51
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Tomascik-Cheeseman LM, Coleman MA, Marchetti F, Nelson DO, Kegelmeyer LM, Nath J, Wyrobek AJ. Differential basal expression of genes associated with stress response, damage control, and DNA repair among mouse tissues. Mutat Res 2004; 561:1-14. [PMID: 15238225 DOI: 10.1016/j.mrgentox.2004.02.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2003] [Revised: 02/06/2004] [Accepted: 02/06/2004] [Indexed: 11/20/2022]
Abstract
Efficient recognition and repair of DNA damage is essential for maintaining genomic integrity. Tissues and cell types within tissues appear to vary in both DNA damage susceptibilities and cancer incidences, yet the molecular mechanisms underlying these differences are not well understood. The purpose of this study was to characterize the baseline transcription profiles of selected genes involved in DNA damage recognition and repair processes among several tissues of healthy adult B6C3F1 mice (testis, brain, liver, spleen and heart), which are routinely used by the National Toxicology Program (NTP) to conduct long-term chemical carcinogenicity studies. Stress response, damage control and DNA repair-associated genes were differentially expressed among the tissues examined. Overall, stress response genes exhibited the greatest variation among tissues with the highest expression in liver and heart while DNA repair genes exhibited the least variation. Damage control genes associated with cell cycle regulation and DNA repair genes generally had the highest expression in testis. The expression levels of several genes were rank correlated with the spontaneous cancer incidences among these tissues. Variations in basal expression of DNA damage recognition and repair-associated genes among healthy tissues may contribute to their differential response to genotoxic agents and susceptibility to genetic disease.
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Affiliation(s)
- Lisa M Tomascik-Cheeseman
- Biology and Biotechnology Research Program, Lawrence Livermore National Laboratory, P.O. Box 808, L-448 Livermore, CA 94550, USA
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52
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Khil PP, Smirnova NA, Romanienko PJ, Camerini-Otero RD. The mouse X chromosome is enriched for sex-biased genes not subject to selection by meiotic sex chromosome inactivation. Nat Genet 2004; 36:642-6. [PMID: 15156144 DOI: 10.1038/ng1368] [Citation(s) in RCA: 264] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2003] [Accepted: 03/25/2004] [Indexed: 11/09/2022]
Abstract
Sex chromosomes are subject to sex-specific selective evolutionary forces. One model predicts that genes with sex-biased expression should be enriched on the X chromosome. In agreement with Rice's hypothesis, spermatogonial genes are over-represented on the X chromosome of mice and sex- and reproduction-related genes are over-represented on the human X chromosome. Male-biased genes are under-represented on the X chromosome in worms and flies, however. Here we show that mouse spermatogenesis genes are relatively under-represented on the X chromosome and female-biased genes are enriched on it. We used Spo11(-/-) mice blocked in spermatogenesis early in meiosis to evaluate the temporal pattern of gene expression in sperm development. Genes expressed before the Spo11 block are enriched on the X chromosome, whereas those expressed later in spermatogenesis are depleted. Inactivation of the X chromosome in male meiosis may be a universal driving force for X-chromosome demasculinization.
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Affiliation(s)
- Pavel P Khil
- Genetics and Biochemistry Branch, NIDDK, National Institutes of Health, 5 Memorial Drive, Bethesda, Maryland 20892, USA
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53
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Kodzius R, Matsumura Y, Kasukawa T, Shimokawa K, Fukuda S, Shiraki T, Nakamura M, Arakawa T, Sasaki D, Kawai J, Harbers M, Carninci P, Hayashizaki Y. Absolute expression values for mouse transcripts: re-annotation of the READ expression database by the use of CAGE and EST sequence tags. FEBS Lett 2004; 559:22-6. [PMID: 14960301 DOI: 10.1016/s0014-5793(04)00018-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2003] [Revised: 12/26/2003] [Accepted: 01/05/2004] [Indexed: 11/18/2022]
Abstract
The RIKEN expression array database (READ) provides comprehensive gene expression data for the mouse, which were obtained as relative values from microarray double-staining experiments with E17.5 mRNA as common reference. To assign absolute expression values for mouse transcripts within READ, we applied the E17.5 reference sample to CAGE (cap analysis of gene expression) and expressed sequence tag (EST) high-throughput tag sequencing. Newly assigned values within the READ database were validated by comparison to expression data from serial analysis of gene expression, CAGE and EST experiments. These experiments confirmed the great significance of the absolute expression values within the improved READ database. The new Absolute READ database on absolute expression data is available under.
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Affiliation(s)
- Rimantas Kodzius
- Genome Science Laboratory, RIKEN, Wako Main Campus, Hirosawa 2-1, Wako, Saitama 351-0198, Japan
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54
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Castrillo JI, Oliver SG. Yeast as a Touchstone in Post-genomic Research: Strategies for Integrative Analysis in Functional Genomics. BMB Rep 2004; 37:93-106. [PMID: 14761307 DOI: 10.5483/bmbrep.2004.37.1.093] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The new complexity arising from the genome sequencing projects requires new comprehensive post-genomic strategies: advanced studies in regulatory mechanisms, application of new high-throughput technologies at a genome-wide scale, at the different levels of cellular complexity (genome, transcriptome, proteome and metabolome), efficient analysis of the results, and application of new bioinformatic methods in an integrative or systems biology perspective. This can be accomplished in studies with model organisms under controlled conditions. In this review a perspective of the favourable characteristics of yeast as a touchstone model in post-genomic research is presented. The state-of-the art, latest advances in the field and bottlenecks, new strategies, new regulatory mechanisms, applications (patents) and high-throughput technologies, most of them being developed and validated in yeast, are presented. The optimal characteristics of yeast as a well-defined system for comprehensive studies under controlled conditions makes it a perfect model to be used in integrative, "systems biology" studies to get new insights into the mechanisms of regulation (regulatory networks) responsible of specific phenotypes under particular environmental conditions, to be applied to more complex organisms (e.g. plants, human).
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Affiliation(s)
- Juan I Castrillo
- School of Biological Sciences, University of Manchester, 2205 Stopford Building, Oxford Road, Manchester M13 9PT, UK.
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55
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Zhang Q, Ushijima R, Kawai T, Tanaka H. Which to use? - microarray data analysis in input and output data processing. CHEM-BIO INFORMATICS JOURNAL 2004. [DOI: 10.1273/cbij.4.56] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Qingwei Zhang
- Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University
- Pharmaceutical Research Laboratory, AJINOMOTO Co., Inc. [present address]
| | - Rie Ushijima
- Laboratory of Seeds Finding Technology, Eisai Co., Ltd
| | | | - Hiroshi Tanaka
- Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental University
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56
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Futaki S, Hayashi Y, Yamashita M, Yagi K, Bono H, Hayashizaki Y, Okazaki Y, Sekiguchi K. Molecular basis of constitutive production of basement membrane components. Gene expression profiles of Engelbreth-Holm-Swarm tumor and F9 embryonal carcinoma cells. J Biol Chem 2003; 278:50691-701. [PMID: 12968032 DOI: 10.1074/jbc.m304985200] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Engelbreth-Holm-Swarm (EHS) tumors produce large amounts of basement membrane (BM) components that are widely used as cell culture substrates mimicking BM functions. To delineate the tissue/organ origin of the tumor and the mechanisms operating in the BM overproduction, a genome-wide expression profile of EHS tumor was analyzed using RIKEN cDNA microarrays containing approximately 40,000 mouse cDNA clones. Expression profiles of F9 embryonal carcinoma cells that produce laminin-1 and other BM components upon differentiation into parietal endoderm-like cells (designated F9-PE) were also analyzed. Hierarchical clustering analysis showed that the gene expression profiles of EHS and F9-PE were the most similar among 49 mouse tissues/organs in the RIKEN Expression Array Database, suggesting that EHS tumor is parietal endoderm-derived. Quantitative PCR analysis confirmed that not only BM components but also the machineries required for efficient production of BM components, such as enzymes involved in post-translational modification and molecular chaperones, were highly expressed in both EHS and F9-PE. Pairs of similar transcription factor isoforms, such as Gata4/Gata6, Sox7/Sox17, and Cited1/Cited2, were also highly expressed in both EHS tumor and F9-PE. Time course analysis of F9 differentiation showed that up-regulation of the transcription factors was associated with those of BM components, suggesting their involvement in parietal endoderm specification and overproduction of the BM components.
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Affiliation(s)
- Sugiko Futaki
- Sekiguchi Biomatrix Signaling Project, ERATO, Japanese Science and Technology Agency (JST), Aichi Medical University, 21 Karimata, Yazako Nagakute-cho, Aichi-gun, Aichi, 480-1195, Japan
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57
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Tomaru Y, Kondo S, Suzuki M, Hayashizaki Y. A comprehensive search for HNF-3α-regulated genes in mouse hepatoma cells by 60K cDNA microarray and chromatin immunoprecipitation/PCR analysis. Biochem Biophys Res Commun 2003; 310:667-74. [PMID: 14521963 DOI: 10.1016/j.bbrc.2003.08.148] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To characterize the regulatory pattern by a specific transcription regulatory factor, we used a combination of expression analysis with the mouse cDNA microarray composed of 60,000 cDNA clones and cross-linking/chromatin immunoprecipitation (X-ChIP) followed by comparative PCR. Overexpression of mouse hepatocyte nuclear factor-3alpha (HNF-3alpha) in a mouse hepatoma cell line resulted in accompanied perturbed expression of more than 1500 genes. Search for HNF-3alpha consensus recognition sequences in the upstream regions of their coding sequences, which were mapped on the mouse genome, enabled us to mine 300 genes as the potential HNF-3alpha-regulated genes and classify 135 annotated ones into several functional categories. Further X-ChIP/PCR analysis demonstrated in vivo binding of HNF-3alpha to the 5(')-flanking sequences of 25 members selected out of these genes. Besides known HNF-3alpha-regulated genes such as albumin and alpha-fetoprotein genes, the genes newly identified as the HNF-3alpha-regulated ones include three encoding CDP-diacylglycerol-inositol 3-phosphatidyltransferase, phosphatidylserine decarboxylase, and phospholipase A2, which are located en suite in the lipid metabolic pathway in liver. The potential usefulness of the present approach to extensive characterization of gene expression framework directed by a specific transcription regulatory factor is discussed.
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Affiliation(s)
- Yasuhiro Tomaru
- Laboratory of Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama, Kanagawa 230-0045, Japan
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58
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59
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Kasukawa T, Furuno M, Nikaido I, Bono H, Hume DA, Bult C, Hill DP, Baldarelli R, Gough J, Kanapin A, Matsuda H, Schriml LM, Hayashizaki Y, Okazaki Y, Quackenbush J. Development and evaluation of an automated annotation pipeline and cDNA annotation system. Genome Res 2003; 13:1542-51. [PMID: 12819153 PMCID: PMC403710 DOI: 10.1101/gr.992803] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Manual curation has long been held to be the "gold standard" for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed problems with this approach, including inaccurate and inconsistent assignment of gene names, as well as many good assignments that were difficult to reproduce using only computational methods. For the FANTOM2 annotation of more than 60,000 cDNA clones, we developed a number of methods and tools to circumvent some of these problems, including an automated annotation pipeline that provides high-quality preliminary annotation for each sequence by introducing an "uninformative filter" that eliminates uninformative annotations, controlled vocabularies to accurately reflect both the functional assignments and the evidence supporting them, and a highly refined, Web-based manual annotation tool that allows users to view a wide array of sequence analyses and to assign gene names and putative functions using a consistent nomenclature. The ultimate utility of our approach is reflected in the low rate of reassignment of automated assignments by manual curation. Based on these results, we propose a new standard for large-scale annotation, in which the initial automated annotations are manually investigated and then computational methods are iteratively modified and improved based on the results of manual curation.
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Affiliation(s)
- Takeya Kasukawa
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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60
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Numata K, Kanai A, Saito R, Kondo S, Adachi J, Wilming LG, Hume DA, Hayashizaki Y, Tomita M. Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res 2003; 13:1301-6. [PMID: 12819127 PMCID: PMC403720 DOI: 10.1101/gr.1011603] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
With the sequencing and annotation of genomes and transcriptomes of several eukaryotes, the importance of noncoding RNA (ncRNA)-RNA molecules that are not translated to protein products-has become more evident. A subclass of ncRNA transcripts are encoded by highly regulated, multi-exon, transcriptional units, are processed like typical protein-coding mRNAs and are increasingly implicated in regulation of many cellular functions in eukaryotes. This study describes the identification of candidate functional ncRNAs from among the RIKEN mouse full-length cDNA collection, which contains 60,770 sequences, by using a systematic computational filtering approach. We initially searched for previously reported ncRNAs and found nine murine ncRNAs and homologs of several previously described nonmouse ncRNAs. Through our computational approach to filter artifact-free clones that lack protein coding potential, we extracted 4280 transcripts as the largest-candidate set. Many clones in the set had EST hits, potential CpG islands surrounding the transcription start sites, and homologies with the human genome. This implies that many candidates are indeed transcribed in a regulated manner. Our results demonstrate that ncRNAs are a major functional subclass of processed transcripts in mammals.
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Affiliation(s)
- Koji Numata
- Graduate School of Media and Governance, Bioinformatics Program, Keio University, Fujisawa, Kanagawa 252-8520, Japan
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61
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Abbott CA. 11th Intelligent Systems for Molecular Biology 2003 (ISMB 2003). Comp Funct Genomics 2003; 4:654-9. [PMID: 18629025 PMCID: PMC2447307 DOI: 10.1002/cfg.336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2003] [Revised: 09/25/2003] [Accepted: 09/29/2003] [Indexed: 01/22/2023] Open
Abstract
This report profiles the keynote talks given at ISMB03 in Brisbane, Australia by Ron Shamir, David Haussler, John Mattick, Yoshihide Hayashizaki, Sydney Brenner, the
Overton Prize winner, Jim Kent, and the ISCB Senior Accomplishment Awardee,
David Sankov.
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Affiliation(s)
- Catherine A. Abbott
- School of Biological Sciences, Flinders University, GPO BOX 2100, Adelaide, SA, Australia
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62
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Hayashizaki Y. Mouse Genome Encyclopedia Project. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2003; 68:195-204. [PMID: 15338618 DOI: 10.1101/sqb.2003.68.195] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- Y Hayashizaki
- Laboratory for Genome Exploration Research Group, Riken Genomic Sciences Center, Riken Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
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