Animals ; DNA, Fungal ; Phosphorylation ; RNA Polymerase II ; Sequence Homology, Nucleic Acid ; T-Box Domain Proteins ; genetics

The evolutionarily conserved RNA Polymerase II Rpb4/7 sub-complex has been thoroughly studied in yeast and impacts gene expression at multiple levels including transcription, mRNA processing and decay. In addition Rpb4/7 exerts differential effects on gene expression in yeast and Rpb4 is not obligatory for yeast (S. cerevisiae) survival. Specialised roles for human (hs) Rpb4/7 have not been extensively described and we have probed this question by depleting hsRpb4/7 in established human cell lines using RNA interference. We find that Rpb4/7 protein levels are inter-dependent and accordingly, the functional effects of depleting either protein are co-incident. hsRpb4/7 exhibits gene-specific effects and cells initially remain viable upon hsRpb4/7 depletion. However prolonged hsRpb4/7 depletion is cytotoxic in the range of cell lines tested. Protracted cell death occurs by an unknown mechanism and in some cases is accompanied by a pronounced elongated cell morphology. In conclusion we provide evidence for a gene-specific role of hsRpb4/7 in human cell viability.
Cell Line ; Cell Nucleus ; metabolism ; Cell Survival ; drug effects ; Gene Expression Profiling ; HeLa Cells ; Humans ; RNA Interference ; RNA Polymerase II ; antagonists & inhibitors ; genetics ; metabolism ; RNA, Small Interfering ; pharmacology

The swine influenza virus (SIV) strain A/Swine/TianJin/01/2004(H1N1) (A/S/TJ/04) was rescued successfully by an eight-plasmid rescue system. The cDNAs of SIV 8 gene segments were synthesized by RT-PCR and cloned into the RNA polymerase I/II bidirection expression vector PHW2000 independently, resulting in 8 recombinant plasmids. The 8 recombinant plasmids were cotransfected into COS-1 cell, 30 h later TPCK-trypsin was added to 0.5 microg/mL. The COS-1 cell and supernatant were harvested 48 h after cotransfection and were inoculated into the allantoic cavity of 9-day-old specific-pathogen free (SPF) chicken eggs. The allantoic fluid of dead eggs was harvested and passaged 3 generations in SPF chicken eggs to get infective virus. The successful rescue of A/S/TJ/04 SIV was identified by hemagglutination assay, hemagglutination inhibition assay, sequence analysis and electron microscope observation. The successful rescue of SIV built a platform for the research of the relationship between genome structure and function of SIV, the mechanisms of trans-species transmission of influenza virus and for the generation of new SIV as vaccine.
Animals ; COS Cells ; Cercopithecus aethiops ; Chick Embryo ; Chickens ; Influenza A Virus, H1N1 Subtype ; genetics ; physiology ; Plasmids ; genetics ; RNA Polymerase I ; genetics ; RNA Polymerase II ; genetics ; Recombination, Genetic ; genetics ; Swine ; Transfection ; Virus Replication

OBJECTIVETo study the imprinting status and expression level of insulin-like growth factor 2 (IGF2) gene in colorectal cancer and to provide a clue for the mechanism of carcinogenesis of colorectal cancer.

METHODSThe expression levels of IGF2 in the paired colorectal cancer and adjacent normal tissue were examined and compared by use of semi-quantitative reverse transcription-polymerase chain reaction. The imprinting status of IGF2 was detected by restriction fragment length polymorphism. The relationships between the expression level of IGF2, its imprinting status, and the carcinogenesis of colorectal cancer were analyzed.

RESULTSIGF2 was overexpressed in 82.4% (28/34) of colorectal cancer tissues which was significantly higher than those of the matched normal tissues (P<0.01, t=3.01). 87.5% (14/16) of colorectal cancer showed loss of imprinting(LOI), while 71.4%(10/14) of normal tissues also displayed LOI of IGF2.

CONCLUSIONOverexpression of IGF2 was found to play an important role in carcinogenesis of colorectal cancer. LOI of IGF2 may be a prophase manifestation of colorectal cancer.

Colorectal Neoplasms ; genetics ; pathology ; DNA, Neoplasm ; genetics ; metabolism ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Female ; Gene Expression Regulation, Neoplastic ; Genomic Imprinting ; Humans ; Insulin-Like Growth Factor II ; genetics ; Male ; Middle Aged ; RNA, Neoplasm ; genetics ; metabolism ; Reverse Transcriptase Polymerase Chain Reaction

OBJECTIVETo develop a simple method for genotyping of hepatitis E virus (HEV) and to investigate HEV genotype distribution in Nanjing area.

METHODSTwenty-seven full HEV sequences currently-available in GenBank were analyzed with MegAlign and MapDraw programs of DNA STAR software. Degenerate primers were designed and applied to amplify a fragment in HEV ORF1 region. HEV genotypes were determined by the size of the PCR products and by single restriction endonuclease analysis.

RESULTSThe PCR products of HEV genotype 1 and 2 were 275 bp and 269 bp in size. Distinctively, the PCR products of genotype 3 and 4 were 317 bp and 314 bp in size. Moreover, the PCR products of genotype 1 could be digested by Nae 1, but the products of genotype 2 could not. Distinctively, the PCR products of HEV genotype 3 could be digested by Not 1, but the products of genotype 4 could not. Six HEV reference strains standing for different HEV genotypes were clustered into their own types as predicted. Within 43 HEV IgM-positive clinical specimens collected in Nanjing, 19 were HEV PCR-positive and identified as genotype 4.

CONCLUSIONA simple method of PCR combined with single restriction endonuclease analysis is developed for HEV genotyping. This assay allows rapid identification of a large number of HEV isolates directly from clinical specimens. Among patients with hepatitis E in Nanjing, most were infected with HEV genotype 4.

DNA Restriction Enzymes ; metabolism ; DNA, Complementary ; genetics ; metabolism ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Genotype ; Hepatitis E ; blood ; genetics ; immunology ; Hepatitis E virus ; genetics ; Humans ; Polymerase Chain Reaction ; methods ; RNA, Viral ; genetics ; Reverse Transcriptase Polymerase Chain Reaction

Animals ; Base Sequence ; Clustered Regularly Interspaced Short Palindromic Repeats ; genetics ; Gene Expression ; Genetic Engineering ; methods ; Mice ; Molecular Sequence Data ; Mutation ; Promoter Regions, Genetic ; genetics ; RNA Polymerase II ; genetics ; RNA, Guide ; genetics

Prostate-specific membrane antigen (PSMA), the research of which has flourished in recent years, is a specific prostate cancer marker. PSMA plays a more and more important role in the early diagnosis, gene treatment and prognosis of the disease course of prostate cancer. This review focuses on the progress in researches of the structure, function, expression traits and gene expression of the PSMA protein, prostate cancer radioimmunoimaging, DNA vaccines and suicide gene therapy based on PSMA, as well as the role of PSMA in the clinical diagnosis and treatment of prostate cancer.
Antigens, Surface ; genetics ; Gene Expression Regulation, Neoplastic ; Glutamate Carboxypeptidase II ; genetics ; Humans ; Male ; Prostate-Specific Antigen ; genetics ; Prostatic Neoplasms ; diagnosis ; genetics ; therapy ; RNA, Messenger ; genetics ; metabolism ; Reverse Transcriptase Polymerase Chain Reaction

OBJECTIVETo provide DNA molecular marker for identification of Nelumbo nucifera by exploring the differences of nrDNA-ITS sequence of N. nucifera originated from different habitats.

METHODTo compare nrDNA-ITS base sequence using specific PCR-ITS.

RESULTThe completed sequence of ITS and 5.8 S rDNA, and the partial sequences of 18S rDNA and 26S rDNA, totally 750 bp, from N. nucifera were obtained. The differences among N. nucifera from different habitats and from different cultivars were found.

CONCLUSIONThe method can be used to identify N. nucifera among different species and to distinguish their fakes. It provided the basis for identifying N. nucifera from different geographical regions by comparison of their ITS sequences.

Base Sequence ; China ; DNA, Plant ; chemistry ; genetics ; metabolism ; DNA, Ribosomal Spacer ; classification ; genetics ; Deoxyribonuclease EcoRI ; metabolism ; Deoxyribonucleases, Type II Site-Specific ; metabolism ; Drug Contamination ; prevention & control ; Geography ; Nelumbo ; classification ; genetics ; Phylogeny ; Plants, Medicinal ; classification ; genetics ; Polymerase Chain Reaction ; RNA, Ribosomal ; genetics ; RNA, Ribosomal, 18S ; genetics ; RNA, Ribosomal, 5.8S ; genetics ; Sequence Analysis, DNA ; Species Specificity

Human leukocyte antigen (HLA) class II molecules are polymorphic cell surface glycoproteins that are crucial for the cellular interaction in immune response. The expression of class II molecules is regulated in a tissue-specific and cytokine-inducible manner, and is mainly restricted to the antigen presenting cells. However, some tumor cells also express class II molecules, and in some class-II-negative tumor cells, class II expression is inducible by interferon (IFN)-gamma. However, their expression varies, even though the tumor cells originate from the same histological origin; some tumor cells show strong expression, others show weak or no expression. To determine whether this differential expression of class II molecules on tumor cells is transcriptionally regulated, FACS analysis and Northern hybridization were performed using a panel of melanoma cell lines, IGR3, Malme-3M, SK-Mel-24, and SK-Mel-28 to analyze the cell surface expression and mRNA transcription rate of HLA-DR before and after treatment with IFN-gamma. FACS analysis showed that before IFN-gamma treatment, IGR3 and Malme-3M cells barely expressed HLA-DR. On the contrary, almost all of the SK-Mel-24 cells (> 90%) and a relatively high rate (> 50%) of SK-Mel-28 cells expressed HLA-DR. After IFN-gamma treatment, HLA-DR expression was induced in Malme-3M cells and SK-Mel-28 cells which displayed elevated levels of HLA-DR expression in a time-dependent manner. However, IGR3 cells never responded to IFN-gamma. Northern analysis showed that treatment with IFN-gamma led to the steady-state mRNA augmentation of the HLA-DR gene in Malme-3M and SK-Mel-28, whereas in IGR3, IFN-gamma did not augment the transcriptional rate of the HLA-DR gene. To further clarify this differential modulation, sequencing analysis of PCR product of the HLA-DR proximal promoter region was done, since the transcription rate of the class II gene is controlled by the well-conserved proximal promoter region. Six independent clones from PCR products of the HLA-DRA proximal promoter region and 16 clones from PCR products of the HLA-DRB proximal promoter region were isolated from the above cell lines and sequenced. Comparison of the nucleotide sequences of all 6 clones of DRA promoter showed that the sequences are extremely similar in both regulatory sequences and their intervening sequences. Sixteen clones of HLA-DRB promoter showed sequence variations such as substitution and insertion/deletion, and these 16 clones could be further grouped into 6 homologues with sequence homology. These data established that the melanoma cell lines studied here showed a differential susceptibility to IFN-gamma on the modulation of HLA-DR molecules, that this modulation is transcriptionally regulated, and that the difference in promoter activity by sequence variation might contribute to such a differential transcriptional regulation at the promoter level.
Base Sequence ; Gene Expression Regulation, Neoplastic/drug effects* ; HLA-DR Antigens/genetics* ; Human ; Interferon Type II/pharmacology* ; Melanoma/genetics* ; Molecular Sequence Data ; Polymerase Chain Reaction ; Promoter Regions (Genetics) ; RNA, Messenger/analysis ; Tumor Cells, Cultured

The core promoter is an important yet often overlooked component in the regulation of transcription by RNA polymerase II. In fact, the core promoter is the ultimate target of action of all of the factors and coregulators that control the transcriptional activity of every gene. In this review, I describe our current knowledge of a downstream core promoter element termed the DPE, which is a TFIID recognition site that is conserved from Drosophila to humans. The DPE is located from +28 to +32 relative to the +1 transcription start site, and is mainly present in core promoters that lack a TATA box motif. Moreover, in Drosophila, the DPE appears to be about as common as the TATA box. There are distinct mechanisms of basal transcription from DPE- versus TATA-dependent core promoters. For instance, NC2/Dr1-Drap1 is a repressor of TATA-dependent transcription and an activator of DPE-dependent transcription. In addition, DPE-specific and TATA-specific transcriptional enhancers have been identified. These findings further indicate that the core promoter is an active participant in the regulation of eukaryotic gene expression.
Animals ; Base Sequence ; DNA-Binding Proteins/metabolism ; Enhancer Elements (Genetics) ; Feedback, Biochemical ; Gene Expression Regulation ; Human ; Models, Genetic ; *Promoter Regions (Genetics) ; RNA Polymerase II/*metabolism ; Transcription Factors/chemistry/genetics/*metabolism ; *Transcription, Genetic