CiteULike: maximilianh's library [779 articles]

A genome-wide view of the spectrum of spontaneous mutations in yeast.

Michael Lynch — 2008-07-03T10:09:08-00:00

Proceedings of the National Academy of Sciences of the United States of America (26 June 2008)

The mutation process ultimately defines the genetic features of all populations and, hence, has a bearing on a wide range of issues involving evolutionary genetics, inheritance, and genetic disorders, including the predisposition to cancer. Nevertheless, formidable technical barriers have constrained our understanding of the rate at which mutations arise and the molecular spectrum of their effects. Here, we report on the use of complete-genome sequencing in the characterization of spontaneously arising mutations in the yeast Saccharomyces cerevisiae. Our results confirm some findings previously obtained by indirect methods but also yield numerous unexpected findings, in particular a very high rate of point mutation and skewed distribution of base-substitution types in the mitochondrion, a very high rate of segmental duplication and deletion in the nuclear genome, and substantial deviations in the mutational profile among various model organisms.

Reconstructing ordinal relationships in the Demospongiae using mitochondrial genomic data.

Dennis V Lavrov — 2008-06-30T08:08:12-00:00

Molecular phylogenetics and evolution (16 May 2008)

Class Demospongiae (phylum Porifera) encompasses most of sponges' morphological and species diversity. It also represents one of the most challenging and understudied groups in animal phylogenetics, with many higher-level relationships still being unresolved. Among the unanswered questions are the most fundamental, including those about the monophyly of the Demospongiae and the relationships among the 14 recognized orders within the class. The lack of resolved phylogeny hampers progress in studies of demosponge biology, evolution and biodiversity and may interfere with the efficient conservation and economic use of this group. We addressed the question of demosponge relationships using mitochondrial genomic data. We assembled a mitochondrial genomic dataset comprising all orders of demosponges that includes 17 new and five previously published complete demosponge mitochondrial genomes. To test for the congruence between mtDNA-based and nuclear rRNA-based phylogenies, we also determined and analyzed 18S rRNA sequences for the same set of species. Our results provide strong support for five major clades within the Demospongiae: Homoscleromorpha=G0 (order Homosclerophorida), Keratosa=G1 (orders Dendroceratida, Dictyoceratida, and Verticillitida), Myxospongiae=G2 (orders Chondrosida, Halisarcida, and Verongida), marine Haplosclerida=G3 and the rest of demosponges=G4 (orders Agelasida, Astrophorida, Hadromerida, Halichondrida, Poecilosclerida, Spirophorida, and freshwater Haploscerida), and for the (G0((G1+G2)(G3+G4)) relationships among these clades. Conversely, mitochondrial genomic data do not support the monophylies of traditional subclasses Ceractinomorpha and Tetractinomorpha as well as several currently recognized orders of demosponges. Furthermore, we demonstrate that mitochondrial gene arrangements can also be informative for the inference of order-level demosponge relationships and propose a modified method for the analysis of gene order data that works well when translocation of tRNA genes are more frequent than other rearrangements.

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences

Lucas Ward — 2008-06-27T14:58:42-00:00

Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i165-171.

Motivation: The identification of transcription factor (TF) binding sites and the regulatory circuitry that they define is currently an area of intense research. Data from whole-genome chromatin immunoprecipitation (ChIP-chip), whole-genome expression microarrays, and sequencing of multiple closely related genomes have all proven useful. By and large, existing methods treat the interpretation of functional data as a classification problem (between bound and unbound DNA), and the analysis of comparative data as a problem of local alignment (to recover phylogenetic footprints of presumably functional elements). Both of these approaches suffer from the inability to model and detect low-affinity binding sites, which have recently been shown to be abundant and functional. Results: We have developed a method that discovers functional regulatory targets of TFs by predicting the total affinity of each promoter for those factors and then comparing that affinity across orthologous promoters in closely related species. At each promoter, we consider the minimum affinity among orthologs to be the fraction of the affinity that is functional. Because we calculate the affinity of the entire promoter, our method is independent of local alignment. By comparing with functional annotation information and gene expression data in Saccharomyces cerevisiae, we have validated that this biophysically motivated use of evolutionary conservation gives rise to dramatic improvement in prediction of regulatory connectivity and factor-factor interactions compared to the use of a single genome. We propose novel biological functions for several yeast TFs, including the factors Snt2 and Stb4, for which no function has been reported. Our affinity-based approach towards comparative genomics may allow a more quantitative analysis of the principles governing the evolution of non-coding DNA. Availability: The MatrixREDUCE software package is available from http://www.bussemakerlab.org/software/MatrixREDUCE Contact: Harmen.Bussemaker@columbia.edu Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btn154

The GlxR regulon of the amino acid producer Corynebacterium glutamicum: In silico and in vitro detection of DNA binding sites of a global transcription regulator.

Thomas A Kohl — 2008-06-26T15:31:52-00:00

Journal of biotechnology (3 June 2008)

The glxR (cg0350) gene of Corynebacterium glutamicum ATCC 13032 encodes a DNA-binding trancription regulator of the CRP/FNR protein family. Five genomic DNA regions known to be bound GlxR provided the seed information for DNA binding site discovery by expectation maximization and Gibbs sampling approaches. The detection of additional motifs in the genome sequence of C. glutamicum was performed with a position weight matrix and a profile hidden Markov model, both deduced from the initial motif discovery. A combined iterative search for GlxR binding sites revealed 201 potential operator sequences. The interaction of purified GlxR protein with 51 selected binding sites was demonstrated in vitro by performing electrophoretic mobility shift assays with double-stranded 40-mer oligonucleotides. Considering potential operon structures and the genomic organization of C. glutamicum, the expression of 53 transcription units comprising 96 genes may be controlled directly by GlxR. The DNA binding site of GlxR is apparently specified by the consensus sequence TGTGANNTANNTCACA. Integration of the data into the transcriptional regulatory network model of C. glutamicum revealed a high connectivity of the deduced regulatory interactions and suggested that GlxR controls at least (i) sugar uptake, glycolysis, and gluconeogenesis, (ii) acetate, lactate, gluconate, and ethanol metabolism, (iii) aromatic compound degradation, (iv) aerobic and anaerobic respiration, (v) glutamate uptake and nitrogen assimilation, (vi) fatty acid biosynthesis, (vii) deoxyribonucleotide biosynthesis, (viii) the cellular stress response, and (ix) resuscitation.

Non-random retention of protein-coding overlapping genes in Metazoa

Giulia Solda' — 2008-04-17T06:42:58-00:00

BMC Genomics, Vol. 9 (16 April 2008), 174.

Discovering sequence motifs.

TL Bailey — 2008-06-22T20:36:04-00:00

Methods in molecular biology (Clifton, N.J.), Vol. 452 (2008), pp. 231-251.

Sequence motif discovery algorithms are an important part of the computational biologist's toolkit. The purpose of motif discovery is to discover patterns in biopolymer (nucleotide or protein) sequences in order to better understand the structure and function of the molecules the sequences represent. This chapter provides an overview of the use of sequence motif discovery in biology and a general guide to the use of motif discovery algorithms. The chapter discusses the types of biological features that DNA and protein motifs can represent and their usefulness. It also defines what sequence motifs are, how they are represented, and general techniques for discovering them. The primary focus is on one aspect of motif discovery: discovering motifs in a set of unaligned DNA or protein sequences. Also presented are steps useful for checking the biological validity and investigating the function of sequence motifs using methods such as motif scanning--searching for matches to motifs in a given sequence or a database of sequences. A discussion of some limitations of motif discovery concludes the chapter.

Mapping and sequencing of structural variation from eight human genomes

Jeffrey Kidd — 2008-04-30T19:31:59-00:00

Nature, Vol. 453, No. 7191., pp. 56-64.

A regulatory code for neurogenic gene expression in the Drosophila embryo.

M Markstein — 2006-09-29T22:03:20-00:00

Development, Vol. 131, No. 10. (May 2004), pp. 2387-2394.

Bioinformatics methods have identified enhancers that mediate restricted expression in the Drosophila embryo. However, only a small fraction of the predicted enhancers actually work when tested in vivo. In the present study, co-regulated neurogenic enhancers that are activated by intermediate levels of the Dorsal regulatory gradient are shown to contain several shared sequence motifs. These motifs permitted the identification of new neurogenic enhancers with high precision: five out of seven predicted enhancers direct restricted expression within ventral regions of the neurogenic ectoderm. Mutations in some of the shared motifs disrupt enhancer function, and evidence is presented that the Twist and Su(H) regulatory proteins are essential for the specification of the ventral neurogenic ectoderm prior to gastrulation. The regulatory model of neurogenic gene expression defined in this study permitted the identification of a neurogenic enhancer in the distant Anopheles genome. We discuss the prospects for deciphering regulatory codes that link primary DNA sequence information with predicted patterns of gene expression.

Expression-Guided In Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells

Anthony Philippakis — 2006-07-06T00:25:45-00:00

PLoS Computational Biology, Vol. 2, No. 5. (1 May 2006), e53.

While combinatorial models of transcriptional regulation can be inferred for metazoan systems from a priori biological knowledge, validation requires extensive and time-consuming experimental work. Thus, there is a need for computational methods that can evaluate hypothesized cis regulatory codes before the difficult task of experimental verification is undertaken. We have developed a novel computational framework (termed “CodeFinder”) that integrates transcription factor binding site and gene expression information to evaluate whether a hypothesized transcriptional regulatory model (TRM; i.e., a set of co-regulating transcription factors) is likely to target a given set of co-expressed genes. Our basic approach is to simultaneously predict cis regulatory modules (CRMs) associated with a given gene set and quantify the enrichment for combinatorial subsets of transcription factor binding site motifs comprising the hypothesized TRM within these predicted CRMs. As a model system, we have examined a TRM experimentally demonstrated to drive the expression of two genes in a sub-population of cells in the developing Drosophila mesoderm, the somatic muscle founder cells. This TRM was previously hypothesized to be a general mode of regulation for genes expressed in this cell population. In contrast, the present analyses suggest that a modified form of this cis regulatory code applies to only a subset of founder cell genes, those whose gene expression responds to specific genetic perturbations in a similar manner to the gene on which the original model was based. We have confirmed this hypothesis by experimentally discovering six (out of 12 tested) new CRMs driving expression in the embryonic mesoderm, four of which drive expression in founder cells.

Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site

Geetu Tuteja — 2008-06-16T22:31:48-00:00

Nucl. Acids Res. (13 June 2008), gkn366.

Foxa2 is a critical transcription factor that controls liver development and plays an important role in hepatic gluconeogensis in adult mice. Here, we use genome-wide location analysis for Foxa2 to identify its targets in the adult liver. We then show by computational analyses that Foxa2 containing cis-regulatory modules are not constructed from a random assortment of binding sites for other transcription factors expressed in the liver, but rather that their composition depends on the strength of the Foxa2 consensus site present. Genes containing a cis-regulatory module with a medium or weak Foxa2 consensus site are much more liver-specific than the genes with a strong consensus site. We not only provide a better understanding of the mechanisms of Foxa2 regulation but also introduce a novel method for identification of different cis-regulatory modules involving a single factor. 10.1093/nar/gkn366

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.

BP Berman — 2004-11-22T00:17:30-00:00

Genome Biol, Vol. 5, No. 9. (2004)

BACKGROUND: The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. RESULTS: We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene, and assayed embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the remaining 18 do not appear to have enhancer activity. We used the Drosophila pseudoobscura genome to compare patterns of evolution in and around the 15 positive and 18 false-positive predictions. Although conservation of primary sequence cannot distinguish true from false positives, conservation of binding-site clustering accurately discriminates functional binding-site clusters from those with no function. We incorporated conservation of binding-site clustering into a new genome-wide enhancer screen, and predict several hundred new regulatory sequences, including 85 adjacent to genes with embryonic patterns. CONCLUSIONS: Measuring conservation of sequence features closely linked to function--such as binding-site clusterin--makes better use of comparative sequence data than commonly used methods that examine only sequence identity.

Specific DNA-binding by Apicomplexan AP2 transcription factors

Erandi De Silva — 2008-06-10T12:36:17-00:00

Proceedings of the National Academy of Sciences (9 June 2008), 0801993105.

Malaria remains one of the most prevalent infectious diseases worldwide, affecting more than half a billion people annually. Despite many years of research, the mechanisms underlying transcriptional regulation in the malaria-causing Plasmodium spp., and in Apicomplexan parasites generally, remain poorly understood. In Plasmodium, few regulatory elements sufficient to drive gene expression have been characterized, and their cognate DNA-binding proteins remain unknown. This study characterizes the DNA-binding specificities of two members of the recently identified Apicomplexan AP2 (ApiAP2) family of putative transcriptional regulators from Plasmodium falciparum. The ApiAP2 proteins contain AP2 domains homologous to the well characterized plant AP2 family of transcriptional regulators, which play key roles in development and environmental stress response pathways. We assayed ApiAP2 protein-DNA interactions using protein-binding microarrays and combined these results with computational predictions of coexpressed target genes to couple these putative trans factors to corresponding cis-regulatory motifs in Plasmodium. Furthermore, we show that protein-DNA sequence specificity is conserved in orthologous proteins between phylogenetically distant Apicomplexan species. The identification of the DNA-binding specificities for ApiAP2 proteins lays the foundation for the exploration of their role as transcriptional regulators during all stages of parasite development. Because of their origin in the plant lineage, ApiAP2 proteins have no homologues in the human host and may prove to be ideal antimalarial targets. 10.1073/pnas.0801993105

Associating transcription factor-binding site motifs with target GO terms and target genes

Mikael Boden — 2008-06-11T06:46:49-00:00

Nucl. Acids Res. (10 June 2008), gkn374.

The roles and target genes of many transcription factors (TFs) are still unknown. To predict the roles of TFs, we present a computational method for associating Gene Ontology (GO) terms with TF-binding motifs. The method works by ranking all genes as potential targets of the TF, and reporting GO terms that are significantly associated with highly ranked genes. We also present an approach, whereby these predicted GO terms can be used to improve predictions of TF target genes. This uses a novel gene-scoring function that reflects the insight that genes annotated with GO terms predicted to be associated with the TF are more likely to be its targets. We construct validation sets of GO terms highly associated with known targets of various yeast and human TF. On the yeast reference sets, our prediction method identifies at least one correct GO term for 73% of the TF, 49% of the correct GO terms are predicted and almost one-third of the predicted GO terms are correct. Results on human reference sets are similarly encouraging. Validation of our target gene prediction method shows that its accuracy exceeds that of simple motif scanning. 10.1093/nar/gkn374

Systematic identification of cell cycle regulated transcription factors from microarray time series data

Chao Cheng — 2008-03-04T17:29:12-00:00

BMC Genomics, Vol. 9 (03 March 2008), 116.

Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites

Nak-Kyeong Kim — 2008-06-04T19:30:27-00:00

BMC Bioinformatics, Vol. 9 (04 June 2008), 262.

Subfunctionalization of Duplicated Zebrafish pax6 Genes by cis-Regulatory Divergence

Dirk Kleinjan — 2008-02-24T04:18:14-00:00

PLoS Genetics, Vol. 4, No. 2. (1 February 2008), e29.

Gene duplication is a major driver of evolutionary divergence. In most vertebrates a single PAX6 gene encodes a transcription factor required for eye, brain, olfactory system, and pancreas development. In zebrafish, following a postulated whole-genome duplication event in an ancestral teleost, duplicates pax6a and pax6b jointly fulfill these roles. Mapping of the homozygously viable eye mutant sunrise identified a homeodomain missense change in pax6b, leading to loss of target binding. The mild phenotype emphasizes role-sharing between the co-orthologues. Meticulous mapping of isolated BACs identified perturbed synteny relationships around the duplicates. This highlights the functional conservation of pax6 downstream (3′) control sequences, which in most vertebrates reside within the introns of a ubiquitously expressed neighbour gene, ELP4, whose pax6a-linked exons have been lost in zebrafish. Reporter transgenic studies in both mouse and zebrafish, combined with analysis of vertebrate sequence conservation, reveal loss and retention of specific cis-regulatory elements, correlating strongly with the diverged expression of co-orthologues, and providing clear evidence for evolution by subfunctionalization.

CTCF Genomic Binding Sites in Drosophila and the Organisation of the Bithorax Complex.

Eimear E Holohan — 2007-07-12T08:07:40-00:00

PLoS Genet, Vol. 3, No. 7. (6 July 2007)

Insulator or enhancer-blocking elements are proposed to play an important role in the regulation of transcription by preventing inappropriate enhancer/promoter interaction. The zinc-finger protein CTCF is well studied in vertebrates as an enhancer blocking factor, but Drosophila CTCF has only been characterised recently. To date only one endogenous binding location for CTCF has been identified in the Drosophila genome, the Fab-8 insulator in the Abdominal-B locus in the Bithorax complex (BX-C). We carried out chromatin immunopurification coupled with genomic microarray analysis to identify CTCF binding sites within representative regions of the Drosophila genome, including the 3-Mb Adh region, the BX-C, and the Antennapedia complex. Location of in vivo CTCF binding within these regions enabled us to construct a robust CTCF binding-site consensus sequence. CTCF binding sites identified in the BX-C map precisely to the known insulator elements Mcp, Fab-6, and Fab-8. Other CTCF binding sites correlate with boundaries of regulatory domains allowing us to locate three additional presumptive insulator elements; "Fab-2," "Fab-3," and "Fab-4." With the exception of Fab-7, our data indicate that CTCF is directly associated with all known or predicted insulators in the BX-C, suggesting that the functioning of these insulators involves a common CTCF-dependent mechanism. Comparison of the locations of the CTCF sites with characterised Polycomb target sites and histone modification provides support for the domain model of BX-C regulation.

NcDNAlign: Plausible multiple alignments of non-protein-coding genomic sequences.

Dominic Rose — 2008-06-03T09:56:01-00:00

Genomics (27 May 2008)

Genome-wide multiple sequence alignments (MSAs) are a necessary prerequisite for an increasingly diverse collection of comparative genomic approaches. Here we present a versatile method that generates high-quality MSAs for non-protein-coding sequences. The NcDNAlign pipeline combines pairwise BLAST alignments to create initial MSAs, which are then locally improved and trimmed. The program is optimized for speed and hence is particulary well-suited to pilot studies. We demonstrate the practical use of NcDNAlign in three case studies: the search for ncRNAs in gammaproteobacteria and the analysis of conserved noncoding DNA in nematodes and teleost fish, in the latter case focusing on the fate of duplicated ultra-conserved regions. Compared to the currently widely used genome-wide alignment program TBA, our program results in a 20- to 30-fold reduction of CPU time necessary to generate gammaproteobacterial alignments. A showcase application of bacterial ncRNA prediction based on alignments of both algorithms results in similar sensitivity, false discovery rates, and up to 100 putatively novel ncRNA structures. Similar findings hold for our application of NcDNAlign to the identification of ultra-conserved regions in nematodes and teleosts. Both approaches yield conserved sequences of unknown function, result in novel evolutionary insights into conservation patterns among these genomes, and manifest the benefits of an efficient and reliable genome-wide alignment package. The software is available under the GNU Public License at http://www.bioinf.uni-leipzig.de/Software/NcDNAlign/.

Uncovering cis regulatory codes using synthetic promoter shuffling.

A Kinkhabwala — 2008-05-30T14:24:21-00:00

PLoS ONE, Vol. 3, No. 4. (2008)

Revealing the spectrum of combinatorial regulation of transcription at individual promoters is essential for understanding the complex structure of biological networks. However, the computations represented by the integration of various molecular signals at complex promoters are difficult to decipher in the absence of simple cis regulatory codes. Here we synthetically shuffle the regulatory architecture--operator sequences binding activators and repressors--of a canonical bacterial promoter. The resulting library of complex promoters allows for rapid exploration of promoter encoded logic regulation. Among all possible logic functions, NOR and ANDN promoter encoded logics predominate. A simple transcriptional cis regulatory code determines both logics, establishing a straightforward map between promoter structure and logic phenotype. The regulatory code is determined solely by the type of transcriptional regulation combinations: two repressors generate a NOR: NOT (a OR b) whereas a repressor and an activator generate an ANDN: a AND NOT b. Three-input versions of both logics, having an additional repressor as an input, are also present in the library. The resulting complex promoters cover a wide dynamic range of transcriptional strengths. Synthetic promoter shuffling represents a fast and efficient method for exploring the spectrum of complex regulatory functions that can be encoded by complex promoters. From an engineering point of view, synthetic promoter shuffling enables the experimental testing of the functional properties of complex promoters that cannot necessarily be inferred ab initio from the known properties of the individual genetic components. Synthetic promoter shuffling may provide a useful experimental tool for studying naturally occurring promoter shuffling.

RSAT: regulatory sequence analysis tools

Morgane Thomas-Chollier — 2008-05-23T13:55:20-00:00

Nucl. Acids Res. (21 May 2008), gkn304.

The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. The suite includes programs for sequence retrieval, pattern discovery, phylogenetic footprint detection, pattern matching, genome scanning and feature map drawing. Random controls can be performed with random gene selections or by generating random sequences according to a variety of background models (Bernoulli, Markov). Beyond the original word-based pattern-discovery tools (oligo-analysis and dyad-analysis), we recently added a battery of tools for matrix-based detection of cis-acting elements, with some original features (adaptive background models, Markov-chain estimation of P-values) that do not exist in other matrix-based scanning tools. The web server offers an intuitive interface, where each program can be accessed either separately or connected to the other tools. In addition, the tools are now available as web services, enabling their integration in programmatic workflows. Genomes are regularly updated from various genome repositories (NCBI and EnsEMBL) and 682 organisms are currently supported. Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published. 10.1093/nar/gkn304

Transfer of a large gene regulatory apparatus to a new developmental address in echinoid evolution

Feng Gao — 2008-04-23T12:40:37-00:00

Proceedings of the National Academy of Sciences, Vol. 105, No. 16. (22 April 2008), pp. 6091-6096.

Of the five echinoderm classes, only the modern sea urchins (euechinoids) generate a precociously specified embryonic micromere lineage that ingresses before gastrulation and then secretes the biomineral embryonic skeleton. The gene regulatory network (GRN) underlying the specification and differentiation of this lineage is now known. Many of the same differentiation genes as are used in the biomineralization of the embryo skeleton are also used to make the similar biomineral of the spines and test plates of the adult body. Here, we determine the components of the regulatory state upstream of these differentiation genes that are shared between embryonic and adult skeletogenesis. An abrupt "break point" in the micromere GRN is thus revealed, on one side of which most of the regulatory genes are used in both, and on the other side of which the regulatory apparatus is entirely micromere-specific. This reveals the specific linkages of the micromere GRN forged in the evolutionary process by which the skeletogenic gene batteries were caused to be activated in the embryonic micromere lineage. We also show, by comparison with adult skeletogenesis in the sea star, a distant echinoderm outgroup, that the regulatory apparatus responsible for driving the skeletogenic differentiation gene batteries is an ancient pleisiomorphic aspect of the echinoderm-specific regulatory heritage. 10.1073/pnas.0801201105

Convergent evolution of clustering of Iroquois homeobox genes across metazoans.

Manuel Irimia — 2008-05-17T09:00:50-00:00

Molecular biology and evolution (9 May 2008)

Vertebrate and Drosophila Iroquois genes are organized in clusters of three genes sharing blocks of conserved regulatory sequences. Here, we report a three-gene cluster in the basal, pre-duplicative chordate amphioxus. Surprisingly, however, the origin of the amphioxus cluster is independent of those in vertebrates and drosophilids. Investigation of genomic organization of Iroquois genes in other 17 metazoan genomes revealed a fourth independent three-gene cluster organization in polychaetes, as well as additional two- and four-gene clusters in other clades, in one of the most striking examples of convergence in genomic organization described so far. The recurrent independent evolution of Iroquois clusters suggests a functional importance of this organization for these genes, perhaps related to the sharing of regulatory elements. Consistent with this, comparative analysis of genomic regions flanking the three amphioxus Irx genes revealed several blocks of sequences, conserved for at least 100 million years. Finally, we discuss the possible causes and implications of the convergent evolution of this genomic and regulatory organization throughout metazoans.

Interchromosomal associations between alternatively expressed loci

Charalampos Spilianakis — 2005-05-09T03:02:46-00:00

Nature (08 May 2005)

Interchromosomal Interactions and Olfactory Receptor Choice

Stavros Lomvardas — 2008-03-18T12:02:56-00:00

Cell, Vol. 126, No. 2. (28 July 2006), pp. 403-413.

Summary The expression of a single odorant receptor (OR) gene from a large gene family in individual sensory neurons is an essential feature of the organization and function of the olfactory system. We have used chromosome conformation capture to demonstrate the specific association of an enhancer element, H, on chromosome 14 with multiple OR gene promoters on different chromosomes. DNA and RNA fluorescence in situ hybridization (FISH) experiments allow us to visualize the colocalization of the H enhancer with the single OR allele that is transcribed in a sensory neuron. In transgenic mice bearing additional H elements, sensory neurons that express OR pseudogenes also express a second functional receptor. These data suggest a model of receptor choice in which a single trans-acting enhancer element may allow the stochastic activation of only one OR allele in an olfactory sensory neuron.

A transcriptional enhancer from the coding region of ADAMTS5.

KK Barthel — 2008-05-16T11:37:54-00:00

PLoS ONE, Vol. 3, No. 5. (2008)

BACKGROUND: The revelation that the human genome encodes only approximately 25,000 genes and thus cannot account for phenotypic complexity has been one of the biggest surprises in the post-genomic era. However, accumulating evidence suggests that transcriptional regulation may be in large part responsible for this observed mammalian complexity. Consequently, there has been a strong drive to locate cis-regulatory regions in mammalian genomes in order to understand the unifying principles governing these regions, including their genomic distribution. Although a number of systematic approaches have been developed, these all discount coding sequence. METHODOLOGY/PRINCIPAL FINDINGS: Using the computational tool PRI (Pattern-defined Regulatory Islands), which does not mask coding sequence, we identified a regulatory region associated with the gene ADAMTS5 that encompasses the entirety of the essential coding exon 2. We demonstrate through a combination of chromatin immunoprecipitation and reporter gene studies that this region can not only bind the myogenic transcription factors MYOD and myogenin and the E-protein HEB but can also function as a very strong myogenic transcriptional enhancer. CONCLUSIONS/SIGNIFICANCE: Thus, we report the identification and detailed characterization of an exonic enhancer. Ultimately, this leads to the interesting question of why evolution would be so parsimonious in the functional assignment of sequence.

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

Anton Valouev — 2008-05-15T22:59:25-00:00

Genome Res. (13 May 2008), gr.076463.108.

Using the massively parallel technique of Sequencing by Oligonucleotide Ligation and Detection (SOLiD) we have assessed the in vivo positions of more than 44 million putative nucleosome cores in the multicellular genetic model organism Caenorhabditis elegans. These analyses provide a global view of the chromatin architecture of a multicellular animal at extremely high density and resolution. While we observe some degree of reproducible positioning throughout the genome in our mixed stage population of animals, we note that the major chromatin feature in the worm is a diversity of allowed nucleosome positions at the vast majority of individual loci. While absolute positioning of nucleosomes can vary substantially, relative positioning of nucleosomes (in a repeated array structure likely to be maintained at least in part by steric constraints) appears to be a significant property of chromatin structure. The high density of nucleosomal reads enabled a substantial extension of previous analysis describing the usage of individual oligonucleotide sequences along the span of the nucleosome core and linker. We release this dataset, via the UCSC Genome Browser, as a resource for the high-resolution analysis of chromatin conformation and DNA accessibility at individual loci within the C. elegans genome. 10.1101/gr.076463.108

Multigene Analyses of Bilaterian Animals Corroborate the Monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia

Herve Philippe — 2005-04-16T08:03:51-00:00

Molecular Biology and Evolution, Vol. 22, No. 5. (15 May 2005), pp. 1246-1253.

OGtree: a tool for creating genome trees of prokaryotes based on overlapping genes.

Li-Wei Jiang — 2008-05-11T21:20:05-00:00

Nucleic acids research (2 May 2008)

OGtree is a web-based tool for constructing genome trees of prokaryotic species based on a measure of combining overlapping-gene content and overlapping-gene order in their whole genomes. The overlapping genes (OGs) are defined as adjacent genes whose coding sequences overlap partially or entirely. In fact, OGs are ubiquitous in microbial genomes and more conserved between species than non-OGs. Based on these properties, it has been suggested that OGs can serve as better phylogenetic characters than non-OGs for reconstructing the evolutionary relationships among microbial genomes. OGtree takes the accession numbers of prokaryotic genomes as its input. It then downloads their complete genomes from the National Centre for Biotechnology Information and identifies OGs in each genome and their orthologous OGs in other genomes. Next, OGtree computes an overlapping-gene distance between each pair of input genomes based on a combination of their OG content and orthologous OG order. Finally, it utilizes distance-based methods of building tree to reconstruct the genome trees of input prokaryotic genomes according to their pairwise OG distance. OGtree is available online at http://bioalgorithm.life.nctu.edu.tw/OGtree/.

Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets.

Chaim Linhart — 2008-04-18T07:36:36-00:00

Genome research (14 April 2008)

We present a three-fold contribution to the computational task of motif discovery, a key component in the effort of delineating the regulatory map of a genome: 1) We constructed a comprehensive large-scale, publicly-available compendium of transcription factor and microRNA target gene sets derived from diverse high-throughput experiments in several metazoans. We used the compendium as a benchmark for motif discovery tools. 2) We developed Amadeus, a highly efficient, user-friendly software platform for genome-scale detection of novel motifs, applicable to a wide range of motif discovery tasks. Amadeus improves upon extant tools in terms of accuracy, running time, output information and ease-of-use, and is the only program that attained a high success rate on the metazoan compendium. 3) We demonstrate that by searching for motifs based on their genome-wide localization or chromosomal distributions (without using a pre-defined target set), Amadeus uncovers diverse known phenomena, as well as novel regulatory motifs.

The Otx binding site is required for the activation of HpOtxL mRNA expression in the sea urchin, Hemicentrotus pulcherrimus.

Y Hayashibara — 2008-05-09T15:02:28-00:00

Development, growth & differentiation, Vol. 46, No. 1. (February 2004), pp. 61-67.

Two distinct types of orthodenticle-related (HpOtxE and HpOtxL) mRNA are transcribed from a single HpOtx gene by altering the transcription start site and by alternative splicing, and their expressions are differentially regulated during early development of the sea urchin Hemicentrotus pulcherrimus. To understand the mechanism of this regulation, we screened for the enhancer element involved in the stage-specific expression of HpOtxL mRNA. Different portions of the HpOtx gene, including the 5'-flanking region and the first intron, were ligated to the minimal HpOtxL promoter driving a luciferase gene, and their constructs were introduced into fertilized eggs using a particle gun. The enhancer element responsible for proper expression consistent with that of the endogenous HpOtxL was found in the first intron of the HpOtx gene. External and internal deletion analyses showed that the 334 bp region (from +8838 bp to +9171 bp) was required for enhancer activity. In addition, deletion of an Otx binding site within the 334 bp region markedly reduced reporter expression. These results suggest that the Otx binding site within the HpOtxL enhancer is required for the activation of HpOtxL mRNA expression. The promoter preference of the HpOtxL enhancer is also discussed.

Acetylated YY1 regulates Otx2 expression in anterior neuroectoderm at two cis-sites 90 kb apart

Nobuyoshi Takasaki — 2007-03-02T05:22:10-00:00

The EMBO Journal, Vol. aop, No. current. (01 March 2007)

An evaluation of information content as a metric for the inference of putative conserved noncoding regions in DNA sequences using a genetic algorithms approach.

CB Congdon — 2008-05-07T17:36:13-00:00

IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, Vol. 5, No. 1. (r 2008), pp. 1-14.

In previous work, we presented GAMI, an approach to motif inference that uses a genetic algorithms search. GAMI is designed specifically to find putative conserved regulatory motifs in noncoding regions of divergent species, and is designed to allow for analysis of long nucleotide sequences. In this work, we compare GAMI's performance when run with its original fitness function (a simple count of the number of matches) and when run with information content, as well as several variations on these metrics. Results indicate that information content does not identify highly conserved regions, and thus is not the appropriate metric for this task, while variations on information content as well as the original metric succeed in identifying putative conserved regions.

Lifting the veil on the transcriptome

Kevin Callahan — 2008-04-24T19:33:41-00:00

Genome Biology, Vol. 9 (24 April 2008), 218.

Global chromatin domain organization of the Drosophila genome.

E de Wit — 2008-05-07T14:55:40-00:00

PLoS genetics, Vol. 4, No. 3. (March 2008)

In eukaryotes, neighboring genes can be packaged together in specific chromatin structures that ensure their coordinated expression. Examples of such multi-gene chromatin domains are well-documented, but a global view of the chromatin organization of eukaryotic genomes is lacking. To systematically identify multi-gene chromatin domains, we constructed a compendium of genome-scale binding maps for a broad panel of chromatin-associated proteins in Drosophila melanogaster. Next, we computationally analyzed this compendium for evidence of multi-gene chromatin domains using a novel statistical segmentation algorithm. We find that at least 50% of all fly genes are organized into chromatin domains, which often consist of dozens of genes. The domains are characterized by various known and novel combinations of chromatin proteins. The genes in many of the domains are coregulated during development and tend to have similar biological functions. Furthermore, during evolution fewer chromosomal rearrangements occur inside chromatin domains than outside domains. Our results indicate that a substantial portion of the Drosophila genome is packaged into functionally coherent, multi-gene chromatin domains. This has broad mechanistic implications for gene regulation and genome evolution.

CompariMotif: quick and easy comparisons of sequence motifs

Richard Edwards — 2008-05-07T14:30:49-00:00

Bioinformatics, Vol. 24, No. 10. (15 May 2008), pp. 1307-1309.

Summary: CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs. Availability: CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/ Contact: r.edwards@southampton.ac.uk Supplementary information: Further details are available at http://bioinformatics.ucd.ie/shields/software/comparimotif/ 10.1093/bioinformatics/btn105

Combining Statistical Alignment and Phylogenetic Footprinting to Detect Regulatory Elements.

R Satija — 2008-03-21T18:29:17-00:00

Bioinformatics (18 March 2008)

MOTIVATION: Traditional alignment-based phylogenetic footprinting approaches make predictions on the basis of a single assumed alignment. The predictions are therefore highly sensitive to alignment errors or regions of alignment uncertainty. Alternatively, statistical alignment methods provide a framework for performing phylogenetic analyses by examining a distribution of alignments. RESULTS: We developed a novel algorithm for predicting functional elements by combining statistical alignment and phylogenetic footprinting (SAPF). SAPF simultaneously performs both alignment and annotation by combining phylogenetic footprinting techniques with an HMM transducer-based multiple alignment model, and can analyze sequence data from multiple sequences. We assessed SAPF's predictive performance on two simulated datasets and three well-annotated cis-regulatory modules from newly sequenced Drosophila genomes. The results demonstrate that removing the traditional dependence on a single alignment can significantly augment the predictive performance, especially when there is uncertainty in the alignment of functional regions. AVAILABILITY: SAPF is freely available to download online at http://www.stats.ox.ac.uk/~satija/SAPF/ CONTACT: satija@stats.ox.ac.uk.

The words of the regulatory code are arranged in a variable manner in highly conserved enhancers.

Sepand Rastegar — 2008-05-06T22:56:41-00:00

Developmental biology (4 April 2008)

The cis-regulatory regions of many developmental regulators and transcription factors are believed to be highly conserved in the genomes of vertebrate species, suggesting specific regulatory mechanisms for these gene classes. We functionally characterized five notochord enhancers, whose sequence is highly conserved, and systematically mutated two of them. Two subregions were identified to be essential for expression in the notochord of the zebrafish embryo. Synthetic enhancers containing the two essential regions in front of a TATA-box drive expression in the notochord while concatemerization of the subregions alone is not sufficient, indicating that the combination of the two sequence elements is required for notochord expression. Both regions are present in the five functionally characterized notochord enhancers. However, the position, the distance and relative orientation of the two sequence motifs can vary substantially within the enhancer sequences. This suggests that the regulatory grammar itself does not dictate the high evolutionary conservation between these orthologous cis-regulatory sequences. Rather, it represents a less well-conserved layer of sequence organization within these sequences.

ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species

Bart Hooghe — 2008-05-06T14:55:58-00:00

Nucl. Acids Res. (3 May 2008), gkn195.

Transcription factors (TFs) are key components in signaling pathways, and the presence of their binding sites in the promoter regions of DNA is essential for their regulation of the expression of the corresponding genes. Orthologous promoter sequences are commonly used to increase the specificity with which potentially functional transcription factor binding sites (TFBSs) are recognized and to detect possibly important similarities or differences between the different species. The ConTra (conserved TFBSs) web server provides the biologist at the bench with a user-friendly tool to interactively visualize TFBSs predicted using either TransFac (1) or JASPAR (2) position weight matrix libraries, on a promoter alignment of choice. The visualization can be preceded by a simple scoring analysis to explore which TFs are the most likely to bind to the promoter of interest. The ConTra web server is available at http://bioit.dmbr.ugent.be/ConTra/index.php. 10.1093/nar/gkn195

Detecting cis-regulatory binding sites for cooperatively binding proteins

Liesbeth van Oeffelen — 2008-05-06T13:26:56-00:00

Nucl. Acids Res., Vol. 36, No. 8. (1 May 2008), e46.

Several methods are available to predict cis-regulatory modules in DNA based on position weight matrices. However, the performance of these methods generally depends on a number of additional parameters that cannot be derived from sequences and are difficult to estimate because they have no physical meaning. As the best way to detect cis-regulatory modules is the way in which the proteins recognize them, we developed a new scoring method that utilizes the underlying physical binding model. This method requires no additional parameter to account for multiple binding sites; and the only necessary parameters to model homotypic cooperative interactions are the distances between adjacent protein binding sites in basepairs, and the corresponding cooperative binding constants. The heterotypic cooperative binding model requires one more parameter per cooperatively binding protein, which is the concentration multiplied by the partition function of this protein. In a case study on the bacterial ferric uptake regulator, we show that our scoring method for homotypic cooperatively binding proteins significantly outperforms other PWM-based methods where biophysical cooperativity is not taken into account. 10.1093/nar/gkn140

Determinants of a transcriptionally competent environment at the GM-CSF promoter

KH Brettingham-Moore — 2008-05-06T14:24:27-00:00

Nucl. Acids Res., Vol. 36, No. 8. (1 May 2008), pp. 2639-2653.

Granulocyte macrophage-colony stimulating factor (GM-CSF) is produced by T cells, but not B cells, in response to immune signals. GM-CSF gene activation in response to T-cell stimulation requires remodelling of chromatin associated with the gene promoter, and these changes do not occur in B cells. While the CpG methylation status of the murine GM-CSF promoter shows no correlation with the ability of the gene to respond to activation, we find that the basal chromatin environment of the gene promoter influences its ability to respond to immune signals. In unstimulated T cells but not B cells, the GM-CSF promoter is selectively marked by enrichment of histone acetylation, and association of the chromatin-remodelling protein BRG1. BRG1 is removed from the promoter upon activation concomitant with histone depletion and BRG1 is required for efficient chromatin remodelling and transcription. Increasing histone acetylation at the promoter in T cells is paralleled by increased BRG1 recruitment, resulting in more rapid chromatin remodelling, and an associated increase in GM-CSF mRNA levels. Furthermore, increasing histone acetylation in B cells removes the block in chromatin remodelling and transcriptional activation of the GM-CSF gene. These data are consistent with a model in which histone hyperacetylation and BRG1 enrichment at the GM-CSF promoter, generate a chromatin environment competent to respond to immune signals resulting in gene activation. 10.1093/nar/gkn117

MicroRNAs and the advent of vertebrate morphological complexity

Alysha Heimberg — 2008-02-20T21:17:00-00:00

Proceedings of the National Academy of Sciences (14 February 2008), 0712259105.

The causal basis of vertebrate complexity has been sought in genome duplication events (GDEs) that occurred during the emergence of vertebrates, but evidence beyond coincidence is wanting. MicroRNAs (miRNAs) have recently been identified as a viable causal factor in increasing organismal complexity through the action of these approx22-nt noncoding RNAs in regulating gene expression. Because miRNAs are continuously being added to animalian genomes, and, once integrated into a gene regulatory network, are strongly conserved in primary sequence and rarely secondarily lost, their evolutionary history can be accurately reconstructed. Here, using a combination of Northern analyses and genomic searches, we show that 41 miRNA families evolved at the base of Vertebrata, as they are found and/or detected in lamprey, but not in either ascidians or amphioxus (or any other nonchordate taxon). When placed into temporal context, the rate of miRNA acquisition and the extent of phenotypic evolution are anomalously high early in vertebrate history, far outstripping any other episode in chordate evolution. The genomic position of miRNA paralogues in humans, together with gene trees incorporating lamprey orthologues, indicates that although GDEs can account for an increase in the diversity of miRNA family members, which occurred before the last common ancestor of all living vertebrates, GDEs cannot account for the origin of these novel families themselves. We hypothesize that lying behind the origin of vertebrate complexity is the dramatic expansion of the noncoding RNA inventory including miRNAs, rather than an increase in the protein-encoding inventory caused by GDEs. 10.1073/pnas.0712259105

Computational intelligence approaches for pattern discovery in biological systems

Gary Fogel — 2008-05-06T12:22:08-00:00

Brief Bioinform (5 May 2008), bbn021.

Biology, chemistry and medicine are faced by tremendous challenges caused by an overwhelming amount of data and the need for rapid interpretation. Computational intelligence (CI) approaches such as artificial neural networks, fuzzy systems and evolutionary computation are being used with increasing frequency to contend with this problem, in light of noise, non-linearity and temporal dynamics in the data. Such methods can be used to develop robust models of processes either on their own or in combination with standard statistical approaches. This is especially true for database mining, where modeling is a key component of scientific understanding. This review provides an introduction to current CI methods, their application to biological problems, and concludes with a commentary about the anticipated impact of these approaches in bioinformatics. 10.1093/bib/bbn021

Genome-wide transcription and the implications for genomic organization.

Philipp Kapranov — 2007-05-10T13:57:03-00:00

Nat Rev Genet (8 May 2007)

Recent evidence of genome-wide transcription in several species indicates that the amount of transcription that occurs cannot be entirely accounted for by current sets of genome-wide annotations. Evidence indicates that most of both strands of the human genome might be transcribed, implying extensive overlap of transcriptional units and regulatory elements. These observations suggest that genomic architecture is not colinear, but is instead interleaved and modular, and that the same genomic sequences are multifunctional: that is, used for multiple independently regulated transcripts and as regulatory regions. What are the implications and consequences of such an interleaved genomic architecture in terms of increased information content, transcriptional complexity, evolution and disease states?

Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions.

Mahesh Yaragatti — 2008-05-01T09:02:43-00:00

Genome research (25 April 2008)

The identification of transcriptional regulatory modules within mammalian genomes is a prerequisite to understanding the mechanisms controlling regulated gene expression. While high-throughput microarray- and sequencing-based approaches have been used to map the genomic locations of sites of nuclease hypersensitivity or target DNA sequences bound by specific protein factors, the identification of regulatory elements using functional assays, which would provide important complementary data, has been relatively rare. Here we present a method that permits the functional identification of active transcriptional regulatory modules using a simple procedure for the isolation and analysis of DNA derived from nucleosome-free regions (NFRs), the 2% of the cellular genome that contains these elements. The more than 100 new active regulatory DNAs identified in this manner from F9 cells correspond to both promoter-proximal and distal elements, and display several features predicted for endogenous transcriptional regulators, including localization within DNase-accessible chromatin and CpG islands, and proximity to expressed genes. Furthermore, comparison with published ChIP-seq data of ES-cell chromatin shows that the functional elements we identified correspond with genomic regions enriched for H3K4me3, a histone modification associated with active transcriptional regulatory elements, and that the correspondence of H3K4me3 with our promoter-distal elements is largely ES-cell specific. The majority of the distal elements exhibit enhancer activity. Importantly, these functional DNA fragments are an average 149 bp in length, greatly facilitating future applications to identify transcription factor binding sites mediating their activity. Thus, this approach provides a tool for the high-resolution identification of the functional components of active promoters and enhancers.

Nuclear Dvl, c-Jun, beta-catenin, and TCF form a complex leading to stabilization of beta-catenin-TCF interaction.

XQ Gan — 2008-05-01T08:25:43-00:00

The Journal of cell biology, Vol. 180, No. 6. (24 March 2008), pp. 1087-1100.

In canonical Wnt signaling, Dishevelled (Dvl) is a critical cytoplasmic regulator that releases beta-catenin from degradation. Here, we find that Dvl and c-Jun form a complex with beta-catenin-T-cell factor 4 (TCF-4) on the promoter of Wnt target genes and regulate gene transcription. The complex forms via two interactions of nuclear Dvl with c-Jun and beta-catenin, respectively, both of which bind to TCF. Disrupting the interaction of Dvl with either c-Jun or beta-catenin suppresses canonical Wnt signaling-stimulated transcription, and the reduction of Dvl diminished beta-catenin-TCF-4 association on Wnt target gene promoters in vivo. Expression of a TCF-Dvl fusion protein largely rescued the c-Jun knockdown Wnt signaling deficiency in mammalian cells and zebrafish. Thus, we confirm that c-Jun functions in canonical Wnt signaling and show that c-Jun functions as a scaffold in the beta-catenin-TCFs transcription complex bridging Dvl to TCF. Our results reveal a mechanism by which nuclear Dvl cooperates with c-Jun to regulate gene transcription stimulated by the canonical Wnt signaling pathway.

Studying the functional conservation of cis-regulatory modules and their transcriptional output

Denis Bauer — 2008-04-29T09:23:48-00:00

BMC Bioinformatics, Vol. 9 (29 April 2008), 220.

Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting.

S De Bodt — 2008-04-30T14:54:19-00:00

Molecular biology and evolution, Vol. 23, No. 6. (June 2006), pp. 1293-1303.

The MIKC MADS-box gene family has been shaped by extensive gene duplications giving rise to subfamilies of genes with distinct functions and expression patterns. However, within these subfamilies the functional assignment is not that clear-cut, and considerable functional redundancy exists. One way to investigate the diversity in regulation present in these subfamilies is promoter sequence analysis. With the advent of genome sequencing projects, we are now able to exert a comparative analysis of Arabidopsis and poplar promoters of MADS-box genes belonging to the same subfamily. Based on the principle of phylogenetic footprinting, sequences conserved between the promoters of homologous genes are thought to be functional. Here, we have investigated the evolution of MADS-box genes at the promoter level and show that many genes have diverged in their regulatory sequences after duplication and/or speciation. Furthermore, using phylogenetic footprinting, a distinction can be made between redundancy, neo/nonfunctionalization, and subfunctionalization.

Highly similar noncoding genomic DNA sequences: ultraconserved, or merely widespread?

DA Hickey — 2008-04-30T12:01:04-00:00

Genome / National Research Council Canada = Génome / Conseil national de recherches Canada, Vol. 51, No. 5. (May 2008), pp. 396-397.

In this note, I propose an explanation for the seeming contradiction between bioinformatics-based predictions of an essential function for ultraconserved DNA sequences, and the lack of an experimental demonstration of such function.

Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus.

Hanna Petrykowska — 2008-04-28T17:09:26-00:00

Genome research (24 April 2008)

Silencers and enhancer-blockers (EBs) are cis-acting, negative regulatory elements (NREs) that control interactions between promoters and enhancers. Although relatively uncharacterized in terms of biological mechanisms, these elements are likely to be abundant in the genome. We developed an experimental strategy to identify silencers and EBs using transient transfection assays. A known insulator and EB from the chicken beta-globin locus, cHS4, served as a control element for these assays. We examined forty-seven sequences from a 1.8 Mb region of human chromosome 7 for silencer and EB activities. The majority of functional elements displayed directional and promoter-specific activities. A limited number of sequences acted in a dual manner, as both silencers and EBs. We examined genomic data, epigenetic modifications and sequence motifs within these regions. Strong silencer elements contained a novel CT-rich motif, often in multiple copies. Deletion of the motif from three regions caused a measurable loss of silencing ability in these sequences. Moreover, five duplicate occurrences of this motif were identified in the cHS4 insulator. These motifs provided an explanation for an uncharacterized silencing activity we measured in the insulator element. Overall, we identified 15 novel NREs, which contribute new insights into the prevalence and composition of sequences that negatively regulate gene expression.

Implementing arithmetic and other analytic operations by transcriptional regulation.

SM Cory — 2008-04-28T17:06:57-00:00

PLoS computational biology, Vol. 4, No. 4. (April 2008)

The transcriptional regulatory machinery of a gene can be viewed as a computational device, with transcription factor concentrations as inputs and expression level as the output. This view begs the question: what kinds of computations are possible? We show that different parameterizations of a simple chemical kinetic model of transcriptional regulation are able to approximate all four standard arithmetic operations: addition, subtraction, multiplication, and division, as well as various equality and inequality operations. This contrasts with other studies that emphasize logical or digital notions of computation in biological networks. We analyze the accuracy and precision of these approximations, showing that they depend on different sets of parameters, and are thus independently tunable. We demonstrate that networks of these "arithmetic" genes can be combined to accomplish yet more complicated computations by designing and simulating a network that detects statistically significant elevations in a time-varying signal. We also consider the much more general problem of approximating analytic functions, showing that this can be achieved by allowing multiple transcription factor binding sites on the promoter. These observations are important for the interpretation of naturally occurring networks and imply new possibilities for the design of synthetic networks.