Modulation of Gene Expression by Gene Architecture and Promoter Structure

Regulation of gene expression is achieved by the presence of cis regulatory elements; these signatures are interspersed in the noncoding region and also situated in the coding region of the genome. These elements orchestrate the gene expression process by regulating the different steps involved in the flow of genetic information. Transcription (DNA to RNA) and translation (RNA to Protein) are controlled at different levels by different regulatory elements present in the genome. Current chapter describes the structural and functional elements present in the coding and noncoding region of the genome. Further we discuss role of regulatory elements in regulation of gene expression in prokaryotes and eukaryotes. Finally, we also discuss DNA structural properties of regulatory regions and their role in gene expression. Identification and characterization of cis regulatory elements would be useful to engineer the regulation of gene expression

C-H..O hydrogen bonds in minor groove of A-tracts in DNA double helices

Analysis of available β-DNA type oligomeric crystal structures as well as protein-bound DNA fragments (solved using data with resolution <2.6 Å) indicates that in both data sets, a majority of the (3′-Ade) H2..O2(3′-Thy/Cyt) distances in AA.TT and GA.TC dinucleotide steps, are considerably shorter than their values in a uniform fibre model, and are smaller than their optimum separation distance. Since the electropositive C2-H2 group of adenine is in close proximity of the electronegative keto oxygen atoms of both pyrimidine bases in the antiparallel strand of the double-helical DNA structures, it suggests the possibility of intra-base-pair as well as cross-strand C-H..O hydrogen bonds in the minor groove. The C2-H2..O2 hydrogen bonds within the A.T base-pairs could be a natural consequence of Watson-Crick pairing. However, the close cross-strand interactions between the bases at the 3′-ends of the AA.TT and GA.TC steps arise due to the local sequence-dependent geometry of these steps. While the base-pair propeller twist in these steps is comparable to the fibre model, some of the other local parameters such as base-pair opening angle and inter-base-pair slide show coordinated changes, leading to these shorter C2-H2..O2 distances. Hence, in addition to the well-known minor groove hydration, it appears that favourable C2-H2..O2 cross-strand interactions may play a role in imparting a characteristic geometry to AA.TT and GA.TC steps, as well as An. Tn and GAn. TnC tracts, which leads to a narrow minor groove in these regions

Structural properties of promoters: similarities and differences between prokaryotes and eukaryotes

During the process of transcription, RNA polymerase can exactly locate a promoter sequence in the complex maze of a genome. Several experimental studies and computational analyses have shown that the promoter sequences apparently possess some special properties, such as unusual DNA structures and low stability, which make them distinct from the rest of the genome. But most of these studies have been carried out on a particular set of promoter sequences or on promoter sequences from similar organisms. To examine whether the promoters from a wide variety of organisms share these special properties, we have carried out an analysis of sets of promoters from bacteria, vertebrates and plants. These promoters were analyzed with respect to the prediction of three different properties, such as DNA curvature, bendability and stability, which are relevant to transcription. All the promoter sequences are predicted to share certain features, such as stability and bendability profiles, but there are significant differences in DNA curvature profiles and nucleotide composition between the different organisms. These similarities and differences are correlated with some of the known facts about transcription process in the promoters from the three groups of organisms

An ensemble of B-DNA dinucleotide geometries lead to characteristic nucleosomal DNA structure and provide plasticity required for gene expression

<p>Abstract</p> <p>Background</p> <p>A nucleosome is the fundamental repeating unit of the eukaryotic chromosome. It has been shown that the positioning of a majority of nucleosomes is primarily controlled by factors other than the intrinsic preference of the DNA sequence. One of the key questions in this context is the role, if any, that can be played by the variability of nucleosomal DNA structure.</p> <p>Results</p> <p>In this study, we have addressed this question by analysing the variability at the dinucleotide and trinucleotide as well as longer length scales in a dataset of nucleosome X-ray crystal structures. We observe that the nucleosome structure displays remarkable local level structural versatility within the B-DNA family. The nucleosomal DNA also incorporates a large number of kinks.</p> <p>Conclusions</p> <p>Based on our results, we propose that the local and global level versatility of B-DNA structure may be a significant factor modulating the formation of nucleosomes in the vicinity of high-plasticity genes, and in varying the probability of binding by regulatory proteins. Hence, these factors should be incorporated in the prediction algorithms and there may not be a unique 'template' for predicting putative nucleosome sequences. In addition, the multimodal distribution of dinucleotide parameters for some steps and the presence of a large number of kinks in the nucleosomal DNA structure indicate that the linear elastic model, used by several algorithms to predict the energetic cost of nucleosome formation, may lead to incorrect results.</p

Modelling studies on neurodegenerative disease causing triplet repeat sequences d(GGC/GCC)<SUB>n</SUB> and d(CAG/CTG)<SUB>n</SUB>

Model building and molecular mechanics studies have been carried out to examine the potential structures for d(GGC/GCC)5 and d(CAG/CTG)5 that might relate to their biological function and association with triplet repeat expansion diseases. Model building studies suggested that hairpin and quadruplex structures could be formed with these repeat sequences. Molecular mechanics studies have demonstrated that the hairpin and hairpin dimer structures of triplet repeat sequences formed by looping out of the two strands are as favourable as the corresponding B-DNA type hetero duplex structures. Further, at high salt condition, Greek key type quadruplex structures are energetically comparable with hairpin dimer and B-DNA type duplex structures. All tetrads in the quadruplex structures are well stacked and provide favourable stacking energy values. Interestingly, in the energy minimized hairpin dimer and Greek key type quadruplex structures, all the bases even in the non-G tetrads are cyclically hydrogen bonded, even though the A, C and T-tetrads were not hydrogen bonded in the starting structures

Prescription analysis of hypolipidaemic agents in the department of cardiology in a tertiary care hospital

ABSTRACTBackground: The objective of the present study was to evaluate the prescribing pattern of hypolipidaemic drugs in the outpatient department of cardiology in a tertiary care hospital.Methods: A cross-sectional study was conducted in the department of cardiology for the period of 3 months. A total of 526 prescriptions were analyzed for variants such as the disease patterns, the type of hypolipidaemic drugs which are prescribed for those diseases, the prescribing daily dose of the hypolipidaemic drugs and the prescribing daily dose/daily defined dose ratio of the drugs.Results: On evaluation of the prescriptions, it was conferred that both the patients of normal lipid profile (34.77%) and abnormal lipid profile (65.18%) were prescribed hypolipidaemic drug. Diabetes with hypertension (35.74%) was the most common disease for which hypolipidaemic drugs were prescribed. Atorvastatin (30.98%) was the most common drug which was prescribed as monotherapy, whereas atorvastatin with aspirin and clopidogrel (17.49%) was the most common drug prescribed in combination.Conclusions: Use of statin has become very prevalent with increasing trends of use in both normal and abnormal lipid profile patients, suggesting consideration of rational use of statins to follow good prescribing pattern so that morbidity and mortality can be prevented

PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes

<p>Abstract</p> <p>Background</p> <p>As more and more genomes are being sequenced, an overview of their genomic features and annotation of their functional elements, which control the expression of each gene or transcription unit of the genome, is a fundamental challenge in genomics and bioinformatics.</p> <p>Findings</p> <p>Relative stability of DNA sequence has been used to predict promoter regions in 913 microbial genomic sequences with GC-content ranging from 16.6% to 74.9%. Irrespective of the genome GC-content the relative stability based promoter prediction method has already been proven to be robust in terms of recall and precision. The predicted promoter regions for the 913 microbial genomes have been accumulated in a database called PromBase. Promoter search can be carried out in PromBase either by specifying the gene name or the genomic position. Each predicted promoter region has been assigned to a reliability class (low, medium, high, very high and highest) based on the difference between its average free energy and the downstream region. The recall and precision values for each class are shown graphically in PromBase. In addition, PromBase provides detailed information about base composition, CDS and CG/TA skews for each genome and various DNA sequence dependent structural properties (average free energy, curvature and bendability) in the vicinity of all annotated translation start sites (TLS).</p> <p>Conclusion</p> <p>PromBase is a database, which contains predicted promoter regions and detailed analysis of various genomic features for 913 microbial genomes. PromBase can serve as a valuable resource for comparative genomics study and help the experimentalist to rapidly access detailed information on various genomic features and putative promoter regions in any given genome. This database is freely accessible for academic and non- academic users via the worldwide web <url>http://nucleix.mbu.iisc.ernet.in/prombase/</url>.</p

Modelling studies on neurodegenerative disease-causing triplet repeat sequences d(GGC/GCC)<SUB>n</SUB> and d(CAG/CTG)<SUB>n</SUB>

Model building and molecular mechanics studies have been carried out to examine the potential structures for d(GGC/GCC)5 and d(CAG/CTG)5 that might relate to their biological function and association with triplet repeat expansion diseases. Model building studies suggested that hairpin and quadruplex structures could be formed with these repeat sequences. Molecular mechanics studies have demonstrated that the hairpin and hairpin dimer structures of triplet repeat sequences formed by looping out of the two strands are as favourable as the corresponding B-DNA type hetero duplex structures. Further, at high salt condition, Greek key type quadruplex structures are energetically comparable with hairpin dimer and B-DNA type duplex structures. All tetrads in the quadruplex structures are well stacked and provide favourable stacking energy values. Interestingly, in the energy minimized hairpin dimer and Greek key type quadruplex structures, all the bases even in the non-G tetrads are cyclically hydrogen bonded, even though the A, C and T-tetrads were not hydrogen bonded in the starting structures

A comparative assessment of safety and tolerability of metoprolol versus carvedilol in patients of chronic stable angina

Background: Angina pectoris is a clinical manifestation characterized by chest pain typically in substerum radiating to left arm, jaw, back lasting for 1-5 minutes and is relieved by rest. Beta blockers are one of the drugs indicated in angina. The aim of the study is to compare safety and tolerability of metoprolol and carvedilol in patients of chronic stable angina.Methods: The study done is randomized, open label, parallel type where tablet carvedilol and tab metoprolol is given in a group of 50 patients each. The patients were followed thereafter on 8th, 16th, 24th week to study safety in terms of haematological parameters like complete blood count, liver function tests, renal function tests, serum sodium, serum potassium, fasting blood glucose, 2 hours post prandial blood glucose, HbA1C, and Lipid profile and tolerability in terms of side effects. The study was conducted for one year and the data was assessed by relevant statistical analysis where p value <0.05 was considered significant.Results: It was seen that the disease was most common in the age group of 51-60 years with male preponderance, and carvedilol was found to cause non-significant decrease in Serum Triglyceride with no change in total cholesterol, HDL-C, LDL-C was found. No significant changes were observed in metoprolol group. There was no significant difference observed when blood sugar profile and other haematological parameters were considered. Both drugs were considered to be equally tolerable.Conclusions: Compared with carvedilol and metoprolol in patients of chronic stable angina, carvedilol resulted in better lipid profile whereas metoprolol showed no changes in lipid parameters

Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs

<p>Abstract</p> <p>Background</p> <p>An important question of biological relevance is the polymorphism of the double-helical DNA structure in its free form, and the changes that it undergoes upon protein-binding. We have analysed a database of free DNA crystal structures to assess the inherent variability of the free DNA structure and have compared it with a database of protein-bound DNA crystal structures to ascertain the protein-induced variations.</p> <p>Results</p> <p>Most of the dinucleotide steps in free DNA display high flexibility, assuming different conformations in a sequence-dependent fashion. With the exception of the AA/TT and GA/TC steps, which are 'A-phobic', and the GG/CC step, which is 'A-philic', the dinucleotide steps show no preference for A or B forms of DNA. Protein-bound DNA adopts the B-conformation most often. However, in certain cases, protein-binding causes the DNA backbone to take up energetically unfavourable conformations. At the gross structural level, several protein-bound DNA duplexes are observed to assume a curved conformation in the absence of any large distortions, indicating that a series of normal structural parameters at the dinucleotide and trinucleotide level, similar to the ones in free B-DNA, can give rise to curvature at the overall level.</p> <p>Conclusion</p> <p>The results illustrate that the free DNA molecule, even in the crystalline state, samples a large amount of conformational space, encompassing both the A and the B-forms, in the absence of any large ligands. A-form as well as some non-A, non-B, distorted geometries are observed for a small number of dinucleotide steps in DNA structures bound to the proteins belonging to a few specific families. However, for most of the bound DNA structures, across a wide variety of protein families, the average step parameters for various dinucleotide sequences as well as backbone torsion angles are observed to be quite close to the free 'B-like' DNA oligomer values, highlighting the flexibility and biological significance of this structural form.</p