201
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Toky V, Sharma S, Arora BB, Chhibber S. Establishment of a sepsis model following implantation ofKlebsiella pneumoniae-infected fibrin clot into the peritoneal cavity of mice. Folia Microbiol (Praha) 2003; 48:665-9. [PMID: 14976726 DOI: 10.1007/bf02993476] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Successful establishment of sepsis by entrapping a dose of 150 colony forming units of Klebsiella pneumoniae in a fibrin clot following implantation into the peritoneal cavity of mice is reported. The dose in the fibrin clot gave 50% mortality in mice, spread over a period of one week. All the infected mice showed positive blood culture up to 6 d post-infection; histopathology revealed inflammatory changes in both liver and spleen. Introduction of K. pneumoniae into experimental mice without entrapment in fibrin clot caused no mortality and blood culture remained positive only up to 2 d; histopathology of liver and spleen throughout the period of study showed relatively mild inflammatory changes, which almost cleared during 14 d post-infection. The use of the fibrin-clot model may thus be considered to be useful in studying both the initial and the persisting stage of infection in the peritoneum, whence a slow release of bacteria into the blood takes place which finally leads to sepsis and septicemia.
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Affiliation(s)
- V Toky
- Department of Microbiology, Panjab University, Chandigarh, India
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202
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Hennig S, Groth D, Lehrach H. Automated Gene Ontology annotation for anonymous sequence data. Nucleic Acids Res 2003; 31:3712-5. [PMID: 12824400 PMCID: PMC168988 DOI: 10.1093/nar/gkg582] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Gene Ontology (GO) is the most widely accepted attempt to construct a unified and structured vocabulary for the description of genes and their products in any organism. Annotation by GO terms is performed in most of the current genome projects, which besides generality has the advantage of being very convenient for computer based classification methods. However, direct use of GO in small sequencing projects is not easy, especially for species not commonly represented in public databases. We present a software package (GOblet), which performs annotation based on GO terms for anonymous cDNA or protein sequences. It uses the species independent GO structure and vocabulary together with a series of protein databases collected from various sites, to perform a detailed GO annotation by sequence similarity searches. The sensitivity and the reference protein sets can be selected by the user. GOblet runs automatically and is available as a public service on our web server. The paper also addresses the reliability of automated GO annotations by using a reference set of more than 6000 human proteins. The GOblet server is accessible at http://goblet.molgen.mpg.de.
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Affiliation(s)
- Steffen Hennig
- Max-Planck Institute for Molecular Genetics, Ihnestrasse 73, D-14195 Berlin, Germany.
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203
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Abstract
Large-scale genome sequencing is providing a comprehensive view of the complex evolutionary forces that have shaped the structure of eukaryotic chromosomes. Comparative sequence analyses reveal patterns of apparently random rearrangement interspersed with regions of extraordinarily rapid, localized genome evolution. Numerous subtle rearrangements near centromeres, telomeres, duplications, and interspersed repeats suggest hotspots for eukaryotic chromosome evolution. This localized chromosomal instability may play a role in rapidly evolving lineage-specific gene families and in fostering large-scale changes in gene order. Computational algorithms that take into account these dynamic forces along with traditional models of chromosomal rearrangement show promise for reconstructing the natural history of eukaryotic chromosomes.
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Affiliation(s)
- Evan E Eichler
- Department of Genetics, Center for Human Genetics and Center for Computational Genomics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA.
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204
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Affiliation(s)
- Stefan H E Kaufmann
- Department of Immunology, Max-Planck-Institute for Infection Biology, Schumannstrasse 21-22, 10117 Berlin, Germany.
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205
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Silar P, Barreau C, Debuchy R, Kicka S, Turcq B, Sainsard-Chanet A, Sellem CH, Billault A, Cattolico L, Duprat S, Weissenbach J. Characterization of the genomic organization of the region bordering the centromere of chromosome V of Podospora anserina by direct sequencing. Fungal Genet Biol 2003; 39:250-63. [PMID: 12892638 DOI: 10.1016/s1087-1845(03)00025-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A Podospora anserina BAC library of 4800 clones has been constructed in the vector pBHYG allowing direct selection in fungi. Screening of the BAC collection for centromeric sequences of chromosome V allowed the recovery of clones localized on either sides of the centromere, but no BAC clone was found to contain the centromere. Seven BAC clones containing 322,195 and 156,244bp from either sides of the centromeric region were sequenced and annotated. One 5S rRNA gene, 5 tRNA genes, and 163 putative coding sequences (CDS) were identified. Among these, only six CDS seem specific to P. anserina. The gene density in the centromeric region is approximately one gene every 2.8kb. Extrapolation of this gene density to the whole genome of P. anserina suggests that the genome contains about 11,000 genes. Synteny analyses between P. anserina and Neurospora crassa show that co-linearity extends at the most to a few genes, suggesting rapid genome rearrangements between these two species.
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MESH Headings
- Amino Acid Sequence
- Centromere/chemistry
- Centromere/genetics
- Chromosomes, Artificial, Bacterial
- Chromosomes, Fungal/genetics
- Chromosomes, Fungal/ultrastructure
- DNA, Intergenic/analysis
- Gene Rearrangement
- Genes, Fungal
- Genes, rRNA
- Genome, Fungal
- Genomic Library
- Introns
- Molecular Sequence Data
- Physical Chromosome Mapping
- RNA, Transfer/genetics
- Sequence Analysis, DNA
- Sequence Homology
- Sordariales/genetics
- Synteny
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Affiliation(s)
- Philippe Silar
- Institut de Génétique et Microbiologie, UMR CNRS 8621, Bât. 400, Université de Paris Sud, 91405 Orsay Cedex, France.
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206
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Abstract
The compilation of a dense gene map and eventually a whole genome sequence (WGS) of the domestic cat holds considerable value for human genome annotation, for veterinary medicine, and for insight into the evolution of genome organization among mammals. Human association and veterinary studies of the cat, its domestic breeds, and its charismatic wild relatives of the family Felidae have rendered the species a powerful model for human hereditary diseases, for infectious disease agents, for adaptive evolutionary divergence, for conservation genetics, and for forensic applications. Here we review the advantages, rationale, and present strategy of a feline genome project, and we describe the disease models, comparative genomics, and biological applications posed by the full resolution of the cat's genome.
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Affiliation(s)
- Stephen J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, Maryland 21702-1201, USA.
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207
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Zhu L, Swergold GD, Seldin MF. Examination of sequence homology between human chromosome 20 and the mouse genome: intense conservation of many genomic elements. Hum Genet 2003; 113:60-70. [PMID: 12644935 DOI: 10.1007/s00439-003-0920-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2002] [Accepted: 01/14/2003] [Indexed: 10/25/2022]
Abstract
The conservation of genomic organization of mammalian species has been of interest for its usefulness in characterizing the genetics of traits and diseases and as one tool for examining evolution. The recent rough draft sequencing of the mouse and human genomes provides the opportunity for more detailed analyses. The current study examines the extent of homology between human chromosome 20 and the mouse genome by comparing putative coding and non-coding sequence to provide insight into organizational and sequence similarities between the species. The relative position of each of 460 putative coding orthologues was the same in both species, except for a single genomic segment rearrangement. The similarity extended to exon/intron structure, the size of introns, as well as strong evidence for the conservation of position of ancient LINE-1, LINE-2 and LTR repetitive sequence and the subtelomeric region of the long arm of human chromosome 20 and that of mouse chromosome 2. There was also evidence for conservation of a limited amount of non-coding single-copy sequence. Together these data provide additional insight into the extent of conservation of mammalian genomic organization and sequence.
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Affiliation(s)
- Lingxiang Zhu
- Rowe Program in Genetics, Department of Biological Chemistry and Department of Medicine, University of California at Davis, Davis, CA 95616, USA
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208
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Jaillon O, Dossat C, Eckenberg R, Eiglmeier K, Segurens B, Aury JM, Roth CW, Scarpelli C, Brey PT, Weissenbach J, Wincker P. Assessing the Drosophila melanogaster and Anopheles gambiae genome annotations using genome-wide sequence comparisons. Genome Res 2003; 13:1595-9. [PMID: 12840038 PMCID: PMC403732 DOI: 10.1101/gr.922503] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We performed genome-wide sequence comparisons at the protein coding level between the genome sequences of Drosophila melanogaster and Anopheles gambiae. Such comparisons detect evolutionarily conserved regions (ecores) that can be used for a qualitative and quantitative evaluation of the available annotations of both genomes. They also provide novel candidate features for annotation. The percentage of ecores mapping outside annotations in the A. gambiae genome is about fourfold higher than in D. melanogaster. The A. gambiae genome assembly also contains a high proportion of duplicated ecores, possibly resulting from artefactual sequence duplications in the genome assembly. The occurrence of 4063 ecores in the D. melanogaster genome outside annotations suggests that some genes are not yet or only partially annotated. The present work illustrates the power of comparative genomics approaches towards an exhaustive and accurate establishment of gene models and gene catalogues in insect genomes.
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Affiliation(s)
- Olivier Jaillon
- Genoscope/Centre National de Séquençage and CNRS UMR 8030, 91057 Evry Cedex, France
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209
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Cawley S, Pachter L, Alexandersson M. SLAM web server for comparative gene finding and alignment. Nucleic Acids Res 2003; 31:3507-9. [PMID: 12824355 PMCID: PMC168989 DOI: 10.1093/nar/gkg583] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2003] [Revised: 04/03/2003] [Accepted: 04/03/2003] [Indexed: 11/14/2022] Open
Abstract
SLAM is a program that simultaneously aligns and annotates pairs of homologous sequences. The SLAM web server integrates SLAM with repeat masking tools and the AVID alignment program to allow for rapid alignment and gene prediction in user submitted sequences. Along with annotations and alignments for the submitted sequences, users obtain a list of predicted conserved non-coding sequences (and their associated alignments). The web site also links to whole genome annotations of the human, mouse and rat genomes produced with the SLAM program. The server can be accessed at http://bio.math.berkeley.edu/slam.
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Affiliation(s)
- Simon Cawley
- Affymetrix Inc., 6550 Vallejo St, Suite 100, Emeryville, CA 94608, USA.
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210
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Bambrick LL, Yarowsky PJ, Krueger BK. Altered astrocyte calcium homeostasis and proliferation in theTs65Dn mouse, a model of Down syndrome. J Neurosci Res 2003; 73:89-94. [PMID: 12815712 DOI: 10.1002/jnr.10630] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Genes from the Down syndrome (DS) critical region of human chromosome 21, which contribute to the pathology of DS, are also found on mouse chromosome 16. Several animal models of DS with triplication of genes from the DS critical region have been generated, including mouse trisomy 16 (Ts16) and a partial trisomic mouse, Ts65Dn. Using computer-assisted imaging of fura-2 fluorescence, we found an elevation of intracellular cytoplasmic calcium in cortical astrocytes from neonatal Ts65Dn mouse brain, similar to that observed previously in embryonic Ts16 astrocytes. Furthermore, astrocytes from both Ts65Dn and Ts16 cortex fail to respond to the anti-proliferative actions of glutamate. These results suggest that defective regulation of cell proliferation and cellular calcium can result from triplication of DS critical region genes.
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Affiliation(s)
- Linda L Bambrick
- Department of Anesthesiology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
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211
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Pevzner P, Tesler G. Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proc Natl Acad Sci U S A 2003; 100:7672-7. [PMID: 12810957 PMCID: PMC164646 DOI: 10.1073/pnas.1330369100] [Citation(s) in RCA: 238] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2003] [Accepted: 05/05/2003] [Indexed: 11/18/2022] Open
Abstract
The human and mouse genomic sequences provide evidence for a larger number of rearrangements than previously thought and reveal extensive reuse of breakpoints from the same short fragile regions. Breakpoint clustering in regions implicated in cancer and infertility have been reported in previous studies; we report here on breakpoint clustering in chromosome evolution. This clustering reveals limitations of the widely accepted random breakage theory that has remained unchallenged since the mid-1980s. The genome rearrangement analysis of the human and mouse genomes implies the existence of a large number of very short "hidden" synteny blocks that were invisible in the comparative mapping data and ignored in the random breakage model. These blocks are defined by closely located breakpoints and are often hard to detect. Our results suggest a model of chromosome evolution that postulates that mammalian genomes are mosaics of fragile regions with high propensity for rearrangements and solid regions with low propensity for rearrangements.
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Affiliation(s)
- Pavel Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0114, USA
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212
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He QM, Wei YQ, Tian L, Zhao X, Su JM, Yang L, Lu Y, Kan B, Lou YY, Huang MJ, Xiao F, Liu JY, Hu B, Luo F, Jiang Y, Wen YJ, Deng HX, Li J, Niu T, Yang JL. Inhibition of tumor growth with a vaccine based on xenogeneic homologous fibroblast growth factor receptor-1 in mice. J Biol Chem 2003; 278:21831-6. [PMID: 12651849 DOI: 10.1074/jbc.m300880200] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Angiogenesis is important for the growth of solid tumors. The breaking of the immune tolerance against the molecule associated with angiogenesis should be a useful approach for cancer therapy. However, the immunity to self-molecules is difficult to elicit by a vaccine based on autologous or syngeneic molecules due to immune tolerance. Basic fibroblast growth factor (bFGF) is a specific and potent angiogenic factor implicated in tumor growth. The biological activity of bFGF is mediated through interaction with its high-affinity receptor, fibroblast growth factor receptor-1 (FGFR-1). In this study, we selected Xenopus FGFR-1 as a model antigen by the breaking of immune tolerance to explore the feasibility of cancer therapy in murine tumor models. We show here that vaccination with Xenopus FGFR-1 (pxFR1) is effective at antitumor immunity in three murine models. FGFR-1-specific autoantibodies in sera of pxFR1-immunized mice could be found in Western blotting analysis. The purified immunoglobulins were effective at the inhibition of endothelial cell proliferation in vitro and at the antitumor activity in vivo. The antitumor activity and production of FGFR-1-specific autoantibodies could be abrogated by depletion of CD4+ T lymphocytes. Histological examination revealed that the autoantibody was deposited on the endothelial cells within tumor tissues from pxFR1-immunized mice, and intratumoral angiogenesis was significantly suppressed. Furthermore, the inhibition of angiogenesis could also be found in alginate-encapsulate tumor cell assay. These observations may provide a new vaccine strategy for cancer therapy through the induction of autoimmunity against FGFR-1 associated with angiogenesis in a cross-reaction.
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MESH Headings
- Alginates/chemistry
- Animals
- Antineoplastic Agents/pharmacology
- Blotting, Western
- CD4-Positive T-Lymphocytes/metabolism
- Cancer Vaccines
- Cell Division
- Cloning, Molecular
- DNA, Complementary/metabolism
- Dose-Response Relationship, Drug
- Endothelium, Vascular/chemistry
- Endothelium, Vascular/immunology
- Enzyme-Linked Immunosorbent Assay
- Fibroblast Growth Factor 2/metabolism
- Immunoglobulins/chemistry
- Mice
- Neoplasm Transplantation
- Neoplasms/drug therapy
- Neoplasms/prevention & control
- Neovascularization, Pathologic
- Plasmids/metabolism
- Receptor Protein-Tyrosine Kinases/metabolism
- Receptor, Fibroblast Growth Factor, Type 1
- Receptors, Fibroblast Growth Factor/metabolism
- Time Factors
- Transfection
- Tumor Cells, Cultured
- Xenopus
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Affiliation(s)
- Qiu-ming He
- Key Laboratory of Biotherapy of Human Diseases, Ministry of Education, People's Republic of China and Cancer Center, West China Hospital, Guo Xue Xiang No. 37, Sichuan 610041, People's Republic of China
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213
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Zhang L, Pavlovic V, Cantor CR, Kasif S. Human-mouse gene identification by comparative evidence integration and evolutionary analysis. Genome Res 2003; 13:1190-202. [PMID: 12743024 PMCID: PMC403647 DOI: 10.1101/gr.703903] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2002] [Accepted: 02/03/2003] [Indexed: 11/24/2022]
Abstract
The identification of genes in the human genome remains a challenge, as the actual predictions appear to disagree tremendously and vary dramatically on the basis of the specific gene-finding methodology used. Because the pattern of conservation in coding regions is expected to be different from intronic or intergenic regions, a comparative computational analysis can lead, in principle, to an improved computational identification of genes in the human genome by using a reference, such as mouse genome. However, this comparative methodology critically depends on three important factors: (1) the selection of the most appropriate reference genome. In particular, it is not clear whether the mouse is at the correct evolutionary distance from the human to provide sufficiently distinctive conservation levels in different genomic regions, (2) the selection of comparative features that provide the most benefit to gene recognition, and (3) the selection of evidence integration architecture that effectively interprets the comparative features. We address the first question by a novel evolutionary analysis that allows us to explicitly correlate the performance of the gene recognition system with the evolutionary distance (time) between the two genomes. Our simulation results indicate that there is a wide range of reference genomes at different evolutionary time points that appear to deliver reasonable comparative prediction of human genes. In particular, the evolutionary time between human and mouse generally falls in the region of good performance; however, better accuracy might be achieved with a reference genome further than mouse. To address the second question, we propose several natural comparative measures of conservation for identifying exons and exon boundaries. Finally, we experiment with Bayesian networks for the integration of comparative and compositional evidence.
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Affiliation(s)
- Lingang Zhang
- Center for Advanced Biotechnology, Boston University, Boston, Massachusetts 02215, USA
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214
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Kawasawa Y, McKenzie LM, Hill DP, Bono H, Yanagisawa M. G protein-coupled receptor genes in the FANTOM2 database. Genome Res 2003; 13:1466-77. [PMID: 12819145 PMCID: PMC403690 DOI: 10.1101/gr.1087603] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
G protein-coupled receptors (GPCRs) comprise the largest family of receptor proteins in mammals and play important roles in many physiological and pathological processes. Gene expression of GPCRs is temporally and spatially regulated, and many splicing variants are also described. In many instances, different expression profiles of GPCR gene are accountable for the changes of its biological function. Therefore, it is intriguing to assess the complexity of the transcriptome of GPCRs in various mammalian organs. In this study, we took advantage of the FANTOM2 (Functional Annotation Meeting of Mouse cDNA 2) project, which aimed to collect full-length cDNAs inclusively from mouse tissues, and found 410 candidate GPCR cDNAs. Clustering of these clones into transcriptional units (TUs) reduced this number to 213. Out of these, 165 genes were represented within the known 308 GPCRs in the Mouse Genome Informatics (MGI) resource. The remaining 48 genes were new to mouse, and 14 of them had no clear mammalian ortholog. To dissect the detailed characteristics of each transcript, tissue distribution pattern and alternative splicing were also ascertained. We found many splicing variants of GPCRs that may have a relevance to disease occurrence. In addition, the difficulty in cloning tissue-specific and infrequently transcribed GPCRs is discussed further.
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MESH Headings
- Alternative Splicing/genetics
- Animals
- DNA, Complementary/genetics
- Databases, Genetic/statistics & numerical data
- GTP-Binding Proteins/classification
- GTP-Binding Proteins/genetics
- Humans
- Membrane Proteins/classification
- Membrane Proteins/genetics
- Mice
- Nerve Tissue Proteins
- Organ Specificity/genetics
- Proteome/genetics
- Receptor, Anaphylatoxin C5a
- Receptors, Cell Surface/classification
- Receptors, Cell Surface/genetics
- Receptors, Chemokine/classification
- Receptors, Chemokine/genetics
- Receptors, Cytokine/classification
- Receptors, Cytokine/genetics
- Receptors, G-Protein-Coupled
- Receptors, Galanin
- Receptors, Lysophospholipid
- Receptors, Neuropeptide/classification
- Receptors, Neuropeptide/genetics
- Receptors, Odorant/classification
- Receptors, Odorant/genetics
- Receptors, Purinergic/classification
- Receptors, Purinergic/genetics
- Receptors, Purinergic P2/genetics
- Signal Transduction/genetics
- Transcription, Genetic/genetics
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Affiliation(s)
- Yuka Kawasawa
- Howard Hughes Medical Institute, Department of Molecular Genetics, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390-9050, USA.
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215
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Wortman JR, Haas BJ, Hannick LI, Smith RK, Maiti R, Ronning CM, Chan AP, Yu C, Ayele M, Whitelaw CA, White OR, Town CD. Annotation of the Arabidopsis genome. PLANT PHYSIOLOGY 2003; 132:461-8. [PMID: 12805579 PMCID: PMC166989 DOI: 10.1104/pp.103.022251] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2003] [Revised: 03/07/2003] [Accepted: 03/18/2003] [Indexed: 05/18/2023]
Affiliation(s)
- Jennifer R Wortman
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
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216
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Kanapin A, Batalov S, Davis MJ, Gough J, Grimmond S, Kawaji H, Magrane M, Matsuda H, Schönbach C, Teasdale RD, Yuan Z. Mouse proteome analysis. Genome Res 2003; 13:1335-44. [PMID: 12819131 PMCID: PMC403658 DOI: 10.1101/gr.978703] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2002] [Accepted: 03/05/2003] [Indexed: 11/25/2022]
Abstract
A general overview of the protein sequence set for the mouse transcriptome produced during the FANTOM2 sequencing project is presented here. We applied different algorithms to characterize protein sequences derived from a nonredundant representative protein set (RPS) and a variant protein set (VPS) of the mouse transcriptome. The functional characterization and assignment of Gene Ontology terms was done by analysis of the proteome using InterPro. The Superfamily database analyses gave a detailed structural classification according to SCOP and provide additional evidence for the functional characterization of the proteome data. The MDS database analysis revealed new domains which are not presented in existing protein domain databases. Thus the transcriptome gives us a unique source of data for the detection of new functional groups. The data obtained for the RPS and VPS sets facilitated the comparison of different patterns of protein expression. A comparison of other existing mouse and human protein sequence sets (e.g., the International Protein Index) demonstrates the common patterns in mammalian proteomes. The analysis of the membrane organization within the transcriptome of multiple eukaryotes provides valuable statistics about the distribution of secretory and transmembrane proteins
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Affiliation(s)
- Alexander Kanapin
- EMBL Outstation-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.
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217
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Sander TL, Stringer KF, Maki JL, Szauter P, Stone JR, Collins T. The SCAN domain defines a large family of zinc finger transcription factors. Gene 2003; 310:29-38. [PMID: 12801630 DOI: 10.1016/s0378-1119(03)00509-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The SCAN domain is a highly conserved dimerization motif that is vertebrate-specific and found near the N-terminus of C(2)H(2) zinc finger proteins (SCAN-ZFP). Although the function of most SCAN-ZFPs is unknown, some have been implicated in the transcriptional regulation of growth factors, genes involved in lipid metabolism, as well as other genes involved in cell survival and differentiation. Here we utilize a bioinformatics approach to define the structures and gene locations of the 71 members of the human SCAN domain family, as well as to assess the conserved syntenic segments in the mouse genome and identify potential orthologs. The genes encoding SCAN domains are clustered, often in tandem arrays, in both the human and mouse genomes and are capable of generating isoforms that may affect the function of family members. Twenty-three members of the mouse SCAN family appear to be orthologous with human family members, and human-specific cluster expansions were observed. Remarkably, the SCAN domains in lower vertebrates are not associated with C(2)H(2) zinc finger genes, but are contained in large retrovirus-like polyproteins. Collectively, these studies define a large family of vertebrate-specific transcriptional regulators that may have rapidly expanded during recent evolution.
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Affiliation(s)
- Tara L Sander
- Department of Pathology, Children's Hospital Boston, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
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218
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Thanaraj TA, Clark F, Muilu J. Conservation of human alternative splice events in mouse. Nucleic Acids Res 2003; 31:2544-52. [PMID: 12736303 PMCID: PMC156037 DOI: 10.1093/nar/gkg355] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Human and mouse genomes share similar long-range sequence organization, and have most of their genes being homologous. As alternative splicing is a frequent and important aspect of gene regulation, it is of interest to assess the level of conservation of alternative splicing. We examined mouse transcript data sets (EST and mRNA) for the presence of transcripts that both make spliced-alignment with the draft mouse genome sequence and demonstrate conservation of human transcript-confirmed alternative and constitutive splice junctions. This revealed 15% of alternative and 67% of constitutive splice junctions as conserved; however, these numbers are patently dependent on the extent of transcript coverage. Transcript coverage of conserved splice patterns is found to correlate well between human and mouse. A model, which extrapolates from observed levels of conservation at increasing levels of transcript support, estimates overall conservation of 61% of alternative and 74% of constitutive splice junctions, albeit with broad confidence intervals. Observed numbers of conserved alternative splicing events agreed with those expected on the basis of the model. Thus, it is apparent that many, and probably most, alternative splicing events are conserved between human and mouse. This, combined with the preservation of alternative frame stop codons in conserved frame breaking events, indicates a high level of commonality in patterns of gene expression between these two species.
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Affiliation(s)
- T A Thanaraj
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.
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219
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Scherer SW, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K, Herbrick JA, Carson AR, Parker-Katiraee L, Skaug J, Khaja R, Zhang J, Hudek AK, Li M, Haddad M, Duggan GE, Fernandez BA, Kanematsu E, Gentles S, Christopoulos CC, Choufani S, Kwasnicka D, Zheng XH, Lai Z, Nusskern D, Zhang Q, Gu Z, Lu F, Zeesman S, Nowaczyk MJ, Teshima I, Chitayat D, Shuman C, Weksberg R, Zackai EH, Grebe TA, Cox SR, Kirkpatrick SJ, Rahman N, Friedman JM, Heng HHQ, Pelicci PG, Lo-Coco F, Belloni E, Shaffer LG, Pober B, Morton CC, Gusella JF, Bruns GAP, Korf BR, Quade BJ, Ligon AH, Ferguson H, Higgins AW, Leach NT, Herrick SR, Lemyre E, Farra CG, Kim HG, Summers AM, Gripp KW, Roberts W, Szatmari P, Winsor EJT, Grzeschik KH, Teebi A, Minassian BA, Kere J, Armengol L, Pujana MA, Estivill X, Wilson MD, Koop BF, Tosi S, Moore GE, Boright AP, Zlotorynski E, Kerem B, Kroisel PM, Petek E, Oscier DG, Mould SJ, Döhner H, Döhner K, Rommens JM, Vincent JB, Venter JC, Li PW, Mural RJ, Adams MD, Tsui LC. Human chromosome 7: DNA sequence and biology. Science 2003; 300:767-72. [PMID: 12690205 PMCID: PMC2882961 DOI: 10.1126/science.1083423] [Citation(s) in RCA: 149] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. This approach enabled the discovery of candidate genes for developmental diseases including autism.
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Affiliation(s)
- Stephen W. Scherer
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8, Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 1A8,To whom correspondence should be addressed.
| | - Joseph Cheung
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Jeffrey R. MacDonald
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Lucy R. Osborne
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
| | - Kazuhiko Nakabayashi
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Jo-Anne Herbrick
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Andrew R. Carson
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Layla Parker-Katiraee
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8, Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
| | - Jennifer Skaug
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Razi Khaja
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Junjun Zhang
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Alexander K. Hudek
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Martin Li
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - May Haddad
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Gavin E. Duggan
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Bridget A. Fernandez
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada, A1B 3V6
| | - Emiko Kanematsu
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Simone Gentles
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | | | - Sanaa Choufani
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Dorota Kwasnicka
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | | | | | | | - Qing Zhang
- Celera Genomics, Rockville, MD 20850, USA
| | - Zhiping Gu
- Celera Genomics, Rockville, MD 20850, USA
| | - Fu Lu
- Celera Genomics, Rockville, MD 20850, USA
| | - Susan Zeesman
- Hamilton Health Sciences Centre and McMaster University, Hamilton, Ontario, Canada, L8N 3Z5
| | - Malgorzata J. Nowaczyk
- Hamilton Health Sciences Centre and McMaster University, Hamilton, Ontario, Canada, L8N 3Z5
| | - Ikuko Teshima
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada, M5G 1X8
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada, M5G 1X8
| | - Cheryl Shuman
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada, M5G 1X8
| | - Rosanna Weksberg
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada, M5G 1X8
| | - Elaine H. Zackai
- Division of Human Genetics and Molecular Biology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104–4301, USA
| | | | - Sarah R. Cox
- University of Phoenix Genetics Program, Phoenix, AZ 85016, USA
| | - Susan J. Kirkpatrick
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nazneen Rahman
- Section of Cancer Genetics, Institute of Cancer Research, Sutton, Surrey, SM2 5NG, UK
| | - Jan M. Friedman
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada, V6H 3N1
| | - Henry H. Q. Heng
- Wayne State University School of Medicine, Detroit, MI 48202, USA
| | - Pier Giuseppe Pelicci
- European Institute of Oncology, Department of Experimental Oncology, 20141 Milan, Italy, Firc Institute for Molecular Oncology, Cancer Genetics Unit, 20134 Milan, Italy
| | - Francesco Lo-Coco
- Universita di Roma Tor Vergata, Dipartimento di Biopatologia e Diagnostica per Immagini, 00133 Rome, Italy
| | - Elena Belloni
- European Institute of Oncology, Department of Experimental Oncology, 20141 Milan, Italy, Firc Institute for Molecular Oncology, Cancer Genetics Unit, 20134 Milan, Italy
| | - Lisa G. Shaffer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Barbara Pober
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520–8005, USA
| | - Cynthia C. Morton
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA, Harvard Partners Center for Genetics and Genomics, Harvard Medical School, Boston, MA 02115, USA
| | - James F. Gusella
- Molecular Neurogenetics Laboratory, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Gail A. P. Bruns
- Department of Pediatrics, The Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bruce R. Korf
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA, Harvard Partners Center for Genetics and Genomics, Harvard Medical School, Boston, MA 02115, USA
| | - Bradley J. Quade
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Azra H. Ligon
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Heather Ferguson
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anne W. Higgins
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Natalia T. Leach
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Steven R. Herrick
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Emmanuelle Lemyre
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Chantal G. Farra
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Hyung-Goo Kim
- Molecular Neurogenetics Laboratory, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Anne M. Summers
- Department of Genetics, North York General Hospital, Toronto, Ontario, Canada, M2K 1E1
| | - Karen W. Gripp
- Division of Medical Genetics, A. I. duPont Hospital for Children, Wilmington, DE 19899, USA
| | - Wendy Roberts
- The Child Development Centre, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Peter Szatmari
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada, L8N 3Z5
| | - Elizabeth J. T. Winsor
- Prenatal Diagnosis Program and Department of Laboratory Medicine and Pathobiology, University Health Network, The University of Toronto, Toronto, Ontario, Canada, M5G 1X5
| | - Karl-Heinz Grzeschik
- Medizinisches Zentrum für Humangenetik der Universität Marburg, D35037 Marburg, Germany
| | - Ahmed Teebi
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada, M5G 1X8
| | - Berge A. Minassian
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8, Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8
| | - Juha Kere
- Department of Biosciences, Karolinska Institute, at Novum and Clinical Research Centre, Huddinge University Hospital, S-141 57 Stockholm, Sweden
| | - Lluis Armengol
- Program in Genes and Disease, Centre for Genomic Regulation, 08003 Barcelona, Catalonia, Spain
| | - Miguel Angel Pujana
- Program in Genes and Disease, Centre for Genomic Regulation, 08003 Barcelona, Catalonia, Spain
| | - Xavier Estivill
- Program in Genes and Disease, Centre for Genomic Regulation, 08003 Barcelona, Catalonia, Spain
| | - Michael D. Wilson
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada, V8W 3N5
| | - Ben F. Koop
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada, V8W 3N5
| | - Sabrina Tosi
- MRC Molecular Haematology Unit, Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Gudrun E. Moore
- Department of Fetal and Maternal Medicine, Institute of Reproductive and Developmental Biology, Imperial College, Faculty of Medicine, Hammersmith Campus, London W12 0NN, UK
| | - Andrew P. Boright
- Division of Endocrinology, Department of Medicine, University Health Network, University of Toronto, Toronto, Ontario, Canada, M5G 2C4
| | - Eitan Zlotorynski
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, 91904 Israel
| | - Batsheva Kerem
- Department of Genetics, The Life Sciences Institute, The Hebrew University, Jerusalem, 91904 Israel
| | - Peter M. Kroisel
- Institute of Medical Biology and Human Genetics, Karl-Franzens University of Graz, A-8010 Graz, Austria
| | - Erwin Petek
- Institute of Medical Biology and Human Genetics, Karl-Franzens University of Graz, A-8010 Graz, Austria
| | - David G. Oscier
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, BH7 7DW UK
| | - Sarah J. Mould
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, BH7 7DW UK
| | - Hartmut Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany, 89081
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany, 89081
| | - Johanna M. Rommens
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8, Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
| | - John B. Vincent
- Centre for Addiction and Mental Health, Clarke Institute and Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada, M5T 1R8
| | | | | | | | | | - Lap-Chee Tsui
- Department of Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Ontario, Canada, M5G 1X8, Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 1A8
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220
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Cooper GM, Brudno M, Green ED, Batzoglou S, Sidow A. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res 2003; 13:813-20. [PMID: 12727901 PMCID: PMC430923 DOI: 10.1101/gr.1064503] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Comparative sequence analyses on a collection of carefully chosen mammalian genomes could facilitate identification of functional elements within the human genome and allow quantification of evolutionary constraint at the single nucleotide level. High-resolution quantification would be informative for determining the distribution of important positions within functional elements and for evaluating the relative importance of nucleotide sites that carry single nucleotide polymorphisms (SNPs). Because the level of resolution in comparative sequence analyses is a direct function of sequence diversity, we propose that the information content of a candidate mammalian genome be defined as the sequence divergence it would add relative to already-sequenced genomes. We show that reliable estimates of genomic sequence divergence can be obtained from small genomic regions. On the basis of a multiple sequence alignment of approximately 1.4 megabases each from eight mammals, we generate such estimates for five unsequenced mammals. Estimates of the neutral divergence in these data suggest that a small number of diverse mammalian genomes in addition to human, mouse, and rat would allow single nucleotide resolution in comparative sequence analyses.
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Affiliation(s)
- Gregory M Cooper
- Department of Genetics, Stanford University, Stanford, California 94305, USA
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221
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Chen JW, Ghosh R, Finberg RW, Bergelson JM. Structure and chromosomal localization of the murine coxsackievirus and adenovirus receptor gene. DNA Cell Biol 2003; 22:253-9. [PMID: 12823902 DOI: 10.1089/104454903321908647] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We analyzed BAC genomic clones encoding the murine coxsackievirus and adenovirus receptor (mCAR). The mCAR gene is situated on the distal portion of murine chromosome 16, and is composed of at least eight exons, with intron-exon boundaries similar to those reported for the human CAR gene. We previously described two cDNAs encoding mCAR isoforms: the extracellular and transmembrane portions of both are encoded by exons 1-6; the cytoplasmic domain of mCAR 1 is encoded by exon 7, whereas mCAR 2 results from an RNA splice linking the proximal portion of exon 7 to an alternative exon 8. RT-PCR analysis of the mCAR RNA 5'-terminus suggests that transcription may begin 141-161 nucleotides upstream of the ATG translational start site.
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Affiliation(s)
- Jin-Wen Chen
- Division of Immunologic & Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
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222
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Ureta-Vidal A, Ettwiller L, Birney E. Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat Rev Genet 2003; 4:251-62. [PMID: 12671656 DOI: 10.1038/nrg1043] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The increasing number of complete and nearly complete metazoan genome sequences provides a significant amount of material for large-scale comparative genomic analysis. Finding new effective methods to analyse such enormous datasets has been the object of intense research. Three main areas in comparative genomics have recently shown important developments: whole-genome alignment, gene prediction and regulatory-region prediction. Each of these areas improves the methods of deciphering long genomic sequences and uncovering what lies hidden in them.
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Affiliation(s)
- Abel Ureta-Vidal
- EnsEMBL Project, Room A2-06, EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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223
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Wiltshire T, Pletcher MT, Batalov S, Barnes SW, Tarantino LM, Cooke MP, Wu H, Smylie K, Santrosyan A, Copeland NG, Jenkins NA, Kalush F, Mural RJ, Glynne RJ, Kay SA, Adams MD, Fletcher CF. Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse. Proc Natl Acad Sci U S A 2003; 100:3380-5. [PMID: 12612341 PMCID: PMC152301 DOI: 10.1073/pnas.0130101100] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The nature and organization of polymorphisms, or differences, between genomes of individuals are of great interest, because these variations can be associated with or even underlie phenotypic traits, including disease susceptibility. To gain insight into the genetic and evolutionary factors influencing such biological variation, we have examined the arrangement (haplotype) of single-nucleotide polymorphisms across the genomes of eight inbred strains of mice. These analyses define blocks of high or low diversity, often extending across tens of megabases that are delineated by abrupt transitions. These observations provide a striking contrast to the haplotype structure of the human genome.
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Affiliation(s)
- Tim Wiltshire
- Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121, USA.
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224
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Waterston RH, Lander ES, Sulston JE. More on the sequencing of the human genome. Proc Natl Acad Sci U S A 2003; 100:3022-4; author reply 3025-6. [PMID: 12631699 PMCID: PMC152236 DOI: 10.1073/pnas.0634129100] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Robert H Waterston
- Department of Genome Sciences, University of Washington, Box 357730, Seattle, WA 98195, USA.
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225
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Adams MD, Sutton GG, Smith HO, Myers EW, Venter JC. The independence of our genome assemblies. Proc Natl Acad Sci U S A 2003; 100:3025-6. [PMID: 16576752 PMCID: PMC152237 DOI: 10.1073/pnas.0637478100] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mark D Adams
- Celera Genomics, 45 West Gude Drive, Rockville, MD 20850; Institute for Biological Energy Alternatives, 1901 Research Boulevard, Suite 600, Rockville, MD 20850; Department of Electrical Engineering and Computer Sciences, 231 Cory Hall, University of California, Berkeley, CA 94720; and Center for the Advancement of Genomics, 1901 Research Boulevard, Suite 600, Rockville, MD 20850
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226
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Abstract
Changes in technology in the past decade have had such an impact on the way that molecular evolution research is done that it is difficult now to imagine working in a world without genomics or the Internet. In 1992, GenBank was less than a hundredth of its current size and was updated every three months on a huge spool of tape. Homology searches took 30 minutes and rarely found a hit. Now it is difficult to find sequences with only a few homologs to use as examples for teaching bioinformatics. For molecular evolution researchers, the genomics revolution has showered us with raw data and the information revolution has given us the wherewithal to analyze it. In broad terms, the most significant outcome from these changes has been our newfound ability to examine the evolution of genomes as a whole, enabling us to infer genome-wide evolutionary patterns and to identify subsets of genes whose evolution has been in some way atypical.
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Affiliation(s)
- Kenneth H Wolfe
- Department of Genetics, Smurfit Institute, University of Dublin, Trinity College, Dublin 2, Ireland.
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227
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Forsyth S, Horvath A, Coughlin P. A review and comparison of the murine alpha1-antitrypsin and alpha1-antichymotrypsin multigene clusters with the human clade A serpins. Genomics 2003; 81:336-45. [PMID: 12659817 DOI: 10.1016/s0888-7543(02)00041-1] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The major human plasma protease inhibitors, alpha(1)-antitrypsin and alpha(1)-antichymotrypsin, are each encoded by a single gene, whereas in the mouse they are represented by clusters of 5 and 14 genes, respectively. Although there is a high degree of overall sequence similarity within these groupings, the reactive-center loop (RCL) domain, which determines target protease specificity, is markedly divergent. The literature dealing with members of these mouse serine protease inhibitor (serpin) clusters has been complicated by inconsistent nomenclature. Furthermore, some investigators, unaware of the complexity of the family, have failed to distinguish between closely related genes when measuring expression levels or functional activity. We have reviewed the literature dealing with the mouse equivalents of human alpha(1)-antitrypsin and alpha(1)-antichymotrypsin and made use of the recently completed mouse genome sequence to propose a systematic nomenclature. We have also examined the extended mouse clade "a" serpin cluster at chromosome 12F1 and compared it with the syntenic region at human chromosome 14q32. In summarizing the literature and suggesting a standardized nomenclature, we aim to provide a logical structure on which future research may be based.
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Affiliation(s)
- Sharon Forsyth
- Department of Medicine, Monash University, Melbourne 3128, Australia
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228
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Liu G, Zhao S, Bailey JA, Sahinalp SC, Alkan C, Tuzun E, Green ED, Eichler EE. Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome. Genome Res 2003; 13:358-68. [PMID: 12618366 PMCID: PMC430288 DOI: 10.1101/gr.923303] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2002] [Accepted: 01/02/2003] [Indexed: 01/04/2023]
Abstract
We performed a detailed analysis of both single-nucleotide and large insertion/deletion events based on large-scale comparison of 10.6 Mb of genomic sequence from lemur, baboon, and chimpanzee to human. Using a human genomic reference, optimal global alignments were constructed from large (>50-kb) genomic sequence clones. These alignments were examined for the pattern, frequency, and nature of mutational events. Whereas rates of single-nucleotide substitution remain relatively constant (1-2 x 10(-9) substitutions/site/year), rates of retrotransposition vary radically among different primate lineages. These differences have lead to a 15%-20% expansion of human genome size over the last 50 million years of primate evolution, 90% of it due to new retroposon insertions. Orthologous comparisons with the chimpanzee suggest that the human genome continues to significantly expand due to shifts in retrotransposition activity. Assuming that the primate genome sequence we have sampled is representative, we estimate that human euchromatin has expanded 30 Mb and 550 Mb compared to the primate genomes of chimpanzee and lemur, respectively.
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Affiliation(s)
- Ge Liu
- Department of Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
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229
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Venter JC, Levy S, Stockwell T, Remington K, Halpern A. Massive parallelism, randomness and genomic advances. Nat Genet 2003; 33 Suppl:219-27. [PMID: 12610531 DOI: 10.1038/ng1114] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In reviewing the past decade, it is clear that genomics was, and still is, driven by innovative technologies, perhaps more so than any other scientific area in recent memory. From the outset, computing, mathematics and new automated laboratory techniques have been key components in allowing the field to move forward rapidly. We highlight some key innovations that have come together to nurture the explosive growth that makes a new era of genomics a reality. We also document how these new approaches have fueled further innovations and discoveries.
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Affiliation(s)
- J Craig Venter
- The Center for the Advancement of Genomics, 1901 Research Blvd., Rockville, Maryland 20850, USA.
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230
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Karlsson J, Zhao X, Lonskaya I, Neptin M, Holmdahl R, Andersson A. Novel quantitative trait loci controlling development of experimental autoimmune encephalomyelitis and proportion of lymphocyte subpopulations. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2003; 170:1019-26. [PMID: 12517969 DOI: 10.4049/jimmunol.170.2.1019] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The B10.RIII mouse strain (H-2(r)) develops chronic experimental autoimmune encephalomyelitis (EAE) upon immunization with the myelin basic protein 89-101 peptide. EAE was induced and studied in a backcross between B10.RIII and the EAE-resistant RIIIS/J strain (H-2(r)), and a complete genome scan with microsatellite markers was performed. Five loci were significantly linked to different traits and clinical subtypes of EAE on chromosomes 1, 5, 11, 15, and 16, three of the loci having sex specificity. The quantitative trait locus on chromosome 15 partly overlapped with the Eae2 locus, previously identified in crosses between the B10.RIII and RIIIS/J mouse strains. The loci on chromosomes 11 and 16 overlapped with Eae loci identified in other mouse crosses. By analyzing the backcross animals for lymphocyte phenotypes, the proportion of B and T cells in addition to the levels of CD4(+)CD8(-) and CD4(-)CD8(+) T cells and the CD4(+)/CD8(+) ratio in spleen were linked to different loci on chromosomes 1, 2, 3, 5, 6, 11, and 15. On chromosome 16, we found significant linkage to spleen cell proliferation. Several linkages overlapped with the quantitative trait loci for disease phenotypes. The identification of subphenotypes that are linked to the same loci as disease traits could be most useful in the search for candidate genes and biological pathways involved in the pathological process.
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MESH Headings
- Animals
- Crosses, Genetic
- Encephalomyelitis, Autoimmune, Experimental/epidemiology
- Encephalomyelitis, Autoimmune, Experimental/genetics
- Encephalomyelitis, Autoimmune, Experimental/immunology
- Encephalomyelitis, Autoimmune, Experimental/pathology
- Female
- Genetic Linkage/immunology
- Genotype
- Immunophenotyping
- Incidence
- Lymphocyte Count
- Lymphocyte Subsets/immunology
- Lymphocyte Subsets/metabolism
- Lymphocyte Subsets/pathology
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred Strains
- Quantitative Trait Loci/immunology
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Affiliation(s)
- Jenny Karlsson
- Department for Cell and Molecular Biology, Section for Medical Inflammation Research, University of Lund, Sweden
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231
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Davies PA, Wang W, Hales TG, Kirkness EF. A novel class of ligand-gated ion channel is activated by Zn2+. J Biol Chem 2003; 278:712-7. [PMID: 12381728 DOI: 10.1074/jbc.m208814200] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In mammals, the superfamily of "Cys loop," ligand-gated ion channels (LGICs), is assembled from a pool of more than 40 homologous subunits. These subunits have been classified into four families representing channels that are gated by acetylcholine, serotonin, gamma-aminobutyric acid, or glycine. By searching anonymous genomic sequence data for exons that encode characteristic motifs of the channel subunits, we have identified a novel LGIC that defines a fifth family member. Putative exons were used to isolate a full-length cDNA that encodes a protein of 411 amino acid residues. This protein (ZAC) contains all of the motifs that are characteristic of Cys loop channel subunits but cannot be assigned to any of the four established families on the basis of sequence similarity. Genes for ZAC are present in human and dog but appear to have been lost from mouse and rat genomes. Transcripts of ZAC subunits were detected in human placenta, trachea, spinal cord, stomach, and fetal brain. Transfection of human embryonic kidney cells with ZAC subunit cDNA caused expression of spontaneous current. By screening with a broad range of potential agonists and antagonists, we determined that tubocurarine inhibits the spontaneous current whereas Zn(2+) activates the expressed receptors. The absence of Zn(2+)-activated channels in rats and mice may explain why this fifth member of the LGIC superfamily has evaded detection until now.
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Affiliation(s)
- Paul A Davies
- Department of Pharmacology, George Washington University Medical Center, Washington, D. C. 20037, USA
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232
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Branchi I, Bichler Z, Berger-Sweeney J, Ricceri L. Animal models of mental retardation: from gene to cognitive function. Neurosci Biobehav Rev 2003; 27:141-53. [PMID: 12732230 DOI: 10.1016/s0149-7634(03)00016-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
About 2-3% of all children are affected by mental retardation, and genetic conditions rank among the leading causes of mental retardation. Alterations in the information encoded by genes that regulate critical steps of brain development can disrupt the normal course of development, and have profound consequences on mental processes. Genetically modified mouse models have helped to elucidate the contribution of specific gene alterations and gene-environment interactions to the phenotype of several forms of mental retardation. Mouse models of several neurodevelopmental pathologies, such as Down and Rett syndromes and X-linked forms of mental retardation, have been developed. Because behavior is the ultimate output of brain, behavioral phenotyping of these models provides functional information that may not be detectable using molecular, cellular or histological evaluations. In particular, the study of ontogeny of behavior is recommended in mouse models of disorders having a developmental onset. Identifying the role of specific genes in neuropathologies provides a framework in which to understand key stages of human brain development, and provides a target for potential therapeutic intervention.
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Affiliation(s)
- Igor Branchi
- Section of Behavioural Pathophysiology, Laboratorio di Fisiopatologia di Organo e di Sistema, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Roma, Italy.
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233
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Stryke D, Kawamoto M, Huang CC, Johns SJ, King LA, Harper CA, Meng EC, Lee RE, Yee A, L'Italien L, Chuang PT, Young SG, Skarnes WC, Babbitt PC, Ferrin TE. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Nucleic Acids Res 2003; 31:278-81. [PMID: 12520002 PMCID: PMC165511 DOI: 10.1093/nar/gkg064] [Citation(s) in RCA: 205] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The BayGenomics gene-trap resource (http://baygenomics.ucsf.edu) provides researchers with access to thousands of mouse embryonic stem (ES) cell lines harboring characterized insertional mutations in both known and novel genes. Each cell line contains an insertional mutation in a specific gene. The identity of the gene that has been interrupted can be determined from a DNA sequence tag. Approximately 75% of our cell lines contain insertional mutations in known mouse genes or genes that share strong sequence similarities with genes that have been identified in other organisms. These cell lines readily transmit the mutation to the germline of mice and many mutant lines of mice have already been generated from this resource. BayGenomics provides facile access to our entire database, including sequence tags for each mutant ES cell line, through the World Wide Web. Investigators can browse our resource, search for specific entries, download any portion of our database and BLAST sequences of interest against our entire set of cell line sequence tags. They can then obtain the mutant ES cell line for the purpose of generating knockout mice.
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Affiliation(s)
- Doug Stryke
- Department of Pharmaceutical Chemistry, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143, USA
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234
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Brosius J. The contribution of RNAs and retroposition to evolutionary novelties. CONTEMPORARY ISSUES IN GENETICS AND EVOLUTION 2003. [DOI: 10.1007/978-94-010-0229-5_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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235
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236
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Clark AG, Glanowski S, Nielsen R, Thomas P, Kejariwal A, Todd MJ, Tanenbaum DM, Civello D, Lu F, Murphy B, Ferriera S, Wang G, Zheng X, White TJ, Sninsky JJ, Adams MD, Cargill M. Positive selection in the human genome inferred from human-chimp-mouse orthologous gene alignments. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 68:471-7. [PMID: 15338650 DOI: 10.1101/sqb.2003.68.479] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- A G Clark
- Molecular Biology & Genetics, Cornell University, Ithaca, New York 14853, USA
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237
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Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 2003; 13:91-6. [PMID: 12529310 PMCID: PMC430950 DOI: 10.1101/gr.828403] [Citation(s) in RCA: 203] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2002] [Accepted: 10/30/2002] [Indexed: 10/27/2022]
Abstract
We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal changes were simultaneously made and applied to the assembly of the mouse genome, during a six-month period of development: (1) Supercontigs (scaffolds) were iteratively broken and rejoined using several criteria, yielding a 64-fold increase in length (N50), and apparent elimination of all global misjoins; (2) gaps between contigs in supercontigs were filled (partially or completely) by insertion of reads, as suggested by pairing within the supercontig, increasing the N50 contig length by 50%; (3) memory usage was reduced fourfold. The outcome of this mouse assembly and its analysis are described in (Mouse Genome Sequencing Consortium 2002).
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Affiliation(s)
- David B Jaffe
- Whitehead Institute/MIT Center for Genome Research, Cambridge, Massachusetts 02141, USA.
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238
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Pevzner P, Tesler G. Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Genome Res 2003; 13:37-45. [PMID: 12529304 PMCID: PMC430962 DOI: 10.1101/gr.757503] [Citation(s) in RCA: 214] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Although analysis of genome rearrangements was pioneered by Dobzhansky and Sturtevant 65 years ago, we still know very little about the rearrangement events that produced the existing varieties of genomic architectures. The genomic sequences of human and mouse provide evidence for a larger number of rearrangements than previously thought and shed some light on previously unknown features of mammalian evolution. In particular, they reveal that a large number of microrearrangements is required to explain the differences in draft human and mouse sequences. Here we describe a new algorithm for constructing synteny blocks, study arrangements of synteny blocks in human and mouse, derive a most parsimonious human-mouse rearrangement scenario, and provide evidence that intrachromosomal rearrangements are more frequent than interchromosomal rearrangements. Our analysis is based on the human-mouse breakpoint graph, which reveals related breakpoints and allows one to find a most parsimonious scenario. Because these graphs provide important insights into rearrangement scenarios, we introduce a new visualization tool that allows one to view breakpoint graphs superimposed with genomic dot-plots.
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Affiliation(s)
- Pavel Pevzner
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093-0114, USA.
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239
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Couronne O, Poliakov A, Bray N, Ishkhanov T, Ryaboy D, Rubin E, Pachter L, Dubchak I. Strategies and tools for whole-genome alignments. Genome Res 2003; 13:73-80. [PMID: 12529308 PMCID: PMC430965 DOI: 10.1101/gr.762503] [Citation(s) in RCA: 159] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2002] [Accepted: 11/06/2002] [Indexed: 11/25/2022]
Abstract
The availability of the assembled mouse genome makes possible, for the first time, an alignment and comparison of two large vertebrate genomes. We investigated different strategies of alignment for the subsequent analysis of conservation of genomes that are effective for assemblies of different quality. These strategies were applied to the comparison of the working draft of the human genome with the Mouse Genome Sequencing Consortium assembly, as well as other intermediate mouse assemblies. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. We obtained such coverage while preserving specificity. With a view towards the end user, we developed a suite of tools and Web sites for automatically aligning and subsequently browsing and working with whole-genome comparisons. We describe the use of these tools to identify conserved non-coding regions between the human and mouse genomes, some of which have not been identified by other methods.
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Affiliation(s)
- Olivier Couronne
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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240
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Zambrowicz BP, Sands AT. Knockouts model the 100 best-selling drugs--will they model the next 100? Nat Rev Drug Discov 2003; 2:38-51. [PMID: 12509758 DOI: 10.1038/nrd987] [Citation(s) in RCA: 265] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The biopharmaceutical industry is currently faced with a tremendous number of potential drug targets identified through the sequencing of the human genome. The challenge ahead is to delineate those targets with the greatest value for therapeutic intervention. Here, we critically evaluate mouse-knockout technology for target discovery and validation. A retrospective evaluation of the knockout phenotypes for the targets of the 100 best-selling drugs indicates that these phenotypes correlate well with known drug efficacy, illuminating a productive path forward for discovering future drug targets. Prospective mining of the druggable genome is being catalysed by large-scale mouse knockout programs combined with phenotypic screens focused on identifying targets that modulate mammalian physiology in a therapeutically relevant manner.
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Affiliation(s)
- Brian P Zambrowicz
- Lexicon Genetics Incorporated, 8800 Technology Forest Place, The Woodlands, TX 77381, USA.
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241
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Frazer KA, Elnitski L, Church DM, Dubchak I, Hardison RC. Cross-species sequence comparisons: a review of methods and available resources. Genome Res 2003; 13:1-12. [PMID: 12529301 PMCID: PMC430969 DOI: 10.1101/gr.222003] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
With the availability of whole-genome sequences for an increasing number of species, we are now faced with the challenge of decoding the information contained within these DNA sequences. Comparative analysis of DNA sequences from multiple species at varying evolutionary distances is a powerful approach for identifying coding and functional noncoding sequences, as well as sequences that are unique for a given organism. In this review, we outline the strategy for choosing DNA sequences from different species for comparative analyses and describe the methods used and the resources publicly available for these studies.
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Affiliation(s)
- Kelly A Frazer
- Perlegen Sciences, Mountain View, California 94043, USA.
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242
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Bray N, Dubchak I, Pachter L. AVID: A global alignment program. Genome Res 2003; 13:97-102. [PMID: 12529311 PMCID: PMC430967 DOI: 10.1101/gr.789803] [Citation(s) in RCA: 287] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2002] [Accepted: 11/07/2002] [Indexed: 11/25/2022]
Abstract
In this paper we describe a new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole genome human/mouse alignments. We have also performed a quantitative comparison of AVID with other popular alignment tools. To this end, we have established a format for the representation of alignments and methods for their comparison. These formats and methods should be useful for future studies. The tools we have developed for the alignment comparisons, as well as the AVID program, are publicly available. See Web Site References section for AVID Web address and Web addresses for other programs discussed in this paper.
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Affiliation(s)
- Nick Bray
- Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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243
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Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, et alWaterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, Antonarakis SE, Attwood J, Baertsch R, Bailey J, Barlow K, Beck S, Berry E, Birren B, Bloom T, Bork P, Botcherby M, Bray N, Brent MR, Brown DG, Brown SD, Bult C, Burton J, Butler J, Campbell RD, Carninci P, Cawley S, Chiaromonte F, Chinwalla AT, Church DM, Clamp M, Clee C, Collins FS, Cook LL, Copley RR, Coulson A, Couronne O, Cuff J, Curwen V, Cutts T, Daly M, David R, Davies J, Delehaunty KD, Deri J, Dermitzakis ET, Dewey C, Dickens NJ, Diekhans M, Dodge S, Dubchak I, Dunn DM, Eddy SR, Elnitski L, Emes RD, Eswara P, Eyras E, Felsenfeld A, Fewell GA, Flicek P, Foley K, Frankel WN, Fulton LA, Fulton RS, Furey TS, Gage D, Gibbs RA, Glusman G, Gnerre S, Goldman N, Goodstadt L, Grafham D, Graves TA, Green ED, Gregory S, Guigó R, Guyer M, Hardison RC, Haussler D, Hayashizaki Y, Hillier LW, Hinrichs A, Hlavina W, Holzer T, Hsu F, Hua A, Hubbard T, Hunt A, Jackson I, Jaffe DB, Johnson LS, Jones M, Jones TA, Joy A, Kamal M, Karlsson EK, Karolchik D, Kasprzyk A, Kawai J, Keibler E, Kells C, Kent WJ, Kirby A, Kolbe DL, Korf I, Kucherlapati RS, Kulbokas EJ, Kulp D, Landers T, Leger JP, Leonard S, Letunic I, Levine R, Li J, Li M, Lloyd C, Lucas S, Ma B, Maglott DR, Mardis ER, Matthews L, Mauceli E, Mayer JH, McCarthy M, McCombie WR, McLaren S, McLay K, McPherson JD, Meldrim J, Meredith B, Mesirov JP, Miller W, Miner TL, Mongin E, Montgomery KT, Morgan M, Mott R, Mullikin JC, Muzny DM, Nash WE, Nelson JO, Nhan MN, Nicol R, Ning Z, Nusbaum C, O'Connor MJ, Okazaki Y, Oliver K, Overton-Larty E, Pachter L, Parra G, Pepin KH, Peterson J, Pevzner P, Plumb R, Pohl CS, Poliakov A, Ponce TC, Ponting CP, Potter S, Quail M, Reymond A, Roe BA, Roskin KM, Rubin EM, Rust AG, Santos R, Sapojnikov V, Schultz B, Schultz J, Schwartz MS, Schwartz S, Scott C, Seaman S, Searle S, Sharpe T, Sheridan A, Shownkeen R, Sims S, Singer JB, Slater G, Smit A, Smith DR, Spencer B, Stabenau A, Stange-Thomann N, Sugnet C, Suyama M, Tesler G, Thompson J, Torrents D, Trevaskis E, Tromp J, Ucla C, Ureta-Vidal A, Vinson JP, Von Niederhausern AC, Wade CM, Wall M, Weber RJ, Weiss RB, Wendl MC, West AP, Wetterstrand K, Wheeler R, Whelan S, Wierzbowski J, Willey D, Williams S, Wilson RK, Winter E, Worley KC, Wyman D, Yang S, Yang SP, Zdobnov EM, Zody MC, Lander ES. Initial sequencing and comparative analysis of the mouse genome. Nature 2002; 420:520-62. [PMID: 12466850 DOI: 10.1038/nature01262] [Show More Authors] [Citation(s) in RCA: 4941] [Impact Index Per Article: 214.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2002] [Accepted: 10/31/2002] [Indexed: 12/18/2022]
Abstract
The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.
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MESH Headings
- Animals
- Base Composition
- Chromosomes, Mammalian/genetics
- Conserved Sequence/genetics
- CpG Islands/genetics
- Evolution, Molecular
- Gene Expression Regulation
- Genes/genetics
- Genetic Variation/genetics
- Genome
- Genome, Human
- Genomics
- Humans
- Mice/classification
- Mice/genetics
- Mice, Knockout
- Mice, Transgenic
- Models, Animal
- Multigene Family/genetics
- Mutagenesis
- Neoplasms/genetics
- Physical Chromosome Mapping
- Proteome/genetics
- Pseudogenes/genetics
- Quantitative Trait Loci/genetics
- RNA, Untranslated/genetics
- Repetitive Sequences, Nucleic Acid/genetics
- Selection, Genetic
- Sequence Analysis, DNA
- Sex Chromosomes/genetics
- Species Specificity
- Synteny
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244
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245
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Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CAM, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, et alOkazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A, Schönbach C, Gojobori T, Baldarelli R, Hill DP, Bult C, Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H, Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF, Forrest A, Frazer KS, Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N, Jackson IJ, Jarvis ED, Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y, Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L, McKenzie L, Miki H, Nagashima T, Numata K, Okido T, Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R, Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC, Reed DJ, Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CAM, Setou M, Shimada K, Sultana R, Takenaka Y, Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG, Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y, Zimmer A, Carninci P, Hayatsu N, Hirozane-Kishikawa T, Konno H, Nakamura M, Sakazume N, Sato K, Shiraki T, Waki K, Kawai J, Aizawa K, Arakawa T, Fukuda S, Hara A, Hashizume W, Imotani K, Ishii Y, Itoh M, Kagawa I, Miyazaki A, Sakai K, Sasaki D, Shibata K, Shinagawa A, Yasunishi A, Yoshino M, Waterston R, Lander ES, Rogers J, Birney E, Hayashizaki Y. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 2002; 420:563-73. [PMID: 12466851 DOI: 10.1038/nature01266] [Show More Authors] [Citation(s) in RCA: 1263] [Impact Index Per Article: 54.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2002] [Accepted: 10/28/2002] [Indexed: 01/10/2023]
Abstract
Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
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MESH Headings
- Alternative Splicing/genetics
- Amino Acid Motifs
- Animals
- Chromosomes, Mammalian/genetics
- Cloning, Molecular
- DNA, Complementary/genetics
- Databases, Genetic
- Expressed Sequence Tags
- Genes/genetics
- Genomics/methods
- Humans
- Membrane Proteins/genetics
- Mice/genetics
- Physical Chromosome Mapping
- Protein Structure, Tertiary
- Proteome/chemistry
- Proteome/genetics
- RNA, Antisense/genetics
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Untranslated/analysis
- RNA, Untranslated/genetics
- Transcription Initiation Site
- Transcription, Genetic/genetics
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Affiliation(s)
- Y Okazaki
- [1] Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
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246
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Dermitzakis ET, Reymond A, Lyle R, Scamuffa N, Ucla C, Deutsch S, Stevenson BJ, Flegel V, Bucher P, Jongeneel CV, Antonarakis SE. Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature 2002; 420:578-82. [PMID: 12466853 DOI: 10.1038/nature01251] [Citation(s) in RCA: 173] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2002] [Accepted: 10/30/2002] [Indexed: 11/08/2022]
Abstract
The use of comparative genomics to infer genome function relies on the understanding of how different components of the genome change over evolutionary time. The aim of such comparative analysis is to identify conserved, functionally transcribed sequences such as protein-coding genes and non-coding RNA genes, and other functional sequences such as regulatory regions, as well as other genomic features. Here, we have compared the entire human chromosome 21 with syntenic regions of the mouse genome, and have identified a large number of conserved blocks of unknown function. Although previous studies have made similar observations, it is unknown whether these conserved sequences are genes or not. Here we present an extensive experimental and computational analysis of human chromosome 21 in an effort to assign function to sequences conserved between human chromosome 21 (ref. 8) and the syntenic mouse regions. Our data support the presence of a large number of potentially functional non-genic sequences, probably regulatory and structural. The integration of the properties of the conserved components of human chromosome 21 to the rapidly accumulating functional data for this chromosome will improve considerably our understanding of the role of sequence conservation in mammalian genomes.
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Affiliation(s)
- Emmanouil T Dermitzakis
- Division of Medical Genetics, 1 Rue Michel-Servet, University of Geneva Medical School and University Hospitals of Geneva, CH-1211 Geneva, Switzerland
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247
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Marshall KE, Godden EL, Yang F, Burgers S, Buck KJ, Sikela JM. In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases. Genome Biol 2002; 3:RESEARCH0078. [PMID: 12537567 PMCID: PMC151180 DOI: 10.1186/gb-2002-3-12-research0078] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2002] [Revised: 10/17/2002] [Accepted: 10/22/2002] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The identification of genes underlying complex traits has been aided by quantitative trait locus (QTL) mapping approaches, which in turn have benefited from advances in mammalian genome research. Most recently, whole-genome draft sequences and assemblies have been generated for mouse strains that have been used for a large fraction of QTL mapping studies. Here we show how such strain-specific mouse genome sequence databases can be used as part of a high-throughput pipeline for the in silico discovery of gene-coding variations within murine QTLs. As a test of this approach we focused on two QTLs on mouse chromosomes 1 and 13 that are involved in physical dependence on alcohol. RESULTS Interstrain alignment of sequences derived from the relevant mouse strain genome sequence databases for 199 QTL-localized genes spanning 210,020 base-pairs of coding sequence identified 21 genes with different coding sequences for the progenitor strains. Several of these genes, including four that exhibit strong phenotypic links to chronic alcohol withdrawal, are promising candidates to underlie these QTLs. CONCLUSIONS This approach has wide general utility, and should be applicable to any of the several hundred mouse QTLs, encompassing over 60 different complex traits, that have been identified using strains for which relatively complete genome sequences are available.
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Affiliation(s)
- Kriste E Marshall
- Department of Pharmacology and Human Medical Genetics Program, University of Colorado Health Sciences Center, Denver CO 80262, USA
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248
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Forde CE, McCutchen-Maloney SL. Characterization of transcription factors by mass spectrometry and the role of SELDI-MS. MASS SPECTROMETRY REVIEWS 2002; 21:419-439. [PMID: 12666149 DOI: 10.1002/mas.10040] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Over the last decade, much progress has been made in the field of biological mass spectrometry, with numerous advances in technology, resolution, and affinity capture. The field of genomics has also been transformed by the sequencing and characterization of entire genomes. Some of the next challenges lie in understanding the relationship between the genome and the proteome, the protein complement of the genome, and in characterizing the regulatory processes involved in progressing from gene to functional protein. In this new age of proteomics, development of mass spectrometry methods to characterize transcription factors promises to add greatly to our understanding of regulatory networks that govern expression. However, at this time, regulatory networks of transcription factors are mostly uncharted territory. In this review, we summarize the latest advances in characterization of transcription factors by mass spectrometry including affinity capture, identification of complexes of DNA-binding proteins, structural characterization, determination of protein-DNA and protein-protein interactions, assessment of modification sites and metal binding, studies of functional activity, and the latest chip technologies that use SELDI-MS that allow the rapid capture and identification of transcription factors.
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Affiliation(s)
- Cameron E Forde
- Biodefense Division, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, California 94550, USA
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249
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Holt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JMC, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, et alHolt RA, Subramanian GM, Halpern A, Sutton GG, Charlab R, Nusskern DR, Wincker P, Clark AG, Ribeiro JMC, Wides R, Salzberg SL, Loftus B, Yandell M, Majoros WH, Rusch DB, Lai Z, Kraft CL, Abril JF, Anthouard V, Arensburger P, Atkinson PW, Baden H, de Berardinis V, Baldwin D, Benes V, Biedler J, Blass C, Bolanos R, Boscus D, Barnstead M, Cai S, Center A, Chaturverdi K, Christophides GK, Chrystal MA, Clamp M, Cravchik A, Curwen V, Dana A, Delcher A, Dew I, Evans CA, Flanigan M, Grundschober-Freimoser A, Friedli L, Gu Z, Guan P, Guigo R, Hillenmeyer ME, Hladun SL, Hogan JR, Hong YS, Hoover J, Jaillon O, Ke Z, Kodira C, Kokoza E, Koutsos A, Letunic I, Levitsky A, Liang Y, Lin JJ, Lobo NF, Lopez JR, Malek JA, McIntosh TC, Meister S, Miller J, Mobarry C, Mongin E, Murphy SD, O'Brochta DA, Pfannkoch C, Qi R, Regier MA, Remington K, Shao H, Sharakhova MV, Sitter CD, Shetty J, Smith TJ, Strong R, Sun J, Thomasova D, Ton LQ, Topalis P, Tu Z, Unger MF, Walenz B, Wang A, Wang J, Wang M, Wang X, Woodford KJ, Wortman JR, Wu M, Yao A, Zdobnov EM, Zhang H, Zhao Q, Zhao S, Zhu SC, Zhimulev I, Coluzzi M, della Torre A, Roth CW, Louis C, Kalush F, Mural RJ, Myers EW, Adams MD, Smith HO, Broder S, Gardner MJ, Fraser CM, Birney E, Bork P, Brey PT, Venter JC, Weissenbach J, Kafatos FC, Collins FH, Hoffman SL. The genome sequence of the malaria mosquito Anopheles gambiae. Science 2002; 298:129-49. [PMID: 12364791 DOI: 10.1126/science.1076181] [Show More Authors] [Citation(s) in RCA: 1427] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.
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Affiliation(s)
- Robert A Holt
- Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.
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250
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Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, Shallom SJ, van Aken SE, Riedmuller SB, Feldblyum TV, Cho JK, Quackenbush J, Sedegah M, Shoaibi A, Cummings LM, Florens L, Yates JR, Raine JD, Sinden RE, Harris MA, Cunningham DA, Preiser PR, Bergman LW, Vaidya AB, van Lin LH, Janse CJ, Waters AP, Smith HO, White OR, Salzberg SL, Venter JC, Fraser CM, Hoffman SL, Gardner MJ, Carucci DJ. Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii. Nature 2002; 419:512-9. [PMID: 12368865 DOI: 10.1038/nature01099] [Citation(s) in RCA: 539] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2002] [Accepted: 08/30/2002] [Indexed: 12/18/2022]
Abstract
Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease.
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Affiliation(s)
- Jane M Carlton
- The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA.
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