90,493 research outputs found
TYPE II DNA: when the interfacial energy becomes negative
An important step in transcription of a DNA base sequence to a protein is the
initiation from the exact starting point, called promoter region. We propose a
physical mechanism for identification of the promoter region, which relies on a
new classification of DNAs into two types, Type-I and Type-II, like
superconductors, depending on the sign of the energy of the interface
separating the zipped and the unzipped phases. This is determined by the
energies of helical ordering and stretching over two independent length scales.
The negative interfacial energy in Type II DNA leads to domains of helically
ordered state separated by defect regions, or blobs, enclosed by the
interfaces. The defect blobs, pinned by non-coding promoter regions, would be
physically distinct from all other types of bubbles. We also show that the
order of the melting transition under a force is different for Type I and Type
II.Comment: 4 pages, 2 figures, Eq.(4) corrected in 4th versio
TaqMan Genotyping Assay Method for Single Nucleotide Polymorphisms (SNPs) detection in promoter region of N-Acetyltransferase 2 (NAT2) gene
  The N-acetyltransferase 2 (NAT2) polymorphism in coding region has been studies intensively. However, there are limited studies for promoter region of NAT2 gene. Several reported study showed that the promoter region polymorphism of NAT2 gene is genotyped by PCR-sequencing approach. In this paper, we describe TaqMan based assays for the NAT2 polymorphism genotyping in promoter region with following SNP: rs4646243 [T>C], rs4646244 [T>A], rs4646267 [A>G], rs4345600 [A>G], and rs4646246 [A>G]. Our result showed a good separation cluster, trailing cluster and some mix cluster. TaqMan genotyping assay has shown a sensitivity and specificity to detect polymorphism in NAT2 promoter region
Role of tumour necrosis factor gene polymorphisms (-308 and -238) in breast cancer susceptibility and severity
Introduction
Genetic polymorphisms in the promoter region of the tumour necrosis factor (TNF) gene can regulate gene expression and have been associated with inflammatory and malignant conditions. We have investigated two polymorphisms in the promoter of the TNF gene (-308 G>A and -238 G>A) for their role in breast cancer susceptibility and severity by means of an allelic association study.
Methods
Using a case–control study design, breast cancer patients (n = 709) and appropriate age-matched and sex-matched controls obtained from the Breast Screening Unit (n = 498) were genotyped for these TNF polymorphisms, using a high-throughput allelic discrimination method.
Results
Allele frequencies for both polymorphisms were similar in both breast cancer cases and controls. However, the -308 polymorphism was found to be associated with vascular invasion in breast tumours (P = 0.024). Comparison with other standard prognostic indices did not show any association for either genotype.
Conclusions
We demonstrated no association between the -308G>A polymorphism and the -238G>A polymorphism in the promoter region of TNF and susceptibility to breast cancer, in a large North European population. However, the -308 G>A polymorphism was found to be associated with the presence of vascular invasion in breast tumours
Association of genetic and epigenetic modification in MTHFR gene with coronary artery disease patients in North Indian population
Background: Methylene tetra hydro folate reductase (MTHFR) gene polymorphism C677T (rs180113) and DNA methylation in promoter region of MTHFR gene may contribute to the development of coronary artery disease however the results have been inconsistent across studies with different populations, so the aim of our study is to explore the association of polymorphism in MTHFR gene and methylation in promoter region with coronary artery disease (CAD) and other risk factor (lipid profile, homocysteine, vitamin B12 and folic acid levels)Â leading to CAD in of north Indian population.
Methods: Total 100 CAD patients and 100 healthy controls were enrolled in the study. Genotyping of rs1801133 SNP (C677T) is done by PCR-RFLP and DNA methylation study in promoter region by methylation specific PCR. Lipid profile analysis by automated chemistry analyzers, serum homocysteine, folic acid and vitamin B12 was assayed by ELISA.
Results: As per our finding the T allele (OR=3.03, 95% CI=1.74-5.27) and hyper methylation in promoter region of MTHFR increases the odds of coronary artery disease, (OR=3.05, 95% CI=1.7-5.6). Study participants with CT and TT genotype had significantly higher homocysteine (Hcy) (p=0.001), lower folic acid level (p=0.0), and HDL levels (p<0.0001) than those with CC genotype. The study subjects with hyper methylated promoter region have a significantly high homocystenemia levels (p=0.001).
Conclusions: The TT genotype of the MTHFR C677T gene polymorphism and hyper methylation in promoter region of MTHFR, is associated with CAD and can be useful in identification of new biomarkers, development of preventive and therapeutic strategies for CAD.
The epigenetic factor BORIS/CTCFL regulates the NOTCH3 gene expression in cancer cells.
Aberrant upregulation of NOTCH3 gene plays a critical role in cancer pathogenesis. However, the underlying mechanisms are still unknown. We tested here the hypothesis that aberrant epigenetic modifications in the NOTCH3 promoter region might account for its upregulation in cancer cells. We compared DNA and histone methylation status of NOTCH3 promoter region in human normal blood cells and T cell acute lymphoblastic leukemia (T-ALL) cell lines, differentially expressing NOTCH3. We found that histone methylation, rather than DNA hypomethylation, contributes towards establishing an active chromatin status of NOTCH3 promoter in NOTCH3 overexpressing cancer cells. We discovered that the chromatin regulator protein BORIS/CTCFL plays an important role in regulating NOTCH3 gene expression. We observed that BORIS is present in T-ALL cell lines as well as in cell lines derived from several solid tumors overexpressing NOTCH3. Moreover, BORIS targets NOTCH3 promoter in cancer cells and it is able to induce and to maintain a permissive/active chromatin conformation. Importantly, the association between NOTCH3 overexpression and BORIS presence was confirmed in primary T-ALL samples from patients at the onset of the disease. Overall, our results provide novel insights into the determinants of NOTCH3 overexpression in cancer cells, by revealing a key role for BORIS as the main mediator of transcriptional deregulation of NOTCH3. Copyright © 2014 Elsevier B.V. All rights reserved
Comparative promoter region analysis powered by CORG
BACKGROUND: Promoters are key players in gene regulation. They receive signals from various sources (e.g. cell surface receptors) and control the level of transcription initiation, which largely determines gene expression. In vertebrates, transcription start sites and surrounding regulatory elements are often poorly defined. To support promoter analysis, we present CORG , a framework for studying upstream regions including untranslated exons (5' UTR). DESCRIPTION: The automated annotation of promoter regions integrates information of two kinds. First, statistically significant cross-species conservation within upstream regions of orthologous genes is detected. Pairwise as well as multiple sequence comparisons are computed. Second, binding site descriptions (position-weight matrices) are employed to predict conserved regulatory elements with a novel approach. Assembled EST sequences and verified transcription start sites are incorporated to distinguish exonic from other sequences. As of now, we have included 5 species in our analysis pipeline (man, mouse, rat, fugu and zebrafish). We characterized promoter regions of 16,127 groups of orthologous genes. All data are presented in an intuitive way via our web site. Users are free to export data for single genes or access larger data sets via our DAS server . The benefits of our framework are exemplarily shown in the context of phylogenetic profiling of transcription factor binding sites and detection of microRNAs close to transcription start sites of our gene set. CONCLUSION: The CORG platform is a versatile tool to support analyses of gene regulation in vertebrate promoter regions. Applications for CORG cover a broad range from studying evolution of DNA binding sites and promoter constitution to the discovery of new regulatory sequence elements (e.g. microRNAs and binding sites)
Polymorphisms of beta-lactoglobulin promoter region in three Sicilian goat breeds
Several beta-lactoglobulin (BLG) polymorphisms
have been described within the proximal promoter
region and coding region of the caprine gene, although no
genetic variants affecting the protein amino acid composition
and/or expression level have been characterized so
far. Binding sites for several transcription factors (TFs) are
present in the BLG promoter region. The aims of this work
were to sequence the full-length promoter region of three
Sicilian goat breeds in order to identify polymorphisms,
analyze the identified haplotypes, search for differences
between breeds for the presence of polymorphisms in this
gene region, search for putative TFs binding sites, and
check if polymorphisms lay within the identified TFs
binding sites. The promoter region of BLG gene in Sicilian
goat breeds showed high level of polymorphism due to the
presence of 36 single nucleotide polymorphisms (SNPs).
Association between polymorphic sites was computed
within the whole sample analyzed and 18 haplotypes were
inferred. Binding sites for three milk protein binding factors (MPBFs) and four nuclear factor-I (NF-I) were
found within BLG promoter region based on the ovine
sequence. The identification of some SNPs within TFs
binding sites allowed hypothesizing the loss of TFs. Further
studies are in progress to evaluate the effect of these
mutations on binding affinity of TFs, the functional interaction
of the TFs with the goat BLG promoter, and the
relationship of the polymorphisms with BLG gene
expression and milk production and composition
Down-Regulation of Serum/Glucocorticoid Regulated Kinase 1 in Colorectal Tumours Is Largely Independent of Promoter Hypermethylation
Background: We have previously shown that serum/glucocorticoid regulated kinase 1 (SGK1) is down-regulated in colorectal cancers (CRC) with respect to normal tissue. As hyper-methylation of promoter regions is a well-known mechanism of gene silencing in cancer, we tested whether the SGK1 promoter region was methylated in colonic tumour samples. Methodology/Principal Findings: We investigated the methylation profile of the two CpG islands present in the promoter region of SGK1 in a panel of 5 colorectal cancer cell lines by sequencing clones of bisulphite-treated DNA samples. We further confirmed our findings in a panel of 10 normal and 10 tumour colonic tissue samples of human origin. We observed CpG methylation only in the smaller and more distal CpG island in the promoter region of SGK1 in both normal and tumour samples of colonic origin. We further identified a single nucleotide polymorphism (SNP, rs1743963) which affects methylation of the corresponding CpG. Conclusions/Significance: Our results show that even though partial methylation of the promoter region of SGK1 is present
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