine (NE) transporter (NET), a target of many clinically prescribed antidepressants, regulates noradrenergic neurotransmission by efficiently clearing NE from synaptic spaces after release. To advance our understanding of NET gene structure, regulation, and potential associations with complex behavioral trait loci, we amplified a mouse norepinephrine transporter (mNET) cDNA from placenta total RNA and utilized mNET probes to isolate and characterize the mNET gene. Inferred translation of the major open reading frame of the mNET cDNA predicts a 617-amino acid protein with 12 putative membrane-spanning regions and 94% identity to human NET. The coding exons of the mNET cDNA were found to be spread across >36 kb of 129/Svj genomic DNA, with exon-intron boundaries bearing consensus gt/ag splice sites. Sequence upstream (202 bp) of the inferred translation initiation site matched the sequence of 5' rapid amplification of cDNA ends products from brain mRNA with no evidence for intervening introns and is preceded by a TATA box and canonical transcriptional regulatory elements that may play a role in mNET expression in vivo. Probes derived from mNET cDNA identified species-specific MspI restriction fragment length variations within the mNET gene that were utilized to position the gene (Slc6a5) to murine chromosome 8, one recombinant distal to D8Mit15. This site is within a recently defined quantitative trait locus defined for ethanol sensitivity in LSXSS recombinant inbred mice, Lore4. The status of Slc6a5 as a candidate gene for alcohol sensitivity is discussed with respect to studies noting ethanol-induced alterations in brain NE receptors, NE receptor-linked adenylate cyclase, and NE transport.

Amino Acid Sequence↗

PubMed2000

Analysis of the human neurofibromatosis type 2 gene promoter and its expression.

OBJECTIVE: It is hypothesized that transcriptional regulation plays an important role for neurofibromatosis type 2 (NF2) expression in Schwann cells and other cell types. The objective of this study is the isolation and characterization of the transcriptional regulatory elements of the NF2 gene. STUDY DESIGN AND SETTING: A bacterial artificial chromosome library and a partial genomic DNA library were used to isolate the human NF2 gene; NF2 promoter-luciferase constructs were generated, and promoter activities were assayed. This study was carried out in a molecular biology laboratory. RESULTS: A bacterial artificial chromosome clone with an approximately 100-kilobase insert containing nearly the entire human NF2 gene has been isolated. An additional 5' NF2 sequence has also been cloned. Transient transfection experiments demonstrate strong promoter activity from the NF2 5' flanking DNA. CONCLUSIONS: The NF2 gene is approximately 100 kilobases long. Both positive and negative regulatory elements are present in NF2 5' flanking regions. SIGNIFICANCE: Better understanding of the NF2 gene and its regulation will improve molecular diagnostics and ultimately treatment of patients with NF2.

Base Sequence↗

PubMed1985

Bovine papillomavirus contains multiple transforming genes.

Bovine papillomavirus type 1 (BPV-1) and its cloned full-length DNA can transform rodent cells in vitro, and the viral DNA persists as an extrachromosomal multicopy plasmid in these transformed cells. Previous studies have identified at least five discrete viral RNAs that are expressed in BPV-1 transformed cells and have shown that these transcripts share a 3' coterminus. To further define the structure of these RNAs and to characterize the functions of individual viral transcripts, we constructed a cDNA library with mRNA from BPV-1-transformed mouse C127 cells using an Okayama and Berg plasmid. From a library of 10(5) independent clones, 200 BPV-1 specific clones were isolated and characterized. Sequence analysis has revealed differential splicing patterns for the mRNA species in BPV-1 transformed cells. In conjunction with the open reading frames (ORFs) deduced from the BPV-1 DNA sequence, it is possible to predict the structure of the potential encoded proteins. The vector used to generate these cDNA clones contains mammalian cell transcriptional regulatory elements, facilitating their functional characterization. We have identified two distinct classes of cDNA clones that can each independently transform mouse C127 cells. One class of cDNA clones contains the E2 ORF intact and the second contains the E6 ORF intact. These two putative viral functions appear to act synergistically in transforming mouse C127 cells in vitro.

Animals↗

PubMed1990

Embryonic stem cell virus, a recombinant murine retrovirus with expression in embryonic stem cells.

The expression of Moloney murine leukemia virus and vectors derived from it is restricted in undifferentiated mouse embryonal carcinoma and embryonal stem (ES) cells. We have developed a retroviral vector, the murine embryonic stem cell virus (MESV), that is active in embryonal carcinoma and ES cells. MESV was derived from a retroviral mutant [PCC4-cell-passaged myeloproliferative sarcoma virus (PCMV)] expressed in embryonal carcinoma cells but not in ES cells. The enhancer region of PCMV was shown to be functional in both cell types, but sequences within the 5' untranslated region of PCMV were found to restrict viral expression in ES cells. Replacement of this region by related sequences obtained from the dl-587rev retrovirus results in MESV, a modified PCMV virus that confers G418 resistance to fibroblasts and ES cells with similar efficiencies. Expression of MESV in ES cells is mediated by transcriptional regulatory elements within the 5' long terminal repeat of the viral genome.

Animals↗

PubMed1993

Chimeric-transgenic mice represent a powerful tool for studying how the proliferation and differentiation programs of intestinal epithelial cell lineages are regulated.

An in vivo system has been developed for examining the effects of wild-type or mutant proteins on cell fate determination in the mouse intestinal epithelium or on the proliferation and differentiation programs of its component epithelial lineages. This system takes advantage of the fact that at the conclusion of gut morphogenesis, each intestinal crypt is composed of a monoclonal population of cells descended from a single active multipotent stem cell, each villus is supplied by several monoclonal crypts, and the four principal cell types of the intestinal epithelium differentiate during a rapid, geographically well-organized migration along the crypt-to-villus axis. Embryonic stem (ES) cells (129/Sv origin) are initially transfected with recombinant DNAs consisting of a reporter of interest linked to transcriptional regulatory elements that control the cell lineage-specific, differentiation-dependent, and axial patterns of expression of fatty acid binding protein genes in the gut. Stably transfected ES cells are subsequently introduced into host C57BL/6 blastocysts to generate chimeric-transgenic mice. At the borders of ES cell-derived and host blastocyst-derived epithelium, intestinal villi are found that are supplied by both ES cell- and host blastocyst-derived crypts. These villi can be rapidly identified in fixed whole-mount preparations of intestine using the alpha-L-fucose-specific Ulex europaeus agglutinin type I (UEA-I) lectin. They appear striped because UEA-I recognizes a cell-surface carbohydrate polymorphism between the inbred strains used to generate the chimeric animals. The strength of this system derives from the fact that two gut epithelial populations can be compared and contrasted that occupy virtually identical positions along the crypt-to-villus and duodenal-to-colonic axes within the same animal and differ only by the presence or absence of a single gene product. The band of blastocyst-derived epithelium in these striped, polyclonal villi can be used as an internal control to assess the biological effect of the transfected gene product produced in the adjacent stripe of ES-derived cells. The system can be used for either gain-of-function or loss-of-function experiments.

Animals↗