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Origins of chromosomal rearrangement hotspots in the human genome:: evidence from the AZFa deletion hotspots -: art. no. R55

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GENOME BIOLOGY 2004年第8期5卷 1-19页

作者： Hurles, ME Willey, D Matthews, L Hussain, SS Univ Cambridge McDonald Inst Archaeol Res Mol Genet Lab Cambridge CB2 3ER England Wellcome Trust Sanger Inst Cambridge CB10 1SA England

Background: The origins of the recombination hotspots that are a common feature of both allelic and non-allelic homologous recombination in the human genome are poorly understood. We have investigated, by comparative sequencing, the evolution of two hotspots of non-allelic homologous recombination on the Y chromosome that lie within paralogous sequences known to sponsor deletions resulting in male infertility. Results: These recombination hotspots are characterized by signatures of concerted evolution, which indicate that gene conversion between paralogs has been predominant in shaping their recent evolution. By contrast, the paralogous sequences that surround the hotspots exhibit little evidence of gene conversion. A second feature of these rearrangement hotspots is the extreme interspecific sequence divergence (around 2.5%) that places them among the most divergent orthologous sequences between humans and chimpanzees. Conclusions: Several hominid-specific gene conversion events have rendered these hotspots better substrates for chromosomal rearrangements in humans than in chimpanzees or gorillas. Monte Carlo simulations of sequence evolution suggest that extreme sequence divergence is a direct consequence of gene conversion between paralogs. We propose that the coincidence of signatures of concerted evolution and recurrent breakpoints of chromosomal rearrangement (mapped at the sequence level) may enable the identification of putative rearrangement hotspots from analysis of comparative sequences from great apes.

关键词： additional data file Gene Conversion Segmental Duplication Concerted Evolution Phylogenetic Network

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Egr1 regulates the coordinated expression of numerous EGF receptor target genes as identified by ChIP on chip

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GENOME BIOLOGY 2008年第11期9卷 R166-R166页

作者： Arora, Shilpi Wang, Yipeng Jia, Zhenyu Vardar-Sengul, Saynur Munawar, Ayla Doctor, Kutbuddin S. Birrer, Michael McClelland, Michael Adamson, Eileen Mercola, Dan Univ Calif Irvine Dept Pathol & Lab Med Irvine CA 92697 USA Sidney Kimmel Canc Ctr San Diego CA 92121 USA Ege Univ Sch Dent Dept Periodontol TR-35100 Izmir Turkey Burnham Inst Med Res La Jolla CA 92037 USA NCI NIH Cell & Canc Biol Res Bethesda MD 20892 USA

Background: UV irradiation activates the EGF receptor, induces Egr1 expression and promotes apoptosis in a variety of cell types. We examined the hypothesis that Egr1 regulates genes that mediate this process by use of a chip-on-chip protocol in human tumorigenic prostate M12 cells. Results: UV irradiation led to significant binding of 288 gene promoters by Egr1. A major functional subgroup consisted of apoptosis related genes. The largest subgroup of 24 genes;belong to the EGFR-signal transduction pathway. Egr1 promoter binding had a significant impact on gene expression of target genes. Conventional ChIP and qRTPCR were used to validate promoter binding and expression changes. siRNA experiments were used to demonstrate the specific role of Egr1 in gene regulation. UV-stimulation promotes growth arrest and apoptosis of M12 cells and our data clearly show that downstream target of EGFR, namely Egr1, mediates this apoptotic response. Our study also identified numerous previously unknown targets of Egr1. These include FasL, MAX and RRAS2, which may play a role in the apoptotic response/growth arrest. Conclusion: Our results indicate that M12 cells undergo Egr1-dependent apoptotic response upon UV-stimulation and led to the identification of downstream targets of Egr1, which mediate EGFR function.

关键词： Epidermal Growth Factor Receptor Prostate Cancer Cell additional data file Suramin Epidermal Growth Factor Receptor Expression

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An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome -: art. no. R3

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GENOME BIOLOGY 2004年第1期5卷 1-17页

作者： Hild, M Beckmann, B Haas, SA Koch, B Solovyev, V Busold, C Fellenberg, K Boutros, M Vingron, M Sauer, F Hoheisel, JD Paro, R Max Planck Inst Mol Genet D-14195 Berlin Germany Heidelberg Univ ZMBH D-69120 Heidelberg Germany Deutsch Krebsforschungszentrum Div Funct Genome Anal D-69120 Heidelberg Germany Softberry Inc Mt Kisko NY 10549 USA Univ Calif Riverside Dept Biochem Riverside CA 92521 USA

Background: While the genome sequences for a variety of organisms are now available, the precise number of the genes encoded is still a matter of debate. For the human genome several stringent annotation approaches have resulted in the same number of potential genes, but a careful comparison revealed only limited overlap. This indicates that only the combination of different computational prediction methods and experimental evaluation of such in silico data will provide more complete genome annotations. In order to get a more complete gene content of the Drosophila melanogaster genome, we based our new D. melanogaster whole-transcriptome microarray, the Heidelberg FlyArray, on the combination of the Berkeley Drosophila Genome Project (BDGP) annotation and a novel ab initio gene prediction of lower stringency using the Fgenesh software. Results: Here we provide evidence for the transcription of approximately 2,600 additional genes predicted by Fgenesh. Validation of the developmental profiling data by RT-PCR and in situ hybridization indicates a lower limit of 2,000 novel annotations, thus substantially raising the number of genes that make a fly. Conclusions: The successful design and application of this novel Drosophila microarray on the basis of our integrated in silico/wet biology approach confirms our expectation that in silico approaches alone will always tend to be incomplete. The identification of at least 2,000 novel genes highlights the importance of gathering experimental evidence to discover all genes within a genome. Moreover, as such an approach is independent of homology criteria, it will allow the discovery of novel genes unrelated to known protein families or those that have not been strictly conserved between species.

关键词： additional data file Gene Prediction Embryonic Stage additional Exon Berkeley Drosophila Genome Project

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Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships

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GENOME BIOLOGY 2007年第3期8卷 R44-R44页

作者： Dabney, Alan R. Storey, John D. Univ Washington Dept Biostat Seattle WA 98195 USA Univ Washington Dept Genome Sci Seattle WA 98195 USA Texas A&M Univ Dept Stat College Stn TX 77843 USA

In normalizing two-channel expression arrays, the ANOVA approach explicity incorporates the experimental design in its model, and the MA-plot based approach accounts for intensivity-dependent biases. However, both approaches can lead to inacurate normalization in fairly common scenarios. We propose a method called eCADS for normalizing two-channel microarrays that accounts for both experimental design and intensity-dependent biases. Under reasonable experimental designs, eCADS preserves differential expression relationships and requires only a single array per sample pair.

关键词： additional data file Array Function Microarray Quality Control Array Effect Direct Comparison Experiment

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A physical map of the bovine genome

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GENOME BIOLOGY 2007年第8期8卷 R165-R165页

作者： Snelling, Warren M. Chiu, Readman Schein, Jacqueline E. Hobbs, Matthew Abbey, Colette A. Adelson, David L. Aerts, Jan Bennett, Gary L. Bosdet, Ian E. Boussaha, Mekki Brauning, Rudiger Caetano, Alexandre R. Costa, Marcos M. Crawford, Allan M. Dalrymple, Brian P. Eggen, Andre Wind, Annelie Everts-van der Floriot, Sandrine Gautier, Mathieu Gill, Clare A. Green, Ronnie D. Holt, Robert Jann, Oliver Jones, Steven J. M. Kappes, Steven M. Keele, John W. de Jong, Pieter J. Larkin, Denis M. Lewin, Harris A. McEwan, John C. McKay, Stephanie Marra, Marco A. Mathewson, Carrie A. Matukumalli, Lakshmi K. Moore, Stephen S. Murdoch, Brenda Nicholas, Frank W. Osoegawa, Kazutoyo Roy, Alice Salih, Hanni Schibler, Laurent Schnabel, Robert D. Silveri, Licia Skow, Loren C. Smith, Timothy P. L. Sonstegard, Tad S. Taylor, Jeremy F. Tellam, Ross Van Tassell, Curtis P. Williams, John L. Womack, James E. Wye, Natasja H. Yang, George Zhao, Shaying USDA ARS Meat Anim Res Ctr Clay Ctr NE 68933 USA British Columbia Canc Agcy Genome Sci Ctr Vancouver BC V5Z 4E6 Canada Univ Sydney Fac Vet Sci Cooperat Res Ctr Innovat Dairy Prod Sydney NSW 2006 Australia Texas A&M Univ College Stn TX 77843 USA Roslin Inst Roslin EH25 9PS Midlothian Scotland INRA UR339 Lab Genet Biochim & Cytogenet F-78350 Jouy En Josas France AgResearch Mosgiel New Zealand Embrapa Recursos Genet & Biotecnol BR-70770900 Brasilia DF Brazil CSIRO Livestock Ind St Lucia Qld 4067 Australia Univ Illinois Dept Anim Sci Urbana IL 61801 USA USDA ARS Natl Program Staff Beltsville MD 20705 USA Childrens Hosp Oakland Res Inst Oakland CA 94609 USA Univ Illinois Inst Genom Biol Urbana IL 61801 USA Univ Alberta Dept Agr Food & Nutr Sci Edmonton AB T6G 2P5 Canada USDA ARS BARC Bovine Funct Genom Lab Washington DC 20250 USA Genoscope F-91057 Evry France Univ Missouri Div Anim Sci Anim Sci Res Ctr Columbia MO 65211 USA Univ Cattolica Sacro Cuore Ist Zootecn I-29100 Piacenza Italy Inst Genom Res Rockville MD 20850 USA

Background: Cattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-byclone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project. Results: A bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly. Conclusion: Further refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans.

关键词： Quantitative Trait Locus Bacterial Artificial Chromosome additional data file Bacterial Artificial Chromosome Clone Bacterial Artificial Chromosome Library

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The design of transcription-factor binding sites is affected by combinatorial regulation

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GENOME BIOLOGY 2005年第12期6卷 R103-R103页

作者： Bilu, Y Barkai, N Weizmann Inst Sci Dept Mol Genet IL-76100 Rehovot Israel Weizmann Inst Sci Dept Phys Complex Syst IL-76100 Rehovot Israel

Background: Transcription factors regulate gene expression by binding to specific cis-regulatory elements in gene promoters. Although DNA sequences that serve as transcription-factor binding sites have been characterized and associated with the regulation of numerous genes, the principles that govern the design and evolution of such sites are poorly understood. Results: Using the comprehensive mapping of binding-site locations available in Saccharomyces cerevisiae, we examined possible factors that may have an impact on binding-site design. We found that binding sites tend to be shorter and fuzzier when they appear in promoter regions that bind multiple transcription factors. We further found that essential genes bind relatively fewer transcription factors, as do divergent promoters. We provide evidence that novel binding sites tend to appear in specific promoters that are already associated with multiple sites. Conclusion: Two principal models may account for the observed correlations. First, it may be that the interaction between multiple factors compensates for the decreased specificity of each specific binding sequence. In such a scenario, binding-site fuzziness is a consequence of the presence of multiple binding sites. Second, binding sites may tend to appear in promoter regions that are subject to low selective pressure, which also allows for fuzzier motifs. The latter possibility may account for the relatively low number of binding sites found in promoters of essential genes and in divergent promoters.

关键词： Promoter Region Transcription Factor Binding Site additional data file Essential Gene Specific Transcription Factor

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Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans

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GENOME BIOLOGY 2006年第11期7卷 R108-R108页

作者： David, Helga Hofmann, Gerald Oliveira, Ana Paula Jarmer, Hanne Nielsen, Jens Fluxome Sci AS DK-2800 Lyngby Denmark Tech Univ Denmark BioCent DTU Ctr Microbial Biotechnol DK-2800 Lyngby Denmark Tech Univ Denmark BioCent DTU Ctr Biol Sequence Anal DK-2800 Lyngby Denmark

Background: Aspergillus nidulans (the asexual form of Emericella nidulans) is a model organism for aspergilli, which are an important group of filamentous fungi that encompasses human and plant pathogens as well as industrial cell factories. Aspergilli have a highly diversified metabolism and, because of their medical, agricultural and biotechnological importance, it would be valuable to have an understanding of how their metabolism is regulated. We therefore conducted a genome-wide transcription analysis of A. nidulans grown on three different carbon sources (glucose, glycerol, and ethanol) with the objective of identifying global regulatory structures. Furthermore, we reconstructed the complete metabolic network of this organism, which resulted in linking 666 genes to metabolic functions, as well as assigning metabolic roles to 472 genes that were previously uncharacterized. Results: Through combination of the reconstructed metabolic network and the transcription data, we identified subnetwork structures that pointed to coordinated regulation of genes that are involved in many different parts of the metabolism. Thus, for a shift from glucose to ethanol, we identified coordinated regulation of the complete pathway for oxidation of ethanol, as well as upregulation of gluconeogenesis and downregulation of glycolysis and the pentose phosphate pathway. Furthermore, on change in carbon source from glucose to ethanol, the cells shift from using the pentose phosphate pathway as the major source of NADPH (nicotinamide adenine dinucleotide phosphatase, reduced form) for biosynthesis to use of the malic enzyme. Conclusion: Our analysis indicates that some of the genes are regulated by common transcription factors, making it possible to establish new putative links between known transcription factors and genes through clustering.

关键词： Carbon Source Gene Ontology Trehalose Metabolic Network additional data file

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Transcriptome analysis reveals new insight into appressorium formation and function in the rice blast fungus Magnaporthe oryzae

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GENOME BIOLOGY 2008年第5期9卷 R85-R85页

作者： Oh, Yeonyee Donofrio, Nicole Pan, Huaqin Coughlan, Sean Brown, Douglas E. Meng, Shaowu Mitchell, Thomas Dean, Ralph A. N Carolina State Univ Ctr Integrated Fungal Res Raleigh NC 27695 USA Agilent Technol Little Falls DE 19808 USA

Background: Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processes regulating appressorium formation are incompletely understood. Results: We analyzed genome-wide gene expression changes during spore germination and appressorium formation on a hydrophobic surface compared to induction by cAMP. During spore germination, 2,154 (approximately 21%) genes showed differential expression, with the majority being up-regulated. During appressorium formation, 357 genes were differentially expressed in response to both stimuli. These genes, which we refer to as appressorium consensus genes, were functionally grouped into Gene Ontology categories. Overall, we found a significant decrease in expression of genes involved in protein synthesis. Conversely, expression of genes associated with protein and amino acid degradation, lipid metabolism, secondary metabolism and cellular transportation exhibited a dramatic increase. We functionally characterized several differentially regulated genes, including a subtilisin protease (SPM1) and a NAD specific glutamate dehydrogenase (Mgd1), by targeted gene disruption. These studies revealed hitherto unknown findings that protein degradation and amino acid metabolism are essential for appressorium formation and subsequent infection. Conclusion: We present the first comprehensive genome-wide transcript profile study and functional analysis of infection structure formation by a fungal plant pathogen. Our data provide novel insight into the underlying molecular mechanisms that will directly benefit efforts to identify fungal pathogenicity factors and aid the development of new disease management strategies.

关键词： Gene Ontology additional data file Spore Germination Appressorium Formation Germ Tube Elongation

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Systematic quantification of gene interactions by phenotypic array analysis

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GENOME BIOLOGY 2004年第7期5卷 1-18页

作者： Hartman, JL Tippery, NP Fred Hutchinson Canc Res Ctr Seattle WA 98109 USA

A phenotypic array method, developed for quantifying cell growth, was applied to the haploid and homozygous diploid yeast deletion strain sets. A growth index was developed to screen for nonadditive interacting effects between gene deletion and induced perturbations. From a genome screen for hydroxyurea (HU) chemical-genetic interactions, 298 haploid deletion strains were selected for further analysis. The strength of interactions was quantified using a wide range of HU concentrations affecting reference strain growth. The selectivity of interaction was determined by comparison with drugs targeting other cellular processes. Bio-modules were defined as gene clusters with shared strength and selectivity of interaction profiles. The functions and connectivity of modules involved in processes such as DNA repair, protein secretion and metabolic control were inferred from their respective gene composition. The work provides an example of, and a general experimental framework for, quantitative analysis of gene interaction networks that buffer cell growth.

关键词： additional data file TBHP Growth Index Deletion Strain Interaction Index

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At-TAX:: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana

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GENOME BIOLOGY 2008年第7期9卷 R112-R112页

作者： Laubinger, Sascha Zeller, Georg Henz, Stefan R. Sachsenberg, Timo Widmer, Christian K. Naouar, Naira Vuylsteke, Marnik Schoelkopf, Bernhard Raetsch, Gunnar Weigel, Detlef Max Planck Inst Dev Biol Dept Mol Biol D-72076 Tubingen Germany Max Planck Gesell Friedrich Miescher Lab D-72076 Tubingen Germany Univ Ghent VIB Dept Plant Syst Biol B-9052 Ghent Belgium Univ Ghent Dept Mol Genet B-9052 Ghent Belgium Max Planck Inst Biol Cybernet Dept Empir Inference D-72076 Tubingen Germany

Gene expression maps for model organisms, including Arabidopsis thaliana, have typically been created using gene-centric expression arrays. Here, we describe a comprehensive expression atlas, Arabidopsis thaliana Tiling Array Express (At-TAX), which is based on whole-genome tiling arrays. We demonstrate that tiling arrays are accurate tools for gene expression analysis and identified more than 1,000 unannotated transcribed regions. Visualizations of gene expression estimates, transcribed regions, and tiling probe measurements are accessible online at the At-TAX homepage.

关键词： additional data file Annotate Gene Locked Nucleic Acid Tiling Array Gene Expression Estimate

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