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Rosikiewicz W, Suzuki Y, Makalowska I. OverGeneDB: a database of 5' end protein coding overlapping genes in human and mouse genomes. Nucleic Acids Res 2019; 46:D186-D193. [PMID: 29069459 PMCID: PMC5753363 DOI: 10.1093/nar/gkx948] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/20/2017] [Indexed: 01/24/2023] Open
Abstract
Gene overlap plays various regulatory functions on transcriptional and post-transcriptional levels. Most current studies focus on protein-coding genes overlapping with non-protein-coding counterparts, the so called natural antisense transcripts. Considerably less is known about the role of gene overlap in the case of two protein-coding genes. Here, we provide OverGeneDB, a database of human and mouse 5′ end protein-coding overlapping genes. The database contains 582 human and 113 mouse gene pairs that are transcribed using overlapping promoters in at least one analyzed library. Gene pairs were identified based on the analysis of the transcription start site (TSS) coordinates in 73 human and 10 mouse organs, tissues and cell lines. Beside TSS data, resources for 26 human lung adenocarcinoma cell lines also contain RNA-Seq and ChIP-Seq data for seven histone modifications and RNA Polymerase II activity. The collected data revealed that the overlap region is rarely conserved between the studied species and tissues. In ∼50% of the overlapping genes, transcription started explicitly in the overlap regions. In the remaining half of overlapping genes, transcription was initiated both from overlapping and non-overlapping TSSs. OverGeneDB is accessible at http://overgenedb.amu.edu.pl.
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Affiliation(s)
- Wojciech Rosikiewicz
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-712 Poznan, Poland
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 272-8562, Japan
| | - Izabela Makalowska
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, 61-712 Poznan, Poland
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Wezyk M, Szybinska A, Wojsiat J, Szczerba M, Day K, Ronnholm H, Kele M, Berdynski M, Peplonska B, Fichna JP, Ilkowski J, Styczynska M, Barczak A, Zboch M, Filipek-Gliszczynska A, Bojakowski K, Skrzypczak M, Ginalski K, Kabza M, Makalowska I, Barcikowska-Kotowicz M, Wojda U, Falk A, Zekanowski C. Overactive BRCA1 Affects Presenilin 1 in Induced Pluripotent Stem Cell-Derived Neurons in Alzheimer's Disease. J Alzheimers Dis 2019; 62:175-202. [PMID: 29439343 DOI: 10.3233/jad-170830] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The BRCA1 protein, one of the major players responsible for DNA damage response has recently been linked to Alzheimer's disease (AD). Using primary fibroblasts and neurons reprogrammed from induced pluripotent stem cells (iPSC) derived from familial AD (FAD) patients, we studied the role of the BRCA1 protein underlying molecular neurodegeneration. By whole-transcriptome approach, we have found wide range of disturbances in cell cycle and DNA damage response in FAD fibroblasts. This was manifested by significantly increased content of BRCA1 phosphorylated on Ser1524 and abnormal ubiquitination and subcellular distribution of presenilin 1 (PS1). Accordingly, the iPSC-derived FAD neurons showed increased content of BRCA1(Ser1524) colocalized with degraded PS1, accompanied by an enhanced immunostaining pattern of amyloid-β. Finally, overactivation of BRCA1 was followed by an increased content of Cdc25C phosphorylated on Ser216, likely triggering cell cycle re-entry in FAD neurons. This study suggests that overactivated BRCA1 could both influence PS1 turnover leading to amyloid-β pathology and promote cell cycle re-entry-driven cell death of postmitotic neurons in AD.
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Affiliation(s)
- Michalina Wezyk
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Aleksandra Szybinska
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Wojsiat
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Marcelina Szczerba
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Kelly Day
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Harriet Ronnholm
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Malin Kele
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Mariusz Berdynski
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland.,Department of Pharmacology and Clinical Neuroscience, Umea Universitet, Umea, Sweden
| | - Beata Peplonska
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Jakub Piotr Fichna
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Jan Ilkowski
- Department of Emergency Medicine, Faculty of Health Sciences, Poznan University of Medical Sciences, Poznan, Poland
| | - Maria Styczynska
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Anna Barczak
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Marzena Zboch
- Center of Alzheimer's Disease of Wroclaw Medical University, Scinawa, Poland
| | - Anna Filipek-Gliszczynska
- Clinical Department of Neurology, Extrapyramidal Disorders and Alzheimer's Outpatient Clinic, Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Krzysztof Bojakowski
- Clinical Department of General and Vascular Surgery, Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Warsaw, Poland
| | - Magdalena Skrzypczak
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Michal Kabza
- Department of Integrated Genomics, Institute of Anthropology, Adam Mickiewicz University, Poznan, Poland
| | - Izabela Makalowska
- Department of Integrated Genomics, Institute of Anthropology, Adam Mickiewicz University, Poznan, Poland
| | - Maria Barcikowska-Kotowicz
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
| | - Urszula Wojda
- Laboratory of Preclinical Testing of Higher Standard, Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Cezary Zekanowski
- Department of Neurodegenerative Disorders, Laboratory of Neurogenetics, Mossakowski Medical Research Centre Polish Academy of Sciences, Warsaw, Poland
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Golanowska M, Potrykus M, Motyka-Pomagruk A, Kabza M, Bacci G, Galardini M, Bazzicalupo M, Makalowska I, Smalla K, Mengoni A, Hugouvieux-Cotte-Pattat N, Lojkowska E. Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species. Front Microbiol 2018; 9:1940. [PMID: 30233505 PMCID: PMC6127512 DOI: 10.3389/fmicb.2018.01940] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 07/31/2018] [Indexed: 11/30/2022] Open
Abstract
Bacteria belonging to the genera Dickeya and Pectobacterium are responsible for significant economic losses in a wide variety of crops and ornamentals. During last years, increasing losses in potato production have been attributed to the appearance of Dickeya solani. The D. solani strains investigated so far share genetic homogeneity, although different virulence levels were observed among strains of various origins. The purpose of this study was to investigate the genetic traits possibly related to the diverse virulence levels by means of comparative genomics. First, we developed a new genome assembly pipeline which allowed us to complete the D. solani genomes. Four de novo sequenced and ten publicly available genomes were used to identify the structure of the D. solani pangenome, in which 74.8 and 25.2% of genes were grouped into the core and dispensable genome, respectively. For D. solani panregulon analysis, we performed a binding site prediction for four transcription factors, namely CRP, KdgR, PecS and Fur, to detect the regulons of these virulence regulators. Most of the D. solani potential virulence factors were predicted to belong to the accessory regulons of CRP, KdgR, and PecS. Thus, some differences in gene expression could exist between D. solani strains. The comparison between a highly and a low virulent strain, IFB0099 and IFB0223, respectively, disclosed only small differences between their genomes but significant differences in the production of virulence factors like pectinases, cellulases and proteases, and in their mobility. The D. solani strains also diverge in the number and size of prophages present in their genomes. Another relevant difference is the disruption of the adhesin gene fhaB2 in the highly virulent strain. Strain IFB0223, which has a complete adhesin gene, is less mobile and less aggressive than IFB0099. This suggests that in this case, mobility rather than adherence is needed in order to trigger disease symptoms. This study highlights the utility of comparative genomics in predicting D. solani traits involved in the aggressiveness of this emerging plant pathogen.
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Affiliation(s)
- Malgorzata Golanowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Marta Potrykus
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Agata Motyka-Pomagruk
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Michal Kabza
- Department of Integrative Genomics, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Giovanni Bacci
- Department of Biology, University of Florence, Florence, Italy
| | - Marco Galardini
- EMBL, EBI, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | | | - Izabela Makalowska
- Department of Integrative Genomics, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Kornelia Smalla
- Department of Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut - Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Alessio Mengoni
- Department of Biology, University of Florence, Florence, Italy
| | - Nicole Hugouvieux-Cotte-Pattat
- UMR5240 Microbiologie Adaptation et Pathogénie, Univ Lyon, CNRS, Univ Claude Bernard Lyon 1, INSA Lyon, Villeurbanne, France
| | - Ewa Lojkowska
- Department of Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
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Pande A, Brosius J, Makalowska I, Makalowski W, Raabe CA. Transcriptional interference by small transcripts in proximal promoter regions. Nucleic Acids Res 2018; 46:1069-1088. [PMID: 29309647 PMCID: PMC5815073 DOI: 10.1093/nar/gkx1242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 01/15/2023] Open
Abstract
Proximal promoter regions (PPR) are heavily transcribed yielding different types of small RNAs. The act of transcription within PPRs might regulate downstream gene expression via transcriptional interference (TI). For analysis, we investigated capped and polyadenylated small RNA transcripts within PPRs of human RefSeq genes in eight different cell lines. Transcripts of our datasets overlapped with experimentally determined transcription factor binding sites (TFBS). For TFBSs intersected by these small RNA transcripts, we established negative correlation of sRNA expression levels and transcription factor (TF) DNA binding affinities; suggesting that the transcripts acted via TI. Accordingly, datasets were designated as TFbiTrs (TF-binding interfering transcripts). Expression of most TFbiTrs was restricted to certain cell lines. This facilitated the analysis of effects related to TFbiTr expression for the same RefSeq genes across cell lines. We consistently uncovered higher relative TF/DNA binding affinities and concomitantly higher expression levels for RefSeq genes in the absence of TFbiTrs. Analysis of corresponding chromatin landscapes supported these results. ChIA-PET revealed the participation of distal enhancers in TFbiTr transcription. Enhancers regulating TFbiTrs, in effect, act as repressors for corresponding downstream RefSeq genes. We demonstrate the significant impact of TI on gene expression using selected small RNA datasets.
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Affiliation(s)
- Amit Pande
- Institute of Bioinformatics, University of Muenster, Niels-Stensen-Strasse 14, D-48149 Muenster, Germany
- Institute of Experimental Pathology (ZMBE), Centre for Molecular Biology of Inflammation, University of Muenster, Von-Esmarch-Strasse 56, D-48149 Muenster, Germany
- Brandenburg Medical School (MHB), Fehrbelliner Strasse 38, D-16816 Neuruppin, Germany
| | - Jürgen Brosius
- Institute of Experimental Pathology (ZMBE), Centre for Molecular Biology of Inflammation, University of Muenster, Von-Esmarch-Strasse 56, D-48149 Muenster, Germany
- Brandenburg Medical School (MHB), Fehrbelliner Strasse 38, D-16816 Neuruppin, Germany
| | - Izabela Makalowska
- Laboratory of Functional Genomics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznań, Poland
| | - Wojciech Makalowski
- Institute of Bioinformatics, University of Muenster, Niels-Stensen-Strasse 14, D-48149 Muenster, Germany
| | - Carsten A Raabe
- Institute of Experimental Pathology (ZMBE), Centre for Molecular Biology of Inflammation, University of Muenster, Von-Esmarch-Strasse 56, D-48149 Muenster, Germany
- Brandenburg Medical School (MHB), Fehrbelliner Strasse 38, D-16816 Neuruppin, Germany
- Institute of Medical Biochemistry (ZMBE), Centre for Molecular Biology of Inflammation, University of Muenster, Von-Esmarch-Strasse 56, D-48149 Muenster, Germany
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Rosikiewicz W, Kabza M, Kosinski JG, Ciomborowska-Basheer J, Kubiak MR, Makalowska I. RetrogeneDB-a database of plant and animal retrocopies. Database (Oxford) 2018; 2017:3964680. [PMID: 29220443 PMCID: PMC5509963 DOI: 10.1093/database/bax038] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/14/2017] [Indexed: 01/08/2023]
Abstract
For a long time, retrocopies were considered ‘junk DNA’, but numerous studies have shown that retrocopies may gain functionality and become so-called retrogenes. Retrogenes may code fully functional proteins that coexist with parental gene products or may even replace them. Retrocopies may also function as regulatory RNAs and, for example, become a source of small interfering RNAs, act as trans natural antisense transcripts or as alternative targets for miRNAs. Numerous researchers have emphasized that retrogenes play a crucial role in various organisms’ developmental stages and diseases. Despite the ever-growing evidence of the importance of retrocopies, resources dedicated to retroposition are very limited. Here, we report an update of the RetrogeneDB, which, to the best of our knowledge, is the largest database dedicated to retrocopies. It provides annotations of 86 458 retrocopies in 62 animal and 37 plant species. The database contains information about the retrocopies’ localization, open reading frame conservation, expression, RNA Polymerase II activity and the alternative transcription start site studies. Orthologous relationships between retrogenes were also determined, which made retrocopy conservation studies much more valuable. Additionally, based on the RNA-Seq data from the Geuvadis project, the expression levels of retrocopies were estimated in a total of 50 individuals from 5 human populations. The information is now presented in a new, more user-friendly web interface, with easy access to the source data, which may be used for the downstream analysis. RetrogeneDB is freely available at http://yeti.amu.edu.pl/retrogenedb. Database URL:http://yeti.amu.edu.pl/retrogenedb Secondary database URL:http://rhesus.amu.edu.pl/retrogenedb
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Affiliation(s)
- Wojciech Rosikiewicz
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Michal Kabza
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Jan G Kosinski
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Joanna Ciomborowska-Basheer
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Magdalena R Kubiak
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
| | - Izabela Makalowska
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614, Poznan, Poland
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Galka-Marciniak P, Olejniczak M, Starega-Roslan J, Szczesniak MW, Makalowska I, Krzyzosiak WJ. siRNA release from pri-miRNA scaffolds is controlled by the sequence and structure of RNA. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2016; 1859:639-49. [DOI: 10.1016/j.bbagrm.2016.02.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 01/17/2023]
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Olejniczak M, Urbanek MO, Jaworska E, Witucki L, Szczesniak MW, Makalowska I, Krzyzosiak WJ. Sequence-non-specific effects generated by various types of RNA interference triggers. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 2016; 1859:306-14. [DOI: 10.1016/j.bbagrm.2015.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 10/26/2015] [Accepted: 11/17/2015] [Indexed: 12/16/2022]
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Jensen PJ, Halbrendt N, Fazio G, Makalowska I, Altman N, Praul C, Maximova SN, Ngugi HK, Crassweller RM, Travis JW, McNellis TW. Rootstock-regulated gene expression patterns associated with fire blight resistance in apple. BMC Genomics 2012; 13:9. [PMID: 22229964 PMCID: PMC3277459 DOI: 10.1186/1471-2164-13-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2011] [Accepted: 01/09/2012] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Desirable apple varieties are clonally propagated by grafting vegetative scions onto rootstocks. Rootstocks influence many phenotypic traits of the scion, including resistance to pathogens such as Erwinia amylovora, which causes fire blight, the most serious bacterial disease of apple. The purpose of the present study was to quantify rootstock-mediated differences in scion fire blight susceptibility and to identify transcripts in the scion whose expression levels correlated with this response. RESULTS Rootstock influence on scion fire blight resistance was quantified by inoculating three-year old, orchard-grown apple trees, consisting of 'Gala' scions grafted to a range of rootstocks, with E. amylovora. Disease severity was measured by the extent of shoot necrosis over time. 'Gala' scions grafted to G.30 or MM.111 rootstocks showed the lowest rates of necrosis, while 'Gala' on M.27 and B.9 showed the highest rates of necrosis. 'Gala' scions on M.7, S.4 or M.9F56 had intermediate necrosis rates. Using an apple DNA microarray representing 55,230 unique transcripts, gene expression patterns were compared in healthy, un-inoculated, greenhouse-grown 'Gala' scions on the same series of rootstocks. We identified 690 transcripts whose steady-state expression levels correlated with the degree of fire blight susceptibility of the scion/rootstock combinations. Transcripts known to be differentially expressed during E. amylovora infection were disproportionately represented among these transcripts. A second-generation apple microarray representing 26,000 transcripts was developed and was used to test these correlations in an orchard-grown population of trees segregating for fire blight resistance. Of the 690 transcripts originally identified using the first-generation array, 39 had expression levels that correlated with fire blight resistance in the breeding population. CONCLUSIONS Rootstocks had significant effects on the fire blight susceptibility of 'Gala' scions, and rootstock-regulated gene expression patterns could be correlated with differences in susceptibility. The results suggest a relationship between rootstock-regulated fire blight susceptibility and sorbitol dehydrogenase, phenylpropanoid metabolism, protein processing in the endoplasmic reticulum, and endocytosis, among others. This study illustrates the utility of our rootstock-regulated gene expression data sets for candidate trait-associated gene data mining.
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Affiliation(s)
- Philip J Jensen
- Department of Plant Pathology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Noemi Halbrendt
- Department of Plant Pathology, The Pennsylvania State University, University Park, PA 16802, USA
- The Pennsylvania State University Fruit Research and Extension Center, Biglerville, PA 17307, USA
| | - Gennaro Fazio
- USDA/ARS, Plant Genetics Research Unit, Geneva, NY 14456, USA
| | - Izabela Makalowska
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Naomi Altman
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Craig Praul
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Siela N Maximova
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802, USA
| | - Henry K Ngugi
- Department of Plant Pathology, The Pennsylvania State University, University Park, PA 16802, USA
- The Pennsylvania State University Fruit Research and Extension Center, Biglerville, PA 17307, USA
| | - Robert M Crassweller
- Department of Horticulture, The Pennsylvania State University, University Park, PA 16802, USA
| | - James W Travis
- Department of Plant Pathology, The Pennsylvania State University, University Park, PA 16802, USA
- The Pennsylvania State University Fruit Research and Extension Center, Biglerville, PA 17307, USA
| | - Timothy W McNellis
- Department of Plant Pathology, The Pennsylvania State University, University Park, PA 16802, USA
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Szcześniak MW, Deorowicz S, Gapski J, Kaczyński Ł, Makalowska I. miRNEST database: an integrative approach in microRNA search and annotation. Nucleic Acids Res 2011; 40:D198-204. [PMID: 22135287 PMCID: PMC3245016 DOI: 10.1093/nar/gkr1159] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Despite accumulating data on animal and plant microRNAs and their functions, existing public miRNA resources usually collect miRNAs from a very limited number of species. A lot of microRNAs, including those from model organisms, remain undiscovered. As a result there is a continuous need to search for new microRNAs. We present miRNEST (http://mirnest.amu.edu.pl), a comprehensive database of animal, plant and virus microRNAs. The core part of the database is built from our miRNA predictions conducted on Expressed Sequence Tags of 225 animal and 202 plant species. The miRNA search was performed based on sequence similarity and as many as 10 004 miRNA candidates in 221 animal and 199 plant species were discovered. Out of them only 299 have already been deposited in miRBase. Additionally, miRNEST has been integrated with external miRNA data from literature and 13 databases, which includes miRNA sequences, small RNA sequencing data, expression, polymorphisms and targets data as well as links to external miRNA resources, whenever applicable. All this makes miRNEST a considerable miRNA resource in a sense of number of species (544) that integrates a scattered miRNA data into a uniform format with a user-friendly web interface.
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Affiliation(s)
- Michał Wojciech Szcześniak
- Laboratory of Bioinformatics, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland.
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Park J, Park B, Veeraraghavan N, Jung K, Lee YH, Blair JE, Geiser DM, Isard S, Mansfield MA, Nikolaeva E, Park SY, Russo J, Kim SH, Greene M, Ivors KL, Balci Y, Peiman M, Erwin DC, Coffey MD, Rossman A, Farr D, Cline E, Grünwald NJ, Luster DG, Schrandt J, Martin F, Ribeiro OK, Makalowska I, Kang S. Phytophthora Database: A Forensic Database Supporting the Identification and Monitoring of Phytophthora. Plant Dis 2008; 92:966-972. [PMID: 30769728 DOI: 10.1094/pdis-92-6-0966] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytophthora spp. represent a serious threat to agricultural and ecological systems. Many novel Phytophthora spp. have been reported in recent years, which is indicative of our limited understanding of the ecology and diversity of Phytophthora spp. in nature. Systematic cataloging of genotypic and phenotypic information on isolates of previously described species serves as a baseline for identification, classification, and risk assessment of new Phytophthora isolates. The Phytophthora Database (PD) was established to catalog such data in a web-accessible and searchable format. To support the identification of new Phytophthora isolates via comparison of their sequences at one or more loci with the corresponding sequences derived from the isolates archived in the PD, we generated and deposited sequence data from more than 1,500 isolates representing the known diversity in the genus. Data search and analysis tools in the PD include BLAST, Phyloviewer (a program for building phylogenetic trees using sequences of selected isolates), and Virtual Gel (a program for generating expected restriction patterns for given sequences). The PD also provides a customized means of storing and sharing data via the web. The PD serves as a model that easily can be adopted to develop databases for other important pathogen groups.
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Affiliation(s)
- Jongsun Park
- School of Agricultural Biotechnology and Fungal Bioinformatics Laboratory, Seoul National University, Seoul, Korea
| | | | | | - Kyongyong Jung
- School of Agricultural Biotechnology and Fungal Bioinformatics Laboratory, Seoul National University
| | - Yong-Hwan Lee
- School of Agricultural Biotechnology and Fungal Bioinformatics Laboratory, Seoul National University
| | - Jaime E Blair
- Department of Plant Pathology, Pennsylvania State University
| | - David M Geiser
- Department of Plant Pathology, Pennsylvania State University
| | - Scott Isard
- Department of Plant Pathology, Pennsylvania State University
| | | | | | - Sook-Young Park
- Department of Plant Pathology, Pennsylvania State University
| | | | - Seong H Kim
- Pennsylvania Department of Agriculture, Harrisburg 17110
| | - Matthew Greene
- Mountain Horticultural Crops Research & Extension Center, North Carolina State University, Fletcher 28732
| | - Kelly L Ivors
- Mountain Horticultural Crops Research & Extension Center, North Carolina State University, Fletcher 28732
| | - Yilmaz Balci
- Division of Plant & Soil Sciences, West Virginia University, Morgantown 26506
| | - Masoomeh Peiman
- Department of Plant Pathology, University of California, Riverside 92521
| | - Donald C Erwin
- Department of Plant Pathology, University of California, Riverside 92521
| | - Michael D Coffey
- Department of Plant Pathology, University of California, Riverside 92521
| | - Amy Rossman
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Systematic Botany & Mycology Laboratory, Beltsville, MD 20705
| | - David Farr
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Systematic Botany & Mycology Laboratory, Beltsville, MD 20705
| | - Erica Cline
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Systematic Botany & Mycology Laboratory, Beltsville, MD 20705
| | | | - Douglas G Luster
- USDA-ARS, Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702
| | | | | | | | | | - Seogchan Kang
- Department of Plant Pathology, Pennsylvania State University
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11
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Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda JI, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo MDF, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res 2007; 36:D793-9. [PMID: 18089548 PMCID: PMC2238988 DOI: 10.1093/nar/gkm999] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein-protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.
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Affiliation(s)
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- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan
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12
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Kang S, Blair JE, Geiser DM, Khang CH, Park SY, Gahegan M, O'Donnell K, Luster DG, Kim SH, Ivors KL, Lee YH, Lee YW, Grünwald NJ, Martin FM, Coffey MD, Veeraraghavan N, Makalowska I. Plant pathogen culture collections: it takes a village to preserve these resources vital to the advancement of agricultural security and plant pathology. Phytopathology 2006; 96:920-925. [PMID: 18944046 DOI: 10.1094/phyto-96-0920] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
ABSTRACT Plant pathogen culture collections are essential resources in our fight against plant disease and for connecting discoveries of the present with established knowledge of the past. However, available infrastructure in support of culture collections is in serious need of improvement, and we continually face the risk of losing many of these collections. As novel and reemerging plant pathogens threaten agriculture, their timely identification and monitoring depends on rapid access to cultures representing the known diversity of plant pathogens along with genotypic, phenotypic, and epidemiological data associated with them. Archiving such data in a format that can be easily accessed and searched is essential for rapid assessment of potential risk and can help track the change and movement of pathogens. The underexplored pathogen diversity in nature further underscores the importance of cataloguing pathogen cultures. Realizing the potential of pathogen genomics as a foundation for developing effective disease control also hinges on how effectively we use the sequenced isolate as a reference to understand the genetic and phenotypic diversity within a pathogen species. In this letter, we propose a number of measures for improving pathogen culture collections.
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13
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Cui L, Veeraraghavan N, Richter A, Wall K, Jansen RK, Leebens-Mack J, Makalowska I, dePamphilis CW. ChloroplastDB: the Chloroplast Genome Database. Nucleic Acids Res 2006; 34:D692-6. [PMID: 16381961 PMCID: PMC1347418 DOI: 10.1093/nar/gkj055] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Chloroplast Genome Database (ChloroplastDB) is an interactive, web-based database for fully sequenced plastid genomes, containing genomic, protein, DNA and RNA sequences, gene locations, RNA-editing sites, putative protein families and alignments (http://chloroplast.cbio.psu.edu/). With recent technical advances, the rate of generating new organelle genomes has increased dramatically. However, the established ontology for chloroplast genes and gene features has not been uniformly applied to all chloroplast genomes available in the sequence databases. For example, annotations for some published genome sequences have not evolved with gene naming conventions. ChloroplastDB provides unified annotations, gene name search, BLAST and download functions for chloroplast encoded genes and genomic sequences. A user can retrieve all orthologous sequences with one search regardless of gene names in GenBank. This feature alone greatly facilitates comparative research on sequence evolution including changes in gene content, codon usage, gene structure and post-transcriptional modifications such as RNA editing. Orthologous protein sets are classified by TribeMCL and each set is assigned a standard gene name. Over the next few years, as the number of sequenced chloroplast genomes increases rapidly, the tools available in ChloroplastDB will allow researchers to easily identify and compile target data for comparative analysis of chloroplast genes and genomes.
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Affiliation(s)
| | - Narayanan Veeraraghavan
- Center for Computational Genomics, Huck Institutes of Life Sciences, The Pennsylvania State UniversityUniversity Park, PA 16802, USA
| | - Alexander Richter
- Center for Computational Genomics, Huck Institutes of Life Sciences, The Pennsylvania State UniversityUniversity Park, PA 16802, USA
| | | | - Robert K. Jansen
- Section of Integrative Biology, The University of Texas at AustinAustin, TX 78712, USA
| | | | - Izabela Makalowska
- Center for Computational Genomics, Huck Institutes of Life Sciences, The Pennsylvania State UniversityUniversity Park, PA 16802, USA
| | - Claude W. dePamphilis
- To whom correspondence should be addressed. Tel: +1 814 863 6412; Fax: +1 814 865 9131;
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14
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Lamason RL, Mohideen MAPK, Mest JR, Wong AC, Norton HL, Aros MC, Jurynec MJ, Mao X, Humphreville VR, Humbert JE, Sinha S, Moore JL, Jagadeeswaran P, Zhao W, Ning G, Makalowska I, McKeigue PM, O'donnell D, Kittles R, Parra EJ, Mangini NJ, Grunwald DJ, Shriver MD, Canfield VA, Cheng KC. SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 2006; 310:1782-6. [PMID: 16357253 DOI: 10.1126/science.1116238] [Citation(s) in RCA: 725] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Lighter variations of pigmentation in humans are associated with diminished number, size, and density of melanosomes, the pigmented organelles of melanocytes. Here we show that zebrafish golden mutants share these melanosomal changes and that golden encodes a putative cation exchanger slc24a5 (nckx5) that localizes to an intracellular membrane, likely the melanosome or its precursor. The human ortholog is highly similar in sequence and functional in zebrafish. The evolutionarily conserved ancestral allele of a human coding polymorphism predominates in African and East Asian populations. In contrast, the variant allele is nearly fixed in European populations, is associated with a substantial reduction in regional heterozygosity, and correlates with lighter skin pigmentation in admixed populations, suggesting a key role for the SLC24A5 gene in human pigmentation.
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Affiliation(s)
- Rebecca L Lamason
- Jake Gittlen Cancer Research Foundation, Department of Pathology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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15
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Abstract
Overlapping genes in mammalian genomes are unexpected phenomena even though hundreds of pairs of protein coding overlapping genes have been reported so far. Overlapping genes can be divided into different categories based on direction of transcription as well as on sequence segments being shared between overlapping coding regions. The biologic functions of natural antisense transcripts, their involvement in physiological processes and gene regulation in living organisms are not fully understood. Number of documented examples indicates that they may exert control at various levels of gene expression, such as transcription, mRNA processing, splicing, stability, transport, and translation. Similarly, evolutionary origin of such genes is not known, existing hypotheses can explain only selected cases of mammalian gene overlaps which could originate as result of rearrangements, overprinting and/or adoption of signals in the neighboring gene locus.
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Affiliation(s)
- Izabela Makalowska
- The Huck Institute of the Life Sciences, The Pennsylvania State University, 502 Wartik Lab, University Park, PA 16802, USA.
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16
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Abstract
In mammals, the cell surface receptors encoded by the leukocyte receptor complex (LRC) regulate the activity of T lymphocytes and B lymphocytes, as well as that of natural killer cells, and thus provide protection against pathogens and parasites. The chicken genome encodes many Ig-like receptors that are homologous to the LRC receptors. The chicken Ig-like receptor (CHIR) genes are members of a large monophyletic gene family and are organized into genomic clusters, which are in conserved synteny with the mammalian LRC. One-third of CHIR genes encode polypeptide molecules that contain both activating and inhibitory motifs. These genes are present in different phylogenetic groups, suggesting that the primordial CHIR gene could have encoded both types of motifs in a single molecule. In contrast to the mammalian LRC genes, the CHIR genes with similar function (inhibition or activation) are evolutionarily closely related. We propose that, in addition to recombination, single nucleotide substitutions played an important role in the generation of receptors with different functions. Structural models and amino acid analyses of the CHIR proteins reveal the presence of different types of Ig-like domains in the same phylogenetic groups, as well as sharing of conserved residues and conserved changes of residues between different CHIR groups and between CHIRs and LRCs. Our data support the notion that the CHIR gene clusters are regions homologous to the mammalian LRC gene cluster and favor a model of evolution by repeated processes of birth and death (expansion-contraction) of the Ig-like receptor genes.
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Affiliation(s)
- Nikolas Nikolaidis
- Institute of Molecular Evolutionary Genetics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
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17
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Geiser DM, del Mar Jiménez-Gasco M, Kang S, Makalowska I, Veeraraghavan N, Ward TJ, Zhang N, Kuldau GA, O'donnell K. FUSARIUM-ID v. 1.0: A DNA Sequence Database for Identifying Fusarium. European Journal of Plant Pathology 2004; 110:473-479. [PMID: 0 DOI: 10.1023/b:ejpp.0000032386.75915.a0] [Citation(s) in RCA: 472] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
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18
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Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda JI, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo MDF, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, R. Gopinath G, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol 2004; 2:e162. [PMID: 15103394 PMCID: PMC393292 DOI: 10.1371/journal.pbio.0020162] [Citation(s) in RCA: 267] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Accepted: 04/01/2004] [Indexed: 01/08/2023] Open
Abstract
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
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Affiliation(s)
- Tadashi Imanishi
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Takeshi Itoh
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 2Bioinformatics Laboratory, Genome Research Department, National Institute of Agrobiological SciencesIbarakiJapan
| | - Yutaka Suzuki
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
- 68Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of TokyoTokyoJapan
| | - Claire O'Donovan
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Satoshi Fukuchi
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | | | - Roberto A Barrero
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Takuro Tamura
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
- 8BITS CompanyShizuokaJapan
| | - Yumi Yamaguchi-Kabata
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Motohiko Tanino
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Kei Yura
- 9Quantum Bioinformatics Group, Center for Promotion of Computational Science and Engineering, Japan Atomic Energy Research InstituteKyotoJapan
| | - Satoru Miyazaki
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Kazuho Ikeo
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Keiichi Homma
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Arek Kasprzyk
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Tetsuo Nishikawa
- 10Reverse Proteomics Research InstituteChibaJapan
- 11Central Research Laboratory, HitachiTokyoJapan
| | - Mika Hirakawa
- 12Bioinformatics Center, Institute for Chemical Research, Kyoto UniversityKyotoJapan
| | - Jean Thierry-Mieg
- 13National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MarylandUnited States of America
- 14Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique MathematiqueMontpellierFrance
| | - Danielle Thierry-Mieg
- 13National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MarylandUnited States of America
- 14Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique MathematiqueMontpellierFrance
| | - Jennifer Ashurst
- 15The Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Libin Jia
- 16National Cancer Institute, National Institutes of HealthBethesda, MarylandUnited States of America
| | - Mitsuteru Nakao
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Michael A Thomas
- 17Department of Biological Sciences, Idaho State UniversityPocatello, IdahoUnited States of America
| | - Nicola Mulder
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Youla Karavidopoulou
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Lihua Jin
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Sangsoo Kim
- 18Korea Research Institute of Bioscience and BiotechnologyTaejeonKorea
| | | | - Boris Lenhard
- 19Center for Genomics and Bioinformatics, Karolinska InstitutetStockholmSweden
| | - Eric Eveno
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | - Yoshiyuki Suzuki
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Chisato Yamasaki
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Jun-ichi Takeda
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Craig Gough
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Phillip Hilton
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Yasuyuki Fujii
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Hiroaki Sakai
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
- 22Tokyo Research Laboratories, Kyowa Hakko Kogyo CompanyTokyoJapan
| | - Susumu Tanaka
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Clara Amid
- 23MIPS—Institute for Bioinformatics, GSF—National Research Center for Environment and HealthNeuherbergGermany
| | - Matthew Bellgard
- 24Centre for Bioinformatics and Biological Computing, School of Information Technology, Murdoch UniversityMurdoch, Western AustraliaAustralia
| | - Maria de Fatima Bonaldo
- 25Medical Education and Biomedical Research Facility, University of IowaIowa City, IowaUnited States of America
| | - Hidemasa Bono
- 26Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Susan K Bromberg
- 27Medical College of Wisconsin, MilwaukeeWisconsinUnited States of America
| | - Anthony J Brookes
- 19Center for Genomics and Bioinformatics, Karolinska InstitutetStockholmSweden
| | - Elspeth Bruford
- 28HUGO Gene Nomenclature Committee, University College LondonLondonUnited Kingdom
| | | | - Claude Chelala
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
| | - Christine Couillault
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | | | - Marie-Anne Debily
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
| | | | - Inna Dubchak
- 32Lawrence Berkeley National Laboratory, BerkeleyCaliforniaUnited States of America
| | - Toshinori Endo
- 33Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental UniversityTokyoJapan
| | | | - Eduardo Eyras
- 15The Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Kaoru Fukami-Kobayashi
- 35Bioresource Information Division, RIKEN BioResource Center, RIKEN Tsukuba InstituteIbarakiJapan
| | - Gopal R. Gopinath
- 36Genome Knowledgebase, Cold Spring Harbor LaboratoryCold Spring Harbor, New YorkUnited States of America
| | - Esther Graudens
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | - Yoonsoo Hahn
- 18Korea Research Institute of Bioscience and BiotechnologyTaejeonKorea
| | - Michael Han
- 23MIPS—Institute for Bioinformatics, GSF—National Research Center for Environment and HealthNeuherbergGermany
| | - Ze-Guang Han
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
- 37Chinese National Human Genome Center at ShanghaiShanghaiChina
| | - Kousuke Hanada
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Hideki Hanaoka
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Erimi Harada
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Katsuyuki Hashimoto
- 38Division of Genetic Resources, National Institute of Infectious DiseasesTokyoJapan
| | - Ursula Hinz
- 34Swiss Institute of BioinformaticsGenevaSwitzerland
| | - Momoki Hirai
- 39Graduate School of Frontier Sciences, Department of Integrated Biosciences, University of TokyoChibaJapan
| | - Teruyoshi Hishiki
- 40Functional Genomics Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Ian Hopkinson
- 41Department of Primary Care and Population Sciences, Royal Free University College Medical School, University College LondonLondonUnited Kingdom
- 42Clinical and Molecular Genetics Unit, The Institute of Child HealthLondonUnited Kingdom
| | - Sandrine Imbeaud
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | - Hidetoshi Inoko
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
- 43Department of Genetic Information, Division of Molecular Life Science, School of Medicine, Tokai UniversityKanagawaJapan
| | - Alexander Kanapin
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Yayoi Kaneko
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Takeya Kasukawa
- 26Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Janet Kelso
- 44South African National Bioinformatics Institute, University of the Western CapeBellvilleSouth Africa
| | - Paul Kersey
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | | | | | - Bernhard Korn
- 46RZPD Resource Center for Genome ResearchHeidelbergGermany
| | - Vladimir Kuryshev
- 47Molecular Genome Analysis, German Cancer Research Center-DKFZHeidelbergGermany
| | - Izabela Makalowska
- 48Pennsylvania State UniversityUniversity Park, PennsylvaniaUnited States of America
| | - Takashi Makino
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Shuhei Mano
- 43Department of Genetic Information, Division of Molecular Life Science, School of Medicine, Tokai UniversityKanagawaJapan
| | - Regine Mariage-Samson
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
| | - Jun Mashima
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Hideo Matsuda
- 49Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka UniversityOsakaJapan
| | - Hans-Werner Mewes
- 23MIPS—Institute for Bioinformatics, GSF—National Research Center for Environment and HealthNeuherbergGermany
| | - Shinsei Minoshima
- 50Medical Photobiology Department, Photon Medical Research Center, Hamamatsu University School of MedicineShizuokaJapan
- 52Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | | | - Hideki Nagasaki
- 51Computational Biology Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Naoki Nagata
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Rajni Nigam
- 27Medical College of Wisconsin, MilwaukeeWisconsinUnited States of America
| | - Osamu Ogasawara
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | | | - Masafumi Ohtsubo
- 52Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Norihiro Okada
- 53Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of TechnologyKanagawaJapan
| | - Toshihisa Okido
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Satoshi Oota
- 35Bioresource Information Division, RIKEN BioResource Center, RIKEN Tsukuba InstituteIbarakiJapan
| | - Motonori Ota
- 54Global Scientific Information and Computing Center, Tokyo Institute of TechnologyTokyoJapan
| | - Toshio Ota
- 22Tokyo Research Laboratories, Kyowa Hakko Kogyo CompanyTokyoJapan
| | - Tetsuji Otsuki
- 55Molecular Biology Laboratory, Medicinal Research Laboratories, Taisho Pharmaceutical CompanySaitamaJapan
| | | | - Annemarie Poustka
- 47Molecular Genome Analysis, German Cancer Research Center-DKFZHeidelbergGermany
| | - Shuang-Xi Ren
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
- 37Chinese National Human Genome Center at ShanghaiShanghaiChina
| | - Naruya Saitou
- 56Department of Population Genetics, National Institute of GeneticsShizuokaJapan
| | - Katsunaga Sakai
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Shigetaka Sakamoto
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Ryuichi Sakate
- 39Graduate School of Frontier Sciences, Department of Integrated Biosciences, University of TokyoChibaJapan
| | - Ingo Schupp
- 47Molecular Genome Analysis, German Cancer Research Center-DKFZHeidelbergGermany
| | - Florence Servant
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Stephen Sherry
- 13National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MarylandUnited States of America
| | - Rie Shiba
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Nobuyoshi Shimizu
- 52Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Mary Shimoyama
- 27Medical College of Wisconsin, MilwaukeeWisconsinUnited States of America
| | | | - Bento Soares
- 25Medical Education and Biomedical Research Facility, University of IowaIowa City, IowaUnited States of America
| | - Charles Steward
- 15The Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Makiko Suwa
- 51Computational Biology Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Mami Suzuki
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Aiko Takahashi
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Gen Tamiya
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
- 43Department of Genetic Information, Division of Molecular Life Science, School of Medicine, Tokai UniversityKanagawaJapan
| | - Hiroshi Tanaka
- 33Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental UniversityTokyoJapan
| | - Todd Taylor
- 57Human Genome Research Group, Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Joseph D Terwilliger
- 58Columbia University and Columbia Genome CenterNew York, New YorkUnited States of America
| | - Per Unneberg
- 59Department of Biotechnology, Royal Institute of TechnologyStockholmSweden
| | - Vamsi Veeramachaneni
- 48Pennsylvania State UniversityUniversity Park, PennsylvaniaUnited States of America
| | - Shinya Watanabe
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Laurens Wilming
- 15The Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Norikazu Yasuda
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Hyang-Sook Yoo
- 18Korea Research Institute of Bioscience and BiotechnologyTaejeonKorea
| | - Marvin Stodolsky
- 60Biology Division and Genome Task Group, Office of Biological and Environmental Research, United States Department of EnergyWashington, D.CUnited States of America
| | - Wojciech Makalowski
- 48Pennsylvania State UniversityUniversity Park, PennsylvaniaUnited States of America
| | - Mitiko Go
- 61Faculty of Bio-Science, Nagahama Institute of Bio-Science and TechnologyShigaJapan
| | - Kenta Nakai
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Toshihisa Takagi
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Minoru Kanehisa
- 12Bioinformatics Center, Institute for Chemical Research, Kyoto UniversityKyotoJapan
| | - Yoshiyuki Sakaki
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
- 57Human Genome Research Group, Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - John Quackenbush
- 62Institute for Genomic ResearchRockville, MarylandUnited States of America
| | - Yasushi Okazaki
- 26Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Yoshihide Hayashizaki
- 26Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Winston Hide
- 44South African National Bioinformatics Institute, University of the Western CapeBellvilleSouth Africa
| | - Ranajit Chakraborty
- 63Center for Genome Information, Department of Environmental Health, University of CincinnatiCincinnati, OhioUnited States of America
| | - Ken Nishikawa
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Hideaki Sugawara
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Yoshio Tateno
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Zhu Chen
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
- 37Chinese National Human Genome Center at ShanghaiShanghaiChina
- 64State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Second Medical UniversityShanghaiChina
| | | | - Peter Tonellato
- 65PointOne SystemsWauwatosa, WisconsinUnited States of America
| | - Rolf Apweiler
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Kousaku Okubo
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
- 40Functional Genomics Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Lukas Wagner
- 13National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MarylandUnited States of America
| | - Stefan Wiemann
- 47Molecular Genome Analysis, German Cancer Research Center-DKFZHeidelbergGermany
| | - Robert L Strausberg
- 16National Cancer Institute, National Institutes of HealthBethesda, MarylandUnited States of America
| | - Takao Isogai
- 10Reverse Proteomics Research InstituteChibaJapan
- 66Graduate School of Life and Environmental Sciences, University of TsukubaIbarakiJapan
| | - Charles Auffray
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | - Nobuo Nomura
- 40Functional Genomics Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Takashi Gojobori
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
- 67Department of Genetics, Graduate University for Advanced StudiesShizuokaJapan
| | - Sumio Sugano
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
- 40Functional Genomics Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 68Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of TokyoTokyoJapan
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19
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Cohen-Solal KA, Sood R, Marin Y, Crespo-Carbone SM, Sinsimer D, Martino JJ, Robbins C, Makalowska I, Trent J, Chen S. Identification and characterization of mouse Rab32 by mRNA and protein expression analysis. Biochim Biophys Acta 2003; 1651:68-75. [PMID: 14499590 DOI: 10.1016/s1570-9639(03)00236-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Rab proteins, a subfamily of the ras superfamily, are low molecular weight GTPases involved in the regulation of intracellular vesicular transport. Cloning of human RAB32 was recently described. Presently, we report the cloning and characterization of the mouse homologue of Rab32. We show that murine Rab32 exhibits a ubiquitous expression pattern, with tissue-specific variation in expression level. Three cell types with highly specialized organelles, melanocytes, platelets and mast cells, exhibit relatively high level of Rab32. We show that in murine amelanotic in vitro transformed melanocytes as well as in human amelanotic metastatic melanoma cell lines, the expression of Rab32 is markedly reduced or absent, in parallel with the loss of expression of two key enzymes for the production of melanin, tyrosinase and Tyrp1. Therefore, in both mouse and human systems, the expression of Rab32 correlates with the expression of genes involved in pigment production. However, in melanoma samples, amelanotic due to a mutation in the tyrosinase gene, the expression of Rab32 remains at levels comparable to those observed in pigmented melanoma samples. Finally, we observed co-localization of Rab32 and the melanosomal proteins, Tyrp1 and Dct, indicating an association of Rab32 with melanosomes. Based on these data, we propose the inclusion of Rab32 to the so-called melanocyte/platelet family of Rab proteins.
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Affiliation(s)
- Karine A Cohen-Solal
- Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
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20
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Sood R, Makalowska I, Galdzicki M, Hu P, Eddings E, Robbins CM, Moses T, Namkoong J, Chen S, Trent JM. Cloning and characterization of a novel gene, SHPRH, encoding a conserved putative protein with SNF2/helicase and PHD-finger domains from the 6q24 region. Genomics 2003; 82:153-61. [PMID: 12837266 DOI: 10.1016/s0888-7543(03)00121-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Here we report the identification of a novel transcript containing SNF2, PHD-finger, RING-finger, helicase, and linker histone domains mapping to the q24 band region of human chromosome 6. These domains are characteristic of several DNA repair proteins, transcription factors, and helicases. We have cloned both human and mouse homologs of this novel gene using interexon PCR and RACE technologies. The human cDNA, termed SHPRH, is 6018 bp and codes for a putative protein of 1683 amino acids. The mouse cDNA, termed Shprh, is 7225 bp and codes for a putative protein of 1616 amino acids. The deduced amino acid sequences of the two proteins share 86% identity. Both genes are expressed ubiquitously, with a transcript size of approximately 7.5 kb. Mapping of this gene to 6q24, a region reported to contain a tumor suppressor locus, prompted us to evaluate SHPRH by mutation analysis in tumor cell lines. We have identified one truncating and three missense mutations, thus suggesting SHPRH as a possible candidate for the tumor suppressor gene.
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Affiliation(s)
- Raman Sood
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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21
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Pollock PM, Cohen-Solal K, Sood R, Namkoong J, Martino JJ, Koganti A, Zhu H, Robbins C, Makalowska I, Shin SS, Marin Y, Roberts KG, Yudt LM, Chen A, Cheng J, Incao A, Pinkett HW, Graham CL, Dunn K, Crespo-Carbone SM, Mackason KR, Ryan KB, Sinsimer D, Goydos J, Reuhl KR, Eckhaus M, Meltzer PS, Pavan WJ, Trent JM, Chen S. Melanoma mouse model implicates metabotropic glutamate signaling in melanocytic neoplasia. Nat Genet 2003; 34:108-12. [PMID: 12704387 DOI: 10.1038/ng1148] [Citation(s) in RCA: 227] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2002] [Accepted: 03/28/2003] [Indexed: 01/09/2023]
Abstract
To gain insight into melanoma pathogenesis, we characterized an insertional mouse mutant, TG3, that is predisposed to develop multiple melanomas. Physical mapping identified multiple tandem insertions of the transgene into intron 3 of Grm1 (encoding metabotropic glutamate receptor 1) with concomitant deletion of 70 kb of intronic sequence. To assess whether this insertional mutagenesis event results in alteration of transcriptional regulation, we analyzed Grm1 and two flanking genes for aberrant expression in melanomas from TG3 mice. We observed aberrant expression of only Grm1. Although we did not detect its expression in normal mouse melanocytes, Grm1 was ectopically expressed in the melanomas from TG3 mice. To confirm the involvement of Grm1 in melanocytic neoplasia, we created an additional transgenic line with Grm1 expression driven by the dopachrome tautomerase promoter. Similar to the original TG3, the Tg(Grm1)EPv line was susceptible to melanoma. In contrast to human melanoma, these transgenic mice had a generalized hyperproliferation of melanocytes with limited transformation to fully malignant metastasis. We detected expression of GRM1 in a number of human melanoma biopsies and cell lines but not in benign nevi and melanocytes. This study provides compelling evidence for the importance of metabotropic glutamate signaling in melanocytic neoplasia.
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Affiliation(s)
- Pamela M Pollock
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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22
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Giardine B, Elnitski L, Riemer C, Makalowska I, Schwartz S, Miller W, Hardison RC. GALA, a database for genomic sequence alignments and annotations. Genome Res 2003; 13:732-41. [PMID: 12671007 PMCID: PMC430176 DOI: 10.1101/gr.603103] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2002] [Accepted: 01/24/2003] [Indexed: 01/26/2023]
Abstract
We have developed a relational database to contain whole genome sequence alignments between human and mouse with extensive annotations of the human sequence. Complex queries are supported on recorded features, both directly and on proximity among them. Searches can reveal a wide variety of relationships, such as finding all genes expressed in a designated tissue that have a highly conserved noncoding sequence 5' to the start site. Other examples are finding single nucleotide polymorphisms that occur in conserved noncoding regions upstream of genes and identifying CpG islands that overlap the 5' ends of divergently transcribed genes. The database is available online at http://globin.cse.psu.edu/ and http://bio.cse.psu.edu/.
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Affiliation(s)
- Belinda Giardine
- Department of Computer Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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23
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Rosenberg MJ, Agarwala R, Bouffard G, Davis J, Fiermonte G, Hilliard MS, Koch T, Kalikin LM, Makalowska I, Morton DH, Petty EM, Weber JL, Palmieri F, Kelley RI, Schäffer AA, Biesecker LG. Mutant deoxynucleotide carrier is associated with congenital microcephaly. Nat Genet 2002; 32:175-9. [PMID: 12185364 DOI: 10.1038/ng948] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The disorder Amish microcephaly (MCPHA) is characterized by severe congenital microcephaly, elevated levels of alpha-ketoglutarate in the urine and premature death. The disorder is inherited in an autosomal recessive pattern and has been observed only in Old Order Amish families whose ancestors lived in Lancaster County, Pennsylvania. Here we show, by using a genealogy database and automated pedigree software, that 23 nuclear families affected with MCPHA are connected to a single ancestral couple. Through a whole-genome scan, fine mapping and haplotype analysis, we localized the gene affected in MCPHA to a region of 3 cM, or 2 Mb, on chromosome 17q25. We constructed a map of contiguous genomic clones spanning this region. One of the genes in this region, SLC25A19, which encodes a nuclear mitochondrial deoxynucleotide carrier (DNC), contains a substitution that segregates with the disease in affected individuals and alters an amino acid that is highly conserved in similar proteins. Functional analysis shows that the mutant DNC protein lacks the normal transport activity, implying that failed deoxynucleotide transport across the inner mitochondrial membrane causes MCPHA. Our data indicate that mitochondrial deoxynucleotide transport may be essential for prenatal brain growth.
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Affiliation(s)
- Marjorie J Rosenberg
- National Human Genome Research Institute, National Institutes of Health, 49 Convent Drive, Bethesda, Maryland 20892-4472, USA.
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24
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Lin CF, Makalowska I, Wolfsberg T, Makalowski W. Pattern formation and developmental mechanisms. Curr Opin Genet Dev 2002. [DOI: 10.1016/s0959-437x(02)00312-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Makalowska I, Wolfsberg TG, Lorenc A. Genetics of disease. Curr Opin Genet Dev 2002. [DOI: 10.1016/s0959-437x(02)00295-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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26
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Wolfsburg T, Makalowska I, Makalowski W. Chromosomes and expression mechanisms. Curr Opin Genet Dev 2002. [DOI: 10.1016/s0959-437x(02)00275-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Makalowska I, Sood R, Faruque MU, Hu P, Robbins CM, Eddings EM, Mestre JD, Baxevanis AD, Carpten JD. Identification of six novel genes by experimental validation of GeneMachine predicted genes. Gene 2002; 284:203-13. [PMID: 11891061 DOI: 10.1016/s0378-1119(01)00897-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In silico gene identification from finished and unfinished human genome sequence has become critically important in many projects seeking to gain insights into the gene content of genomic regions implicated in diseases. To establish limitations and criteria for in silico gene identification, and to identify novel genes of potential relevance to human prostate cancer and melanoma, 3 Mb of chromosome 1 sequence have been analyzed using GeneMachine. This program is a software suite comprising of sequence similarity programs and four gene identification programs. A total of 49 potential transcripts were selected and 37 of them were selected for experimental validation. We verified 16 of the predicted genes by experimental analysis. The comparison of the predicted transcripts with their cloned forms helped to refine predicted gene models as well as to identify splice variants for several of them. Although sequences matching with ten of our verified genes have been recently deposited in the GenBank, six of them remain novel. Our studies support the feasibility of identifying novel genes from regions of interest using draft human genome sequence.
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Affiliation(s)
- Izabela Makalowska
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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28
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Carpten J, Nupponen N, Isaacs S, Sood R, Robbins C, Xu J, Faruque M, Moses T, Ewing C, Gillanders E, Hu P, Bujnovszky P, Makalowska I, Baffoe-Bonnie A, Faith D, Smith J, Stephan D, Wiley K, Brownstein M, Gildea D, Kelly B, Jenkins R, Hostetter G, Matikainen M, Schleutker J, Klinger K, Connors T, Xiang Y, Wang Z, De Marzo A, Papadopoulos N, Kallioniemi OP, Burk R, Meyers D, Grönberg H, Meltzer P, Silverman R, Bailey-Wilson J, Walsh P, Isaacs W, Trent J. Germline mutations in the ribonuclease L gene in families showing linkage with HPC1. Nat Genet 2002; 30:181-4. [PMID: 11799394 DOI: 10.1038/ng823] [Citation(s) in RCA: 406] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Although prostate cancer is the most common non-cutaneous malignancy diagnosed in men in the United States, little is known about inherited factors that influence its genetic predisposition. Here we report that germline mutations in the gene encoding 2'-5'-oligoadenylate(2-5A)-dependent RNase L (RNASEL) segregate in prostate cancer families that show linkage to the HPC1 (hereditary prostate cancer 1) region at 1q24-25 (ref. 9). We identified RNASEL by a positional cloning/candidate gene method, and show that a nonsense mutation and a mutation in an initiation codon of RNASEL segregate independently in two HPC1-linked families. Inactive RNASEL alleles are present at a low frequency in the general population. RNASEL regulates cell proliferation and apoptosis through the interferon-regulated 2-5A pathway and has been suggested to be a candidate tumor suppressor gene. We found that microdissected tumors with a germline mutation showed loss of heterozygosity and loss of RNase L protein, and that RNASEL activity was reduced in lymphoblasts from heterozyogous individuals compared with family members who were homozygous with respect to the wildtype allele. Thus, germline mutations in RNASEL may be of diagnostic value, and the 2-5A pathway might provide opportunities for developing therapies for those with prostate cancer.
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Affiliation(s)
- J Carpten
- Cancer Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland 20892, USA
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29
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Appukuttan B, Sood R, Ott S, Makalowska I, Patel RJ, Wang X, Robbins CM, Brownstein MJ, Stout JT. Isolation and characterization of the human homeobox gene HOX D1. Mol Biol Rep 2002; 27:195-201. [PMID: 11455954 DOI: 10.1023/a:1011048931477] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Homeobox genes, first identified in Drosophila, encode transcription factors that regulate embryonic development along the anteroposterior axis of an organism. Vertebrate homeobox genes are described on the basis of their homology to the genes found within the Drosophila Antennapedia and Bithorax homeotic gene complexes. Mammals possess four paralogous homeobox (HOX) gene clusters, HOX A, HOX B, HOX C and HOX D, each located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. We report the characterization of the human HOX D1 gene. This gene consists of two exons, encoding a 328 amino acid protein, separated by an intron of 354 bp. The human HOX D1 protein is one amino acid longer (328 amino acids) than the mouse protein (327 amino acids) and is 82% identical to the mouse HOX D1 homolog. The DNA binding homeodomain region of the human protein exhibits a 97% and 80% identity between mouse Hoxd1 and Drosophila labial homeodomains, respectively. The exon/intron and intron/exon splice junctions are conserved in position between human and mouse genes. Determination of the human HOX D1 gene structure permits the use of PCR based analysis of this gene for the assessment of mutations, for diseases that link to the HOXD cluster (such as Duanes Retraction Syndrome (DRS)), or polymorphisms associated with human variation. Molecular characterization of the HOXD1 gene may also permit analysis of the functional role of this gene in human neurogenisis.
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Affiliation(s)
- B Appukuttan
- Casey Eye Institute, Oregon Health Sciences University, Portland
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Stephan DA, Howell GR, Teslovich TM, Coffey AJ, Smith L, Bailey-Wilson JE, Malechek L, Gildea D, Smith JR, Gillanders EM, Schleutker J, Hu P, Steingruber HE, Dhami P, Robbins CM, Makalowska I, Carpten JD, Sood R, Mumm S, Reinbold R, Bonner TI, Baffoe-Bonnie A, Bubendorf L, Heiskanen M, Kallioneimi OP, Baxevanis AD, Joseph SS, Zucchi I, Burk RD, Isaacs W, Ross MT, Trent JM. Physical and transcript map of the hereditary prostate cancer region at xq27. Genomics 2002; 79:41-50. [PMID: 11827456 DOI: 10.1006/geno.2001.6681] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have recently mapped a locus for hereditary prostate cancer (termed HPCX) to the long arm of the X chromosome (Xq25-q27) through a genome-wide linkage study. Here we report the construction of an approximately 9-Mb sequence-ready bacterial clone contig map of Xq26.3-q27.3. The contig was constructed by screening BAC/PAC libraries with markers spaced at approximately 85-kb intervals. We identified overlapping clones by end-sequencing framework clones to generate 407 new sequence-tagged sites, followed by PCR verification of overlaps. Contig assembly was based on clone restriction fingerprinting and the landmark information. We identified a minimal overlap contig for genomic sequencing, which has yielded 7.7 Mb of finished sequence and 1.5 Mb of draft sequence. The transcriptional mapping effort localized 57 known and predicted genes by database searching, STS content mapping, and sequencing, followed by sequence annotation. These transcriptional units represent candidate genes for HPCX and multiple other hereditary diseases at Xq26.3-q27.3.
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Affiliation(s)
- Dietrich A Stephan
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Abstract
Histone proteins are often noted for their high degree of sequence conservation. It is less often recognized that the histones are a heterogeneous protein family. Furthermore, several classes of non-histone proteins containing the histone fold motif exist. Novel histone and histone fold protein sequences continue to be added to public databases every year. The Histone Database (http://genome.nhgri.nih.gov/histones/) is a searchable, periodically updated collection of histone fold-containing sequences derived from sequence-similarity searches of public databases. Sequence sets are presented in redundant and non-redundant FASTA form, hotlinked to GenBank sequence files. Partial sequences are also now included in the database, which has considerably augmented its taxonomic coverage. Annotated alignments of full-length non-redundant sets of sequences are now available in both web-viewable (HTML) and downloadable (PDF) formats. The database also provides summaries of current information on solved histone fold structures, post-translational modifications of histones, and the human histone gene complement.
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Affiliation(s)
- Steven Sullivan
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 45, Room 6AN12J, 45 Center Drive, MSC 6510, Bethesda, MD 20892-6510, USA
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Wolfsberg TG, Makalowska I, Makalowski W. Web alert. Genetics of disease. Curr Opin Genet Dev 2001; 11:237-8. [PMID: 11377956 DOI: 10.1016/s0959-437x(00)00202-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Genetics & Development.
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Affiliation(s)
- T G Wolfsberg
- National Human Genome Research Institute, National Institutes of Health, Building 9, Room B1E01, Bethesda, Maryland 20892-0960, USA.
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Abstract
MOTIVATION A number of free-standing programs have been developed in order to help researchers find potential coding regions and deduce gene structure for long stretches of what is essentially 'anonymous DNA'. As these programs apply inherently different criteria to the question of what is and is not a coding region, multiple algorithms should be used in the course of positional cloning and positional candidate projects to assure that all potential coding regions within a previously-identified critical region are identified. RESULTS We have developed a gene identification tool called GeneMachine which allows users to query multiple exon and gene prediction programs in an automated fashion. BLAST searches are also performed in order to see whether a previously-characterized coding region corresponds to a region in the query sequence. A suite of Perl programs and modules are used to run MZEF, GENSCAN, GRAIL 2, FGENES, RepeatMasker, Sputnik, and BLAST. The results of these runs are then parsed and written into ASN.1 format. Output files can be opened using NCBI Sequin, in essence using Sequin as both a workbench and as a graphical viewer. The main feature of GeneMachine is that the process is fully automated; the user is only required to launch GeneMachine and then open the resulting file with Sequin. Annotations can then be made to these results prior to submission to GenBank, thereby increasing the intrinsic value of these data. AVAILABILITY GeneMachine is freely-available for download at http://genome.nhgri.nih.gov/genemachine. A public Web interface to the GeneMachine server for academic and not-for-profit users is available at http://genemachine.nhgri.nih.gov. The Web supplement to this paper may be found at http://genome.nhgri.nih.gov/genemachine/supplement/.
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Affiliation(s)
- I Makalowska
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Building 49, Room 4A-22, Bethesda, MD 20892, USA
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Makalowska I, Makalowski W, Wolfsberg TG. Pattern formation and developmental mechanisms. Curr Opin Genet Dev 2001. [DOI: 10.1016/s0959-437x(00)00204-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Sood R, Bonner TI, Makalowska I, Stephan DA, Robbins CM, Connors TD, Morgenbesser SD, Su K, Faruque MU, Pinkett H, Graham C, Baxevanis AD, Klinger KW, Landes GM, Trent JM, Carpten JD. Cloning and characterization of 13 novel transcripts and the human RGS8 gene from the 1q25 region encompassing the hereditary prostate cancer (HPC1) locus. Genomics 2001; 73:211-22. [PMID: 11318611 DOI: 10.1006/geno.2001.6500] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aim of this study was to develop a saturated transcript map of the region encompassing the HPC1 locus to identify the susceptibility genes involved in hereditary prostate cancer (OMIM 176807) and hyperparathyroidism-jaw tumor syndrome (OMIM 145001). We previously reported the generation of a 6-Mb BAC/PAC contig of the candidate region and employed various strategies, such as database searching, exon-trapping, direct cDNA hybridization, and sample sequencing of BACs, to identify all potential transcripts. These efforts led to the identification and precise localization on the BAC contig of 59 transcripts representing 22 known genes and 37 potential transcripts represented by ESTs and exon traps. Here we report the detailed characterization of these ESTs into full-length transcript sequences, their expression pattern in various tissues, their genomic organization, and their homology to known genes. We have also identified an Alu insertion polymorphism in the intron of one of the transcripts. Overall, data on 13 novel transcripts and the human RGS8 gene (homologue of the rat RGS8 gene) are presented in this paper. Ten of the 13 novel transcripts are expressed in prostate tissue and represent positional candidates for HPC1.
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Affiliation(s)
- R Sood
- Cancer Genetics Branch, National Human Genome Research Institute, Bethesda, MD 20892, USA.
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Sood R, Makalowska I, Pollock P, Robbins C, Chen S, Trent J. Molecular cloning and expression analysis of human and mouse homologs of a new transcriptional regulator as a candidate tumor suppresor gene. Nat Genet 2001. [DOI: 10.1038/87308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Baxevanis AD, Makalowska I, Trout K, Zhou Q, Zhou ZZ, Stein J, Dougherty ER, Meltzer PS, Chen Y, Bittner ML, Trent JM. An integrated approach to the extraction, storage, processing and analysis of microarray gene expression data. Nat Genet 2001. [DOI: 10.1038/87000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Slaugenhaupt SA, Blumenfeld A, Gill SP, Leyne M, Mull J, Cuajungco MP, Liebert CB, Chadwick B, Idelson M, Reznik L, Robbins CM, Makalowska I, Brownstein MJ, Krappmann D, Scheidereit C, Maayan C, Axelrod FB, Gusella JF. Tissue-specific expression of a splicing mutation in the IKBKAP gene causes familial dysautonomia. Am J Hum Genet 2001; 68:598-605. [PMID: 11179008 PMCID: PMC1274473 DOI: 10.1086/318810] [Citation(s) in RCA: 423] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2000] [Accepted: 01/10/2001] [Indexed: 11/04/2022] Open
Abstract
Familial dysautonomia (FD; also known as "Riley-Day syndrome"), an Ashkenazi Jewish disorder, is the best known and most frequent of a group of congenital sensory neuropathies and is characterized by widespread sensory and variable autonomic dysfunction. Previously, we had mapped the FD gene, DYS, to a 0.5-cM region on chromosome 9q31 and had shown that the ethnic bias is due to a founder effect, with >99.5% of disease alleles sharing a common ancestral haplotype. To investigate the molecular basis of FD, we sequenced the minimal candidate region and cloned and characterized its five genes. One of these, IKBKAP, harbors two mutations that can cause FD. The major haplotype mutation is located in the donor splice site of intron 20. This mutation can result in skipping of exon 20 in the mRNA of patients with FD, although they continue to express varying levels of wild-type message in a tissue-specific manner. RNA isolated from lymphoblasts of patients is primarily wild-type, whereas only the deleted message is seen in RNA isolated from brain. The mutation associated with the minor haplotype in four patients is a missense (R696P) mutation in exon 19, which is predicted to disrupt a potential phosphorylation site. Our findings indicate that almost all cases of FD are caused by an unusual splice defect that displays tissue-specific expression; and they also provide the basis for rapid carrier screening in the Ashkenazi Jewish population.
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Affiliation(s)
- Susan A. Slaugenhaupt
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Anat Blumenfeld
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Sandra P. Gill
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Maire Leyne
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - James Mull
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Math P. Cuajungco
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Christopher B. Liebert
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Brian Chadwick
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Maria Idelson
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Luba Reznik
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Christiane M. Robbins
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Izabela Makalowska
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Michael J. Brownstein
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Daniel Krappmann
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Claus Scheidereit
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Channa Maayan
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - Felicia B. Axelrod
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
| | - James F. Gusella
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown; Harvard Institute of Human Genetics, Harvard Medical School, Boston; Departments of Clinical Biochemistry and Pediatrics, Hadassah University Hospital, Jerusalem; Laboratory of Genetics, National Institute of Mental Health and National Human Genome Research Institute, and Genome Technology Branch, National Human Genome Research Institute, and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda; Max-Delbrück-Centrum for Molecular Medicine, Berlin; and Department of Pediatrics, New York University Medical Center, New York
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Makalowska I, Wolfsberg T, Makalowski W. Web alert. Oncogenes and cell proliferation. Curr Opin Genet Dev 2001; 11:9-10. [PMID: 11163143 DOI: 10.1016/s0959-437x(00)00148-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Genetics & Development.
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Affiliation(s)
- I Makalowska
- National Human Genome Research Institute, National Institutes of Health, Building 49, Room 2B75, Bethesda, Maryland 20892-4431, USA.
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Wolfsberg T, Makalowska I, Makalowski W. Web alert. Genomes and evolution. Curr Opin Genet Dev 2000; 10:591. [PMID: 11088005 DOI: 10.1016/s0959-437x(00)00133-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- T Wolfsberg
- National Human Genome Research Institute, National Institutes of Health, Building 9, Room B1E01, Bethesda, MD 20892-0960, USA.
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Galdzicki M, Makalowska I, Wolfsberg TG. Web alert. Pattern formation and developmental mechanisms. Curr Opin Genet Dev 2000; 10:345-6. [PMID: 11023300 DOI: 10.1016/s0959-437x(00)00093-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- M Galdzicki
- National Human Genome Research Institute, Bethesda, MD 20892-4431, USA.
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Sood R, Makalowska I, Carpten JD, Robbins CM, Stephan DA, Connors TD, Morgenbesser SD, Su K, Pinkett HW, Graham CL, Quesenberry MI, Baxevanis AD, Klinger KW, Trent JM, Bonner TI. The human RGL (RalGDS-like) gene: cloning, expression analysis and genomic organization. Biochim Biophys Acta 2000; 1491:285-8. [PMID: 10760592 DOI: 10.1016/s0167-4781(00)00031-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ral GDP dissociation stimulator (RalGDS) and its family members RGL, RLF and RGL2 are involved in Ras and Ral signaling pathways as downstream effector proteins. Here we report the precise localization and cloning of two forms of human RGL gene differing at the amino terminus. Transcript A, cloned from liver cDNA libraries has the same amino terminus as the mouse RGL, whereas transcript B cloned from brain has a substitution of 45 amino acids for the first nine amino acids. At the genomic level, exon 1 of transcript A is replaced by two alternative exons (1B1 and 1B2) in transcript B. Both forms share exons 2 through 18. The human RGL protein shares 94% amino acid identity with the mouse protein. Northern blot analysis shows that human RGL is expressed in a wide variety of tissues with strong expression being seen in the heart, brain, kidney, spleen and testis.
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Affiliation(s)
- R Sood
- Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Building 36, Room 3D05, 9000 Rockville Pike, Bethesda, MD, USA.
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Carpten JD, Makalowska I, Robbins CM, Scott N, Sood R, Connors TD, Bonner TI, Smith JR, Faruque MU, Stephan DA, Pinkett H, Morgenbesser SD, Su K, Graham C, Gregory SG, Williams H, McDonald L, Baxevanis AD, Klingler KW, Landes GM, Trent JM. A 6-Mb high-resolution physical and transcription map encompassing the hereditary prostate cancer 1 (HPC1) region. Genomics 2000; 64:1-14. [PMID: 10708513 DOI: 10.1006/geno.1999.6051] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Several hereditary disease loci have been genetically mapped to the chromosome 1q24-q31 interval, including the hereditary prostate cancer 1 (HPC1) locus. Here, we report the construction of a 20-Mb yeast artificial chromosome contig and a high-resolution 6-Mb sequence-ready bacterial artificial chromosome (BAC)/P1-derived artificial chromosome (PAC) contig of 1q25 by sequence and computational analysis, STS content mapping, and chromosome walking. One hundred thirty-six new STSs, including 10 novel simple sequence repeat polymorphisms that are being used for genetic refinement of multiple disease loci, have been generated from this contig and are shown to map to the 1q25 interval. The integrity of the 6-Mb BAC/PAC contig has been confirmed by restriction fingerprinting, and this contig is being used as a template for human chromosome 1 genome sequencing. A transcription mapping effort has resulted in the precise localization of 18 known genes and 31 ESTs by database searching, exon trapping, direct cDNA hybridization, and sample sequencing of BACs from the 1q25 contig. An additional 11 known genes and ESTs have been placed within the larger 1q24-q31 interval. These transcription units represent candidate genes for multiple hereditary diseases, including HPC1.
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Affiliation(s)
- J D Carpten
- Cancer Genetics Branch, Bethesda, Maryland 20892, USA.
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Makalowski W, Wolfsberg TG, Makalowska I. Oncogenes and cell proliferation. Curr Opin Genet Dev 2000. [DOI: 10.1016/s0959-437x(99)00054-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Sullivan SA, Aravind L, Makalowska I, Baxevanis AD, Landsman D. The histone database: a comprehensive WWW resource for histones and histone fold-containing proteins. Nucleic Acids Res 2000; 28:320-2. [PMID: 10592260 PMCID: PMC102427 DOI: 10.1093/nar/28.1.320] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Histone Database (HDB) is an annotated and searchable collection of all full-length sequences and structures of histone and non-histone proteins containing the histone fold motif. These sequences are both eukaryotic and archaeal in origin. Several new histone fold-containing proteins have been identified, including Spt7p, and a few false positives have been removed from the earlier version of HDB. Database contents include compilations of post-translational modifications for each of the core and linker histones, as well as genomic information in the form of map loci for the human histone gene complement, with the genetic loci linked to Online Mendelian Inheritance in Man (OMIM). Conflicts between similar sequence entries from a number of source databases are also documented. Newly added to the HDB are multiple sequence alignments in which predicted functions of histone fold amino acid residues are annotated. The database is freely accessible through the WWW at http://genome.nhgri.nih.gov/histones/
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Affiliation(s)
- S A Sullivan
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A Room 8N805, Bethesda, MD 20894, USA
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Chadwick BP, Leyne M, Gill S, Liebert CB, Mull J, Mezey E, Robbins CM, Pinkett HW, Makalowska I, Maayan C, Blumenfeld A, Axelrod FB, Brownstein M, Gusella JF, Slaugenhaupt SA. Cloning, mapping, and expression of a novel brain-specific transcript in the familial dysautonomia candidate region on chromosome 9q31. Mamm Genome 2000; 11:81-3. [PMID: 10603000 DOI: 10.1007/s003350010017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- B P Chadwick
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, Massachusetts, USA
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47
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Wolfsberg TG, Makalowska I, Makalowski W. Genomes and evolution. Web alert. Curr Opin Genet Dev 1999; 9:619. [PMID: 10636697 DOI: 10.1016/s0959-437x(99)00037-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- T G Wolfsberg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.
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48
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Chadwick BP, Gill S, Leyne M, Mull J, Liebert CB, Robbins CM, Pinkett HW, Makalowska I, Maayan C, Blumenfeld A, Axelrod FB, Brownstein M, Slaugenhaupt SA. Cloning, genomic organization and expression of a putative human transmembrane protein related to the Caenorhabditis elegans M01F1.4 gene. Gene 1999; 240:67-73. [PMID: 10564813 DOI: 10.1016/s0378-1119(99)00432-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A novel human transcript CG-2 (C9ORF5), was isolated from the familial dysautonomia candidate region on 9q31 using a combination of cDNA selection and exon trapping. CG-2 was detected as a relatively abundant 8kb transcript in all adult and fetal tissues with the exception of adult thymus. Genomic analysis of CG-2 identified 18 exons that span more than 110kb. The gene encodes a 911-amino-acid protein with a predicted molecular weight of 101kDa and a hypothetical pI of 9.03. Sequence analysis of CG-2 indicates that it is likely to encode a transmembrane protein. Here, we assess CG-2 as a candidate for familial dysautonomia.
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MESH Headings
- Adult
- Amino Acid Sequence
- Animals
- Brain/embryology
- Brain/metabolism
- Caenorhabditis elegans/genetics
- Cell Line
- Chromosome Mapping
- Chromosomes, Human, Pair 9/genetics
- Cloning, Molecular
- Cricetinae
- DNA/chemistry
- DNA/genetics
- DNA Mutational Analysis
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Complementary/isolation & purification
- Databases, Factual
- Dysautonomia, Familial/genetics
- Expressed Sequence Tags
- Gene Expression
- Gene Expression Regulation, Developmental
- Genes/genetics
- Genes, Helminth/genetics
- Humans
- Hybrid Cells
- Membrane Proteins/genetics
- Mice
- Molecular Sequence Data
- Rats
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
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Affiliation(s)
- B P Chadwick
- Molecular Neurogenetics Unit, Massachusetts General Hospital, Charlestown, MA, USA
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49
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Marcelino J, Carpten JD, Suwairi WM, Gutierrez OM, Schwartz S, Robbins C, Sood R, Makalowska I, Baxevanis A, Johnstone B, Laxer RM, Zemel L, Kim CA, Herd JK, Ihle J, Williams C, Johnson M, Raman V, Alonso LG, Brunoni D, Gerstein A, Papadopoulos N, Bahabri SA, Trent JM, Warman ML. CACP, encoding a secreted proteoglycan, is mutated in camptodactyly-arthropathy-coxa vara-pericarditis syndrome. Nat Genet 1999; 23:319-22. [PMID: 10545950 DOI: 10.1038/15496] [Citation(s) in RCA: 214] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Altered growth and function of synoviocytes, the intimal cells which line joint cavities and tendon sheaths, occur in a number of skeletal diseases. Hyperplasia of synoviocytes is found in both rheumatoid arthritis and osteoarthritis, despite differences in the underlying aetiologies of the two disorders. We have studied the autosomal recessive disorder camptodactyly-arthropathy-coxa vara-pericarditis syndrome (CACP; MIM 208250) to identify biological pathways that lead to synoviocyte hyperplasia, the principal pathological feature of this syndrome. Using a positional-candidate approach, we identified mutations in a gene (CACP) encoding a secreted proteoglycan as the cause of CACP. The CACP protein, which has previously been identified as both 'megakaryocyte stimulating factor precursor' and 'superficial zone protein', contains domains that have homology to somatomedin B, heparin-binding proteins, mucins and haemopexins. In addition to expression in joint synovium and cartilage, CACP is expressed in non-skeletal tissues including liver and pericardium. The similarity of CACP sequence to that of other protein families and the expression of CACP in non-skeletal tissues suggest it may have diverse biological activities.
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Affiliation(s)
- J Marcelino
- Department of Genetics and Center for Human Genetics, Case Western Reserve University and University Hospitals of Cleveland, Cleveland, Ohio, USA
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50
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Makalowska I, Makalowski W. Differentiation and gene regulation. Curr Opin Genet Dev 1999. [DOI: 10.1016/s0959-437x(99)00019-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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