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Sanchez-Pulido L, Ponting CP. TM6SF2 and MAC30, new enzyme homologs in sterol metabolism and common metabolic disease. Front Genet 2014; 5:439. [PMID: 25566323 PMCID: PMC4263179 DOI: 10.3389/fgene.2014.00439] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 11/27/2014] [Indexed: 12/14/2022] Open
Abstract
Carriers of the Glu167Lys coding variant in the TM6SF2 gene have recently been identified as being more susceptible to non-alcoholic fatty liver disease (NAFLD), yet exhibit lower levels of circulating lipids and hence are protected against cardiovascular disease. Despite the physiological importance of these observations, the molecular function of TM6SF2 remains unknown, and no sequence similarity with functionally characterized proteins has been identified. In order to trace its evolutionary history and to identify functional domains, we embarked on a computational protein sequence analysis of TM6SF2. We identified a new domain, the EXPERA domain, which is conserved among TM6SF, MAC30/TMEM97 and EBP (D8, D7 sterol isomerase) protein families. EBP mutations are the cause of chondrodysplasia punctata 2 X-linked dominant (CDPX2), also known as Conradi-Hünermann-Happle syndrome, a defective cholesterol biosynthesis disorder. Our analysis of evolutionary conservation among EXPERA domain-containing families and the previously suggested catalytic mechanism for the EBP enzyme, indicate that TM6SF and MAC30/TMEM97 families are both highly likely to possess, as for the EBP family, catalytic activity as sterol isomerases. This unexpected prediction of enzymatic functions for TM6SF and MAC30/TMEM97 is important because it now permits detailed experiments to investigate the function of these key proteins in various human pathologies, from cardiovascular disease to cancer.
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Affiliation(s)
- Luis Sanchez-Pulido
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford Oxford, UK
| | - Chris P Ponting
- Medical Research Council Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford Oxford, UK
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2
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Soldovieri MV, Boutry-Kryza N, Milh M, Doummar D, Heron B, Bourel E, Ambrosino P, Miceli F, De Maria M, Dorison N, Auvin S, Echenne B, Oertel J, Riquet A, Lambert L, Gerard M, Roubergue A, Calender A, Mignot C, Taglialatela M, Lesca G. NovelKCNQ2andKCNQ3Mutations in a Large Cohort of Families with Benign Neonatal Epilepsy: First Evidence for an Altered Channel Regulation by Syntaxin-1A. Hum Mutat 2014; 35:356-67. [DOI: 10.1002/humu.22500] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Accepted: 12/12/2013] [Indexed: 11/06/2022]
Affiliation(s)
| | - Nadia Boutry-Kryza
- Department of Medical Genetics; Hospices Civils de Lyon; France
- Claude Bernard Lyon I University; Lyon France
- CRNL, CNRS UMR 5292, INSERM U1028; Lyon France
| | - Mathieu Milh
- INSERM, UMR_S910; Marseille France
- Department of Neuropediatrics; CHU Timone, APHM; Marseille France
| | - Diane Doummar
- Department of Neuropediatrics; Armand Trousseau Hospital; APHP Paris France
| | - Benedicte Heron
- Department of Neuropediatrics; Armand Trousseau Hospital; APHP Paris France
| | - Emilie Bourel
- Department of Neuropediatrics; Hôpital Nord, CHU d'Amiens; Amiens France
| | - Paolo Ambrosino
- Department of Medicine and Health Science; University of Molise; Campobasso Italy
| | - Francesco Miceli
- Department of Neuroscience; University of Naples Federico II; Naples Italy
| | - Michela De Maria
- Department of Medicine and Health Science; University of Molise; Campobasso Italy
| | - Nathalie Dorison
- Department of Neuropediatrics; Armand Trousseau Hospital; APHP Paris France
| | - Stephane Auvin
- Department of Neuropediatrics; Robert Debré Hospital; APHP Paris France
- INSERM U676; Paris France
| | - Bernard Echenne
- Department of Neuropediatrics; Gui de Chauliac Hospital, CHU de Montpellier; Montpellier France
| | - Julie Oertel
- Department of Medical Genetics; Hopital de l'Archet 2, CHU de Nice; Nice France
| | - Audrey Riquet
- Department of Neuropediatrics; Roger Salengro Hospital; Lille France
| | - Laetitia Lambert
- Department of Medical Genetics; Maternité de Nancy and CHU de Nancy; Nancy France
- INSERM UMR954, Vandoeuvre-les-Nancy; France
| | - Marion Gerard
- Department of Medical Genetics; CHU de Caen; Caen France
| | - Anne Roubergue
- Department of Neuropediatrics; Armand Trousseau Hospital; APHP Paris France
| | - Alain Calender
- Department of Medical Genetics; Hospices Civils de Lyon; France
- Claude Bernard Lyon I University; Lyon France
| | - Cyril Mignot
- Department of Genetics; Clinical Genetics Unit, Hôpital de la Pitié-Salpêtrière; APHP Paris France
- Centre de Référence des Déficiences Intellectuelles de Causes Rares; APHP Paris France
| | - Maurizio Taglialatela
- Department of Medicine and Health Science; University of Molise; Campobasso Italy
- Department of Neuroscience; University of Naples Federico II; Naples Italy
- Unidad de Biofísica; Consejo Superior de Investigaciones Cientificas - Universidad del Pais Vasco; Leioa Spain
| | - Gaetan Lesca
- Department of Medical Genetics; Hospices Civils de Lyon; France
- Claude Bernard Lyon I University; Lyon France
- CRNL, CNRS UMR 5292, INSERM U1028; Lyon France
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3
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Riera C, Lois S, de la Cruz X. Prediction of pathological mutations in proteins: the challenge of integrating sequence conservation and structure stability principles. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Casandra Riera
- Laboratory of Translational Bioinformatics in Neuroscience; VHIR; Barcelona Spain
| | - Sergio Lois
- Laboratory of Translational Bioinformatics in Neuroscience; VHIR; Barcelona Spain
| | - Xavier de la Cruz
- Laboratory of Translational Bioinformatics in Neuroscience; VHIR; Barcelona Spain
- Institució Catalana per la Recerca i Estudis Avançats (ICREA); Barcelona Spain
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4
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5
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Barraclough KA, Staatz CE, Isbel NM, McTaggart SJ. Review: Pharmacodynamic monitoring of immunosuppression in kidney transplantation. Nephrology (Carlton) 2010; 15:522-32. [PMID: 20649871 DOI: 10.1111/j.1440-1797.2010.01349.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Advances in immunosuppressive therapies have improved kidney transplant outcomes. However, immunosuppressant drug-induced toxicities continue to reduce tolerability and impact patient and graft survival. A major ongoing challenge in kidney transplantation is to establish ways of tailoring immunosuppressant therapy so as to maintain efficacy while minimizing toxicity. Pharmacodynamic monitoring by direct measurement of immune cell function has the potential to personalize immunosuppression. The purpose of this review is to provide the clinician with an overview of the methodology and use of immune function monitoring in the field of kidney transplantation.
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Affiliation(s)
- Katherine A Barraclough
- Department of Renal Medicine, University of Queensland at the Princess Alexandra Hospital, Queensland, Australia.
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6
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Hebebrand J, Scherag A, Schimmelmann BG, Hinney A. Child and adolescent psychiatric genetics. Eur Child Adolesc Psychiatry 2010; 19:259-79. [PMID: 20140632 DOI: 10.1007/s00787-010-0091-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 01/08/2010] [Indexed: 01/22/2023]
Abstract
The current status of child and adolescent psychiatric genetics appears promising in light of the initiation of genome-wide association studies (GWAS) for diverse polygenic disorders and the molecular elucidation of monogenic Rett syndrome, for which recent functional studies provide hope for pharmacological treatment strategies. Within the last 50 years, tremendous progress has been made in linking genetic variation to behavioral phenotypes and psychiatric disorders. We summarize the major findings of the Human Genome Project and dwell on largely unsuccessful candidate gene and linkage studies. GWAS for the first time offer the possibility to detect single nucleotide polymorphisms and copy number variants without a priori hypotheses as to their molecular etiology. At the same time it is becoming increasingly clear that very large sample sizes are required in order to enable genome wide significant findings, thus necessitating further large-scaled ascertainment schemes for the successful elucidation of the molecular genetics of childhood and adolescent psychiatric disorders. We conclude by reflecting on different scenarios for future research into the molecular basis of early onset psychiatric disorders. This review represents the introductory article of this special issue of the European Child and Adolescent Psychiatry.
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Affiliation(s)
- Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, LVR-Klinikum Essen, University of Duisburg-Essen, Virchowstrasse 174, Essen, Germany.
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7
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Ryan M, Diekhans M, Lien S, Liu Y, Karchin R. LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. ACTA ACUST UNITED AC 2009; 25:1431-2. [PMID: 19369493 DOI: 10.1093/bioinformatics/btp242] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
SUMMARY LS-SNP/PDB is a new WWW resource for genome-wide annotation of human non-synonymous (amino acid changing) SNPs. It serves high-quality protein graphics rendered with UCSF Chimera molecular visualization software. The system is kept up-to-date by an automated, high-throughput build pipeline that systematically maps human nsSNPs onto Protein Data Bank structures and annotates several biologically relevant features. AVAILABILITY LS-SNP/PDB is available at (http://ls-snp.icm.jhu.edu/ls-snp-pdb) and via links from protein data bank (PDB) biology and chemistry tabs, UCSC Genome Browser Gene Details and SNP Details pages and PharmGKB Gene Variants Downloads/Cross-References pages.
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Affiliation(s)
- Michael Ryan
- Department of Bioinformatics, George Mason University, Fairfax, VA, USA
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8
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Garcia SM, Casanueva MO, Silva MC, Amaral MD, Morimoto RI. Neuronal signaling modulates protein homeostasis in Caenorhabditis elegans post-synaptic muscle cells. Genes Dev 2007; 21:3006-16. [PMID: 18006691 DOI: 10.1101/gad.1575307] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein homeostasis maintains proper intracellular balance by promoting protein folding and clearance mechanisms while minimizing the stress caused by the accumulation of misfolded and damaged proteins. Chronic expression of aggregation-prone proteins is deleterious to the cell and has been linked to a wide range of conformational disorders. The molecular response to misfolded proteins is highly conserved and generally studied as a cell-autonomous process. Here, we provide evidence that neuronal signaling is an important modulator of protein homeostasis in post-synaptic muscle cells. In a forward genetic screen in Caenorhabditis elegans for enhancers of polyglutamine aggregation in muscle cells, we identified unc-30, a neuron-specific transcription factor that regulates the synthesis of the inhibitory neurotransmitter gamma-aminobutyric acid (GABA). We used additional sensors of protein conformational states to show that defective GABA signaling or increased acetylcholine (ACh) signaling causes a general imbalance in protein homeostasis in post-synaptic muscle cells. Moreover, exposure to GABA antagonists or ACh agonists has a similar effect, which reveals that toxins that act at the neuromuscular junction are potent modifiers of protein conformational disorders. These results demonstrate the importance of intercellular communication in intracellular homeostasis.
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Affiliation(s)
- Susana M Garcia
- Department of Biochemistry, Molecular Biology and Cell Biology, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
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9
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Abstract
Accelerated evolution of the field of functional genomics has been greatly facilitated by high-throughput microarray-based gene function studies, relating to the parallel and serial expression measurements of genomes. Microarray experimentation is being applied for the study of basic research questions, drug target discovery, pharmacology, toxicogenomics, target selectivity, disease biomarker determination, development of prognostic tests, and disease subclass determination. This article will review the current applications of microarray technology in the field of organ transplantation and discuss the potential impact of this technology on transplantation medicine.
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Affiliation(s)
- Minnie M Sarwal
- Department of Pediatrics, Stanford University School of Medicine, Palo Alto, CA 94305, USA.
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10
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Ferrer-Costa C, Orozco M, de la Cruz X. Sequence-based prediction of pathological mutations. Proteins 2006; 57:811-9. [PMID: 15390262 DOI: 10.1002/prot.20252] [Citation(s) in RCA: 146] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The development of methods to assess the impact of amino acid mutations on human health has become an important goal in biomedical research, due to the growing number of nonsynonymous SNPs identified. Within this context, computational methods constitute a valuable tool, because they can easily process large amounts of mutations and give useful, almost cost-free, information on their pathological character. In this paper we present a computational approach to the prediction of disease-associated amino acid mutations, using only sequence-based information (amino acid properties, evolutionary information, secondary structure and accessibility predictions, and database annotations) and neural networks, as a model building tool. Mutations are predicted to be either pathological or neutral. Our results show that the method has a good overall success rate, 83%, that can reach 95% when trained for specific proteins. The methodology is fast and flexible enough to provide good estimates of the pathological character of large sets of nonsynonymous SNPs, but can also be easily adapted to give more precise predictions for proteins of special biomedical interest.
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Affiliation(s)
- C Ferrer-Costa
- Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomédica, Parc Científic de Barcelona, Barcelona, Spain
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11
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Abstract
High throughput, high density platforms for transcriptional, proteomic, and metabonomic analyses are opening new doors for improving our understanding of the complexity and redundancy of the immune system in the interplay of the innate and allo-immune responses in organ transplantation. New insights are being obtained into the possible discrepancies between the gold standard of tissue pathological diagnosis and clinical graft outcomes, as new transcriptional categories of transplant rejection evolve. The bystander effects of chronic immunosuppression underlying the complexities of graft dysfunction are beginning to be understood. Non-invasive mechanisms to monitor transplants, by following 'footprints' of biomarker sets that reflect the disease phenotype, are being pursued for their clinical application for direct patient care. Utilization of these same biomarker sets may also offer a unique means to titrate immunosuppression and predict specific graft dysfunction events prior to clinical decline, thus bringing in the potential to reduce patient morbidity from infection and malignancy, preserve graft integrity, and limit the progression of chronic graft injury. Bioinformatics support is integral to the unraveling of the mysteries of the human genome, proteome, and metabolome in disease and in health.
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Affiliation(s)
- Minnie M Sarwal
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94304, USA.
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12
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Ferrer-Costa C, Orozco M, de la Cruz X. Use of bioinformatics tools for the annotation of disease-associated mutations in animal models. Proteins 2006; 61:878-87. [PMID: 16208716 DOI: 10.1002/prot.20664] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Single-point mutations are one of the most frequent causes of genetic variability in both human and close species. The recent availability of different bioinformatics tools for annotating human single nucleotide polymorphisms (SNPs) has opened the possibility of using them to score SNPs from species with a biomedical interest, in particular from mice and other models of human disease. Also, this ability to predict pathogenicity of single point mutations in one species, based on data from another species, opens the possibility to predict the pathological character of single point mutations in humans using data from well-characterized model systems of human disease. This could provide a valuable alternative to the more traditional genetic population approaches. However, transferral of prediction tools may be limited by different factors, from a species bias in the training set, to a large sequence divergence between the proteomes of the training and the target species. Here we study the conditions under which prediction tools can be transferred among species, concentrating in the case of mice. We find that for the majority of the human-mouse homolog pairs, the sequence similarity is large enough to preserve the pathological character of mutations among species, in general. We then establish that prediction/annotation tools developed for one organism can be used to predict the neutral/pathological character of mutations/SNPs in the other organism.
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Affiliation(s)
- Carles Ferrer-Costa
- Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomédica, Parc Científic de Barcelona, Barcelona, Spain
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13
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Jiang MC, Jiang PC, Liao CF, Lee CC. A modified mutation detection method for large-scale cloning of the possible single nucleotide polymorphism sequences. BMB Rep 2005; 38:191-7. [PMID: 15826496 DOI: 10.5483/bmbrep.2005.38.2.191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although the human genome has been nearly completely sequenced, the functions and the roles of the vast majority of the genes, and the influences of single nucleotide polymorphisms (SNPs) in these genes are not entirely known. A modified mutation detection method was developed for large-scale cloning of the possible SNPs between tumor and normal cells for facilitating the identification of genetic factors that associated with cancer formation and progression. The method involves hybridization of restriction enzyme-cut chromosomal DNA, cleavage and modification of the sites of differences by enzymes, and differential cloning of sequence variations with a designed vector. Experimental validations of the presence and location of sequence variations in the isolated clones by PCR and DNA sequencing support the capability of this method in identifying sequence differences between tumor cells and normal cells.
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14
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Abstract
Microarrays, or gene chips, are exciting investigative tools for analyzing expression changes across thousands of genes in concert in tissues and cells of interest. Despite the relatively recent application of microarrays to transplant research, they hold great promise for unraveling the staging of rejection, stratifying patients towards more individualized treatment regimes, and discovering noninvasive biomarkers for monitoring of intragraft events. Bioinformatics tools are being developed to sift through the large data sets generated as "genomic fingerprints" of the underlying biologic pathways. Gene clustering and class prediction tools allow discovery of diagnostic and prognostic molecular signatures of health and disease. Oligonucleotide-based microarrays also have utility in genotyping polymorphic markers. This report reviews the current literature of microarray use in transplantation research, compares currently available array platforms, and discusses future application of this technology to clinical organ transplantation.
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Affiliation(s)
- Elaine S Mansfield
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
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15
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Lesca G, Plauchu H, Coulet F, Lefebvre S, Plessis G, Odent S, Rivière S, Leheup B, Goizet C, Carette MF, Cordier JF, Pinson S, Soubrier F, Calender A, Giraud S. Molecular screening of ALK1/ACVRL1 and ENG genes in hereditary hemorrhagic telangiectasia in France. Hum Mutat 2004; 23:289-99. [PMID: 15024723 DOI: 10.1002/humu.20017] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Hereditary hemmorrhagic telangiectasia (HHT, or Osler-Rendu-Weber syndrome) is an autosomal dominant disease characterized by arteriovenous malformations, affecting 1 out of 10,000 individuals in France. The disease is caused by mutations of two genes: ENG and ALK1 (ACVRL1). We screened the coding sequence of ENG and ALK1 in 160 unrelated French index cases. A germline mutation was identified in 100 individuals (62.5%). A total of 36 mutations were found in ENG, including three nonsense mutations, 19 small insertions/deletions leading to a frameshift, two inframe deletions, seven missense mutations, and five intronic or splice-site mutations. Of the 36 mutations, 33 were novel mutations. A total of 64 mutations were found in ALK1, including six nonsense mutations, 28 small insertions/deletions leading to a frameshift, one inframe deletion, 27 missense mutations, and two intronic or splice-site mutations. Of the 64 mutations, 27 were novel mutations. Mutations were found in most parts of the coding sequence for both genes, except ALK1 exon 5 and ENG exons 12 to 14. Missense mutations in ALK1 were more frequent in exons 7, 8, and 10. ENG cDNA was sequenced for three intronic mutations: c.689+2T>C produced an abnormal transcript excluding exon 5, c.1103+3_1103+8del activated a cryptic splice site 22 bp upstream, and c.1428G>A produced two abnormal transcripts, one including intron 11 and the other excluding exon 10. Although most of the mutations were private, some recurrent mutations in ALK1 were of particular interest. Mutation c.1112_1113dupG (p.Gly371fsX391) was found in 17 unrelated individuals sharing a common haplotype, strongly suggesting a founder effect related to the concentration of patients previously reported in a specific French region (Rhône-Alpes). Three missense mutations involved the same codon: c.1231C>T (p.Arg411Trp), c.1232G>C (p.Arg411Pro), and c.1232G>A (p.Arg411Gln) were found in seven, two, and one patients, respectively. Haplotype analysis was in favor of both a founder effect and a mutation hot-spot.
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Affiliation(s)
- Gaëtan Lesca
- Laboratoire de Génétique, Hôpital Edouard Herriot, Lyon, France.
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Chua MS, Sarwal MM. Microarrays: new tools for transplantation research. Pediatr Nephrol 2003; 18:319-27. [PMID: 12700956 DOI: 10.1007/s00467-003-1083-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2001] [Revised: 11/11/2002] [Accepted: 11/22/2002] [Indexed: 12/25/2022]
Abstract
The advent of DNA microarray technology has greatly enhanced our potential to understand the molecular basis of human diseases and to aid in more accurate classification, diagnosis and/or prognosis. This powerful, flexible and highly informative technique has been adopted by many biomedical research disciplines. The use of DNA microarrays for gene expression profiling of patients undergoing organ transplantation has diagnostic and therapeutic potential. By generating global views of the gene expression changes in renal graft function post transplantation, DNA microarray technology will provide important information to improve our understanding of the molecular basis of various causes of graft dysfunction, and therefore suggest improved diagnosis, disease classification, and treatment.
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Affiliation(s)
- Mei-Sze Chua
- Department of Pediatrics, Stanford University School of Medicine, G320, 300 Pasteur Drive, CA 94305, Stanford, USA
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17
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Abstract
The robotic mouse is an autosomal dominant mutant that arose from a large-scale chemical mutagenesis program. It has a jerky, ataxic gait and develops adult-onset Purkinje cell loss in the cerebellum in a striking region-specific pattern, as well as cataracts. Genetic and physical mapping of the disease locus led to the identification of a missense mutation in a highly conserved region of Af4, a putative transcription factor that has been previously implicated in leukemogenesis. We demonstrate that Af4 is specifically expressed in Purkinje cells, and we hypothesize that the expression of mutant Af4 leads to neurodegeneration. This function was not identified through knock-out studies, highlighting the power of phenotype-driven mutagenesis in the mouse to identify new pathways involved in neurological disease.
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18
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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, 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] [Citation(s) in RCA: 4802] [Impact Index Per Article: 218.3] [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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Ponting CP, Russell RR. The natural history of protein domains. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2002; 31:45-71. [PMID: 11988462 DOI: 10.1146/annurev.biophys.31.082901.134314] [Citation(s) in RCA: 193] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome sequencing and structural genomics projects are providing new insights into the evolutionary history ofprote in domains. As methods for sequence and structure comparison improve, more distantly related domains are shown to be homologous. Thus there is a need for domain families to be classified within a hierarchy similar to Linnaeus' Systema Naturae, the classification of species. With such a hierarchy in mind, we discuss the evolution of domains, their combination into proteins, and evidence as to the likely origin of protein domains. We also discuss when and how analysis of domains can be used to understand details of protein function. Unconventional features of domain evolution such as intragenomic competition, domain insertion, horizontal gene transfer, and convergent evolution are seen as analogs of organismal evolutionary events. These parallels illustrate how the concept of domains can be applied to provide insights into evolutionary biology.
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Affiliation(s)
- Chris P Ponting
- Department of Human Anatomy and Genetics, University of Oxford, MRC Functional Genetics Unit, South Parks Road, Oxford OX1 3QX, UK.
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Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P. Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res 2002; 30:242-4. [PMID: 11752305 PMCID: PMC99073 DOI: 10.1093/nar/30.1.242] [Citation(s) in RCA: 511] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with particular emphasis on mobile eukaryotic domains. Extensive annotation for each domain family is available, providing information relating to function, subcellular localization, phyletic distribution and tertiary structure. The January 2002 release has added more than 200 hand-curated domain models. This brings the total to over 600 domain families that are widely represented among nuclear, signalling and extracellular proteins. Annotation now includes links to the Online Mendelian Inheritance in Man (OMIM) database in cases where a human disease is associated with one or more mutations in a particular domain. We have implemented new analysis methods and updated others. New advanced queries provide direct access to the SMART relational database using SQL. This database now contains information on intrinsic sequence features such as transmembrane regions, coiled-coils, signal peptides and internal repeats. SMART output can now be easily included in users' documents. A SMART mirror has been created at http://smart.ox.ac.uk.
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