oalib
Search Results: 1 - 10 of 100 matches for " "
All listed articles are free for downloading (OA Articles)
Page 1 /100
Display every page Item
Identification and analysis of putative promoter motifs in Flavivirus genome
Pallavi Somvanshi,Vijai Singh,P. K. Seth
Bioinformation , 2008,
Abstract: The genus Flavivirus comprises medically significant pathogenic virus; causing several infections in humans worldwide. Flavivirus genomes are 10-11 kb approximately and encode both structural and non structural region. The non structural region plays fundamental role in the stability, regulation and cell cycle of virus. The complete genomes of 26 Flavivirus were used for identification of promoter motifs through in silico approaches. The promoter sequences were encoded in merely 16 viruses and 10 viruses could not encode it. All these in silico identified promoter motifs was confirmed and verified with the known experimental data. This analysis suggests that presence of promoter may play a crucial role in the pattern of gene expression, regulation networks, cell specificity and development. It may also be useful for designing efficient expression vector and target specific delivery system in the gene therapy.
Identification in silico of putative damage responsive elements (DRE) in promoter regions of the yeast genome
Silva, Walkiria Luckwu de Santana;Cavalcanti, Andre Ricardo de Oliveira;Guimar?es, Katia Silva;Morais Jr., Marcos Antonio de;
Genetics and Molecular Biology , 2005, DOI: 10.1590/S1415-47572005000500025
Abstract: we report an in silico analysis to identify nucleotide sequence motifs in dna repair genes that may define a binding site for regulatory proteins during the induction of those genes by mutagens. the damage responsive elements (dre) weight matrix generated in this analysis was used to search for homologous sequences in the promoter region of all genes, including putative gene and hypothetical open reading frames (orfs), in the saccharomyces genome data base (sgd). the results demonstrated that over one third of the yeast genes in the database presented at least one 15-bp sequence in their promoter region with 85% or more of similarity to the dre consensus sequence. the presence of the dre sequence in the promoter region of regulatory genes and its high similarity to other well reported dna binding sites points to its involvement in the general regulation of not only dna repair genes but yeast genes in general.
Putative cold acclimation pathways in Arabidopsis thaliana identified by a combined analysis of mRNA co-expression patterns, promoter motifs and transcription factors
Aakash Chawade, Marcus Br?utigam, Angelica Lindl?f, Olof Olsson, Bj?rn Olsson
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-304
Abstract: By means of our method, previously published Arabidopsis microarray data from cold acclimated plants at six different time points, promoter motif sequence data extracted from ~24,000 Arabidopsis promoters and known transcription factor binding sites were combined to construct a putative genetic regulatory interaction network. The inferred network includes both previously characterised and hitherto un-described regulatory interactions between transcription factor (TF) genes and genes that encode other TFs or other proteins. Part of the obtained transcription factor regulatory network is presented here. More detailed information is available in the additional files.The rule-based method described here can be used to infer genetic networks by combining data from microarrays, promoter sequences and known promoter binding sites. This method should in principle be applicable to any biological system. We tested the method on the cold acclimation process in Arabidopsis and could identify a more complex putative genetic regulatory network than previously described. However, it should be noted that information on specific binding sites for individual TFs were in most cases not available. Thus, gene targets for the entire TF gene families were predicted. In addition, the networks were built solely by a bioinformatics approach and experimental verifications will be necessary for their final validation. On the other hand, since our method highlights putative novel interactions, more directed experiments could now be performed.Plants have developed a number of different physiological and developmental responses to cope with abiotic stress. One important factor is acclimation, where mild stress conditions greatly enhance tolerance to later, more severe conditions [1]. Transcriptome analysis using microarray technology is a very powerful tool to identify cold responsive genes [2-4]. Amongst these are genes encoding transcription factors (TFs), signal transduction components, osmo-r
Chromatin-driven de novo discovery of DNA binding motifs in the human malaria parasite
Elena Y Harris, Nadia Ponts, Karine G Le Roch, Stefano Lonardi
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-601
Abstract: We propose a methodology for discovering cis-regulatory elements that uses for the first time exclusively dynamic chromatin remodeling data. Our method employs nucleosome positioning data collected at seven time points during the erythrocytic cycle of P. falciparum to discover putative DNA binding motifs and their transcription factor binding sites along with their associated clusters of target genes. Our approach results in 129 putative binding motifs within the promoter region of known genes. About 75% of those are novel, the remaining being highly similar to experimentally validated binding motifs. About half of the binding motifs reported show statistically significant enrichment in functional gene sets and strong positional bias in the promoter region.Experimental results establish the principle that dynamic chromatin remodeling data can be used in lieu of gene expression data to discover binding motifs and their transcription factor binding sites. Our approach can be applied using only dynamic nucleosome positioning data, independent from any knowledge of gene function or expression.One of the major challenges in molecular biology is to characterize the mechanisms governing the regulation of transcription. Mechanisms of regulation can be broadly classified in three classes: (1) interaction of a control factor with DNA, (2) interaction of a control factor with the transcriptional complex, and (3) epigenetic factors. In this paper we are interested in elucidating mechanisms that belong to the first class, in which transcription factor proteins modulate expression levels by binding to one or more specific sites in the promoter region of a gene. The problem of identifying in silico transcription factor binding sites (TFBS) has been studied intensively. As a result a variety of algorithms and tools have been developed (see [1] for a review). Typically, these methodologies involve obtaining a set of genes which are known to be co-expressed or functionally-related an
In silico discovery of transcription regulatory elements in Plasmodium falciparum
Jason A Young, Jeffery R Johnson, Chris Benner, S Frank Yan, Kaisheng Chen, Karine G Le Roch, Yingyao Zhou, Elizabeth A Winzeler
BMC Genomics , 2008, DOI: 10.1186/1471-2164-9-70
Abstract: We have developed an algorithm called Gene Enrichment Motif Searching (GEMS) that uses a hypergeometric-based scoring function and a position-weight matrix optimization routine to identify with high-confidence regulatory elements in the nucleotide-biased and repeat sequence-rich P. falciparum genome. When applied to promoter regions of genes contained within 21 co-expression gene clusters generated from P. falciparum life cycle microarray data using the semi-supervised clustering algorithm Ontology-based Pattern Identification, GEMS identified 34 putative cis-regulatory elements associated with a variety of parasite processes including sexual development, cell invasion, antigenic variation and protein biosynthesis. Among these candidates were novel motifs, as well as many of the elements for which biological experimental evidence already exists in the Plasmodium literature. To provide evidence for the biological relevance of a cell invasion-related element predicted by GEMS, reporter gene and electrophoretic mobility shift assays were conducted.This GEMS analysis demonstrates that in silico regulatory element discovery can be successfully applied to challenging repeat-sequence-rich, base-biased genomes such as that of P. falciparum. The fact that regulatory elements were predicted from a diverse range of functional gene clusters supports the hypothesis that cis-regulatory elements play a role in the transcriptional control of many P. falciparum biological processes. The putative regulatory elements described represent promising candidates for future biological investigation into the underlying transcriptional control mechanisms of gene regulation in malaria parasites.While intense research efforts have focused on understanding how gene expression is regulated in model organisms, there are thousands of species important to human health, the environment, and global economies whose transcriptional control mechanisms are not well represented by current biological models
ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants
Kathryn E Holt, A Harvey Millar, James Whelan
Plant Methods , 2006, DOI: 10.1186/1746-4811-2-8
Abstract: To add to this larger process and to provide alternatives to existing prediction methods, we have developed several tools in the statistical package R. ModuleFinder identifies sets of genes and treatments that we have found to form valuable sets for analysis of the mechanisms underlying gene co-expression. CoReg then links the hierarchical clustering of these co-expressed sets with frequency tables of promoter elements. These promoter elements can be drawn from known elements or all possible combinations of nucleotides in an element of various lengths. These sets of promoter elements represent putative cis-acting regulatory elements common to sets of co-expressed genes and can be prioritised for experimental testing. We have used these new tools to analyze the response of transcripts for nuclear genes encoding mitochondrial proteins in Arabidopsis to a range of chemical stresses. ModuleFinder provided a subset of co-expressed gene modules that are more logically related to biological functions than did subsets derived from traditional hierarchical clustering techniques. Importantly ModuleFinder linked responses in transcripts for electron transport chain components, carbon metabolism enzymes and solute transporter proteins. CoReg identified several promoter motifs that helped to explain the patterns of expression observed.ModuleFinder identifies sets of genes and treatments that form useful sets for analysis of the mechanisms behind co-expression. CoReg links the clustering tree of expression-based relationships in these sets with frequency tables of promoter elements. These sets of promoter elements represent putative cis-acting regulatory elements for sets of genes, and can then be tested experimentally. We consider these tools, both built on an open source software product to provide valuable, alternative tools for the prioritisation of promoter elements for experimental analysis.The regulation of gene expression is one of the most intensively studied areas of bi
Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster  [PDF]
Thomas A Down ,Casey M Bergman,Jing Su,Tim J. P Hubbard
PLOS Computational Biology , 2007, DOI: 10.1371/journal.pcbi.0030007
Abstract: A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs) that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes.
Distribution of short interstitial telomere motifs in two plant genomes: putative origin and function
Christine Gaspin, Jean-Fran?ois Rami, Bernard Lescure
BMC Plant Biology , 2010, DOI: 10.1186/1471-2229-10-283
Abstract: Our analysis showed that the distribution of the telo box (AAACCCTA) in different genomic regions of A. thaliana and O. sativa is not random. As is also the case for plant microsatellites, they are preferentially located in the 5' flanking regions of genes, mainly within the 5' UTR, and distributed as a gradient along the direction of transcription. As previously reported in Arabidopsis, a conserved topological association of telo boxes with site II or TEF cis-acting elements is observed in almost all promoters of genes encoding ribosomal proteins in O. sativa. Such a conserved promoter organization can be found in other genes involved in the biogenesis of the translational machinery including rRNA processing proteins and snoRNAs. Strikingly, the association of telo boxes with site II motifs or TEF boxes is conserved in promoters of genes harbouring snoRNA clusters nested within an intron as well as in the 5' flanking regions of non-intronic snoRNA genes. Thus, the search for associations between telo boxes and site II motifs or TEF box in plant genomes could provide a useful tool for characterizing new cryptic RNA pol II promoters.The data reported in this work support the model previously proposed for the spreading of telo boxes within plant genomes and provide new insights into a putative process for the acquisition of microsatellites in plants. The association of telo boxes with site II or TEF cis-acting elements appears to be an essential feature of plant genes involved in the biogenesis of ribosomes and clearly indicates that most plant snoRNAs are RNA pol II products.Regulatory sequences constitute a small fraction of eukaryotic genomes that determine the level, location and chronology of gene expression. In parallel to functional studies, computational analysis provides different approaches for scanning genomic sequence to identify those regions predicted to participate in gene regulation [1,2]: (i) sequence analysis of co-regulated genes within a given spec
Genome-wide Prediction and Functional Validation of Promoter Motifs Regulating Gene Expression in Spore and Infection Stages of Phytophthora infestans  [PDF]
Sourav Roy,Meenakshi Kagda,Howard S. Judelson
PLOS Pathogens , 2013, DOI: 10.1371/journal.ppat.1003182
Abstract: Most eukaryotic pathogens have complex life cycles in which gene expression networks orchestrate the formation of cells specialized for dissemination or host colonization. In the oomycete Phytophthora infestans, the potato late blight pathogen, major shifts in mRNA profiles during developmental transitions were identified using microarrays. We used those data with search algorithms to discover about 100 motifs that are over-represented in promoters of genes up-regulated in hyphae, sporangia, sporangia undergoing zoosporogenesis, swimming zoospores, or germinated cysts forming appressoria (infection structures). Most of the putative stage-specific transcription factor binding sites (TFBSs) thus identified had features typical of TFBSs such as position or orientation bias, palindromy, and conservation in related species. Each of six motifs tested in P. infestans transformants using the GUS reporter gene conferred the expected stage-specific expression pattern, and several were shown to bind nuclear proteins in gel-shift assays. Motifs linked to the appressoria-forming stage, including a functionally validated TFBS, were over-represented in promoters of genes encoding effectors and other pathogenesis-related proteins. To understand how promoter and genome architecture influence expression, we also mapped transcription patterns to the P. infestans genome assembly. Adjacent genes were not typically induced in the same stage, including genes transcribed in opposite directions from small intergenic regions, but co-regulated gene pairs occurred more than expected by random chance. These data help illuminate the processes regulating development and pathogenesis, and will enable future attempts to purify the cognate transcription factors.
An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance
Ana C Casimiro, Susana Vinga, Ana T Freitas, Arlindo L Oliveira
BMC Bioinformatics , 2008, DOI: 10.1186/1471-2105-9-89
Abstract: We propose to integrate position uniformity tests and over-representation tests to improve the accuracy of the classification of motifs. Using artificial data, we have compared three different statistical tests (Chi-Square, Kolmogorov-Smirnov and a Chi-Square bootstrap) to assess whether a given motif occurs uniformly in the promoter region of a gene. Using the test that performed better in this dataset, we proceeded to study the positional distribution of several well known cis-regulatory elements, in the promoter sequences of different organisms (S. cerevisiae, H. sapiens, D. melanogaster, E. coli and several Dicotyledons plants). The results show that position conservation is relevant for the transcriptional machinery.We conclude that many biologically relevant motifs appear heterogeneously distributed in the promoter region of genes, and therefore, that non-uniformity is a good indicator of biological relevance and can be used to complement over-representation tests commonly used. In this article we present the results obtained for the S. cerevisiae data sets.The computational analysis of DNA sequences represents a major endeavor in the post-genomic era. The increasing number of whole-genome sequencing projects has provided an enormous amount of information which leads to the need of new tools and string processing algorithms to analyze and classify the obtained sequences [1].In this regard, the study of short functional DNA segments, such as transcriptional factor binding sites, has emerged as an important effort to understand key control mechanisms. For example, it is now known that the presence of certain sequences of motifs in promoter regions determines the effective regulation of gene transcription, a central feature of gene regulatory networks.DNA motifs can be represented in a number of different ways. Position specific scoring matrices (PSSMs) and consensi (oligonucleotide sequences) are amongst the most commonly used. However, several other more sophis
Page 1 /100
Display every page Item


Home
Copyright © 2008-2017 Open Access Library. All rights reserved.