1
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Kogenaru S, del Val C, Hotz-Wagenblatt A, Glatting KH. TissueDistributionDBs: a repository of organism-specific tissue-distribution profiles. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0670-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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2
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Zhang Z, Zhang B, Nie X, Liu Q, Xie F, Shang D. Transcriptome Analysis and Identification of Genes Related to Immune Function in Skin of the Chinese Brown Frog. Zoolog Sci 2009; 26:80-6. [DOI: 10.2108/zsj.26.80] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Zhewen Zhang
- Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery, Liaoning Normal University, Dalian 116029, China
| | - Bing Zhang
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
| | - Xiaona Nie
- College of Computer and Information Technology, Liaoning Normal University, Dalian 116029, China
| | - Qingkun Liu
- College of Computer and Information Technology, Liaoning Normal University, Dalian 116029, China
| | - Fuding Xie
- College of Computer and Information Technology, Liaoning Normal University, Dalian 116029, China
| | - Dejing Shang
- Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery, Liaoning Normal University, Dalian 116029, China
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3
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Zhang YZ, Chen J, Nie ZM, Lü ZB, Wang D, Jiang CY, He PA, Liu LL, Lou YL, Song L, Wu XF. Expression of open reading frames in silkworm pupal cDNA library. Appl Biochem Biotechnol 2007; 136:327-43. [PMID: 17625237 DOI: 10.1007/s12010-007-9029-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 11/24/2022]
Abstract
A cDNA library containing 2409 singletons was constructed from whole silkworm pupae (Bombyx mori) In addition, the types of genes overexpressed in pupa were analyzed. These genes contained 79 types of proteins with the exception of enzyme, mitochondrial DNA, andribosomal protein. Also analyzed were the expression and nonexpression of open reading frame (ORF) sequences in Escherichia coli. cDNA sequences were compared to the silkworm (B. mori) genome in the GenBank database and the silkworm cDNA database including the SilkBase and KAIKOBLAST databases and 498 novel expressed sequence tags (ESTs) and 217 unknown ESTs were found. After comparison with all available ORF-complete mRNA sequences from the same organism (fruitfly, mosquito, and apis) in the RefSeq collection, 1659 full-length cDNA were identified. In addition, the structure of silkworm mRNA was analyzed, and it was found that 66.8% of silkworm mRNA tailed with poly(A) contained the highly conserved AAUAAA signal and the signal located 10-17 nucleotides upstream of the putative poly(A). Finally, the composition of nucleotides in promoter region for all ESTs was surveyed. The results imply that the TTTTA box may possess some functions in regulating transcription and expression of some genes.
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Affiliation(s)
- Yao-Zhou Zhang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China.
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4
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Coblentz FE, Towle DW, Shafer TH. Expressed sequence tags from normalized cDNA libraries prepared from gill and hypodermal tissues of the blue crab, Callinectes sapidus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2006; 1:200-8. [DOI: 10.1016/j.cbd.2005.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2005] [Revised: 10/10/2005] [Accepted: 10/11/2005] [Indexed: 11/29/2022]
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5
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Morin RD, Chang E, Petrescu A, Liao N, Griffith M, Kirkpatrick R, Butterfield YS, Young AC, Stott J, Barber S, Babakaiff R, Dickson MC, Matsuo C, Wong D, Yang GS, Smailus DE, Wetherby KD, Kwong PN, Grimwood J, Brinkley CP, Brown-John M, Reddix-Dugue ND, Mayo M, Schmutz J, Beland J, Park M, Gibson S, Olson T, Bouffard GG, Tsai M, Featherstone R, Chand S, Siddiqui AS, Jang W, Lee E, Klein SL, Blakesley RW, Zeeberg BR, Narasimhan S, Weinstein JN, Pennacchio CP, Myers RM, Green ED, Wagner L, Gerhard DS, Marra MA, Jones SJ, Holt RA. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res 2006; 16:796-803. [PMID: 16672307 PMCID: PMC1479861 DOI: 10.1101/gr.4871006] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Sequencing of full-insert clones from full-length cDNA libraries from both Xenopus laevis and Xenopus tropicalis has been ongoing as part of the Xenopus Gene Collection Initiative. Here we present 10,967 full ORF verified cDNA clones (8049 from X. laevis and 2918 from X. tropicalis) as a community resource. Because the genome of X. laevis, but not X. tropicalis, has undergone allotetraploidization, comparison of coding sequences from these two clawed (pipid) frogs provides a unique angle for exploring the molecular evolution of duplicate genes. Within our clone set, we have identified 445 gene trios, each comprised of an allotetraploidization-derived X. laevis gene pair and their shared X. tropicalis ortholog. Pairwise dN/dS, comparisons within trios show strong evidence for purifying selection acting on all three members. However, dN/dS ratios between X. laevis gene pairs are elevated relative to their X. tropicalis ortholog. This difference is highly significant and indicates an overall relaxation of selective pressures on duplicated gene pairs. We have found that the paralogs that have been lost since the tetraploidization event are enriched for several molecular functions, but have found no such enrichment in the extant paralogs. Approximately 14% of the paralogous pairs analyzed here also show differential expression indicative of subfunctionalization.
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Affiliation(s)
- Ryan D. Morin
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Elbert Chang
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Anca Petrescu
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Nancy Liao
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Malachi Griffith
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Robert Kirkpatrick
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | | | - Alice C. Young
- NIH Intramural Sequencing Center, National Human Genome Research Institute
| | - Jeffrey Stott
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Sarah Barber
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Ryan Babakaiff
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Mark C. Dickson
- Stanford Human Genome Center and Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Corey Matsuo
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - David Wong
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - George S. Yang
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Duane E. Smailus
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Keith D. Wetherby
- NIH Intramural Sequencing Center, National Human Genome Research Institute
| | - Peggy N. Kwong
- NIH Intramural Sequencing Center, National Human Genome Research Institute
| | - Jane Grimwood
- Stanford Human Genome Center and Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | - Mabel Brown-John
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | | | - Michael Mayo
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Jeremy Schmutz
- Stanford Human Genome Center and Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jaclyn Beland
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Morgan Park
- NIH Intramural Sequencing Center, National Human Genome Research Institute
| | - Susan Gibson
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Teika Olson
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Gerard G. Bouffard
- NIH Intramural Sequencing Center, National Human Genome Research Institute
| | - Miranda Tsai
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Ruth Featherstone
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Steve Chand
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Asim S. Siddiqui
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Wonhee Jang
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA
| | - Ed Lee
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA
| | - Steven L. Klein
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | | | - Barry R. Zeeberg
- Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology
| | | | - John N. Weinstein
- Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology
| | - Christa Prange Pennacchio
- The I.M.A.G.E Consortium, Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Richard M. Myers
- Stanford Human Genome Center and Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Eric D. Green
- NIH Intramural Sequencing Center, National Human Genome Research Institute
| | - Lukas Wagner
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland 20894, USA
| | | | - Marco A. Marra
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Steven J.M. Jones
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
| | - Robert A. Holt
- British Columbia Genome Sciences Centre, BCCA, Vancouver, BC V5Z 1L3 Canada
- Corresponding author.E-mail ; fax (604) 877-6085
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Savolainen P, Fitzsimmons C, Arvestad L, Andersson L, Lundeberg J. ESTs from brain and testis of White Leghorn and red junglefowl: annotation, bioinformatic classification of unknown transcripts and analysis of expression levels. Cytogenet Genome Res 2005; 111:79-87. [PMID: 16093725 DOI: 10.1159/000085674] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2004] [Accepted: 11/30/2004] [Indexed: 11/19/2022] Open
Abstract
We report the generation, assembly and annotation of expressed sequence tags (ESTs) from four chicken cDNA libraries, constructed from brain and testis tissue dissected from red junglefowl and White Leghorn. 21,285 5'-end ESTs were generated and assembled into 2,813 contigs and 9,737 singletons, giving 12,549 tentative unique transcripts. The transcripts were annotated using BLAST by matching to known chicken genes or to putative homologues in other species using the major gene/protein databases. The results for these similarity searches are available on www.sbc.su.se/~arve/chicken. 4,129 (32.9%) of the transcripts remained without a significant match to gene/protein databases, a proportion of unmatched transcripts similar to earlier non-mammalian EST studies. To estimate how many of these transcripts may represent novel genes, they were studied for the presence of coding sequence. It was shown that most of the unique chicken transcripts do not contain coding parts of genes, but it was estimated that at least 400 of the transcripts contain coding sequence, indicating that 3.2% of avian genes belong to previously unknown gene families. Further BLAST search against dbEST left 1,649 (13.1%) of the transcripts unmatched to any library. The number of completely unmatched transcripts containing coding sequence was estimated at 180, giving a measure of the number of putative novel chicken genes identified in this study. 84.3% of the identified transcripts were found only in testis tissue, which has been poorly studied in earlier chicken EST studies. Large differences in expression levels were found between the brain and testis libraries for a large number of transcripts, and among the 525 most frequently represented transcripts, there were at least 20 transcripts with significant difference in expression levels between red junglefowl and White Leghorn.
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Affiliation(s)
- P Savolainen
- Department of Biotechnology, Royal Institute of Technology, Stockholm, Sweden.
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7
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Gilchrist MJ, Zorn AM, Voigt J, Smith JC, Papalopulu N, Amaya E. Defining a large set of full-length clones from a Xenopus tropicalis EST project. Dev Biol 2004; 271:498-516. [PMID: 15223350 DOI: 10.1016/j.ydbio.2004.04.023] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2004] [Revised: 04/07/2004] [Accepted: 04/07/2004] [Indexed: 02/06/2023]
Abstract
Amphibian embryos from the genus Xenopus are among the best species for understanding early vertebrate development and for studying basic cell biological processes. Xenopus, and in particular the diploid Xenopus tropicalis, is also ideal for functional genomics. Understanding the behavior of genes in this accessible model system will have a significant and beneficial impact on the understanding of similar genes in other vertebrate systems. Here we describe the analysis of 219,270 X. tropicalis expressed sequence tags (ESTs) from four early developmental stages. From these, we have deduced a set of unique expressed sequences comprising approximately 20,000 clusters and 16,000 singletons. Furthermore, we developed a computational method to identify clones that contain the complete coding sequence and describe the creation for the first time of a set of approximately 7000 such clones, the full-length (FL) clone set. The entire EST set is cloned in a eukaryotic expression vector and is flanked by bacteriophage promoters for in vitro transcription, allowing functional experiments to be carried out without further subcloning. We have created a publicly available database containing the FL clone set and related clustering data (http://www.gurdon.cam.ac.uk/informatics/Xenopus.html) and we make the FL clone set publicly available as a resource to accelerate the process of gene discovery and function in this model organism. The creation of the unique set of expressed sequences and the FL clone set pave the way toward a large-scale systematic analysis of gene sequence, gene expression, and gene function in this vertebrate species.
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8
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Scheetz TE, Laffin JJ, Berger B, Holte S, Baumes SA, Brown R, Chang S, Coco J, Conklin J, Crouch K, Donohue M, Doonan G, Estes C, Eyestone M, Fishler K, Gardiner J, Guo L, Johnson B, Keppel C, Kreger R, Lebeck M, Marcelino R, Miljkovich V, Perdue M, Qui L, Rehmann J, Reiter RS, Rhoads B, Schaefer K, Smith C, Sunjevaric I, Trout K, Wu N, Birkett CL, Bischof J, Gackle B, Gavin A, Grundstad AJ, Mokrzycki B, Moressi C, O'Leary B, Pedretti K, Roberts C, Robinson NL, Smith M, Tack D, Trivedi N, Kucaba T, Freeman T, Lin JJC, Bonaldo MF, Casavant TL, Sheffield VC, Soares MB. High-throughput gene discovery in the rat. Genome Res 2004; 14:733-41. [PMID: 15060017 PMCID: PMC383320 DOI: 10.1101/gr.1414204] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The rat is an important animal model for human diseases and is widely used in physiology. In this article we present a new strategy for gene discovery based on the production of ESTs from serially subtracted and normalized cDNA libraries, and we describe its application for the development of a comprehensive nonredundant collection of rat ESTs. Our new strategy appears to yield substantially more EST clusters per ESTs sequenced than do previous approaches that did not use serial subtraction. However, multiple rounds of library subtraction resulted in high frequencies of otherwise rare internally primed cDNAs, defining the limits of this powerful approach. To date, we have generated >200,000 3' ESTs from >100 cDNA libraries representing a wide range of tissues and developmental stages of the laboratory rat. Most importantly, we have contributed to approximately 50,000 rat UniGene clusters. We have identified, arrayed, and derived 5' ESTs from >30,000 unique rat cDNA clones. Complete information, including radiation hybrid mapping data, is also maintained locally at http://genome.uiowa.edu/clcg.html. All of the sequences described in this article have been submitted to the dbEST division of the NCBI.
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Affiliation(s)
- Todd E Scheetz
- Center for Bioinformatics and Computational Biology, The University of Iowa, Iowa City, Iowa 52242, USA.
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9
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Krylov V, Mácha J, Tlapáková T, Takác M, Jonák J. The c- src1 gene visualized by in situ hybridization on Xenopus laevis chromosomes. Cytogenet Genome Res 2004; 103:169-72. [PMID: 15004482 DOI: 10.1159/000076307] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2003] [Accepted: 10/13/2003] [Indexed: 11/19/2022] Open
Abstract
Fluorescent in situ hybridization followed by tyramide signal amplification was used to map the site of the c-SRC1 gene on XENOPUS LAEVIS chromosomes. Positive results were obtained with a cDNA probe of about 1 kb. The c-SRC1 gene is located in the subcentromeric region in the long arm of one of the acrocentric chromosomes of the G category (classified according to Graf and Kobel, 1991). The c-SRC1 gene and the XENOPUS major histocompatibility complex (MHC) 1b locus, which consists of 20 tandemly arranged gene copies, are situated on different chromosomes of the G category.
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Affiliation(s)
- V Krylov
- Department of Physiology and Developmental Biology, Faculty of Science, Charles University, Prague, Czech Republic
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10
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Abstract
In Xenopus embryos, body patterning and cell specification are initiated by transcription factors, which are themselves transcribed during oogenesis, and their mRNAs are stored for use after fertilization. We have previously shown that the T-box transcription factor VegT is both necessary and sufficient to initiate transcription of all endoderm, and most mesoderm genes. In the absence of maternal VegT, no mesodermal organs (including the heart) or endodermal organs form. A second maternal transcription factor XTcf3 acts as a global repressor of transcription of dorsal genes, whose repression is inactivated on the dorsal side by a maternally encoded Wnt signaling pathway. In the absence of beta-catenin, no mesodermal or endodermal organs form. We show here that the maternally encoded transcription factor CREB is also essential for development. It is required for the initiation of expression of several mesodermal genes, including Xbra, Xcad2, and -3 and also regulates the cardiogenic gene Nkx 2-5. We show that maternal CREB-depleted embryos develop gastrulation defects that are rescued by the reintroduction of activated CREB mRNA. We conclude that maternal CREB must be added to the list of essential maternal transcription factors regulating cell specification in the early embryo.
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Affiliation(s)
- Nambirajan Sundaram
- Division of Developmental Biology, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, OH 45229-3039, USA
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Venkatesan K, McManus HR, Mello CC, Smith TF, Hansen U. Functional conservation between members of an ancient duplicated transcription factor family, LSF/Grainyhead. Nucleic Acids Res 2003; 31:4304-16. [PMID: 12888489 PMCID: PMC169928 DOI: 10.1093/nar/gkg644] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The LSF/Grainyhead transcription factor family is involved in many important biological processes, including cell cycle, cell growth and development. In order to investigate the evolutionary conservation of these biological roles, we have characterized two new family members in Caenorhabditis elegans and Xenopus laevis. The C.elegans member, Ce-GRH-1, groups with the Grainyhead subfamily, while the X.laevis member, Xl-LSF, groups with the LSF subfamily. Ce-GRH-1 binds DNA in a sequence-specific manner identical to that of Drosophila melanogaster Grainyhead. In addition, Ce-GRH-1 binds to sequences upstream of the C.elegans gene encoding aromatic L-amino-acid decarboxylase and genes involved in post-embryonic development, mab-5 and dbl-1. All three C.elegans genes are homologs of D.melanogaster Grainyhead-regulated genes. RNA-mediated interference of Ce-grh-1 results in embryonic lethality in worms, accompanied by soft, defective cuticles. These phenotypes are strikingly similar to those observed previously in D.melanogaster grainyhead mutants, suggesting conservation of the developmental role of these family members over the course of evolution. Our phylogenetic analysis of the expanded LSF/GRH family (including other previously unrecognized proteins/ESTs) suggests that the structural and functional dichotomy of this family dates back more than 700 million years, i.e. to the time when the first multicellular organisms are thought to have arisen.
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Neumann NF, Galvez F. DNA microarrays and toxicogenomics: applications for ecotoxicology? Biotechnol Adv 2002; 20:391-419. [PMID: 14550024 DOI: 10.1016/s0734-9750(02)00025-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Toxicogenomics attempts to define how the regulation and expression of genes mediate the toxicological effects associated with exposure to a chemical. DNA microarrays are rapidly becoming one of the tools of choice for large-scale toxicogenomic studies. An approach in modern toxicogenomics has been to classify toxicity based on gene transcriptional patterns; comparing the transcriptional responses of a chemical with unknown toxicity to those for which the transcriptional profiles and toxicological endpoints have been well characterized. Recent evidence suggests that gene expression microarrays may be instrumental in defining mechanisms of action of toxicants. However, several assumptions are inherent to a toxicogenomic-based approach in toxicology, many of which remain to be validated. Gene expression profiling using DNA microarrays represents a snapshot of the gene transcriptional responses occurring at a particular time and within a particular tissue. Toxicity, on the other hand, represents a continuum of possible effects governed by both temporal and spatial factors that are inextricably contingent upon the exposure conditions. The perceived toxicological properties of any chemical are dependent on the route, dose, and duration of the exposure, and as such, gene expression patterns are also subject to these variables. Correct interpretation of DNA microarray data for the assessment of the toxicological properties of chemicals will require that temporal and spatial gene expression profiles be accounted for. These considerations are further compounded in ecotoxicological studies, during which altered gene expression patterns induced from exposure to an anthropogenic substance must be discernible over and above the complex effects that phenotypic, genotypic, and environmental variables have on gene expression. To this end, the greatest utility of DNA microarrays in the field of ecotoxicology may be in predicting the toxicological modes of action of anthropogenic substances on host physiology, particularly in non-model organisms. Predictable and accurate assessment of the impacts of a chemical substance in ecotoxicology will require that classical toxicological endpoints be used to validate any effects predicted based on gene expression profiling. Validated expression profiling may subsequently find utility in ecotoxicological-based computer simulation models, such as the Biotic Ligand Model (BLM), in which gene expression information may be integrated with geochemical, pharmacokinetic, and physiological data to accurately assess and predict toxicity of metals to aquatic organisms.
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Affiliation(s)
- Norman F Neumann
- National Water Research Institute, Environment Canada, Canada Center for Inland Waters, 867 Lakeshore Road, Burlington, Ontario, Canada L7R 4A6.
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13
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Tomasevic N, Peculis BA. Xenopus LSm proteins bind U8 snoRNA via an internal evolutionarily conserved octamer sequence. Mol Cell Biol 2002; 22:4101-12. [PMID: 12024024 PMCID: PMC133881 DOI: 10.1128/mcb.22.12.4101-4112.2002] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
U8 snoRNA plays a unique role in ribosome biogenesis: it is the only snoRNA essential for maturation of the large ribosomal subunit RNAs, 5.8S and 28S. To learn the mechanisms behind the in vivo role of U8 snoRNA, we have purified to near homogeneity and characterized a set of proteins responsible for the formation of a specific U8 RNA-binding complex. This 75-kDa complex is stable in the absence of added RNA and binds U8 with high specificity, requiring the conserved octamer sequence present in all U8 homologues. At least two proteins in this complex can be cross-linked directly to U8 RNA. We have identified the proteins as Xenopus homologues of the LSm (like Sm) proteins, which were previously reported to be involved in cytoplasmic degradation of mRNA and nuclear stabilization of U6 snRNA. We have identified LSm2, -3, -4, -6, -7, and -8 in our purified complex and found that this complex associates with U8 RNA in vivo. This purified complex can bind U6 snRNA in vitro but does not bind U3 or U14 snoRNA in vitro, demonstrating that the LSm complex specifically recognizes U8 RNA.
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MESH Headings
- Amino Acid Sequence
- Animals
- Binding Sites
- Cells, Cultured
- Conserved Sequence
- Cross-Linking Reagents/chemistry
- Evolution, Molecular
- Female
- Molecular Sequence Data
- N-Terminal Acetyltransferase C
- Oocytes
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/metabolism
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/immunology
- Ribonucleoprotein, U4-U6 Small Nuclear/isolation & purification
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Ribonucleoproteins, Small Nuclear
- Xenopus/genetics
- Xenopus Proteins/genetics
- Xenopus Proteins/metabolism
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Affiliation(s)
- Nenad Tomasevic
- Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-1766, USA
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Booth RA, Cummings C, Tiberi M, Liu XJ. GIPC participates in G protein signaling downstream of insulin-like growth factor 1 receptor. J Biol Chem 2002; 277:6719-25. [PMID: 11751850 DOI: 10.1074/jbc.m108033200] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Several recent studies have demonstrated that insulin-like growth factor (IGF)-1-induced mitogen-activated protein kinase (MAP kinase) activation is abolished by pertussis toxin, suggesting that trimeric G proteins of the G(i) class are novel cellular targets of the IGF-1 signaling pathway. We report here that the intracellular domain of the Xenopus IGF-1 receptor is capable of binding to the Xenopus homolog of mammalian GIPC, a PDZ domain-containing protein previously identified as a binding partner of G(i)-specific GAP (RGS-GAIP). Binding of xGIPC to xIGF-1 receptor is independent of the kinase activity of the receptor and appears to require the PDZ domain of xGIPC. Injection of two C-terminal truncation mutants that retained the PDZ domain blocked IGF-1-induced Xenopus MAP kinase activation and oocyte maturation. While full-length xGIPC injection did not significantly alter insulin response, it greatly enhanced human RGS-GAIP in stimulating the insulin response in frog oocytes. This represents the first demonstration that GIPC x RGS-GAIP complex acts positively in IGF-1 receptor signal transduction.
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Affiliation(s)
- Ronald A Booth
- Ottawa Health Research Institute, Ottawa Hospital, Ottawa K1Y 4E9, Canada
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