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Cui F, Sirotin MV, Zhurkin VB. Impact of Alu repeats on the evolution of human p53 binding sites. Biol Direct 2011; 6:2. [PMID: 21208455 PMCID: PMC3032802 DOI: 10.1186/1745-6150-6-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Accepted: 01/06/2011] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The p53 tumor suppressor protein is involved in a complicated regulatory network, mediating expression of ~1000 human genes. Recent studies have shown that many p53 in vivo binding sites (BSs) reside in transposable repeats. The relationship between these BSs and functional p53 response elements (REs) remains unknown, however. We sought to understand whether the p53 REs also reside in transposable elements and particularly in the most-abundant Alu repeats. RESULTS We have analyzed ~160 functional p53 REs identified so far and found that 24 of them occur in repeats. More than half of these repeat-associated REs reside in Alu elements. In addition, using a position weight matrix approach, we found ~400,000 potential p53 BSs in Alu elements genome-wide. Importantly, these putative BSs are located in the same regions of Alu repeats as the functional p53 REs - namely, in the vicinity of Boxes A/A' and B of the internal RNA polymerase III promoter. Earlier nucleosome-mapping experiments showed that the Boxes A/A' and B have a different chromatin environment, which is critical for the binding of p53 to DNA. Here, we compare the Alu-residing p53 sites with the corresponding Alu consensus sequences and conclude that the p53 sites likely evolved through two different mechanisms - the sites overlapping with the Boxes A/A' were generated by CG → TG mutations; the other sites apparently pre-existed in the progenitors of several Alu subfamilies, such as AluJo and AluSq. The binding affinity of p53 to the Alu-residing sites generally correlates with the age of Alu subfamilies, so that the strongest sites are embedded in the 'relatively young' Alu repeats. CONCLUSIONS The primate-specific Alu repeats play an important role in shaping the p53 regulatory network in the context of chromatin. One of the selective factors responsible for the frequent occurrence of Alu repeats in introns may be related to the p53-mediated regulation of Alu transcription, which, in turn, influences expression of the host genes.
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Affiliation(s)
- Feng Cui
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Michael V Sirotin
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Victor B Zhurkin
- Laboratory of Cell Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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Banares S, Zeh K, Krajewska M, Kermer P, Baribault H, Reed JC, Krajewski S. Novel pan-neuronal Cre-transgenic line for conditional ablation of genes in the nervous system. Genesis 2005; 42:6-16. [PMID: 15828007 DOI: 10.1002/gene.20117] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Tissue-specific gene ablation is accomplished by combining conventional gene targeting approaches with site-specific recombinases such as the Cre/loxP system. Despite the use of a cardiac-specific rat myosin light chain II promoter, our transgenic line (CRE3) had little or no Cre expression in the heart; however, strong Cre activity was detected in the brain as early as gestation day E11.5. This was determined by several methods including crossing our mouse line with a lacZ indicator line (ROSA26). Transgenic Cre, in this mouse line, mediated DNA recombination of loxP-flanked genes selectively in neurons throughout the gray matter of the brain, cerebellum, spinal cord, as well as retina, dorsal, and sympathetic ganglia. Cre protein was also detected by immunohistochemistry exclusively in neurons, but not in other types of cells or tissues. Thus, our transgenic CRE3 mice provide pan-neuronal expression of CRE for carrying out conditional deletion of genes in neurons and their progenitors.
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Abstract
Studies of cellular interactions are critical to the understanding of tumorigenesis. Although many studies have demonstrated a monoclonal composition of advanced neoplasms in humans and mice, the clonal composition of smaller, antecedent lesions has been studied less thoroughly. To examine the clonal development of breast cancer, we generated chimeric mammary glands using mouse mammary epithelium with an inherited predisposition for neoplasia. Analysis of whey acidic protein-transforming growth factor-alpha transgenic mouse mammary glands, chimeric for two different cell lineage markers, revealed that mammary ducts and alveoli are polyclonal, and putative early preneoplastic lesions, hyperplastic alveolar nodules (HANs), frequently are polyclonal. Furthermore, the chimeric patch patterns in individual HANs were similar to the patterns observed in pregnant chimeric mammary glands. Thus, polyclonality in HANs appears to reflect persistence of the polyclonal architecture of ducts and/or alveoli, suggesting that hyperplasia formation can be the result of non-cell autonomous local tissue microenvironmental influences on groups of cells, rather than clonal progression of a single initiated cell.
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Affiliation(s)
- William C Kisseberth
- Department of Veterinary Clinical Sciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA
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4
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Wen F, Cecena G, Munoz-Ritchie V, Fuchs E, Chambon P, Oshima RG. Expression of conditional cre recombinase in epithelial tissues of transgenic mice. Genesis 2003; 35:100-6. [PMID: 12533792 PMCID: PMC2405925 DOI: 10.1002/gene.10169] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
SUMMARY Keratin 18 (K18) expression is a defining characteristic of internal epithelial cells of mammals. Here, we used the K18 gene and an internal ribosome entry site (IRES) to express green fluorescent protein, human placental alkaline phosphatase, and a modified Cre recombinase in an epithelial specific pattern in transgenic mice. The K18-driven alkaline phosphatase was expressed in liver, kidney, uterine endometrium, and other internal epithelia. The enzymatic activity of the Cre recombinase-mutant estrogen receptor fusion protein was dependent on tamoxifen administration and resulted in a mosaic pattern in internal epithelia, including bladder, uterus, liver, and kidney. This conditional Cre activity in internal epithelial organs should be valuable for strategies utilizing Cre for activation of gene expression. This study demonstrates that the tissue-specific, position-independent transcriptional activity of the K18 gene is not compromised by the use of an IRES element for the expression of a second protein from a bicistronic mRNA.
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Affiliation(s)
- Fang Wen
- The Burnham Institute, La Jolla, California 92037, USA
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5
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Abstract
Locus control regions (LCRs) are operationally defined by their ability to enhance the expression of linked genes to physiological levels in a tissue-specific and copy number-dependent manner at ectopic chromatin sites. Although their composition and locations relative to their cognate genes are different, LCRs have been described in a broad spectrum of mammalian gene systems, suggesting that they play an important role in the control of eukaryotic gene expression. The discovery of the LCR in the beta-globin locus and the characterization of LCRs in other loci reinforces the concept that developmental and cell lineage-specific regulation of gene expression relies not on gene-proximal elements such as promoters, enhancers, and silencers exclusively, but also on long-range interactions of various cis regulatory elements and dynamic chromatin alterations.
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Affiliation(s)
- Qiliang Li
- Division of Medical Genetics, Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
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6
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Rose-Hellekant TA, Gilchrist K, Sandgren EP. Strain background alters mammary gland lesion phenotype in transforming growth factor-alpha transgenic mice. THE AMERICAN JOURNAL OF PATHOLOGY 2002; 161:1439-47. [PMID: 12368216 PMCID: PMC1867309 DOI: 10.1016/s0002-9440(10)64419-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Whey acidic protein (WAP)-transforming growth factor (TGF)-alpha transgenic mice acquire both cancerous and noncancerous mammary lesions. For this study, we evaluated the effect of mouse strain background on the incidence, latency, and histotype of two noncancerous lesions, hyperplastic alveolar nodules (analogous to typical hyperplasias in women), and macrocysts. These lesions display characteristics of fibrocystic changes observed in breasts of women, and in both mice and humans are associated with an uncertain risk of progression to neoplasia. Virgin transgenic mice of the (C57BL/6J;SJL)F2 background developed very few hyperplastic alveolar nodules and no macrocysts. In contrast, when the WAP-TGF-alpha transgene was carried on the FVB/N strain, congenic virgin transgenic mice acquired both lesion types with approximately 100% penetrance. In the (FVB;C57BL/6J)F1 background, hyperplastic alveolar nodule incidence was reduced to approximately the nontransgenic mouse level, and macrocyst latency was increased dramatically. Crossing into C57BL/6 resulted in elimination of the macrocyst phenotype. Finally, FVB strain transgenic mammary epithelium transplanted into nontransgenic recipients of the FVB/N or (FVB;C57BL/6J)F1 backgrounds displayed macrocyst latency characteristic of the recipient, and not donor, mouse strain. Quantitative real-time polymerase chain reaction analysis demonstrated that, despite the difference in macrocyst incidence between (FVB;C57BL/6J)F1 and C57BL/6 virgin transgenic mice (81% versus 0%), the level of TGF-alpha expression was not different. FVB strain transgenic mice expressed only twofold more TGF-alpha than the other backgrounds. These findings indicate that C57BL/6J modifier alleles inhibit mammary lesion incidence and macrocyst latency in a semidominant manner, and that suppression of lesion development can involve host factors that are independent of mammary epithelial genotype.
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Affiliation(s)
- Teresa A Rose-Hellekant
- Department of Pathobiological Sciences, School of Medicine, University of Wisconsin-Madison, 53706, USA
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7
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Koehler DR, Hannam V, Belcastro R, Steer B, Wen Y, Post M, Downey G, Tanswell AK, Hu J. Targeting transgene expression for cystic fibrosis gene therapy. Mol Ther 2001; 4:58-65. [PMID: 11472107 DOI: 10.1006/mthe.2001.0412] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
We have developed an expression cassette for cystic fibrosis (CF) gene therapy using control elements from the human cytokeratin 18 gene (KRT18, also known as K18). KRT18 is naturally expressed in a spatial pattern similar to that of CFTR, the gene mutated in CF. We delivered a KRT18-driven lacZ plasmid complexed with cationic liposomes intravenously to mice and examined expression in various tissues. We found expression in nasal and bronchial epithelium, airway submucosal glands, gall bladder, and kidneys. Expression was low in pancreas and gut, and absent from liver and alveolar lung. This is consistent with the expression pattern reported for a K18lacZ transgenic mouse. Following delivery of a cytomegalovirus (CMV) major immediate-early promoter/enhancer-driven lacZ plasmid, we found expression in bronchi, submucosal glands, alveolar cells, liver, and kidney. We did not detect expression in nose, pancreas, gall bladder, or gut. Using fluorescently labeled plasmid delivered by means of liposomes, we identified the liver, alveolar lung, and kidneys as the major plasmid deposition sites. Our data demonstrate that a KRT18-driven expression vector delivered systemically can target gene expression to CF-affected tissues, despite an uneven distribution of plasmid DNA. A KRT18-based vector may be a useful alternative to viral promoter-based vectors in clinical gene therapy trials to treat CF.
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Affiliation(s)
- D R Koehler
- Programme in Lung Biology Research, Canadian Institutes of Health Research Group in Lung Development, The Hospital for Sick Children, Toronto, Ontario, Canada
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Abstract
AbstractThe c-fes proto-oncogene encodes a 92-kd protein tyrosine kinase whose expression is restricted largely to myeloid and endothelial cells in adult mammals. A 13.2-kilobase (kb) humanc-fes genomic fragment was previously shown to containcis-acting element(s) sufficient for a locus control function in bone marrow macrophages. Locus control regions (LCRs) confer transgene expression in mice that is integration site independent, copy number dependent, and similar to endogenous murine messenger RNA levels. To identify sequences required for this LCR,c-fes transgenes were analyzed in mice. Myeloid-cell–specific, deoxyribonuclease-I–hypersensitive sites localized to the 3′ boundary of exon 1 and intron 3 are required to confer high-level transgene expression comparable to endogenous c-fes, independent of integration site. We define a minimal LCR element as DNA sequences (nucleotides +28 to +2523 relative to the transcription start site) located within intron 1 to intron 3 of the human locus. When this 2.5-kb DNA fragment was linked to a c-fes complementary DNA regulated by its own 446–base-pair promoter, integration-site–independent, copy-number–dependent transcription was observed in myeloid cells in transgenic mice. Furthermore, this 2.5-kb cassette directed expression of a heterologous gene (enhanced green fluorescent protein) exclusively in myeloid cells. The c-fes regulatory unit represents a novel reagent for targeting gene expression to macrophages and neutrophils in transgenic mice.
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A minimal c-fes cassette directs myeloid-specific expression in transgenic mice. Blood 2000. [DOI: 10.1182/blood.v96.9.3040.h8003040_3040_3048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The c-fes proto-oncogene encodes a 92-kd protein tyrosine kinase whose expression is restricted largely to myeloid and endothelial cells in adult mammals. A 13.2-kilobase (kb) humanc-fes genomic fragment was previously shown to containcis-acting element(s) sufficient for a locus control function in bone marrow macrophages. Locus control regions (LCRs) confer transgene expression in mice that is integration site independent, copy number dependent, and similar to endogenous murine messenger RNA levels. To identify sequences required for this LCR,c-fes transgenes were analyzed in mice. Myeloid-cell–specific, deoxyribonuclease-I–hypersensitive sites localized to the 3′ boundary of exon 1 and intron 3 are required to confer high-level transgene expression comparable to endogenous c-fes, independent of integration site. We define a minimal LCR element as DNA sequences (nucleotides +28 to +2523 relative to the transcription start site) located within intron 1 to intron 3 of the human locus. When this 2.5-kb DNA fragment was linked to a c-fes complementary DNA regulated by its own 446–base-pair promoter, integration-site–independent, copy-number–dependent transcription was observed in myeloid cells in transgenic mice. Furthermore, this 2.5-kb cassette directed expression of a heterologous gene (enhanced green fluorescent protein) exclusively in myeloid cells. The c-fes regulatory unit represents a novel reagent for targeting gene expression to macrophages and neutrophils in transgenic mice.
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10
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Chow YH, Plumb J, Wen Y, Steer BM, Lu Z, Buchwald M, Hu J. Targeting transgene expression to airway epithelia and submucosal glands, prominent sites of human CFTR expression. Mol Ther 2000; 2:359-67. [PMID: 11020351 DOI: 10.1006/mthe.2000.0135] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Targeting therapeutic gene expression to disease-affected tissues is an essential component of effective and safe gene therapy. After birth, CFTR gene expression in human lungs is localized predominantly in the epithelial cells lining the upper airways, especially in the ducts and serous tubules of the submucosal glands. We have developed a K18 expression cassette, based on the DNA control elements of the human cytokeratin 18 gene. Temporal and spatial analyses of transgenic mice demonstrated that this expression cassette targets transgene expression to almost all cell types in which CFTR is expressed. Airway epithelium expression started as early as 11.5 days of gestational age and continued into the adulthood of the transgenic mice. In these adult mice, the pattern of the reporter expression strikingly matched that of the human cytokeratin 18 and human CFTR genes. The transgene expression was epithelium-specific and undetectable in connective tissue, muscle, bone, cartilage, blood, and endothelial cells. Significantly, high levels of expression were detected in tracheal submucosal glands. Together, these results suggest that our K18 expression cassette has a high potential for clinical application in gene therapy for patients with cystic fibrosis.
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Affiliation(s)
- Y H Chow
- Programme of Lung Biology Research, The Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
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11
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Abstract
A novel positive/negative selection cassette, puDeltatk, was generated. pu(Delta)tk is a bifunctional fusion protein between puromycin N-acetyltransferase (Puro) and a truncated version of herpes simplex virus type 1 thymidine kinase (DeltaTk). Murine embryonic stem (ES) cells transfected with pu(Delta)tk become resistant to puromycin and sensitive to 1-(-2-deoxy-2-fluoro-1-beta-D-arabino-furanosyl)-5-iodouracil (FIAU). Unlike other HSV1 tk transgenes, puDeltatk is readily transmitted through the male germ line. Thus pu(Delta)tk is a convenient positive/negative selectable marker that can be widely used in many ES cell applications.
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Affiliation(s)
- Y T Chen
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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12
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Willoughby DA, Vilalta A, Oshima RG. An Alu element from the K18 gene confers position-independent expression in transgenic mice. J Biol Chem 2000; 275:759-68. [PMID: 10625605 DOI: 10.1074/jbc.275.2.759] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have identified a 323-base pair fragment of the 5'-flanking sequence of the K18 gene, which confers position-independent and copy number-dependent expression on two heterologous transgenes. This fragment is composed primarily of an Alu repetitive element. Its activity in mice is correlated with its RNA polymerase III promoter activity and its orientation-dependent ability to inhibit potential transcriptional interference in a transfection assay. However, the activity of the Alu element is not correlated with its enhancer blocking activity, a characteristic of insulator elements. In addition, this Alu element did not block the suppressive effect of co-injecting mouse alpha satellite DNA with the transgene. This Alu element is likely responsible for at least part of the protective effects of the sequences flanking the K18. These results suggest that transcriptionally active Alu elements may eliminate transcriptional interference of neighboring genes. This Alu element is one component of the locus control region associated with the K18 gene. Other Alu repetitive elements may also function to define regulatory domains.
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Affiliation(s)
- D A Willoughby
- Burnham Institute, La Jolla Cancer Research Center, La Jolla, California 92037, USA
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13
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Abstract
The beta-globin locus control region (LCR) is the founding member of a novel class of cis-acting regulatory elements that confer high level, tissue-specific, site-of-integration-independent, copy number-dependent expression on linked transgenes located in ectopic chromatin sites. Knowledge from beta-globin and other LCR studies has shed light on our understanding of the long-range interaction between enhancers and promoters, the relationship between chromatin conformation and transcriptional regulation, and the developmental regulation of multiple gene loci. After over a decade of investigation and discovery, we take a retrospective look at the beta-globin LCR and other LCRs, summarize their properties and review models of LCR function.
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Affiliation(s)
- Q Li
- Division of Medical Genetics, Mail Box 357720, Department of Medicine, University of Washington, Seattle, WA 98195, USA.
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14
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Yeung CM, Wong CK, Chung SK, Chung SS, Chow BK. Glucose-dependent insulinotropic polypeptide gene expression in the stomach: revealed by a transgenic mouse study, in situ hybridization and immunohistochemical staining. Mol Cell Endocrinol 1999; 154:161-70. [PMID: 10509810 DOI: 10.1016/s0303-7207(99)00106-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Glucose-dependent insulinotropic polypeptide (GIP) plays an important role in stimulating insulin release in the pancreas as well as inhibiting gastric acid secretion in the stomach. GIP has been found in specific endocrine cells located in the mucosal layer of the small intestine and in the submandibular salivary gland. In this study, the tissue-specific expression of GIP guided by 1.2 kb of the human GIP (hGIP) gene 5' flanking region was investigated by a transgenic mouse approach. A chimeric promoter-reporter gene construct linking the 5'-flanking region of the hGIP gene with the thymidine kinase gene of the herpes simplex virus was introduced into the genomes of mice by microinjection. By reverse transcriptase-PCR (RT-PCR) and thymidine kinase assays, transgene expression was found in the stomach and pancreas. The enzyme activity detected in the stomach was about 6-fold higher than that found in the pancreas, suggesting that GIP may be expressed in the stomach. This observation is supported by RT-PCR studies since both human and mouse GIP transcripts are detected in the stomach and small intestine. In addition, distinct GIP-producing cells were identified in both tissues in mouse by in situ hybridization and immunohistochemical staining. Taken together, our data demonstrate for the first time that GIP is expressed in human and mouse stomach.
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Affiliation(s)
- C M Yeung
- Department of Zoology, The University of Hong Kong, People's Republic of China
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15
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Rhodes K, Oshima RG. A regulatory element of the human keratin 18 gene with AP-1-dependent promoter activity. J Biol Chem 1998; 273:26534-42. [PMID: 9756890 DOI: 10.1074/jbc.273.41.26534] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human keratin 18 (K18) gene is expressed in a restricted but diverse subset of differentiated epithelial tissues and carcinomas. The 10-kilobase pair K18 gene contains all of the genetic information necessary for tissue-specific, copy number-dependent and integration site-independent expression in transgenic mice. We identified a 100-base pair regulatory element that activates the K18 proximal promoter in the presence of the previously identified first intron enhancer. Deletion of the element greatly diminished K18 expression. This regulatory element also has cryptic, AP-1-dependent promoter activity in the absence of the normal promoter, which results in 10-40-fold higher levels of K18 RNA expression in transgenic mice. The high activity of this cryptic promoter is dependent upon the first intron enhancer. These experiments define interactive regulatory regions of the K18 gene that modulate expression in diverse epithelial cell types and identify an unusual regulatory element with promoter activity that may be useful for high level heterologous gene expression in transgenic animals.
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Affiliation(s)
- K Rhodes
- The Burnham Institute, La Jolla, California 92037, USA
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16
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Muth K, Bruyns R, Thorey IS, von Melchner H. Disruption of genes regulated during hematopoietic differentiation of mouse embryonic stem cells. Dev Dyn 1998; 212:277-83. [PMID: 9626502 DOI: 10.1002/(sici)1097-0177(199806)212:2<277::aid-aja12>3.0.co;2-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A retroviral gene trap vector (U3Tkneo) that selects for integrations in or near expressed 5' exons has been used to identify genes that are repressed during hematopoietic differentiation of mouse totipotent embryonic stem cells. The vector contains coding sequences for an HSV-thymidine kinase/neomycin phosphotransferase fusion protein in the U3 region of a Moloney murine leukemia virus LTR and allows selection for (G418) and against (Ganciclovir; GC) U3 gene expression. A total of 208 neomycin-resistant clones were isolated following infection with U3tkneo and screened for integrations into regulated genes by using a two-step, semisolid culture system that supports hematopoietic differentiation. Two clones contained U3Tkneo integrations in genes that were repressed selectively in hematopoietic cells. Analysis of upstream proviral flanking sequences indicated that both integrations occurred into unknown genes. One up-stream sequence identified a cellular transcript that was expressed differentially in the kidneys and liver of adult mice. When this fusion gene was passaged to the germ line, homozygous offspring with nearly null mutations were obtained. However, mutant mice were normal, suggesting that potential loss of function phenotypes are subtle and may be restricted to the kidneys and the liver.
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Affiliation(s)
- K Muth
- Department of Hematology, University of Frankfurt Medical School, Germany
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17
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Jendraschak E, Kaminski WE. Isolation of human promoter regions by Alu repeat consensus-based polymerase chain reaction. Genomics 1998; 50:53-60. [PMID: 9628822 DOI: 10.1006/geno.1998.5290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Knowledge of the promoter structure is critical for an understanding of the regulation of genes. We demonstrate by analysis of 405 human genes that human promoter regions are flanked by upstream Alu repeat elements, typically at a distance of 0.5-5 kb from their protein-coding areas. We identified common Alu repeat consensus sequences (ARC) among the different members of the Alu subfamilies that can be used as universal anchor sites for polymerase chain reaction (PCR) amplification. Utilizing ARC-specific primers and oligonucleotides specific for the 5' end of a selected target gene, we show that sequences spanning unknown human gene promoter regions can be directly amplified by PCR from genomic DNA. This novel technique, termed ARC-PCR, allowed us to characterize the proximal promoters of the human LTA4 hydrolase and SPARC genes, each within 1 day.
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Affiliation(s)
- E Jendraschak
- Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98195, USA
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18
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Neznanov N, Umezawa A, Oshima RG. A regulatory element within a coding exon modulates keratin 18 gene expression in transgenic mice. J Biol Chem 1997; 272:27549-57. [PMID: 9346889 DOI: 10.1074/jbc.272.44.27549] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Multiple tissue-specific, DNase-hypersensitive sites are correlated with known or potential regulatory regions of the human keratin 18 (K18) gene. One of these sites is found within exon 6, close to a potential AP-1 binding site. Footprint analysis confirmed that this site is capable of binding c-Jun and c-Fos in vitro. However, exon 6 can stimulate expression of a reporter gene driven by the K18 proximal promoter independent of AP-1 in F9 cells and additionally modulates AP-1 responsiveness when in combination with an intron enhancer. Analysis in transgenic mice and by transient transfections of mutant forms of the K18 gene showed that exon 6 contributes to the expression of the K18 gene. However, substitution of part of exon 6 with the corresponding part of the keratin 19 gene which lacks an AP-1 site decreased but did not destroy the regulatory activity of the exon. Furthermore, this mutation did not alter either the tissue specificity or the position-independent and copy number-dependent behavior of the K18 gene. In contrast, a frameshift mutation within exon 6 dramatically decreased the expression of the gene. K18 RNA expression from the frameshift mutation was less than 10% of the wild type K18 transgene. This decline in expression was the result of a combination of decreased stability of mutant K18 RNA and the creation of a negative regulatory element that can interact with the first intron regulatory elements and actively suppress K18 expression. These results demonstrate that a protein-coding portion of the K18 gene also has a regulatory function.
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Affiliation(s)
- N Neznanov
- Burnham Institute, La Jolla, California 92037, USA
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19
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Abstract
Keratin 8 (K8) and keratin 18 (K18) are the most common and characteristic members of the large intermediate filament gene family expressed in 'simple' or single layer epithelial tissues of the body. Their persistent expression in tumor cells derived from these epithelia has led to the wide spread use of keratin monoclonal antibodies as aids in the detection and identification of carcinomas. Oncogenes which activate ras signal transduction pathways stimulate expression of the K18 gene through transcription factors including members of the AP-1 (jun and fos) and ETS families. The persistent expression of K8 and K18 may reflect the integrated transcriptional activation of such transcription factors and, in the cases of ectopic expression, an escape from the suppressive epigenetic mechanisms of DNA methylation and chromatin condensation. Comparison of the mechanisms of transcriptional control of K18 expression with expression patterns documented in both normal and pathological conditions leads to the proposal that persistent K8 and K18 expression is a reflection of the action of multiple different oncogenes converging on the nucleus through a limited number of transcription factors to then influence the expression of a large number of genes including these keratins. Furthermore, correlation of various tumor cell characteristics including invasive behavior and drug sensitivity with K8 and K18 expression has stimulated consideration of the possible functions of these proteins in both normal development and in tumorigenesis. Recent developments in the analysis of the functions of these intermediate filament proteins provide new insights into diverse functions influenced by K8 and K18.
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Affiliation(s)
- R G Oshima
- Burnham Institute, La Jolla, CA 92037, USA
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20
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Wu JX, Adamson ED. Kinase-negative mutant epidermal growth factor receptor (EGFR) expression during embryonal stem cell differentiation favours EGFR-independent lineages. Development 1996; 122:3331-42. [PMID: 8898244 DOI: 10.1242/dev.122.10.3331] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
EGF receptors are expressed on most fetal and adult cells but their precise roles are not well known. We previously reported that, in P19 embryonal carcinoma cells, the expression of kinase-negative EGFR inhibits retinoic acid (RA)-induced differentiation to nervous tissue, suggesting that EGFR plays a role in differentiation (J.-X. Wu and E. D. Adamson (1993) Dev. Biol. 159, 208–222). Embryo stem (ES) cells differentiate into a wide range of tissue types after the removal of the cytokine LIF from the culture medium. We demonstrate here that the induction of some early markers of differentiation, tissue-type plasminogen activator (tPA), AFP and keratins 8 and 19 is inhibited, whilst brachyury and myosin are increased, in clones containing kinase-negative mutant EGFR. After an extended period of differentiation, the cell types present in mutant and control cultures differed. Mutant clones produced frequent cardiac and skeletal muscle as the predominant differentiated cell types in vitro; other cells types were sparse or absent. Teratocarcinomas formed by EGFR-deltakinase-expressing ES cells contained frequent skeletal and cardiac muscle as well as apoptotic nuclei, while normal ES cells produced no detectable muscle and less apoptoses. Since mutant differentiated cultures had slower growth rates and increased levels of cell death, we concluded that: (1) inactive EGFR does not allow some cell types to survive and/or proliferate; (2) tissues that do not require EGFR for their survival, development or function predominate in long-term mutant cultures; (3) EGFR activity is not necessary for cardiac and skeletal muscle or endoderm formation and (4) Impaired survival of EGF-dependent lineages leads to preferential selection of muscle in differentiating ES cells.
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Affiliation(s)
- J X Wu
- The Burnham Institute, La Jolla Cancer Research Center, CA 92037, USA
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21
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Hewitt SM, Fraizer GC, Saunders GF. Transcriptional silencer of the Wilms' tumor gene WT1 contains an Alu repeat. J Biol Chem 1995; 270:17908-12. [PMID: 7629096 DOI: 10.1074/jbc.270.30.17908] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Expression of the Wilms' tumor gene WT1 is tightly regulated throughout development. In contrast, the WT1 promoter is promiscuous, functioning in all cell lines tested. We have cloned a transcriptional silencer that is involved in regulation of the WT1 gene. The transcriptional silencer is located in the third intron of the WT1 gene, approximately 12 kilobases from the promoter, and functions to repress transcription from the WT1 promoter in cell lines of non-renal origin. The 460-base pair silencer region is unusual in that it contains a full-length Alu repeat. We have also cloned an enhancer like-element located 1.3 kilobases upstream of the WT1 promoter.
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Affiliation(s)
- S M Hewitt
- Department of Biochemistry and Molecular Biology, University of Texas M. D Anderson Cancer Center, Houston 77030, USA
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22
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Briand P, Kahn A, Vandewalle A. Targeted oncogenesis: A powerful method to derive renal cell lines. Kidney Int 1995; 47:388-94. [PMID: 7723228 DOI: 10.1038/ki.1995.51] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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23
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Casanova L, Bravo A, Were F, Ramírez A, Jorcano JJ, Vidal M. Tissue-specific and efficient expression of the human simple epithelial keratin 8 gene in transgenic mice. J Cell Sci 1995; 108 ( Pt 2):811-20. [PMID: 7539440 DOI: 10.1242/jcs.108.2.811] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Keratin 8 is a type II intermediate filament protein found in simple epithelia. We have introduced a 12 kb DNA fragment of the human K8 locus into the germ line of mice. The transgene, containing 1.1 kb of 5′ flanking sequences, 7.7 kb corresponding to the body of the gene and 3.2 kb of 3′ flanking sequences, was expressed in all six lines obtained. Immunolocalization and RNA analysis of adult tissues showed that the tissue-specific expression pattern of the transgene was almost indistinguishable from that of the endogenous gene. This pattern was found in organs containing single epithelial cell types, such as trachea, lung, stomach, intestine, liver, kidney, thymus and glands. The highest expressing line, however, also produced human K8 in tissues such as stratified epithelia, where it formed part of the pre-existing keratin cytoskeleton of basal cells. Steady state levels of human K8 RNA were proportional to the copy number of the transgene, but transgene expression was less efficient, per gene copy, than that of the endogenous gene. When in the 12 kb DNA fragment the exons and introns of the gene were replaced by the Escherichia coli lacZ gene, the resulting construct showed no expression in transgenic mice. This suggests that 5′ and 3′ flanking sequences, in the absence of intragenic sequences, are not sufficient for K8 expression and that important control elements are located in the body of the K8 gene.
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Affiliation(s)
- L Casanova
- Department of Developmental and Cell Biology, Centro Investigaciones Biológicas, CSIC, Madrid, Spain
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Murphy C, Beckers J, Rüther U. Regulation of the human C-reactive protein gene in transgenic mice. J Biol Chem 1995; 270:704-8. [PMID: 7822299 DOI: 10.1074/jbc.270.2.704] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Human C-reactive protein (hCRP) is a major acute-phase reactant in man. The regulation of the hCRP gene in transgenic mice is similar to that in humans. To map DNA regions required for the correct regulation of the hCRP gene, several constructs have been generated, and their expression in transgenic mice has been analyzed. Constructs lacking DNA regions surrounding the poly(A) site of the gene are not expressed either before or after induction in transgenic mice. Minimal regions 540 base pairs upstream and 1.2 kilobases downstream of the hCRP gene are sufficient for liver-specific expression. Extended 5'- and 3'-flanking regions are required to silence the expression prior to induction. Our findings demonstrate that regulatory sequences shown to confer inducible expression of the hCRP gene in hepatoma cell lines are insufficient in transgenic mice.
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Affiliation(s)
- C Murphy
- European Molecular Biology Laboratory, Heidelberg, Federal Republic of Germany
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25
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Larsen HJ, Brodersen CH, Hjorth JP. High-level salivary gland expression in transgenic mice. Transgenic Res 1994; 3:311-6. [PMID: 7951333 DOI: 10.1007/bf01973591] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A 7.1 kb mini-gene construct containing cloned DNA from the murine parotid secretory protein (PSP) gene with 6.2 kb of the promoter, has previously been shown to direct specific mRNA expression to the salivary glands in transgenic mice. However, the level of transgene expression in the parotid gland was only a few percent of the endogenous level. This indicated that elements necessary for high-level expression are still to be found. In this study, we have searched for such regulatory elements in additional flanking regions by using a 25 kb cloned Pspb fragment containing the complete structural gene, 11.4 kb of 5'-flanking sequence, and 2.5 kb 3'-flanking sequence as a transgene. To distinguish the expression of the transgene from that of the endogenous gene, we took advantage of an allelic difference, using an oligonucleotide that recognized the mRNA from Pspb and the transgene but not that from the other allele, Pspa. The expression of the transgene was examined in animals homozygous for Pspa. Three independent integrations all exhibited a level of parotid-gland-specific expression that corresponded to that of the endogenous gene. Thus, sequences responsible for this high-level PSP mRNA expression are situated within the genomic DNA of the transgene.
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Affiliation(s)
- H J Larsen
- Department of Molecular Biology, University of Aarhus, Denmark
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Faust N, Bonifer C, Wiles MV, Sippel AE. An in vitro differentiation system for the examination of transgene activation in mouse macrophages. DNA Cell Biol 1994; 13:901-7. [PMID: 7917012 DOI: 10.1089/dna.1994.13.901] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
In an effort to study basic principles of marker gene activation during myeloid lineage development, we established an in vitro differentiation system for macrophages based on mouse embryonic stem (ES) cells. Under the influence of defined cytokines, ES cells gave rise to a cell population consisting predominantly of macrophages. We could show, that expression of the mouse lysozyme M gene is a faithful internal standard for indicating the proportion of macrophage cells in the differentiation culture. This controlled in vitro differentiation system can be used for quantitative studies on transgene activation. Undifferentiated ES cells were stably transfected with a construct carrying the chicken lysozyme gene locus, which had been shown previously to express lysozyme RNA cell type specifically and position independently in macrophages of transgenic mice. In undifferentiated transfected ES cell clones, the transgene was consistently inactive. Upon in vitro differentiation, the transgene was expressed exclusively in macrophages and its level of activity was independent of the chromosomal site of integration. The in vitro cell differentiation system presented here will be useful to study the cis- and trans-regulatory requirements of myeloid-specific gene activation and the influence of hematopoietic regulators on myelopoiesis through their effect on transfected marker gene expression.
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Affiliation(s)
- N Faust
- Institut für Biologie III, Universität Freiburg, Germany
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Abstract
In little more than a decade, the techniques developed for altering the genetic makeup of laboratory and livestock animals and plants have changed the landscape of biological research. It is now possible to introduce virtually any cloned gene into the germ line and study the expression pattern and effects of the introduced gene, or transgene. This has allowed the extension of in vitro and in vivo cell-culture studies into whole animal systems in which the introduced gene is subject to all normal regulatory processes from the onset of development. Although there have been reports of foreign gene expression resulting from direct injection of DNA in animals (e.g., Wolff et al., 1990; Zhu et al., 1993), transgenic animals are the primary model system for examining molecular genetic phenomena in vivo.
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Affiliation(s)
- D C Wight
- Edison Biotechnology Institute, Ohio University, Athens 45701
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28
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Tu ZJ, Lazowski KW, Ehlenfeldt RG, Wu G, Lin HH, Kousvelari E, Ann DK. Isoproterenol/tannin-dependent R15 expression in transgenic mice is mediated by an upstream parotid control region. Gene Expr 1993; 3:289-305. [PMID: 8019129 PMCID: PMC6081613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/1993] [Accepted: 12/17/1993] [Indexed: 01/28/2023]
Abstract
Transgenic mice were used to locate the cis-acting DNA elements that are essential for tissue-specific and inducible expression of the rat proline-rich protein gene, R15. Chimeric genes with up to 10 kb of R15 5'-flanking region fused to chloramphenicol acetyltransferase (CAT) or polyomaviral large T-antigen (PyLT) reporter genes were tested. Our results demonstrate that (1) the isoproterenol/tannin-inducible, parotid-specific transgene expression requires an upstream cis-regulatory domain, namely the parotid control region, which extends from -6 to -1.7 kb of the R15 gene; (2) this parotid control region functions with a heterologous promoter and is indispensable for achieving a reproducible chromosomal position-independent transgene expression; (3) deletion of the R15 5'-flanking region up to -1.7 kb results in a pleiotropic effect on the transgene expression, which includes ectopic (nonsalivary) reporter expression and lack of inducibility by either the beta-agonist isoproterenol or dietary tannin stimulation; (4) when the -10 to -6 kb region from the R15 gene is deleted in the construct, the inducible expression in the parotid glands of the transgenic mice decreases by over 30-fold, but position-independent and tissue-specific transgene expression is retained. Moreover, the mechanism of induction by either catecholamine isoproterenol or dietary tannin appears to be through a beta 1-adrenergic receptor-mediated pathway for both normal (non-transgenic) and transgenic animals.
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Affiliation(s)
- Z J Tu
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis 55455
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