Discovery of novel rules for G-quadruplex-forming sequences in plants by using bioinformatics methods(BIOINFORMATICS)

スポンサーリンク

概要

• 論文の詳細を見る

• The G-quadruplex is one of the most frequently studied secondary DNA structures and consists of 4 guanine residues that interact through Watson-Crick and Hoogsteen pairing. The G-quadruplex formation is thought to be a molecular switch for gene expression. Genome-wide analyses of G-quadruplexes have been published for many species; however, only one genome-wide analysis of G-quadruplexes in plants has been reported. Here, we propose a new approach involving a two-step procedure for identifying G-quadruplex-forming sequences (potential G4 DNA motif regions: G4MRs) and classifying positional relationships between G4MRs and genes. By using this approach, we exhaustively searched for G4MRs in the whole genomes of 8 species: Arabidopsis thaliana, Oryza sativa subsp. japonica, Populus trichocarpa, Vitis vinifera, Homo sapiens, Danio rerio, Drosophila melanogaster, and Caenorhabditis elegans. We classified genes on the basis of their positional relationships to their proximal G4MRs. We identified novel rules for G4MRs in plants, such as G4MR-enrichment in the template strands at transcription start sites (TSSs). Next, we focused on the template strands of TSSs and conducted gene ontology (GO) analysis of genes proximal to G4MRs. We identified GO terms such as chloroplast and nucleosome (or histone) in O. sativa. Although these terms were strongly associated in O. sativa, weak associations were identified in other plants. These results will be helpful for elucidating the functional roles of G4 DNA.

著者

• 高橋 広夫

  中部大・応生・応生化

• Machida Chiyoko

  Plant Biology Research Center, Chubu University

• Machida Yasunori

  Division Of Biological Science Graduate School Of Science Nagoya University

• CHA Byung-Yoon

  Research Institute for Biological Functions, Chubu University

• Takahashi Hiro

  Department Of Biotechnology School Of Engineering Nagoya University

• Takahashi Hiro

  Department Of Biological Chemistry College Of Bioscience And Biotechnology Chubu University

• Cha Byung-yoon

  Research Institute For Biological Functions Chubu University

• Takahashi Hiro

  Plant Biology Research Center Chubu University

• Nagai Kazuo

  College of Bioscience and Biotechnology, Chubu University:Research Institute for Biological Functions, Chubu University

• Nakagawa Ayami

  Plant Biology Research Center, Chubu University

• Kojima Shoko

  Plant Biology Research Center, Chubu University

• Takahashi Anna

  College of Bioscience and Biotechnology, Chubu University

• Woo Je-Tae

  College of Bioscience and Biotechnology, Chubu University

• Kojima Shoko

  Plant Biology Research Center, Chubu University:College of Bioscience and Biotechnology, Chubu University

• Woo Je-Tae

  College of Bioscience and Biotechnology, Chubu University:Research Institute for Biological Functions, Chubu University

• Takahashi Hiro

  Plant Biology Research Center, Chubu University:College of Bioscience and Biotechnology, Chubu University:Research Institute for Biological Functions, Chubu University

• 高橋 広夫

  千葉大院・園芸

関連論文

• Identification of ENHANCER OF SHOOT REGENERATION 1-upregulated genes during in vitro shoot regeneration
• 1Dp02 遺伝的アルゴリズムとパーミュテーションテストを組み合わせた遺伝子セットの抽出とその評価方法の開発(生体情報工学,遺伝子工学,核酸工学,一般講演)
• 1D10-1 網羅的な遺伝子発現情報を用いた植物の形態制御関連遺伝子解析(生体情報工学(バイオインフォマティクス),発酵生理学・発酵工学,一般講演)
• PS-203-6 肝内結石症における胆管癌発生へのK-ras遺伝子変異と粘液形質の関与 : 形態学的研究への非線形ニューラルネットワークモデリング解析の応用
• 1D10-2 射影適応共鳴理論とブースティングの組み合わせ手法PART-BFCSを用いたがん組織の発現解析(生体情報工学(バイオインフォマティクス),発酵生理学・発酵工学,一般講演)
• Prediction of Peptide Binding to Major Histocompatibility Complex Class II Molecules through Use of Boosted Fuzzy Classifier with SWEEP Operator Method(BIOINFORMATICS)
• REGULATION OF CELL PROLIFERATION IN TOBACCO : INTERACTION OF NPK1 (MAPKKK) AND NAK1 (KINESIN-LIKE PROTEIN)
• Transient Gene Expression in Plant Cells Mediated by Agrobacterium tumefaciens: Application for the Analysis of Virulence Loci
• Knowledge-based Fuzzy Adaptive Resonance Theory and Its Application to the Analysis of Gene Expression in Plants(BIOINFORMATICS)
• Receptor-like kinases that are essential for protoderm formation in Arabidopsis thaliana
• The ASYMMETRIC LEAVES2 Gene of Arabidopsis thaliana, Required for Formation of a Symmetric Flat Leaf Lamina, Encodes a Member of a Novel Family of Proteins Characterized by Cysteine Repeats and a Leucine Zipper
• ACR4, a Putative Receptor Kinase Gene of Arabidopsis thaliana, that is Expressed in the Outer Cell Layers of Embryos and Plants, is Involved in Proper Embryogenesis
• The ASYMMETRIC LEAVES2 gene of A. thaliana regulates the establishment of midvein as the longitudinal axis of leaf symmetry
• MOLECULAR-GENETIC ANALYSIS OF THE AS2 GENE ON THE MECHANISM OF SYMMETRICAL LEAF DEVEL OPMENT IN Arabidopsis thaliana
• Study on the Role of ATCR4,the Arabidopsis Homolog of Maize CRINKLY4 in Epidermis Differentiation
• The ALE1 gene is involved in endosperm development and epidermal differentiation in arabidopsis
• The role of the ASYMMETRIC LEAVES 2(AS2)gene of Arabidopsis thaliana in leaf development
• A Mitogen-activated Protein Kinase NtMPK4 Activated by SIPKK is Required for Jasmonic Acid Signaling and Involved in Ozone Tolerance via Stomatal Movement in Tobacco
• An Inhibitory Effect of Chrysoeriol on Platelet-Derived Growth Factor (PDGF)-Induced Proliferation and PDGF Receptor Signaling in Human Aortic Smooth Muscle Cells
• Inference of Common Genetic Network Using Fuzzy Adaptive Resonance Theory Associated Matrix Method(BIOINFORMATICS)
• Effect of the WUS (JAM) gene on the regulation of leaf identity in Arabidopsis thaliana
• Prognostic Predictor with Multiple Fuzzy Neural Models Using Expression Profiles from DNA Microarray for Metastases of Breast Cancer(BIOINFORMATICS)
• A New Reliable Cancer Diagnosis Method Using Boosted Fuzzy Classifier with a SWEEP Operator Method
• 2F16-1 射影適応共鳴理論とブースティングを組み合わせた新規ガン診断手法の開発(代謝工学・メタボローム・生体情報工学(バイオインフォマティクス),一般講演)
• DNAチップ解析における遺伝子スクリーニング手法の重要性と新手法の提案 (特集 いま注目のDNAチップ大活用!!) -- (数理統計学とチップ解析)
• Proposal of New Gene Filtering Method, BagPART, for Gene Expression Analysis with Small Sample(BIOINFORMATICS)
• Classification of Intramural Metastases and Lymph Node Metastases of Esophageal Cancer from Gene Expression Based on Boosting and Projective Adaptive Resonance Theory(BIOINFORMATICS)
• Lymphoma Prognostication from Expression Profiling Using a Combination Method of Boosting and Projective Adaptive Resonance Theory
• Honokiol Inhibits Osteoclast Differentiation and Function in Vitro
• Agrobacterium-mediated transformation of the wild orchid species Phalaenopsis amabilis
• The transposition pattern of the Ac element in tobacco cultured cells
• ANALYSES OF THE FUNCTIONS OF AS1 AND AS2 IN ARABIDOPSIS
• ANALYSIS OF THE EXPRESSION PATTERN OF GENES WHICH ARE RELATED TO THE LEAF DEVELOPMENT
• HINKEL kinesin, ANP MAPKKKs and MKK6/ANQ MAPKK, which phosphorylates and activates MPK4 MAPK, constitute a pathway that is required for cytokinesis in Arabidopsis thaliana
• A MAP Kinase Cascade That Controls Plant Cytokinesis
• The Expression Pattern of the Gene for NPK1 Protein Kinase Related to Mitogen-Activated Protein Kinase Kinase Kinase (MAPKKK) in a Tobacco Plant : Correlation with Cell Proliferation
• Arabidopsis AUXIN RESPONSE FACTOR6 and 8 Regulate Jasmonic Acid Biosynthesis and Floral Organ Development via Repression of Class 1 KNOX Genes
• Interaction between Agrobacterium tumefaciens oncoprotein 6b and a tobacco nucleolar protein that is homologous to TNP1 encoded by a transposable element of Antirrhinum majus
• ASYMMETRIC LEAVES2, ASYMMETRIC LEAVES1 and Histone Deacetylases Are Involved in the Spatial Regulation of microRNA in Arabidopsis
• Oncogene 6b from Agrobacterium tumefaciens Induces Abaxial Cell Division at Late Stages of Leaf Development and Modifies Vascular Development in Petioles
• Analysis of the globular arrest 1 mutant of Arabidopsis thaliana which has a defect in the embryogenesis
• Characterization of the embryo yellow mutant of Arabidopsis thaliana which has a defect in the embryogenesis
• Isolation and Characterization of the JUVENILE-LEAF-LESS AND MISSHAPEN-APICAL-MERISTEM (JAM) Gene of Arabidopsis thaliana
• 植物の葉の形造りに関わる遣伝子ネットワーク
• Honokiol Increases ABCA1 Expression Level by Activating Retinoid X Receptor Beta
• Morphological Effects of Sinefungin, an Inhibitor of S-Adenosylmethionine-Dependent Methyltransferases, on Anabaena sp. PCC 7120
• ANALYSES OF THE FUNCTIONAL REGION OF 6b PROTEIN ON T-DNA OF A.tumefaciens AND THE ROLE OF ITS INTERACTING PROTEINS
• Agrobacterium tumefaciens T-DNA 6b gene induces plant cell growth and effects on leaf development
• ISOLATION OF ARABIDOPSIS MUTANTS USINGTHE Ac TRANSPOSABLE EREMENTS AND THE SITE-SPECIFIC RECOMBINATIONSYSTEM
• Plant Cells Without Detectable Plastids are Generated in the crumpled leaf Mutant of Arabidopsis thaliana
• Asymmetric Leaves2 and elongator, a histone acetyltransferase complex, mediate the establishment of polarity in leaves of Arabidopsis thaliana
• A transposon insertion mutant of the NADPH oxidase gp91-phox gene homolog in Arabidopsis
• A defect in at Toc159 of Arabidopsis thaliana causes severe defects in leaf development
• Identification of a monofunctional aspartate kinase gene of Arabidopsis thaliana with spatially and temporally regulated expression
• AN ANALYSIS OF CRUMPLED LEAF MUTANT HAVING PALE GREEN, WAVY, AND DISTORTED LEAVES IN ARABIDOPSIS THALIANA
• AN ANALYSIS OF A LYSINE-SENSITIVE ASPARTATE KINASE HOMOLOG OF ARABIDOPSIS WHICH IS HIGHLY EXPRESSED IN LEAF VEINS
• Honokiol enhances adipocyte differentiation by potentiating insulin signaling in 3T3-L1 preadipocytes
• ASYMMETRIC LEAVES2 and Elongator, a Histone Acetyltransferase Complex, Mediate the Establishment of Polarity in Leaves of Arabidopsis thaliana
• Identification of Alternative Splicing Events Regulated by an Arabidopsis Serine/Arginine-Like Protein, atSR45a, in Response to High-Light Stress using a Tiling Array
• Roles of the ASYMMETRIC LEAVES2 gene in floral organ development in Arabidopsis thaliana
• Discovery of novel rules for G-quadruplex-forming sequences in plants by using bioinformatics methods
• N,N'-diphenethylurea isolated from Okinawan ascidian Didemnum molle enhances adipocyte differentiation in 3T3-L1 cells
• CRUMPLED LEAF (CRL)Homologs of Physcomitrella patens are Involved in the Complete Separation of Dividing Plastids
• Knowledge-based Fuzzy Adaptive Resonance Theory and Its Application to the Analysis of Gene Expression in Plants
• Discovery of novel rules for G-quadruplex-forming sequences in plants by using bioinformatics methods(BIOINFORMATICS)
• Arabidopsis ASYMMETRIC LEAVES2 protein required for leaf morphogenesis consistently forms speckles during mitosis of tobacco BY-2 cells via signals in its specific sequence
• 4Fp19 5'非翻訳領域にコードされた種間保存性の高いペプチドの網羅的探索法の開発(生体情報工学,バイオインフォマティックス/システムバイオロジー/遺伝子工学,一般講演)
• ASYMMETRIC LEAVES2 and FASCIATA2 cooperatively regulate the formation of leaf adaxial-abaxial polarity in Arabidopsis thaliana
• どう活かす他人のデータ : バイオインフォマティクス活用法(続・生物工学基礎講座-バイオよもやま話-)
• Identification of a candidate single-nucleotide polymorphism related to chemotherapeutic response through a combination of knowledge-based algorithm and hypothesis-free genomic data
• Meta-Analyses of Microarrays of Arabidopsis asymmetric leaves1 (as1), as2 and Their Modifying Mutants Reveal a Critical Role for the ETT Pathway in Stabilization of Adaxial-Abaxial Patterning and Cell Division During Leaf Development (Special Focus Issue
• Identification of a candidate single-nucleotide polymorphism related to chemotherapeutic response through a combination of knowledge-based algorithm and hypothesis-free genomic data(BIOINFORMATICS)
• 2P-184 5'非翻訳領域にコードされた種間保存性ペプチドの網羅的探索・進化保存性評価手法の開発(生体情報工学,バイオインフォマティクス,一般講演)
• Changes in mRNA Stability Associated with Cold Stress in Arabidopsis Cells
• Discovery of novel rules for G-quadruplex-forming sequences in plants by using bioinformatics methods

もっと見る 閉じる

スポンサーリンク