PURPOSE: We investigated whether TIGR/MYOC, a candidate gene for the primary open angle glaucoma(POAG) is also involved in the pathogenesis of normal tension glaucoma(NTG) and steroid-induced glau-coma(SIG). METHODS: Genomic DNA was extracted from the peripheral blood samples collected from 72 normal volunteers and 60 POAG, 47 NTG, 61 SIG patients. The genotype distribution of dinucleotide repeat polymorphism, (G-T)n microsatellite located 249 bp upstream of transcription start site was determined by direct sequencing of the Polymerase Chain Reaction(PCR) product. RESULTS: We found 6 alleles in the (G-T)n microsatellite of TIGR/MYOC ranging from 12 to 17, which differ slightly from that of previous reports. There was no obvious difference in the genotype distribution and allele frequency between the POAG group and the control group. However, a significant association of the microsatellite marker with SIG and, to a lesser extent, with NTG was observed. A significant increase in the frequency of (G-T)13/(G-T)13 genotype and a concomitant decrease in the frequency of (G-T)13/(G-T)14 genotype was seen in both the NTG and SIG group compared to that of the control group. In the SIG group, a significant decrease in the frequency of (G-T)14 allele was also observed compared to the control group, although the decrease did not contribute to the increase in the frequency of the allele. CONCLUSIONS: These findings suggest that a polymorphism in the 5 flanking region of the TIGR/MYOC is associated with patients with NTG and SIG.
Alleles ; Dinucleotide Repeats* ; DNA ; Gene Frequency ; Genotype ; Glaucoma* ; Healthy Volunteers ; Humans ; Microsatellite Repeats ; Transcription Initiation Site

We evaluated the role of IL-10- in IL-33-mediated cholesterol reduction in macrophage-derived foam cells (MFCs) and the mechanism by which IL-33 upregulates IL-10. Serum IL-33 and IL-10 levels in coronary artery disease patients were measured. The effects of IL-33 on intra-MFC cholesterol level, IL-10, ABCA1 and CD36 expression, ERK 1/2, Sp1, STAT3 and STAT4 activation, and IL-10 promoter activity were determined. Core sequences were identified using bioinformatic analysis and site-specific mutagenesis. The serum IL-33 levels positively correlated with those of IL-10. IL-33 decreased cellular cholesterol level and upregulated IL-10 and ABCA1 but had no effect on CD36 expression. siRNA-IL-10 partially abolished cellular cholesterol reduction and ABCA1 elevation by IL-33 but did not reverse the decreased CD36 levels. IL-33 increased IL-10 mRNA production but had little effect on its stability. IL-33 induced ERK 1/2 phosphorylation and increased the luciferase expression driven by the IL-10 promoter, with the highest extent within the −2000 to −1752 bp segment of the 5′-flank of the transcription start site; these effects were counteracted by U0126. IL-33 activated Sp1, STAT3 and STAT4, but only the STAT3 binding site was predicted in the above segment. Site-directed mutagenesis of the predicted STAT3-binding sites (CTGCTTCCTGGCAGCAGAA→CTGCCTGGCAGCAGAA) reduced luciferase activity, and a STAT3 inhibitor blocked the regulatory effects of IL-33 on IL-10 expression. Chromatin immunoprecipitation (CHIP) confirmed the STAT3-binding sequences within the −1997 to −1700 and −1091 to −811 bp locus regions. IL-33 increased IL-10 expression in MFCs via activating ERK 1/2 and STAT3, which subsequently promoted IL-10 transcription and thus contributed to the beneficial effects of IL-33 on MFCs.
Binding Sites ; Cholesterol ; Chromatin Immunoprecipitation ; Computational Biology ; Coronary Artery Disease ; Foam Cells* ; Humans ; Interleukin-10* ; Interleukin-33* ; Luciferases ; Macrophages* ; Mutagenesis, Site-Directed ; Phosphorylation ; RNA, Messenger ; Transcription Initiation Site

The cyclic AMP receptor protein (CRP) complexed with cyclic AMP (CRP.cAMP) regulates expression of many genes by binding to sites at or near many promoters of Escherichia coli. The regulatory effect of CRP.cAMP was studied by in vitro transcription assay with lacUV5 promoter derivatives that have the CRP binding site at different locations (-56 to -69 from the transcription start site of lacUV5 promoter) upstream of the promoter. The CRP binding site itself influenced differently on the promoter activity depending on the distances from the promoter. Depending on the helix phasing of the CRP.cAMP relative to RNA polymerase CRP.cAMP activated, repressed or had no effect on the promoter. These results imply that a regulator is not a dedicated protein for repression or activation but that any regulator may have a potential of dual functionalities when it is under appropriate condition.
Binding Sites ; Cyclic AMP ; Cyclic AMP Receptor Protein ; DNA-Directed RNA Polymerases ; Escherichia coli* ; Escherichia* ; Repression, Psychology ; Transcription Initiation Site

HOTAIR is an lncRNA that has been known to have an oncogenic role in different cancers. There is limited knowledge of genetic and epigenetic elements and their interactions for the gene encoding HOTAIR. Therefore, understanding the molecular mechanism and its regulation remains to be challenging. We used different in silico analyses to find genetic and epigenetic elements of HOTAIR gene to gain insight into its regulation. We reported different regulatory elements including canonical promoters, transcription start sites, CpGIs as well as epigenetic marks that are potentially involved in the regulation of HOTAIR gene expression. We identified repeat sequences and single nucleotide polymorphisms that are located within or next to the CpGIs of HOTAIR. Our analyses may help to find potential interactions between genetic and epigenetic elements of HOTAIR gene in the human tissues and show opportunities and limitations for researches on HOTAIR gene in future studies.
Computational Biology ; Computer Simulation* ; CpG Islands ; Epigenomics ; Gene Expression ; Humans ; Polymorphism, Single Nucleotide ; RNA, Long Noncoding* ; Transcription Initiation Site

Over the past decade or so, dramatic developments in our ability to experimentally determine the content and function of genomes have taken place. In particular, next-generation sequencing technologies are now inspiring a new understanding of bacterial transcriptomes on a global scale. In bacterial cells, whole-transcriptome studies have not received attention, owing to the general view that bacterial genomes are simple. However, several recent RNA sequencing results are revealing unexpected levels of complexity in bacterial transcriptomes, indicating that the transcribed regions of genomes are much larger and complex than previously anticipated. In particular, these data show a wide array of small RNAs, antisense RNAs, and alternative transcripts. Here, we review how current transcriptomics are now revolutionizing our understanding of the complexity and regulation of bacterial transcriptomes.
Genome ; Genome, Bacterial ; Hypogonadism ; Mitochondrial Diseases ; Ophthalmoplegia ; RNA ; RNA, Antisense ; RNA, Satellite ; Sequence Analysis, RNA ; Transcription Initiation Site ; Transcriptome

Chromatin structure and dynamics that are influenced by epigenetic marks, such as histone modification and DNA methylation, play a crucial role in modulating gene transcription. To understand the relationship between histone modifications and regulatory elements in breast cancer cells, we compared our chromatin immunoprecipitation sequencing (ChIP-Seq) histone modification patterns for histone H3K4me1, H3K4me3, H3K9/16ac, and H3K27me3 in MCF-7 cells with publicly available formaldehyde-assisted isolation of regulatory elements (FAIRE)-chip signals in human chromosomes 8, 11, and 12, identified by a method called FAIRE. Active regulatory elements defined by FAIRE were highly associated with active histone modifications, like H3K4me3 and H3K9/16ac, especially near transcription start sites. The H3K9/16ac-enriched genes that overlapped with FAIRE signals (FAIRE-H3K9/14ac) were moderately correlated with gene expression levels. We also identified functional sequence motifs at H3K4me1-enriched FAIRE sites upstream of putative promoters, suggesting that regulatory elements could be associated with H3K4me1 to be regarded as distal regulatory elements. Our results might provide an insight into epigenetic regulatory mechanisms explaining the association of histone modifications with open chromatin structure in breast cancer cells.
Breast ; Breast Neoplasms ; Chromatin ; Chromatin Immunoprecipitation ; Chromosomes, Human ; DNA Methylation ; Epigenomics ; Gene Expression ; Histones ; Humans ; MCF-7 Cells ; Transcription Initiation Site

Promoter prediction is a very important problem and is closely related to the main problems of bioinformatics such as the construction of gene regulatory networks and gene function annotation. In this context, we developed an integrated promoter prediction program using hybrid methods, PromoterWizard, which can be employed to detect the core promoter region and the transcription start site (TSS) in vertebrate genomic DNA sequences, an issue of obvious importance for genome annotation efforts. PromoterWizard consists of three main modules and two auxiliary modules. The three main modules include CDRM (Composite Dependency Reflecting Model) module, SVM (Support Vector Machine) module, and ICM (Interpolated Context Model) module. The two auxiliary modules are CpG Island Detector and GCPlot that may contribute to improving the predictive accuracy of the three main modules and facilitating human curator to decide on the final annotation.
Base Sequence ; Chimera ; Computational Biology ; CpG Islands ; Dependency (Psychology) ; Gene Regulatory Networks ; Genome ; Humans ; Promoter Regions, Genetic ; Transcription Initiation Site ; Vertebrates

BACKGROUND: Herpes zoster is a common viral infectious disease that is caused by the varicellar zoster virus (VZV). It has been suggested that impaired cellular immunity is responsible for the reactivation of the virus, but the pathogenesis of viral reactivation is not fully understood yet. Previous research has shown that interleukin (IL)-10 promoter gene polymorphisms influenced the susceptibility of herpes zoster in Europeans (Finnish patients). The wide ethnical differences of polymorphisms of the IL-10 promoter gene are known to exist between European and Asian populations, but it has not yet been confirmed whether IL-10 polymorphisms are susceptible to herpes zoster in Koreans. OBJECTIVE: The aim of this study was to determine whether some type of polymorphisms in Koreans also influence the susceptibility of developing herpes zoster and, if they exist, to compare the ethnic differences of polymorphisms to those in Europeans. METHODS: The three most investigated single nucleotide polymorphisms (SNP(S)) situated at positions -1082 (G/A), -819 (T/C) and -592 (C/A) 5' of the transcription start site and three haplotypes (GCC, ACC and ATA) of these SNPs were analyzed in 74 herpes zoster patients and 216 normal controls. RESULTS: We found that the -1082 G allele was significantly higher in herpes zoster patients (odds ratio, 2.16; 95% confidence interval, 1.15~4.07; p=0.02) and the GCC haplotype was associated with development of herpes zoster in Koreans (odd ratio, 2.34; 95% confidence interval, 1.23~4.45; p=0.01), compared to the ATA haplotype in Finns. CONCLUSION: Our results suggest that susceptibility genes do influence the development of herpes zoster in Koreans and that ethnic differences do exist between Koreans and Europeans (Finns).
Alleles ; Asian Continental Ancestry Group ; Communicable Diseases ; Haplotypes ; Herpes Zoster* ; Humans ; Immunity, Cellular ; Interleukin-10* ; Interleukins ; Polymorphism, Single Nucleotide* ; Transcription Initiation Site

Metastasis is a major cause of therapeutic failure in ovarian cancer. To elucidate molecular mechanisms of ovarian cancer metastasis, we previously established a metastatic xenograft mouse model using human ovarian carcinoma SK-OV-3 cells. Using gene expression profiling, we found that γ-aminobutyric acid (GABA)A receptor π subunit (GABRP) expression was upregulated (>4-fold) in metastatic tissues from our xenograft mice compared with SK-OV-3 cells. Importantly, GABRP knockdown diminished the migration and invasion of SK-OV-3 cells, and reduced extracellular signal-regulated kinase (ERK) activation while overexpression of GABRP exhibited significantly increased cell migration, invasion and ERK activation. Moreover, treatment with the mitogen-activated protein kinase (MAPK)/ERK kinase (MEK) inhibitor U0126 similarly suppressed the migration and invasion of SK-OV-3 cells, implying that GABRP promotes these cellular behaviors by activating the MAPK/ERK pathway. Using genome-wide DNA methylation profiling, we identified hypomethylated CpG sites in the GABRP promoter in metastatic tissues from the xenograft mice compared with SK-OV-3 cells. Treatment with a DNA methyltransferase inhibitor demonstrated that methylation at −963 bp from the GABRP transcription start site (−963 CpG site) was critical for the epigenetic regulation of GABRP. Finally, we analyzed human ovarian cancer patient samples and showed DNA hypomethylation at the GABRP −963 CpG site in advanced stage, but not early-stage, primary tumors compared with their paired normal tissues. These findings suggest that GABRP enhances the aggressive phenotype of ovarian cancer cells, and that the DNA methylation status of the GABRP −963 CpG site may be useful for predicting the metastatic potential in ovarian cancer patients.
Animals ; Cell Movement ; DNA ; DNA Methylation ; Epigenomics* ; Gene Expression Profiling ; Heterografts ; Humans ; Methylation ; Mice ; Neoplasm Metastasis ; Ovarian Neoplasms* ; Phenotype* ; Phosphotransferases ; Protein Kinases ; Transcription Initiation Site

T cell immunoglobulin mucin domain (TIM)-3 is an immunomodulatory molecule and upregulated in T cells by several cytokines. TIM-3 also influences mast cell function but its transcriptional regulation in mast cells has not been clarified. Therefore, we examined the transcript level and the promoter activity of TIM-3 in mast cells. The TIM-3 transcript level was assessed by real-time RT-PCR and promoter activity by luciferase reporter assay. TIM-3 mRNA levels were increased in HMC-1, a human mast cell line by TGF-beta1 stimulation but not by stimulation with interferon (IFN)-alpha, IFN-lambda, TNF-alpha, or IL-10. TIM-3 promoter -349~+144 bp region relative to the transcription start site was crucial for the basal and TGF-beta1-induced TIM-3 promoter activities in HMC-1 cells. TIM-3 promoter activity was increased by overexpression of Smad2 and Smad4, downstream molecules of TGF-beta1 signaling. Our results localize TIM-3 promoter activity to the region spanning -349 to +144 bp in resting and TGF-beta1 stimulated mast cells.
Cytokines ; Humans ; Immunoglobulins ; Interferons ; Interleukin-10 ; Luciferases ; Mast Cells ; Mucins ; RNA, Messenger ; T-Lymphocytes ; Transcription Initiation Site ; Transforming Growth Factor beta1 ; Tumor Necrosis Factor-alpha