CiteULike: dpollard's binding_site

Using DNA duplex stability information for transcription factor binding site discovery.

R Gordân — 2008-02-01T06:20:50-00:00

Pac Symp Biocomput (2008), pp. 453-464.

Transcription factor (TF) binding site discovery is an important step in understanding transcriptional regulation. Many computational tools have already been developed, but their success in detecting TF motifs is still limited. We believe one of the main reasons for the low accuracy of current methods is that they do not take into account the structural aspects of TF-DNA interaction. We have previously shown that knowledge about the structural class of the TF and information about nucleosome occupancy can be used to improve motif discovery. Here, we demonstrate the benefits of using information about the DNA double-helical stability for motif discovery. We notice that, in general, the energy needed to destabilize the DNA double helix is higher at TF binding sites than at random DNA sites. We use this information to derive informative positional priors that we incorporate into a motif finding algorithm. When applied to yeast ChIP-chip data, the new informative priors improve the performance of the motif finder significantly when compared to priors that do not use the energetic stability information.

Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast.

RW Lusk — 2008-02-01T06:17:57-00:00

Pac Symp Biocomput (2008), pp. 489-500.

The identification of transcription factor binding sites commonly relies on the interpretation of scores generated by a position weight matrix. These scores are presumed to reflect on the affinity of the transcription factor for the bound sequence. In almost all applications, a cutoff score is chosen to distinguish between functional and non-functional binding sites. This cutoff is generally based on statistical rather than biological criteria. Furthermore, given the variety of transcription factors, it is unlikely that the use of a common statistical threshold for all transcription factors is appropriate. In order to incorporate biological information into the choice of cutoff score, we developed a simple evolutionary model that assumes that transcription factor binding sites evolve to maintain an affinity greater than some factor-specific threshold. We then compared patterns of substitution in binding sites predicted by this model at different thresholds to patterns of substitution observed at sites bound in vivo by transcription factors in S. cerevisiae. Assuming that the cutoff value that gives the best fit between the observed and predicted values will optimally distinguish functional and non-functional sites, we discovered substantial heterogeneity for appropriate cutoff values among factors. While commonly used thresholds seem appropriate for many factors, some factors appear to function at cutoffs satisfied commonly in the genome. This evidence was corroborated by local patterns of rate variation for examples of stringent and lenient p-value cutoffs. Our analysis further highlights the necessity of taking a factor-specific approach to binding site identification.

Ancient and Recent Positive Selection Transformed Opioid cis-Regulation in Humans.

Matthew V Rockman — 2005-11-14T19:50:57-00:00

PLoS Biol, Vol. 3, No. 12. (15 November 2005)

Changes in the cis-regulation of neural genes likely contributed to the evolution of our species' unique attributes, but evidence of a role for natural selection has been lacking. We found that positive natural selection altered the cis-regulation of human prodynorphin, the precursor molecule for a suite of endogenous opioids and neuropeptides with critical roles in regulating perception, behavior, and memory. Independent lines of phylogenetic and population genetic evidence support a history of selective sweeps driving the evolution of the human prodynorphin promoter. In experimental assays of chimpanzee-human hybrid promoters, the selected sequence increases transcriptional inducibility. The evidence for a change in the response of the brain's natural opioids to inductive stimuli points to potential human-specific characteristics favored during evolution. In addition, the pattern of linked nucleotide and microsatellite variation among and within modern human populations suggests that recent selection, subsequent to the fixation of the human-specific mutations and the peopling of the globe, has favored different prodynorphin cis-regulatory alleles in different parts of the world.

Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus.

MT Hamblin — 2007-12-05T22:52:50-00:00

Am J Hum Genet, Vol. 66, No. 5. (May 2000), pp. 1669-1679.

The Duffy blood group locus, which encodes a chemokine receptor, is characterized by three alleles-FY*A, FY*B, and FY*O. The frequency of the FY*O allele, which corresponds to the absence of Fy antigen on red blood cells, is at or near fixation in most sub-Saharan African populations but is very rare outside Africa. The FST value for the FY*O allele is the highest observed for any allele in humans, providing strong evidence for the action of natural selection at this locus. Homozygosity for the FY*O allele confers complete resistance to vivax malaria, suggesting that this allele has been the target of selection by Plasmodium vivax or some other infectious agent. To characterize the signature of directional selection at this locus, we surveyed DNA sequence variation, both in a 1.9-kb region centered on the FY*O mutation site and in a 1-kb region 5-6 kb away from it, in 17 Italians and in a total of 24 individuals from five sub-Saharan African populations. The level of variation across both regions is two- to threefold lower in the Africans than in the Italians. As a result, the pooled African sample shows a significant departure from the neutral expectation for the number of segregating sites, whereas the Italian sample does not. The FY*O allele occurs on two major haplotypes in three of the five African populations. This finding could be due to recombination, recurrent mutation, population structure, and/or mutation accumulation and drift. Although we are unable to distinguish among these alternative hypotheses, it is likely that the two major haplotypes originated prior to selection on the FY*O mutation.

Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy-negative individuals.

C Tournamille — 2007-12-05T22:50:02-00:00

Nat Genet, Vol. 10, No. 2. (June 1995), pp. 224-228.

The mRNA for the Duffy blood group antigen, the erythrocyte receptor for the Plasmodium vivax malaria parasite, has recently been cloned and shown to encode a widely expressed chemokine receptor. Here, we show that the Duffy antigen/chemokine receptor gene (DARC) is composed of a single exon and that most Duffy-negative blacks carry a silent FY*B allele with a single T to C substitution at nucleotide -46. This mutation impairs the promoter activity in erythroid cells by disrupting a binding site for the GATA1 erythroid transcription factor. With the recent characterization of the FY*A and FY*B alleles, these findings provide the molecular basis of the Duffy blood group system and an explanation for the erythroid-specific repression of the DARC gene in Duffy-negative individuals.

Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila.

N Gompel — 2006-01-18T01:41:02-00:00

Nature, Vol. 433, No. 7025. (3 February 2005), pp. 481-487.

The gain, loss or modification of morphological traits is generally associated with changes in gene regulation during development. However, the molecular bases underlying these evolutionary changes have remained elusive. Here we identify one of the molecular mechanisms that contributes to the evolutionary gain of a male-specific wing pigmentation spot in Drosophila biarmipes, a species closely related to Drosophila melanogaster. We show that the evolution of this spot involved modifications of an ancestral cis-regulatory element of the yellow pigmentation gene. This element has gained multiple binding sites for transcription factors that are deeply conserved components of the regulatory landscape controlling wing development, including the selector protein Engrailed. The evolutionary stability of components of regulatory landscapes, which can be co-opted by chance mutations in cis-regulatory elements, might explain the repeated evolution of similar morphological patterns, such as wing pigmentation patterns in flies.

Regulation of Body Pigmentation by the Abdominal-B Hox Protein and Its Gain and Loss in Drosophila Evolution

Sangyun Jeong — 2006-06-29T22:11:03-00:00

Cell, Vol. 125, No. 7. (30 June 2006), pp. 1387-1399.

SummaryHox genes have been implicated in the evolution of many animal body patterns, but the molecular events underlying trait modification have not been elucidated. Pigmentation of the posterior male abdomen is a recently acquired trait in the Drosophila melanogaster lineage. Here, we show that the Abdominal-B (ABD-B) Hox protein directly activates expression of the yellow pigmentation gene in posterior segments. ABD-B regulation of pigmentation evolved through the gain of ABD-B binding sites in a specific cis-regulatory element of the yellow gene of a common ancestor of sexually dimorphic species. Within the melanogaster species group, male-specific pigmentation has subsequently been lost by at least three different mechanisms, including the mutational inactivation of a key ABD-B binding site in one lineage. These results demonstrate how Hox regulation of traits and target genes is gained and lost at the species level and have general implications for the evolution of body form at higher taxonomic levels.

Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter.

D Pribnow — 2007-11-26T00:26:11-00:00

Proc Natl Acad Sci U S A, Vol. 72, No. 3. (March 1975), pp. 784-788.

Escherichia coli RNA polymerase (EC 2.7.7.6), bound in a tight complex at an early T7 promoter, protects 41 to 43 base pairs of DNA from digestion by DNase. I. The protected DNA fragment contains both the binding site for RNA polymerase and the mRNA initiation point for the promoter. The sequence of the DNA fragment and the sequence of the mRNA that it codes for are presented here. A seven-base-pair sequence, apparently common to all promoters, is implicated in the formation of a tight binary complex with RNA polymerase.

Turnover of binding sites for transcription factors involved in early Drosophila development.

J Costas — 2007-10-16T21:11:16-00:00

Gene, Vol. 310 (22 May 2003), pp. 215-220.

Despite the importance of cis-regulatory regions in evolution, little is know about their evolutionary dynamics. In this report, we analyze the process of evolution of binding sites for transcription factors using as a model a well characterized system, the Drosophila early developmental enhancers. We compare the sequences of eight enhancer regions for early developmental genes between Drosophila melanogaster and other two species, Drosophila virilis and Drosophila pseudoobscura, searching for the presence/absence of 104 biochemically verified binding sites from D. melanogaster. We also modeled the binding specificity of each binding site by the use of well-defined positional weight matrices (PWMs). The comparisons showed that turnover of binding sites seems to fit a molecular clock, at an approximate rate of 0.94% of gain/loss of binding sites per million years. This intense turnover affects both high and low affinity binding sites at the same extent. Furthermore, the subset of overlapping binding sites is also subjected to this high turnover. Conserved binding sites seem to be constrained to maintain not only location but also the exact sequence at each particular position. Finally, we detected a significant decrease in mean PWM scores for the D. virilis binding sites in the case of Hunchback. Possible explanations for this fact are discussed.

Large-Scale Discovery of Promoter Motifs in Drosophila melanogaster

Thomas Down — 2007-01-23T14:07:06-00:00

PLoS Computational Biology, Vol. 3, No. 1. (1 January 2007), e7.

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.

Discovery of Regulatory Elements by a Computational Method for Phylogenetic Footprinting

Mathieu Blanchette — 2006-02-02T20:22:09-00:00

Genome Res., Vol. 12, No. 5. (1 May 2002), pp. 739-748.

Phylogenetic footprinting is a method for the discovery of regulatory elements in a set of orthologous regulatory regions from multiple species. It does so by identifying the best conserved motifs in those orthologous regions. We describe a computer algorithm designed specifically for this purpose, making use of the phylogenetic relationships among the sequences under study to make more accurate predictions. The program is guaranteed to report all sets of motifs with the lowest parsimony scores, calculated with respect to the phylogenetic tree relating the input species. We report the results of this algorithm on several data sets of interest. A large number of known functional binding sites are identified by our method, but we also find several highly conserved motifs for which no function is yet known.

Regulatory element detection using correlation with expression.

HJ Bussemaker — 2006-06-29T13:55:25-00:00

Nat Genet, Vol. 27, No. 2. (February 2001), pp. 167-171.

We present here a new computational method for discovering cis-regulatory elements that circumvents the need to cluster genes based on their expression profiles. Based on a model in which upstream motifs contribute additively to the log-expression level of a gene, this method requires a single genome-wide set of expression ratios and the upstream sequence for each gene, and outputs statistically significant motifs. Analysis of publicly available expression data for Saccharomyces cerevisiae reveals several new putative regulatory elements, some of which plausibly control the early, transient induction of genes during sporulation. Known motifs generally have high statistical significance.

Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information.

VJ Makeev — 2006-04-27T19:16:12-00:00

Nucleic Acids Res, Vol. 31, No. 20. (15 October 2003), pp. 6016-6026.

We explored distance preferences in the arrangement of binding motifs for five transcription factors (Bicoid, Krüppel, Hunchback, Knirps and Caudal) in a large set of Drosophila cis-regulatory modules (CRMs). Analysis of non-overlapping binding motifs revealed the presence of periodic signals specific to particular combinations of binding motifs. The most striking periodic signals (10 bp for Bicoid and 11 bp for Hunchback) suggest preferential positioning of some binding site combinations on the same side of the DNA helix. We also analyzed distance preferences in arrangements of highly correlated overlapping binding motifs, such as Bicoid and Krüppel. Based on the distance analysis, we extracted preferential binding site arrangements and proposed models for potential composite elements (CEs) and antagonistic motif pairs involved in the function of developmental CRMs. Our results suggest that there are distinct hierarchical levels in the organization of transcription regulatory information. We discuss the role of the hierarchy in understanding transcriptional regulation and in detection of transcription regulatory regions in genomes.

Interaction of Gal repressor with inducer and operator: induction of gal transcription from repressor-bound DNA.

S Chatterjee — 2007-10-31T21:24:02-00:00

Proc Natl Acad Sci U S A, Vol. 94, No. 7. (1 April 1997), pp. 2957-2962.

Gal repressor inhibits transcription from the gal promoter (P1) when it binds to the cognate operator (O(E)). The repression is relieved by the presence of the inducer D-galactose. Compared with its interaction with free repressor, D-galactose binds to the repressor-operator complex with 10-fold reduced affinity as determined by fluorescence enhancement measurements. Thermodynamic analysis and fluorescence anisotropy showed that the stability of the repressor-operator complex is reduced by only 7-fold by the presence of the inducer in the complex. The formation of the inducer-repressor-operator ternary complex has been confirmed by CD spectral analysis. Fluorescence spectroscopy and energy transfer experiments suggest that individual allosteric effects of the two ligands, inducer and operator, on Gal repressor are responsible for the slightly weakened stability of the ternary complex compared with the stability of the inducer-repressor and repressor-operator complexes. In vitro transcription results demonstrated full derepression of transcription of the P1 promoter under conditions in which the concentrations of the inducer-repressor binary complex are severalfold higher than the dissociation constant of the inducer-repressor-operator ternary complex into inducer-repressor and free DNA. These results strongly suggest that the inducer binding to the repressor-operator complex does not lead to dissociation of the repressor from the operator during transcription induction. Because Gal repressor inhibits transcription by modulating the alpha subunit of the P1-bound RNA polymerase, we conclude that the inducer binding to the operator-bound repressor only allosterically relieves the inhibitory effect of repressor on RNA polymerase without dissociating the repressor from DNA.

Incorporating evolution of transcription factor binding sites into annotated alignments.

AS Bais — 2007-10-09T17:18:49-00:00

J Biosci, Vol. 32, No. 5. (August 2007), pp. 841-850.

Identifying transcription factor binding sites (TFBSs) is essential to elucidate putative regulatory mechanisms.A common strategy is to combine cross-species conservation with single sequence TFBS annotation to yield "conserved TFBSs". Most current methods in this field adopt a multi-step ap proach that segregates the two aspects.Again,it is widely accepted that the evolutionary dynamics of binding sites differ from those of the surrounding sequence. Hence, it is desirable to have an approach that explicitly takes this factor into account.Although a plethora of approaches have been proposed for the prediction of conserved TFBSs,very few explicitly model TFBS evolutionary properties, while additionally being multi-step. Recently, we introduced a novel approach to simultaneously align and annotate conserved TFBSs in a pair of sequences.Building upon the standard Smith-Waterman algorithm for local alignments, SimAnn introduces additional states for profiles to output extended alignments or annotated alignments.That is, alignments with parts annotated as gap lessly aligned TFBSs (pair-profile hits)are generated.Moreover,the pair- profile related parameters are derived in a sound statistical framework. In this article,we extend this approach to explicitly incorporate evolution of binding sites in the SimAnn framework.We demonstrate the extension in the theoretical derivations through two position-specific evolutionary models,previously used for modelling TFBS evolution.In a simulated setting,we provide a proof of concept that the approach works given the underlying assumptions,as compared to the original work.Finally,using a real dataset of experimentally verified binding sites in human-mouse sequence pairs,we compare the new approach (eSimAnn) to an existing multi-step tool that also considers TFBS evolution. Although it is widely accepted that binding sites evolve differently from the surrounding sequences,most comparative TFBS identification methods do not explicitly consider this.Additionally, prediction of conserved binding sites is carried out in a multi-step approach that segregates alignment from TFBS annotation. In this paper, we demonstrate how the simultaneous alignment and annotation approach of SimAnn can be further extended to incorporate TFBS evolutionary relationships.We study how alignments and binding site predictions interplay at varying evolutionary distances and for various profile qualities.

Systematic detection of statistically overrepresented DNA motif association rules.

JM Lin — 2007-06-14T23:03:18-00:00

Genome Inform, Vol. 17, No. 1. (2006), pp. 124-133.

DNA motifs, or cis-elements, are short nucleotide sequence patterns recognized by various transcription factors (TFs). In promoters, these TFs bind in a complex combinatorial manner in order to regulate the expression of a downstream gene. The combinatorial space is frequently large and difficult to manage since vertebrates have thousands of transcription factors and more than 20,000 genes. We introduce a computer program called CAYCE (Combinatorial AnalYsis of Cis-Elements) that systematically detects statistically overrepresented DNA motif association rules independent of Microarray information. CAYCE is an adaptation of the apriori algorithm traditionally used for association rule mining, but offers three significant advancements. (1) It analyzes multiple occurrences of an item, corresponding to multiple TF binding sites, (2) It compares results with a biologically relevant background, and (3), it provides p-values for straightforward statistical interpretation. CAYCE can be easily applied to any item-set data where the investigator is also interested in multiple occurrences of a single item, and/or overrepresentation of association rules compared with a background. Applying CAYCE to human promoters in 1% of the human genome, we discover that motif clusters containing five repetitions of SP1 are the most statistically significant.

Regulatory conservation of protein coding and miRNA genes in vertebrates: lessons from the opossum genome

Shaun Mahony — 2007-05-17T16:52:19-00:00

Genome Biology, Vol. 8 (16 May 2007), R84.

Binding Site Graphs: A New Graph Theoretical Framework for Prediction of Transcription Factor Binding Sites

Timothy Reddy — 2007-05-11T14:56:35-00:00

PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e90.

Computational prediction of nucleotide binding specificity for transcription factors remains a fundamental and largely unsolved problem. Determination of binding positions is a prerequisite for research in gene regulation, a major mechanism controlling phenotypic diversity. Furthermore, an accurate determination of binding specificities from high-throughput data sources is necessary to realize the full potential of systems biology. Unfortunately, recently performed independent evaluation showed that more than half the predictions from most widely used algorithms are false. We introduce a graph-theoretical framework to describe local sequence similarity as the pair-wise distances between nucleotides in promoter sequences, and hypothesize that densely connected subgraphs are indicative of transcription factor binding sites. Using a well-established sampling algorithm coupled with simple clustering and scoring schemes, we identify sets of closely related nucleotides and test those for known TF binding activity. Using an independent benchmark, we find our algorithm predicts yeast binding motifs considerably better than currently available techniques and without manual curation. Importantly, we reduce the number of false positive predictions in yeast to less than 30%. We also develop a framework to evaluate the statistical significance of our motif predictions. We show that our approach is robust to the choice of input promoters, and thus can be used in the context of predicting binding positions from noisy experimental data. We apply our method to identify binding sites using data from genome scale ChIP–chip experiments. Results from these experiments are publicly available at http://cagt10.bu.edu/BSG. The graphical framework developed here may be useful when combining predictions from numerous computational and experimental measures. Finally, we discuss how our algorithm can be used to improve the sensitivity of computational predictions of transcription factor binding specificities.

Computational annotation of transcription factor binding sites in D. Melanogaster developmental genes.

V Narang — 2007-06-13T21:19:27-00:00

Genome Inform, Vol. 17, No. 2. (2006), pp. 14-24.

Drosophila melanogaster is one of the most important organisms for studying the genetics of development. The precise regulation of genes during early development is enacted through the control of transcription. The control circuitry is hardwired in the genome as clusters of multiple transcription factor binding sites (TFBS) known as cis-regulatory modules (CRMs). A number of TFBS and CRMs have been experimentally annotated in the Drosophila genome. Currently about 661 CRM sequences are known, of which 155 have been annotated with 778 TFBS. This work attempts computational annotation of TFBS in the remaining 506 uncharacterized Drosophila CRMs. The difficulty of this task lies in the fact that experimental data is insufficient for constructing reliable positional weight matrices (PWM) to predict the TFBS. Thus a novel feature extraction and classification method for TFBS detection has been implemented in this work. The method achieves both high sensitivity and low false positive rate in cross-validation studies. As a result of this work, a new database has been compiled which aggregates all the CRM and TFBS annotation information for Drosophila available to date, and appends new TFBS annotations.

Determination of local statistical significance of patterns in Markov sequences with application to promoter element identification.

H Huang — 2006-09-03T04:34:23-00:00

J Comput Biol, Vol. 11, No. 1. (2004), pp. 1-14.

High-level eukaryotic genomes present a particular challenge to the computational identification of transcription factor binding sites (TFBSs) because of their long noncoding regions and large numbers of repeat elements. This is evidenced by the noisy results generated by most current methods. In this paper, we present a p-value-based scoring scheme using probability generating functions to evaluate the statistical significance of potential TFBSs. Furthermore, we introduce the local genomic context into the model so that candidate sites are evaluated based both on their similarities to known binding sites and on their contrasts against their respective local genomic contexts. We demonstrate that our approach is advantageous in the prediction of myogenin and MEF2 binding sites in the human genome. We also apply LMM to large-scale human binding site sequences in situ and found that, compared to current popular methods, LMM analysis can reduce false positive errors by more than 50% without compromising sensitivity. This improvement will be of importance to any subsequent algorithm that aims to detect regulatory modules based on known PSSMs.

Frequent Gain and Loss of Functional Transcription Factor Binding Sites

Scott Doniger — 2007-05-26T03:59:06-00:00

PLoS Computational Biology, Vol. 3, No. 5. (1 May 2007), e99.

Cis-regulatory sequences are not always conserved across species. Divergence within cis-regulatory sequences may result from the evolution of species-specific patterns of gene expression or the flexible nature of the cis-regulatory code. The identification of functional divergence in cis-regulatory sequences is therefore important for both understanding the role of gene regulation in evolution and annotating regulatory elements. We have developed an evolutionary model to detect the loss of constraint on individual transcription factor binding sites (TFBSs). We find that a significant fraction of functionally constrained binding sites have been lost in a lineage-specific manner among three closely related yeast species. Binding site loss has previously been explained by turnover, where the concurrent gain and loss of a binding site maintains gene regulation. We estimate that nearly half of all loss events cannot be explained by binding site turnover. Recreating the mutations that led to binding site loss confirms that these sequence changes affect gene expression in some cases. We also estimate that there is a high rate of binding site gain, as more than half of experimentally identified S. cerevisiae binding sites are not conserved across species. The frequent gain and loss of TFBSs implies that cis-regulatory sequences are labile and, in the absence of turnover, may contribute to species-specific patterns of gene expression.

SPACER: identification of cis-regulatory elements with non-contiguous critical residues.

A Chakravarty — 2007-05-23T00:09:39-00:00

Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 1029-1031.

MOTIVATION: Many transcription factors bind to sites that are long and loosely related to each other. De novo identification of such motifs is computationally challenging. In this article, we propose a novel semi-greedy algorithm over the space of all IUPAC degenerate strings to identify the most over-represented highly degenerate motifs. RESULTS: We present an implementation of this algorithm, named SPACER (Separated Pattern-based Algorithm for cis-Element Recognition) and demonstrate its effectiveness in identifying 'gapped' and highly degenerate motifs. We compare SPACER's performance against ten motif finders on 42 experimentally defined regulons from Bacillus subtilis, Escherichia coli and Saccharomyces cerevisiae. These motif finders cover a wide range of both enumerative and statistical approaches, including programs specifically designed for prokaryotic and 'gapped' motifs. AVAILABILITY: A Java 1.4 implementation is freely available on the Web at http://genie.Dartmouth.edu/SPACER/

A stochastic model for the evolution of transcription factor binding site abundance.

Günter P Wagner — 2007-05-23T00:01:19-00:00

J Theor Biol (7 March 2007)

Both experimental as well as sequence evolution evidence suggests that transcription factor binding sites can undergo divergence and turnover even when the transcriptional output remains conserved. Furthermore, it is likely that there exist lineage specific differences in the retention rate of binding sites that make it desirable to estimate the rate of acquisition and decay of transcription factor binding sites from comparative sequence data. In this paper we propose a stochastic, phenomenological model for binding site turnover. For a given genomic region we assume a constant rate of binding site origination lambda and a constant per site decay rate of mu. We derived an explicit expression for the conditional probability distribution of the number of binding sites n at time t given n(0) binding sites at t=0. The analytical result was compared to a simulation model and we found that it closely predicts the simulated sequence evolution. We then analyzed a small data set of the number of estrogen response elements (ERE) in mammalian HoxA sequences and showed that the data is broadly consistent with the assumption of a stationary turnover process. A regression of shared EREs over the time since divergence led to an estimate of the half-life time for an ERE in the primate HoxA clusters of about 27Myr, which corresponds to a per site decay rate of mu approximately 1.3x10(-8)/year and a rate of origination of lambda approximately 1.6x10(-7)/year. We conclude that the model can be used to estimate the rate of binding site turnover from comparative genomic data.

Mining of putative cis-acting elements for chromatin mediated regulation of Hox genes in mammals by in-silico analysis.

Hemant Bengani — 2007-03-22T23:13:37-00:00

J Exp Zoolog B Mol Dev Evol (14 March 2007)

The remarkable conservation in developmental strategies across phyla is well reflected in the conservation of the homeotic gene complexes responsible for establishing the body plan in embryonic development. On the other hand, changes in the strategy of transcription regulation are believed to form one of the major factors in the evolution of developmental mechanisms and phenotypic evolution of species. Apart from transcription regulation by gene specific transcription factors, the role of regulators mediating modifications of chromatin proteins, especially of HOX gene clusters in Drosophila is well documented. By comparative genomics we have identified novel motifs conserved in mouse, chimpanzee and human in the noncoding upstream/intronic sequences of Hox genes by in silico analysis. These motifs lack the binding sites for known transcription factors and are significantly over represented in the target genes of one of the core components of Polycomb Repressive Complex namely Supressor of zeste 12 (SUZ12) in human embryonic cells reported by Lee et al. [2006a. Cell 125:301-313]. Therefore, we predict that they could be the sites of interaction of chromatin modifying complexes for epigenetic regulation. J. Exp. Zool. (Mol. Dev. Evol.) 308B, 2007. (c) 2007 Wiley-Liss, Inc.

Prediction of cis-regulatory elements using binding site matrices--the successes, the failures and the reasons for both.

T Vavouri — 2006-01-05T21:04:57-00:00

Curr Opin Genet Dev, Vol. 15, No. 4. (August 2005), pp. 395-402.

Protein-DNA interactions control many aspects of animal development and cellular responses to the environment. Although profiling of individual transcription factor binding sites is not a reliable guide for predicting the position of cis-regulatory elements in large genomes, modelling the evolution and the organization of regulatory elements has provided enough information to make some successful predictions. For vertebrate genomes, the field is limited by the lack of sufficient experimental data upon which to build reliable models. Nonetheless, a combination of experimental, computational and comparative data is likely to reveal aspects of complex regulatory networks in vertebrates, just as it has already done for simple eukaryotic genomes.

Conserved sequences and the evolution of gene regulatory signals.

MD Adams — 2006-07-20T15:00:35-00:00

Curr Opin Genet Dev, Vol. 15, No. 6. (December 2005), pp. 628-633.

Studies of evolutionary conservation of gene regulatory signals have led to a paradox: extensive sequence similarity implies functional conservation in non-coding regions across mammalian species; however, this stands in contrast to our understanding of transcriptional regulatory sites composed of degenerate recognition sequences for transcription factors that can maintain functional equivalence despite considerable sequence divergence. The latter observation provides an explanation for the rapid evolution of new traits through the gain and loss of transcription factor binding sites that bring new genes under the control of an existing genetic regulatory network. The former observation might point to novel mechanisms of gene regulation and/or chromosome function that are currently unappreciated. Recent comparative genome analysis has highlighted extensive conserved sequences in mammalian genomes that are beginning to be functionally characterized.

Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.

Trevor W Siggers — 2007-02-09T01:33:17-00:00

Nucleic Acids Res (30 January 2007)

Predicting the binding specificity of transcription factors is a critical step in the characterization and computational identification and of cis-regulatory elements in genomic sequences. Here we use protein-DNA structures to predict binding specificity and consider the possibility of predicting position weight matrices (PWM) for an entire protein family based on the structures of just a few family members. A particular focus is the sensitivity of prediction accuracy to the docking geometry of the structure used. We investigate this issue with the goal of determining how similar two docking geometries must be for binding specificity predictions to be accurate. Docking similarity is quantified using our recently described interface alignment score (IAS). Using a molecular-mechanics force field, we predict high-affinity nucleotide sequences that bind to the second zinc-finger (ZF) domain from the Zif268 protein, using different C(2)H(2) ZF domains as structural templates. We identify a strong relationship between IAS values and prediction accuracy, and define a range of IAS values for which accurate structure-based predictions of binding specificity is to be expected. The implication of our results for large-scale, structure-based prediction of PWMs is discussed.

Dorsal gradient networks in the Drosophila embryo.

A Stathopoulos — 2007-02-05T20:05:06-00:00

Dev Biol, Vol. 246, No. 1. (1 June 2002), pp. 57-67.

Here, we describe one of the major maternal regulatory gradients, Dorsal, and threshold outputs of gene expression that result from the graded distribution of this transcription factor. The analysis of a large number of authentic and synthetic target genes suggests that the Dorsal gradient directly specifies at least four, and possibly as many as seven, different thresholds of gene activity and tissue differentiation. These thresholds initiate the differentiation of the three primary embryonic tissues: the mesoderm, neurogenic ectoderm, and dorsal ectoderm. Moreover, primary readouts of the Dorsal gradient create asymmetries that subdivide each tissue into multiple cell types during gastrulation. Dorsal patterning thresholds represent the culmination of one of the most complete gene regulation network known in development, which begins with the asymmetric positioning of the oocyte nucleus within the egg chamber and leads to the localized activation of the Toll-Dorsal signaling pathway in ventral regions of the early embryo.

A SNP in a half-binding site creates p53 and estrogen receptor control of VEGFR-1.

Daniel Menendez — 2007-02-01T19:54:16-00:00

Mol Cell Biol (22 January 2007)

Interactions between master regulatory pathways provide higher order controls for cellular regulation. Recently, we reported a C>T single nucleotide polymorphism (SNP) in the vascular endothelial growth factor receptor 1 (VEGFR-1/Flt1) promoter that merges human VEGF and p53 pathways. This finding suggested a new layer in environmental controls of a pathway relevant to several diseases. The Flt1-T SNP created what appeared to be a half-site p53 target response element (RE). The absence of information about p53 gene responsiveness mediated by half-site REs led us to address how it influences Flt1 expression. We now identify a second regulatory sequence comprising a partial RE for estrogen receptors (ERs) upstream of the p53 binding site. Surprisingly, this provides for synergistic stimulation of transcription specifically at the Flt1-T allele through the combined action of ligand-bound ER and stress-induced p53. In addition to demonstrating direct control of Flt1 expression by ER and p53 proteins acting as sequence-specific transcription factors at half-site REs, we establish a new interaction between three master regulatory pathways, p53/ER/VEGF. The mechanism of joint regulation through half-sites is likely relevant to transcriptional control of other targets and expands the number of genes that may be directly controlled in master regulatory networks.

Simultaneous alignment and annotation of cis-regulatory regions.

AS Bais — 2007-01-29T08:42:16-00:00

Bioinformatics, Vol. 23, No. 2. (15 January 2007)

MOTIVATION: Current methods that annotate conserved transcription factor binding sites in an alignment of two regulatory regions perform the alignment and annotation step separately and combine the results in the end. If the site descriptions are weak or the sequence similarity is low, the local gap structure of the alignment poses a problem in detecting the conserved sites. It is therefore desirable to have an approach that is able to simultaneously consider the alignment as well as possibly matching site locations. RESULTS: With SimAnn we have developed a tool that serves exactly this purpose. By combining the annotation step and the alignment of the two sequences into one algorithm, it detects conserved sites more clearly. It has the additional advantage that all parameters are calculated based on statistical considerations. This allows for its successful application with any binding site model of interest. We present the algorithm and the approach for parameter selection and compare its performance with that of other, non-simultaneous methods on both simulated and real data. AVAILABILITY: A command-line based C++ implementation of SimAnn is available from the authors upon request. In addition, we provide Perl scripts for calculating the input parameters based on statistical considerations.

PhyloScan: Identification of transcription factor binding sites using cross-species evidence

Steven Carmack — 2007-01-24T08:54:14-00:00

Algorithms for Molecular Biology, Vol. 2 (23 January 2007), 1.