51
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Li Z, Li B, Liu J, Guo Z, Liu Y, Li Y, Shen WH, Huang Y, Huang H, Zhang Y, Dong A. Transcription factors AS1 and AS2 interact with LHP1 to repress KNOX genes in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:959-970. [PMID: 27273574 DOI: 10.1111/jipb.12485] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 05/31/2016] [Indexed: 06/06/2023]
Abstract
Polycomb group proteins are important repressors of numerous genes in higher eukaryotes. However, the mechanism by which Polycomb group proteins are recruited to specific genes is poorly understood. In Arabidopsis, LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), also known as TERMINAL FLOWER 2, was originally proposed as a subunit of polycomb repressive complex 1 (PRC1) that could bind the tri-methylated lysine 27 of histone H3 (H3K27me3) established by the PRC2. In this work, we show that LHP1 mainly functions with PRC2 to establish H3K27me3, but not with PRC1 to catalyze monoubiquitination at lysine 119 of histone H2A. Our results show that complexes of the transcription factors ASYMMETRIC LEAVES 1 (AS1) and AS2 could help to establish the H3K27me3 modification at the chromatin regions of Class-I KNOTTED1-like homeobox (KNOX) genes BREVIPEDICELLUS and KNAT2 via direct interactions with LHP1. Additionally, our transcriptome analysis indicated that there are probably more common target genes of AS1 and LHP1 besides Class-I KNOX genes during leaf development in Arabidopsis.
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Affiliation(s)
- Zhongfei Li
- State Key Laboratory of Genetic Engineering, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Bin Li
- State Key Laboratory of Genetic Engineering, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jian Liu
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhihao Guo
- State Key Laboratory of Genetic Engineering, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yuhao Liu
- State Key Laboratory of Genetic Engineering, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yan Li
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Shanghai State Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cédex, France
| | - Ying Huang
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Shanghai State Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hai Huang
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yijing Zhang
- National Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
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Guo BJ, Wang J, Lin S, Tian Z, Zhou K, Luan HY, Lyu C, Zhang XZ, Xu RG. A genome-wide analysis of the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) gene family in barley (Hordeum vulgare L.). J Zhejiang Univ Sci B 2016; 17:763-774. [PMID: 27704746 PMCID: PMC5064170 DOI: 10.1631/jzus.b1500277] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 04/17/2016] [Indexed: 12/25/2022]
Abstract
ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) genes are a family of plant specific transcription factors, which play an important role in the regulation of plant lateral organ development and metabolism. However, a genome-wide analysis of the AS2/LOB gene family is still not available for barley. In the present study, 24 AS2-like (ASL)/LOB domain (LBD) genes were identified based on the barley (Hordeum vulgare L.) genome sequence. A phylogenetic tree of ASL/LBD proteins from barley, Arabidopsis, maize, and rice was constructed. The ASL/LBD genes were classified into two classes, class I and class II, which were divided into five and two subgroups, respectively. Genes homologous in barley and Arabidopsis were analyzed. In addition, the structure and chromosomal locations of the genes were analyzed. Expression profiles indicated that barley HvASL/LBD genes exhibit a variety of expression patterns, suggesting that they are involved in various aspects of physiological and developmental processes. This genome-wide analysis of the barley AS2/LOB gene family contributes to our understanding of the functions of the AS2/LOB gene family.
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Affiliation(s)
- Bao-jian Guo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou 225009, China
| | - Jun Wang
- Lianyungang Agricultural Science, Lianyungang 222006, China
| | - Shen Lin
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou 225009, China
| | - Zheng Tian
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou 225009, China
| | - Kai Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou 225009, China
| | - Hai-ye Luan
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou 225009, China
| | - Chao Lyu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou 225009, China
| | - Xin-zhong Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou 225009, China
| | - Ru-gen Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Barley Research Institution of Yangzhou University, Yangzhou University, Yangzhou 225009, China
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Matsumura Y, Ohbayashi I, Takahashi H, Kojima S, Ishibashi N, Keta S, Nakagawa A, Hayashi R, Saéz-Vásquez J, Echeverria M, Sugiyama M, Nakamura K, Machida C, Machida Y. A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis. Biol Open 2016; 5:942-54. [PMID: 27334696 PMCID: PMC4958277 DOI: 10.1242/bio.019109] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Although the DEAD-box RNA helicase family is ubiquitous in eukaryotes, its developmental role remains unelucidated. Here, we report that cooperative action between the Arabidopsis nucleolar protein RH10, an ortholog of human DEAD-box RNA helicase DDX47, and the epigenetic repressor complex of ASYMMETRIC-LEAVES1 (AS1) and AS2 (AS1-AS2) is critical to repress abaxial (ventral) genes ETT/ARF3 and ARF4, which leads to adaxial (dorsal) development in leaf primordia at shoot apices. Double mutations of rh10-1 and as2 (or as1) synergistically up-regulated the abaxial genes, which generated abaxialized filamentous leaves with loss of the adaxial domain. DDX47 is part of the small subunit processome (SSUP) that mediates rRNA biogenesis. In rh10-1 we found various defects in SSUP-related events, such as: accumulation of 35S/33S rRNA precursors; reduction in the 18S/25S ratio; and nucleolar hypertrophy. Double mutants of as2 with mutations of genes that encode other candidate SSUP-related components such as nucleolin and putative rRNA methyltransferase exhibited similar synergistic defects caused by up-regulation of ETT/ARF3 and ARF4. These results suggest a tight link between putative SSUP and AS1-AS2 in repression of the abaxial-determining genes for cell fate decisions for adaxial development. Summary: This paper reports the importance of cooperative action between the nucleus-localized epigenetic repressor and the nucleolus-localized proteins involved in ribosomal RNA processing for polarity establishment of Arabidopsis leaves.
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Affiliation(s)
- Yoko Matsumura
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Iwai Ohbayashi
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Hakusan 3-7-1, Bunkyo-ku, Tokyo 112-0001, Japan
| | - Hiro Takahashi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-shi, Chiba 271-8510, Japan
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Nanako Ishibashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Sumie Keta
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Ayami Nakagawa
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Rika Hayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Julio Saéz-Vásquez
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan 66860, France Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan F-66860, France
| | - Manuel Echeverria
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan 66860, France Université de Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan F-66860, France
| | - Munetaka Sugiyama
- Botanical Gardens, Graduate School of Science, The University of Tokyo, Hakusan 3-7-1, Bunkyo-ku, Tokyo 112-0001, Japan
| | - Kenzo Nakamura
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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Chandler JW. Auxin response factors. PLANT, CELL & ENVIRONMENT 2016; 39:1014-28. [PMID: 26487015 DOI: 10.1111/pce.12662] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/22/2015] [Accepted: 10/05/2015] [Indexed: 05/03/2023]
Abstract
Auxin signalling involves the activation or repression of gene expression by a class of auxin response factor (ARF) proteins that bind to auxin response elements in auxin-responsive gene promoters. The release of ARF repression in the presence of auxin by the degradation of their cognate auxin/indole-3-acetic acid repressors forms a paradigm of transcriptional response to auxin. However, this mechanism only applies to activating ARFs, and further layers of complexity of ARF function and regulation are being revealed, which partly reflect their highly modular domain structure. This review summarizes our knowledge concerning ARF binding site specificity, homodimer and heterodimer multimeric ARF association and cooperative function and how activator ARFs activate target genes via chromatin remodelling and evolutionary information derived from phylogenetic comparisons from ARFs from diverse species. ARFs are regulated in diverse ways, and their importance in non-auxin-regulated pathways is becoming evident. They are also embedded within higher-order transcription factor complexes that integrate signalling pathways from other hormones and in response to the environment. The ways in which new information concerning ARFs on many levels is causing a revision of existing paradigms of auxin response are discussed.
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Affiliation(s)
- John William Chandler
- Institute of Developmental Biology, University of Cologne, Cologne Biocenter, Zuelpicher Strasse 47b, Cologne, D-50674, Germany
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55
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Ichihashi Y, Tsukaya H. Behavior of Leaf Meristems and Their Modification. FRONTIERS IN PLANT SCIENCE 2015; 6:1060. [PMID: 26648955 PMCID: PMC4664833 DOI: 10.3389/fpls.2015.01060] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 11/13/2015] [Indexed: 05/06/2023]
Abstract
A major source of diversity in flowering plant form is the extensive variability of leaf shape and size. Leaf formation is initiated by recruitment of a handful of cells flanking the shoot apical meristem (SAM) to develop into a complex three-dimensional structure. Leaf organogenesis depends on activities of several distinct meristems that are established and spatiotemporally differentiated after the initiation of leaf primordia. Here, we review recent findings in the gene regulatory networks that orchestrate leaf meristem activities in a model plant Arabidopsis thaliana. We then discuss recent key studies investigating the natural variation in leaf morphology to understand how the gene regulatory networks modulate leaf meristems to yield a substantial diversity of leaf forms during the course of evolution.
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Affiliation(s)
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of TokyoTokyo, Japan
- Bio-Next Project, Okazaki Institute for Integrative Bioscience, National Institutes of Natural SciencesOkazaki, Japan
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56
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Husbands AY, Benkovics AH, Nogueira FTS, Lodha M, Timmermans MCP. The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity. THE PLANT CELL 2015; 27:3321-35. [PMID: 26589551 PMCID: PMC4707451 DOI: 10.1105/tpc.15.00454] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 10/16/2015] [Accepted: 11/02/2015] [Indexed: 05/22/2023]
Abstract
Flattened leaf architecture is not a default state but depends on positional information to precisely coordinate patterns of cell division in the growing primordium. This information is provided, in part, by the boundary between the adaxial (top) and abaxial (bottom) domains of the leaf, which are specified via an intricate gene regulatory network whose precise circuitry remains poorly defined. Here, we examined the contribution of the ASYMMETRIC LEAVES (AS) pathway to adaxial-abaxial patterning in Arabidopsis thaliana and demonstrate that AS1-AS2 affects this process via multiple, distinct regulatory mechanisms. AS1-AS2 uses Polycomb-dependent and -independent mechanisms to directly repress the abaxial determinants MIR166A, YABBY5, and AUXIN RESPONSE FACTOR3 (ARF3), as well as a nonrepressive mechanism in the regulation of the adaxial determinant TAS3A. These regulatory interactions, together with data from prior studies, lead to a model in which the sequential polarization of determinants, including AS1-AS2, explains the establishment and maintenance of adaxial-abaxial leaf polarity. Moreover, our analyses show that the shared repression of ARF3 by the AS and trans-acting small interfering RNA (ta-siRNA) pathways intersects with additional AS1-AS2 targets to affect multiple nodes in leaf development, impacting polarity as well as leaf complexity. These data illustrate the surprisingly multifaceted contribution of AS1-AS2 to leaf development showing that, in conjunction with the ta-siRNA pathway, AS1-AS2 keeps the Arabidopsis leaf both flat and simple.
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Affiliation(s)
- Aman Y Husbands
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Anna H Benkovics
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | | | - Mukesh Lodha
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Marja C P Timmermans
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 Center for Plant Molecular Biology, University of Tübingen, 72076 Tuebingen, Germany
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Takahashi H, Kaniwa N, Saito Y, Sai K, Hamaguchi T, Shirao K, Shimada Y, Matsumura Y, Ohtsu A, Yoshino T, Doi T, Takahashi A, Odaka Y, Okuyama M, Sawada JI, Sakamoto H, Yoshida T. Construction of possible integrated predictive index based on EGFR and ANXA3 polymorphisms for chemotherapy response in fluoropyrimidine-treated Japanese gastric cancer patients using a bioinformatic method. BMC Cancer 2015; 15:718. [PMID: 26475168 PMCID: PMC4609065 DOI: 10.1186/s12885-015-1721-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 10/08/2015] [Indexed: 12/23/2022] Open
Abstract
Background Variability in drug response between individual patients is a serious concern in medicine. To identify single-nucleotide polymorphisms (SNPs) related to drug response variability, many genome-wide association studies have been conducted. Methods We previously applied a knowledge-based bioinformatic approach to a pharmacogenomics study in which 119 fluoropyrimidine-treated gastric cancer patients were genotyped at 109,365 SNPs using the Illumina Human-1 BeadChip. We identified the SNP rs2293347 in the human epidermal growth factor receptor (EGFR) gene as a novel genetic factor related to chemotherapeutic response. In the present study, we reanalyzed these hypothesis-free genomic data using extended knowledge. Results We identified rs2867461 in annexin A3 (ANXA3) gene as another candidate. Using logistic regression, we confirmed that the performance of the rs2867461 + rs2293347 model was superior to those of the single factor models. Furthermore, we propose a novel integrated predictive index (iEA) based on these two polymorphisms in EGFR and ANXA3. The p value for iEA was 1.47 × 10−8 by Fisher’s exact test. Recent studies showed that the mutations in EGFR is associated with high expression of dihydropyrimidine dehydrogenase, which is an inactivating and rate-limiting enzyme for fluoropyrimidine, and suggested that the combination of chemotherapy with fluoropyrimidine and EGFR-targeting agents is effective against EGFR-overexpressing gastric tumors, while ANXA3 overexpression confers resistance to tyrosine kinase inhibitors targeting the EGFR pathway. Conclusions These results suggest that the iEA index or a combination of polymorphisms in EGFR and ANXA3 may serve as predictive factors of drug response, and therefore could be useful for optimal selection of chemotherapy regimens. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1721-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan. .,Plant Biology Research Center, Chubu University, Matsumoto-cho 1200, Kasugai, Aichi, 487-8501, Japan. .,Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Nahoko Kaniwa
- Division of Medicinal Safety Science, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan.
| | - Yoshiro Saito
- Division of Medicinal Safety Science, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan.
| | - Kimie Sai
- Division of Medicinal Safety Science, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan.
| | - Tetsuya Hamaguchi
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Kuniaki Shirao
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Yasuhiro Shimada
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Yasuhiro Matsumura
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, 6-5-1, Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
| | - Atsushi Ohtsu
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1, Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
| | - Takayuki Yoshino
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1, Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
| | - Toshihiko Doi
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1, Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
| | - Anna Takahashi
- Plant Biology Research Center, Chubu University, Matsumoto-cho 1200, Kasugai, Aichi, 487-8501, Japan.
| | - Yoko Odaka
- Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Misuzu Okuyama
- Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Jun-Ichi Sawada
- Division of Functional Biochemistry and Genomics, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo, 158-8501, Japan. .,Present address: Pharmaceutical and Medical Devices Agency, Shinkasumigaseki-building, 3-3-2 Kasumigaseki, Chiyoda-ku, Tokyo, 100-0013, Japan.
| | - Hiromi Sakamoto
- Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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Machida C, Nakagawa A, Kojima S, Takahashi H, Machida Y. The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 4:655-71. [PMID: 26108442 PMCID: PMC4744985 DOI: 10.1002/wdev.196] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/23/2015] [Accepted: 05/12/2015] [Indexed: 01/17/2023]
Abstract
Leaf primordia are born around meristem‐containing stem cells at shoot apices, grow along three axes (proximal–distal, adaxial–abaxial, medial–lateral), and develop into flat symmetric leaves with adaxial–abaxial polarity. Axis development and polarity specification of Arabidopsis leaves require a network of genes for transcription factor‐like proteins and small RNAs. Here, we summarize present understandings of adaxial‐specific genes, ASYMMETRIC LEAVES1 (AS1) and AS2. Their complex (AS1–AS2) functions in the regulation of the proximal–distal leaf length by directly repressing class 1 KNOX homeobox genes (BP, KNAT2) that are expressed in the meristem periphery below leaf primordia. Adaxial–abaxial polarity specification involves antagonistic interaction of adaxial and abaxial genes including AS1 and AS2 for the development of two respective domains. AS1–AS2 directly represses the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3) and indirectly represses ETT/ARF3 and ARF4 through tasiR‐ARF. Modifier mutations have been identified that abolish adaxialization and enhance the defect in the proximal–distal patterning in as1 and as2. AS1–AS2 and its modifiers synergistically repress both ARFs and class 1 KNOXs. Repression of ARFs is critical for establishing adaxial–abaxial polarity. On the other hand, abaxial factors KANADI1 (KAN1) and KAN2 directly repress AS2 expression. These data delineate a molecular framework for antagonistic gene interactions among adaxial factors, AS1, AS2, and their modifiers, and the abaxial factors ARFs as key regulators in the establishment of adaxial–abaxial polarity. Possible AS1–AS2 epigenetic repression and activities downstream of ARFs are discussed. WIREs Dev Biol 2015, 4:655–671. doi: 10.1002/wdev.196 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Chiyoko Machida
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Ayami Nakagawa
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Shoko Kojima
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Japan
| | - Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Chiba, Japan
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Abstract
The investigation of transcription factor (TF) families is a major focus of postgenomic research. The plant-specific ASYMMETRIC LEAVES2-LIKE (ASL) / LATERAL ORGAN BOUNDARIES Domain (LBD) proteins constitute a major zincfinger-like-domain transcription factor family, and regulate diverse biological processes in plants. However, little is known about LBD genes in maize (Zea mays). In this study, a total of 44 LBD genes were identified in maize genome and were phylogenetically clustered into two groups (I and II), together with LBDs from Arabidopsis. The predicted maize LBDs were distributed across all the 10 chromosomes with different densities. In addition, the gene structures of maize LBDs were analysed. The expression profiles of the maize LBD genes under normal growth conditions were analysed by microarray data and qRT-PCR. The results indicated that LBDs might be involved in various aspects of physiological and developmental processes in maize. To our knowledge, this is the first report of a genomewide analysis of the maize LBD gene family, which would provide valuable information for understanding the classification and putative functions of the gene family.
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Jia X, Ding N, Fan W, Yan J, Gu Y, Tang X, Li R, Tang G. Functional plasticity of miR165/166 in plant development revealed by small tandem target mimic. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 233:11-21. [PMID: 25711809 DOI: 10.1016/j.plantsci.2014.12.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/16/2014] [Accepted: 12/24/2014] [Indexed: 05/20/2023]
Abstract
MicroRNA 165 and 166 (miR165/166) is composed of nine members and targets five members (PHB, PHV, REV, ATHB8 and ATHB15) of the HD-ZIP III transcription factor family. Mutants generated by traditional methods could hardly reveal the overall functions of miR165/166 in plant development. In this study, the expressions of all miR165/166 members were simultaneously blocked by over-expressing STTM165/166-31 in Arabidopsis and tomato for functional dissection of miR165/166 family. Following a down-regulation of over 90% endogenous miR165/166, the target HD-ZIP III genes were correspondingly up-regulated in the STTM transgenic Arabidopsis and tomato plants. Notably, the STTM165/166-31 over-expressed Arabidopsis and tomato displayed pleiotropic effects on development which were not frequently observed in previously identified genetic mutants of either individual miR165/166 gene or any of the five target genes. Furthermore, the transgenic Arabidopsis showed increased IAA content and decreased IAA sensitivity accompanied by enhanced expressions of genes responsible for auxin biosynthesis and signaling, suggesting possible roles of auxin in mediation of miR165/166-regulated processes. Importantly, the transgenic Arabidopsis exhibited the improved behavior under salt stress. Overall, such diverse variations in plant development and physiological process revealed by STTM165/166 demonstrate a key role of miR165/166-mediated network in regulating plant development and responses to abiotic stresses.
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Affiliation(s)
- Xiaoyun Jia
- Shanxi Agricultural University, Taigu 030801, Shanxi, China; Gene Suppression Laboratory, Department of Plant and Soil Sciences and Kentucky Tobacco and Research Development Center, University of Kentucky, Lexington, KY 40546 USA
| | - Na Ding
- Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Weixin Fan
- Shanxi Agricultural University, Taigu 030801, Shanxi, China
| | - Jun Yan
- Gene Suppression Laboratory, Department of Plant and Soil Sciences and Kentucky Tobacco and Research Development Center, University of Kentucky, Lexington, KY 40546 USA
| | - Yiyou Gu
- Gene Suppression Laboratory, Department of Plant and Soil Sciences and Kentucky Tobacco and Research Development Center, University of Kentucky, Lexington, KY 40546 USA; Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Xiaoqing Tang
- Gene Suppression Laboratory, Department of Plant and Soil Sciences and Kentucky Tobacco and Research Development Center, University of Kentucky, Lexington, KY 40546 USA; Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Runzhi Li
- Shanxi Agricultural University, Taigu 030801, Shanxi, China; Gene Suppression Laboratory, Department of Plant and Soil Sciences and Kentucky Tobacco and Research Development Center, University of Kentucky, Lexington, KY 40546 USA.
| | - Guiliang Tang
- Shanxi Agricultural University, Taigu 030801, Shanxi, China; Gene Suppression Laboratory, Department of Plant and Soil Sciences and Kentucky Tobacco and Research Development Center, University of Kentucky, Lexington, KY 40546 USA; Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA.
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Šiukšta R, Vaitkūnienė V, Kaselytė G, Okockytė V, Žukauskaitė J, Žvingila D, Rančelis V. Inherited phenotype instability of inflorescence and floral organ development in homeotic barley double mutants and its specific modification by auxin inhibitors and 2,4-D. ANNALS OF BOTANY 2015; 115:651-63. [PMID: 25660346 PMCID: PMC4343296 DOI: 10.1093/aob/mcu263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
BACKGROUND AND AIMS Barley (Hordeum vulgare) double mutants Hv-Hd/tw2, formed by hybridization, are characterized by inherited phenotypic instability and by several new features, such as bract/leaf-like structures, long naked gaps in the spike, and a wide spectrum of variations in the basic and ectopic flowers, which are absent in single mutants. Several of these features resemble those of mutations in auxin distribution, and thus the aim of this study was to determine whether auxin imbalances are related to phenotypic variations and instability. The effects of auxin inhibitors and 2,4-D (2,4-dichlorophenoxyacetic acid) on variation in basic and ectopic flowers were therefore examined, together with the effects of 2,4-D on spike structure. METHODS The character of phenotypic instability and the effects of auxin inhibitors and 2,4-D were compared in callus cultures and intact plants of single homeotic Hv-tw2 and Hv-Hooded/Kap (in the BKn3 gene) mutants and alternative double mutant lines: offspring from individual plants in distal hybrid generations (F9-F10) that all had the same BKn3 allele as determined by DNA sequencing. For intact plants, two auxin inhibitors, 9-hydroxyfluorene-9-carboxylic acid (HFCA) and p-chlorophenoxyisobutyric acid (PCIB), were used. KEY RESULTS Callus growth and flower/spike structures of the Hv-tw2 mutant differed in their responses to HFCA and PCIB. An increase in normal basic flowers after exposure to auxin inhibitors and a decrease in their frequencies caused by 2,4-D were observed, and there were also modifications in the spectra of ectopic flowers, especially those with sexual organs, but the effects depended on the genotype. Exposure to 2,4-D decreased the frequency of short gaps and lodicule transformations in Hv-tw2 and of long naked gaps in double mutants. CONCLUSIONS The effects of auxin inhibitors and 2,4-D suggest that ectopic auxin maxima or deficiencies arise in various regions of the inflorescence/flower primordia. Based on the phenotypic instability observed, definite trends in the development of ectopic flower structures may be detected, from insignificant outgrowths on awns to flowers with sterile organs. Phenotypically unstable barley double mutants provide a highly promising genetic system for the investigation of gene expression modules and trend orders.
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Affiliation(s)
- Raimondas Šiukšta
- Department of Botany and Genetics, Faculty of Natural Sciences, Vilnius University, M. K. Čiurlionis Str. 21/27, LT-03101 Vilnius, Lithuania and Botanical Garden of Vilnius University, Kairėnai Str. 43, LT-10239 Vilnius, Lithuania Department of Botany and Genetics, Faculty of Natural Sciences, Vilnius University, M. K. Čiurlionis Str. 21/27, LT-03101 Vilnius, Lithuania and Botanical Garden of Vilnius University, Kairėnai Str. 43, LT-10239 Vilnius, Lithuania
| | - Virginija Vaitkūnienė
- Department of Botany and Genetics, Faculty of Natural Sciences, Vilnius University, M. K. Čiurlionis Str. 21/27, LT-03101 Vilnius, Lithuania and Botanical Garden of Vilnius University, Kairėnai Str. 43, LT-10239 Vilnius, Lithuania Department of Botany and Genetics, Faculty of Natural Sciences, Vilnius University, M. K. Čiurlionis Str. 21/27, LT-03101 Vilnius, Lithuania and Botanical Garden of Vilnius University, Kairėnai Str. 43, LT-10239 Vilnius, Lithuania
| | - Greta Kaselytė
- Department of Botany and Genetics, Faculty of Natural Sciences, Vilnius University, M. K. Čiurlionis Str. 21/27, LT-03101 Vilnius, Lithuania and Botanical Garden of Vilnius University, Kairėnai Str. 43, LT-10239 Vilnius, Lithuania
| | - Vaiva Okockytė
- Department of Botany and Genetics, Faculty of Natural Sciences, Vilnius University, M. K. Čiurlionis Str. 21/27, LT-03101 Vilnius, Lithuania and Botanical Garden of Vilnius University, Kairėnai Str. 43, LT-10239 Vilnius, Lithuania
| | - Justina Žukauskaitė
- Department of Botany and Genetics, Faculty of Natural Sciences, Vilnius University, M. K. Čiurlionis Str. 21/27, LT-03101 Vilnius, Lithuania and Botanical Garden of Vilnius University, Kairėnai Str. 43, LT-10239 Vilnius, Lithuania
| | - Donatas Žvingila
- Department of Botany and Genetics, Faculty of Natural Sciences, Vilnius University, M. K. Čiurlionis Str. 21/27, LT-03101 Vilnius, Lithuania and Botanical Garden of Vilnius University, Kairėnai Str. 43, LT-10239 Vilnius, Lithuania
| | - Vytautas Rančelis
- Department of Botany and Genetics, Faculty of Natural Sciences, Vilnius University, M. K. Čiurlionis Str. 21/27, LT-03101 Vilnius, Lithuania and Botanical Garden of Vilnius University, Kairėnai Str. 43, LT-10239 Vilnius, Lithuania
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Abstract
Stem cells are responsible for organogenesis, but it is largely unknown whether and how information from stem cells acts to direct organ patterning after organ primordia are formed. It has long been proposed that the stem cells at the plant shoot apex produce a signal, which promotes leaf adaxial-abaxial (dorsoventral) patterning. Here we show the existence of a transient low auxin zone in the adaxial domain of early leaf primordia. We also demonstrate that this adaxial low auxin domain contributes to leaf adaxial-abaxial patterning. The auxin signal is mediated by the auxin-responsive transcription factor MONOPTEROS (MP), whose constitutive activation in the adaxial domain promotes abaxial cell fate. Furthermore, we show that auxin flow from emerging leaf primordia to the shoot apical meristem establishes the low auxin zone, and that this auxin flow contributes to leaf polarity. Our results provide an explanation for the hypothetical meristem-derived leaf polarity signal. Opposite to the original proposal, instead of a signal derived from the meristem, we show that a signaling molecule is departing from the primordium to the meristem to promote robustness in leaf patterning.
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63
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Wang C, Liu C, Roqueiro D, Grimm D, Schwab R, Becker C, Lanz C, Weigel D. Genome-wide analysis of local chromatin packing in Arabidopsis thaliana. Genome Res 2014; 25:246-56. [PMID: 25367294 PMCID: PMC4315298 DOI: 10.1101/gr.170332.113] [Citation(s) in RCA: 203] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The spatial arrangement of interphase chromosomes in the nucleus is important for gene expression and genome function in animals and in plants. The recently developed Hi-C technology is an efficacious method to investigate genome packing. Here we present a detailed Hi-C map of the three-dimensional genome organization of the plant Arabidopsis thaliana. We find that local chromatin packing differs from the patterns seen in animals, with kilobasepair-sized segments that have much higher intrachromosome interaction rates than neighboring regions, representing a dominant local structural feature of genome conformation in A. thaliana. These regions, which appear as positive strips on two-dimensional representations of chromatin interaction, are enriched in epigenetic marks H3K27me3, H3.1, and H3.3. We also identify more than 400 insulator-like regions. Furthermore, although topologically associating domains (TADs), which are prominent in animals, are not an obvious feature of A. thaliana genome packing, we found more than 1000 regions that have properties of TAD boundaries, and a similar number of regions analogous to the interior of TADs. The insulator-like, TAD-boundary-like, and TAD-interior-like regions are each enriched for distinct epigenetic marks and are each correlated with different gene expression levels. We conclude that epigenetic modifications, gene density, and transcriptional activity combine to shape the local packing of the A. thaliana nuclear genome.
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Affiliation(s)
- Congmao Wang
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Chang Liu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
| | - Damian Roqueiro
- Machine Learning and Computational Biology Research Group, Max Planck Institute for Developmental Biology and Max Planck Institute for Intelligent Systems, 72076 Tübingen, Germany
| | - Dominik Grimm
- Machine Learning and Computational Biology Research Group, Max Planck Institute for Developmental Biology and Max Planck Institute for Intelligent Systems, 72076 Tübingen, Germany
| | - Rebecca Schwab
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Christa Lanz
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
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Costanzo E, Trehin C, Vandenbussche M. The role of WOX genes in flower development. ANNALS OF BOTANY 2014; 114:1545-53. [PMID: 24973416 PMCID: PMC4204783 DOI: 10.1093/aob/mcu123] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 04/29/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND WOX (Wuschel-like homeobOX) genes form a family of plant-specific HOMEODOMAIN transcription factors, the members of which play important developmental roles in a diverse range of processes. WOX genes were first identified as determining cell fate during embryo development, as well as playing important roles in maintaining stem cell niches in the plant. In recent years, new roles have been identified in plant architecture and organ development, particularly at the flower level. SCOPE In this review, the role of WOX genes in flower development and flower architecture is highlighted, as evidenced from data obtained in the last few years. The roles played by WOX genes in different species and different flower organs are compared, and differential functional recruitment of WOX genes during flower evolution is considered. CONCLUSIONS This review compares available data concerning the role of WOX genes in flower and organ architecture among different species of angiosperms, including representatives of monocots and eudicots (rosids and asterids). These comparative data highlight the usefulness of the WOX gene family for evo-devo studies of floral development.
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Affiliation(s)
- Enrico Costanzo
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Christophe Trehin
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France
| | - Michiel Vandenbussche
- Laboratory of Reproduction and Development of Plants, UMR5667 (ENS de Lyon, CNRS, INRA, UCBL), Ecole Normale Supérieure de Lyon, Lyon, France
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Analysis of gene expression profiles of soft tissue sarcoma using a combination of knowledge-based filtering with integration of multiple statistics. PLoS One 2014; 9:e106801. [PMID: 25188299 PMCID: PMC4154757 DOI: 10.1371/journal.pone.0106801] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 08/01/2014] [Indexed: 12/21/2022] Open
Abstract
The diagnosis and treatment of soft tissue sarcomas (STS) have been difficult. Of the diverse histological subtypes, undifferentiated pleomorphic sarcoma (UPS) is particularly difficult to diagnose accurately, and its classification per se is still controversial. Recent advances in genomic technologies provide an excellent way to address such problems. However, it is often difficult, if not impossible, to identify definitive disease-associated genes using genome-wide analysis alone, primarily because of multiple testing problems. In the present study, we analyzed microarray data from 88 STS patients using a combination method that used knowledge-based filtering and a simulation based on the integration of multiple statistics to reduce multiple testing problems. We identified 25 genes, including hypoxia-related genes (e.g., MIF, SCD1, P4HA1, ENO1, and STAT1) and cell cycle- and DNA repair-related genes (e.g., TACC3, PRDX1, PRKDC, and H2AFY). These genes showed significant differential expression among histological subtypes, including UPS, and showed associations with overall survival. STAT1 showed a strong association with overall survival in UPS patients (logrank p = 1.84 × 10(-6) and adjusted p value 2.99 × 10(-3) after the permutation test). According to the literature, the 25 genes selected are useful not only as markers of differential diagnosis but also as prognostic/predictive markers and/or therapeutic targets for STS. Our combination method can identify genes that are potential prognostic/predictive factors and/or therapeutic targets in STS and possibly in other cancers. These disease-associated genes deserve further preclinical and clinical validation.
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66
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Jung HJ, Dong X, Park JI, Thamilarasan SK, Lee SS, Kim YK, Lim YP, Nou IS, Hur Y. Genome-wide transcriptome analysis of two contrasting Brassica rapa doubled haploid lines under cold-stresses using Br135K oligomeric chip. PLoS One 2014; 9:e106069. [PMID: 25167163 PMCID: PMC4148347 DOI: 10.1371/journal.pone.0106069] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/27/2014] [Indexed: 12/02/2022] Open
Abstract
Genome wide transcription analysis in response to stresses is important to provide a basis of effective engineering strategies to improve stress tolerance in crop plants. We assembled a Brassica rapa oligomeric microarray (Br135K microarray) using sequence information from 41,173 unigenes and analyzed the transcription profiles of two contrasting doubled haploid (DH) lines, Chiifu and Kenshin, under cold-treatments. The two DH lines showed great differences in electrolyte leakage below −4°C, but similar patterns from 4°C to −2°C. Cold-treatments induced 885 and 858 genes in Chiifu and Kenshin, respectively. Overall, 134, and 56 genes showed an intrinsic difference in expression in Chiifu and Kenshin, respectively. Among 5,349 genes that showed no hit found (NHF) in public databases, 61 and 24 were specifically expressed in Chiifu and Kenshin, respectively. Many transcription factor genes (TFs) also showed various characteristics of expression. BrMYB12, BrMYBL2, BrbHLHs, BrbHLH038, a C2H2, a WRKY, BrDREB19 and a integrase-type TF were induced in a Chiifu-specific fashion, while a bHLH (Bra001826/AT3G21330), bHLH, cycling Dof factor and two Dof type TFs were Kenshin specific. Similar to previous studies, a large number of genes were differently induced or regulated among the two genotypes, but many genes, including NHFs, were specifically or intrinsically expressed with genotype specificity. Expression patterns of known-cold responsive genes in plants resulted in discrepancy to membrane leakage in the two DH lines, indicating that timing of gene expression is more important to conferring freezing tolerance rather than expression levels. Otherwise, the tolerance will be related to the levels of transcripts before cold-treatment or regulated by other mechanisms. Overall, these results indicate common signaling pathways and various transcriptional regulatory mechanisms are working together during cold-treatment of B. rapa. Our newly developed Br135K oligomeric microarray will be useful for transcriptome profiling, and will deliver valuable insight into cold stresses in B. rapa.
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Affiliation(s)
- Hee-Jeong Jung
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | - Xiangshu Dong
- Department of Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
| | | | - Sang Sook Lee
- Department of Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Yeon-Ki Kim
- GreenGene Biotech Inc., Genomics and Genetics Institute, Yongin, Republic of Korea
| | - Yong-Pyo Lim
- Department of Horticulture, Chungnam National University, Daejeon, Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon, Jeonnam, Republic of Korea
- * E-mail: (ISN); (YH)
| | - Yoonkang Hur
- Department of Biology, College of Biological Science and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
- * E-mail: (ISN); (YH)
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Takahashi H, Sai K, Saito Y, Kaniwa N, Matsumura Y, Hamaguchi T, Shimada Y, Ohtsu A, Yoshino T, Doi T, Okuda H, Ichinohe R, Takahashi A, Doi A, Odaka Y, Okuyama M, Saijo N, Sawada JI, Sakamoto H, Yoshida T. Application of a combination of a knowledge-based algorithm and 2-stage screening to hypothesis-free genomic data on irinotecan-treated patients for identification of a candidate single nucleotide polymorphism related to an adverse effect. PLoS One 2014; 9:e105160. [PMID: 25127363 PMCID: PMC4134257 DOI: 10.1371/journal.pone.0105160] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Accepted: 07/17/2014] [Indexed: 01/27/2023] Open
Abstract
Interindividual variation in a drug response among patients is known to cause serious problems in medicine. Genomic information has been proposed as the basis for “personalized” health care. The genome-wide association study (GWAS) is a powerful technique for examining single nucleotide polymorphisms (SNPs) and their relationship with drug response variation; however, when using only GWAS, it often happens that no useful SNPs are identified due to multiple testing problems. Therefore, in a previous study, we proposed a combined method consisting of a knowledge-based algorithm, 2 stages of screening, and a permutation test for identifying SNPs. In the present study, we applied this method to a pharmacogenomics study where 109,365 SNPs were genotyped using Illumina Human-1 BeadChip in 168 cancer patients treated with irinotecan chemotherapy. We identified the SNP rs9351963 in potassium voltage-gated channel subfamily KQT member 5 (KCNQ5) as a candidate factor related to incidence of irinotecan-induced diarrhea. The p value for rs9351963 was 3.31×10−5 in Fisher's exact test and 0.0289 in the permutation test (when multiple testing problems were corrected). Additionally, rs9351963 was clearly superior to the clinical parameters and the model involving rs9351963 showed sensitivity of 77.8% and specificity of 57.6% in the evaluation by means of logistic regression. Recent studies showed that KCNQ4 and KCNQ5 genes encode members of the M channel expressed in gastrointestinal smooth muscle and suggested that these genes are associated with irritable bowel syndrome and similar peristalsis diseases. These results suggest that rs9351963 in KCNQ5 is a possible predictive factor of incidence of diarrhea in cancer patients treated with irinotecan chemotherapy and for selecting chemotherapy regimens, such as irinotecan alone or a combination of irinotecan with a KCNQ5 opener. Nonetheless, clinical importance of rs9351963 should be further elucidated.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- * E-mail:
| | - Kimie Sai
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Yoshiro Saito
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Nahoko Kaniwa
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Yasuhiro Matsumura
- Division of Developmental Therapeutics, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Tetsuya Hamaguchi
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, Tokyo, Japan
| | - Yasuhiro Shimada
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, Tokyo, Japan
| | - Atsushi Ohtsu
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Takayuki Yoshino
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Toshihiko Doi
- Department of Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Haruhiro Okuda
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Risa Ichinohe
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Faculty of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Anna Takahashi
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Ayano Doi
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Faculty of Horticulture, Chiba University, Matsudo, Chiba, Japan
| | - Yoko Odaka
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Misuzu Okuyama
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Nagahiro Saijo
- National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Jun-ichi Sawada
- Division of Functional Biochemistry and Genomics, National Institute of Health Sciences, Tokyo, Japan
| | - Hiromi Sakamoto
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
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68
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Hawkins C, Liu Z. A model for an early role of auxin in Arabidopsis gynoecium morphogenesis. FRONTIERS IN PLANT SCIENCE 2014; 5:327. [PMID: 25071809 PMCID: PMC4086399 DOI: 10.3389/fpls.2014.00327] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/23/2014] [Indexed: 05/19/2023]
Abstract
The female reproductive organ of angiosperms, the gynoecium, often consists of the fusion of multiple ovule-bearing carpels. It serves the important function of producing and protecting ovules as well as mediating pollination. The gynoecium has likely contributed to the tremendous success of angiosperms over their 160 million year history. In addition, being a highly complex plant organ, the gynoecium is well suited to serving as a model system for use in the investigation of plant morphogenesis and development. The longstanding model of gynoecium morphogenesis in Arabidopsis holds that apically localized auxin biosynthesis in the gynoecium results in an apical to basal gradient of auxin that serves to specify along its length the development of style, ovary, and gynophore in a concentration-dependent manner. This model is based primarily on the observed effects of the auxin transport blocker N-1-naphthylphthalamic acid (NPA) as well as analyses of mutants of Auxin Response Factor (ARF) 3/ETTIN (ETT). Both NPA treatment and ett mutation disrupt gynoecium morphological patterns along the apical-basal axis. More than a decade after the model's initial proposal, however, the auxin gradient on which the model critically depends remains elusive. Furthermore, multiple observations are inconsistent with such an auxin-gradient model. Chiefly, the timing of gynoecium emergence and patterning occurs at a very early stage when the organ has little-to-no apical-basal dimension. Based on these observations and current models of early leaf patterning, we propose an alternate model for gynoecial patterning. Under this model, the action of auxin is necessary for the early establishment of adaxial-abaxial patterning of the carpel primordium. In this case, the observed gynoecial phenotypes caused by NPA and ett are due to the disruption of this early adaxial-abaxial patterning of the carpel primordia. Here we present the case for this model based on recent literature and current models of leaf development.
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Affiliation(s)
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, College ParkMD, USA
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69
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DeMason DA, Chetty V. Phenotypic characterization of the CRISPA (ARP gene) mutant of pea (Pisum sativum; Fabaceae): a reevaluation. AMERICAN JOURNAL OF BOTANY 2014; 101:408-27. [PMID: 24638162 DOI: 10.3732/ajb.1300415] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
PREMISE OF THE STUDY Leaf form and development are controlled genetically. The ARP genes encode MYB transcription factors that interact with Class 1 KNOX genes in a regulatory module that controls meristem-leaf determinations and is highly conserved in plants. ARP loss of function alleles and subsequent KNOX1 overexpression cause many unusual leaf phenotypes including loss or partial loss of the ability to produce a lamina and production of "knots" on leaf blades. CRISPA (CRI) is the ARP gene in pea, and a number of its mutant alleles are known. METHODS We made morphological and anatomical evaluations of cri-1 mutant plants while controlling for genetic background and for heteroblastic effects, and we used aldehyde fixation and resin preparations for anatomical analysis. Further, we compared gene expression in WT and cri-1 shoot tips and HOP1/PsKN1 and CRI expression in other leaf mutants. KEY RESULTS The cri-1 plants had more extensive abnormalities in the proximal than in the distal regions of the leaf, including ectopic stipules, narrow leaflets, and shortened petioles with excessive adaxial expansion. "Knots" were morphologically and anatomically variable but consisted of vascularized out-pocketing of the adaxial leaflet surface. HOP1/PsKN1 and UNI mRNA levels were higher in cri-1 shoot tips, and some auxin-regulated genes were lower. Low LE expression suggests that the GA level is high in cri-1 shoot tips. CONCLUSIONS The CRISPA gene of pea suppresses KNOX1 genes and UNI and functions to (1) maintain proximal-distal regions in their appropriate positions, (2) restrict excessive adaxial cell proliferation, and (3) promote laminar expansion.
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Affiliation(s)
- Darleen A DeMason
- Botany and Plant Sciences, University of California, Riverside, California, 92521 USA
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70
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Zhang F, Wang Y, Li G, Tang Y, Kramer EM, Tadege M. STENOFOLIA recruits TOPLESS to repress ASYMMETRIC LEAVES2 at the leaf margin and promote leaf blade outgrowth in Medicago truncatula. THE PLANT CELL 2014; 26:650-64. [PMID: 24585835 PMCID: PMC3967031 DOI: 10.1105/tpc.113.121947] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 01/28/2014] [Accepted: 02/03/2014] [Indexed: 05/22/2023]
Abstract
The Medicago truncatula WUSCHEL-related homeobox (WOX) gene, STENOFOLIA (STF), plays a key role in leaf blade outgrowth by promoting cell proliferation at the adaxial-abaxial junction. STF functions primarily as a transcriptional repressor, but the underlying molecular mechanism is unknown. Here, we report the identification of a protein interaction partner and a direct target, shedding light on the mechanism of STF function. Two highly conserved motifs in the C-terminal domain of STF, the WUSCHEL (WUS) box and the STF box, cooperatively recruit TOPLESS (Mt-TPL) family corepressors, and this recruitment is required for STF function, as deletion of these two domains (STFdel) impaired blade outgrowth whereas fusing Mt-TPL to STFdel restored function. The homeodomain motif is required for direct repression of ASYMMETRIC LEAVES2 (Mt-AS2), silencing of which partially rescues the stf mutant phenotype. STF and LAMINALESS1 (LAM1) are functional orthologs. A single amino acid (Asn to Ile) substitution in the homeodomain abolished the repression of Mt-AS2 and STF's ability to complement the lam1 mutant of Nicotiana sylvestris. Our data together support a model in which STF recruits corepressors to transcriptionally repress its targets during leaf blade morphogenesis. We propose that recruitment of TPL/TPL-related proteins may be a common mechanism in the repressive function of modern/WUS clade WOX genes.
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Affiliation(s)
- Fei Zhang
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401
| | - Yewei Wang
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401
| | - Guifen Li
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Yuhong Tang
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
| | - Elena M. Kramer
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Million Tadege
- Department of Plant and Soil Sciences, Institute for Agricultural Biosciences, Oklahoma State University, Ardmore, Oklahoma 73401
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71
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Ge L, Chen R. PHANTASTICA regulates leaf polarity and petiole identity in Medicago truncatula. PLANT SIGNALING & BEHAVIOR 2014; 9:e28121. [PMID: 24603499 PMCID: PMC4091575 DOI: 10.4161/psb.28121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Establishment of proper polarities along the adaxial-abaxial, proximodistal, and medial-lateral axes is a critical step for the expansion of leaves from leaf primordia. It has been shown that the MYB domain protein, asymmetric leaves1/rough sheath2/PHANTASTICA (collectively named ARP) plays an important role in this process. Loss of function of ARP leads to severe leaf polarity defects, such as abaxialized or needle-like leaves. In addition to its role in leaf polarity establishment, we have recently shown that the Medicago truncatula ARP gene, MtPHAN, also plays a role in leaf petiole identity regulation. We show that a mutation of MtPHAN results in petioles acquiring characteristics of the motor organ, pulvinus, including small epidermal cells with extensive cell surface modifications and altered vascular tissue development. Taken together, our results reveal a previously unidentified function of ARP in leaf development.
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72
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Fukushima K, Hasebe M. Adaxial-abaxial polarity: the developmental basis of leaf shape diversity. Genesis 2013; 52:1-18. [PMID: 24281766 DOI: 10.1002/dvg.22728] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 11/15/2013] [Accepted: 11/22/2013] [Indexed: 02/05/2023]
Abstract
Leaves of flowering plants are diverse in shape. Part of this morphological diversity can be attributed to differences in spatiotemporal regulation of polarity in the upper (adaxial) and lower (abaxial) sides of developing leaves. In a leaf primordium, antagonistic interactions between polarity determinants specify the adaxial and abaxial domains in a mutually exclusive manner. The patterning of those domains is critical for leaf morphogenesis. In this review, we first summarize the gene networks regulating adaxial-abaxial polarity in conventional bifacial leaves and then discuss how patterning is modified in different leaf type categories.
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Affiliation(s)
- Kenji Fukushima
- Department of Basic Biology, School of Life Science, Graduate University for Advance Studies (SOKENDAI), Okazaki, 444-8585, Japan; National Institute for Basic Biology, Okazaki, 444-8585, Japan
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73
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Chen X, Wang H, Li J, Huang H, Xu L. Quantitative control of ASYMMETRIC LEAVES2 expression is critical for leaf axial patterning in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:4895-905. [PMID: 24006428 PMCID: PMC3830476 DOI: 10.1093/jxb/ert278] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
ASYMMETRIC LEAVES2 (AS2) is one of the key genes required for specifying leaf adaxial identity during leaf adaxial-abaxial polarity establishment. Previous data have shown that, in leaf development, AS2 is directly repressed by an abaxially located transcription factor KANADI1 (KAN1), so that the AS2 transcripts are restricted only in the adaxial leaf domain. It is shown here that, different from the spatial repression by KAN1, the quantitative repression of AS2 in the adaxial domain is also critical for ensuring normal leaf pattern formation. By analysing two gain-of-function as2 mutants, as2-5D and isoginchaku-2D (iso-2D), it is shown that the similar AS2-over-expressed phenotypes of these mutants reflect two different kinds of AS2 misexpression patterns. While as2-5D causes disruption of a KAN1-binding site at the AS2 promoter leading to derepression of AS2 in the abaxial side but without changing its expression level of a leaf, iso-2D results in over-expression of AS2 but without altering its adaxial expression pattern. In addition, it was found that, in iso-2D, levels of histone H3 lysine 27 trimethylation (H3K27me3) and H3K4me3 at the AS2 locus are significantly reduced and increased, respectively, compared with those in the wild type and as2-5D. These results suggest that during leaf patterning, quantitative control of the AS2 expression level might involve epigenetic regulations.
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Affiliation(s)
| | | | | | | | - Lin Xu
- * To whom correspondence should be addressed. E-mail:
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74
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Takahashi H, Nakayama R, Hayashi S, Nemoto T, Murase Y, Nomura K, Takahashi T, Kubo K, Marui S, Yasuhara K, Nakamura T, Sueo T, Takahashi A, Tsutsumiuchi K, Ohta T, Kawai A, Sugita S, Yamamoto S, Kobayashi T, Honda H, Yoshida T, Hasegawa T. Macrophage migration inhibitory factor and stearoyl-CoA desaturase 1: potential prognostic markers for soft tissue sarcomas based on bioinformatics analyses. PLoS One 2013; 8:e78250. [PMID: 24167613 PMCID: PMC3805525 DOI: 10.1371/journal.pone.0078250] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 09/10/2013] [Indexed: 11/18/2022] Open
Abstract
The diagnosis and treatment of soft tissue sarcomas (STSs) has been particularly difficult, because STSs are a group of highly heterogeneous tumors in terms of histopathology, histological grade, and primary site. Recent advances in genome technologies have provided an excellent opportunity to determine the complete biological characteristics of neoplastic tissues, resulting in improved diagnosis, treatment selection, and investigation of therapeutic targets. We had previously developed a novel bioinformatics method for marker gene selection and applied this method to gene expression data from STS patients. This previous analysis revealed that the extracted gene combination of macrophage migration inhibitory factor (MIF) and stearoyl-CoA desaturase 1 (SCD1) is an effective diagnostic marker to discriminate between subtypes of STSs with highly different outcomes. In the present study, we hypothesize that the combination of MIF and SCD1 is also a prognostic marker for the overall outcome of STSs. To prove this hypothesis, we first analyzed microarray data from 88 STS patients and their outcomes. Our results show that the survival rates for MIF- and SCD1-positive groups were lower than those for negative groups, and the p values of the log-rank test are 0.0146 and 0.00606, respectively. In addition, survival rates are more significantly different (p = 0.000116) between groups that are double-positive and double-negative for MIF and SCD1. Furthermore, in vitro cell growth inhibition experiments by MIF and SCD1 inhibitors support the hypothesis. These results suggest that the gene set is useful as a prognostic marker associated with tumor progression.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- * E-mail:
| | - Robert Nakayama
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Cancer Transcriptome Project, National Cancer Center Research Institute, Tokyo, Japan
- Department of Orthopaedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Shuhei Hayashi
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, Kumamoto, Japan
| | - Takeshi Nemoto
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Dermatology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuyuki Murase
- Department of Biotechnology, School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Koji Nomura
- Department of Biotechnology, School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Teruyoshi Takahashi
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Kenji Kubo
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Shigetaka Marui
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Koji Yasuhara
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Tetsuro Nakamura
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Takuya Sueo
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Anna Takahashi
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Kaname Tsutsumiuchi
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
| | - Tsutomu Ohta
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akira Kawai
- Orthopedics Division, National Cancer Center Hospital, Tokyo, Japan
| | - Shintaro Sugita
- Department of Surgical Pathology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Shinjiro Yamamoto
- Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, Kumamoto, Japan
| | - Takeshi Kobayashi
- Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai, Aichi, Japan
- Plant Biology Research Center, Chubu University, Kasugai, Aichi, Japan
| | - Hiroyuki Honda
- Department of Biotechnology, School of Engineering, Nagoya University, Nagoya, Aichi, Japan
| | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Tadashi Hasegawa
- Department of Surgical Pathology, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
- Pathology Division, National Cancer Center Hospital, Tokyo, Japan,
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75
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Merelo P, Xie Y, Brand L, Ott F, Weigel D, Bowman JL, Heisler MG, Wenkel S. Genome-wide identification of KANADI1 target genes. PLoS One 2013; 8:e77341. [PMID: 24155946 PMCID: PMC3796457 DOI: 10.1371/journal.pone.0077341] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 08/21/2013] [Indexed: 11/28/2022] Open
Abstract
Plant organ development and polarity establishment is mediated by the action of several transcription factors. Among these, the KANADI (KAN) subclade of the GARP protein family plays important roles in polarity-associated processes during embryo, shoot and root patterning. In this study, we have identified a set of potential direct target genes of KAN1 through a combination of chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) and genome-wide transcriptional profiling using tiling arrays. Target genes are over-represented for genes involved in the regulation of organ development as well as in the response to auxin. KAN1 affects directly the expression of several genes previously shown to be important in the establishment of polarity during lateral organ and vascular tissue development. We also show that KAN1 controls through its target genes auxin effects on organ development at different levels: transport and its regulation, and signaling. In addition, KAN1 regulates genes involved in the response to abscisic acid, jasmonic acid, brassinosteroids, ethylene, cytokinins and gibberellins. The role of KAN1 in organ polarity is antagonized by HD-ZIPIII transcription factors, including REVOLUTA (REV). A comparison of their target genes reveals that the REV/KAN1 module acts in organ patterning through opposite regulation of shared targets. Evidence of mutual repression between closely related family members is also shown.
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Affiliation(s)
- Paz Merelo
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Yakun Xie
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Lucas Brand
- School of Biological Sciences, Monash University, Melbourne, Australia
| | - Felix Ott
- Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Max-Planck-Institute for Developmental Biology, Tübingen, Germany
| | - John L. Bowman
- School of Biological Sciences, Monash University, Melbourne, Australia
- * E-mail: (JLB); (MGH); (SW)
| | - Marcus G. Heisler
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- School of Biologlical Sciences, Sydney University, Sydney, Australia
- * E-mail: (JLB); (MGH); (SW)
| | - Stephan Wenkel
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
- * E-mail: (JLB); (MGH); (SW)
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76
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Takahashi H, Kaniwa N, Saito Y, Sai K, Hamaguchi T, Shirao K, Shimada Y, Matsumura Y, Ohtsu A, Yoshino T, Takahashi A, Odaka Y, Okuyama M, Sawada JI, Sakamoto H, Yoshida T. Identification of a candidate single-nucleotide polymorphism related to chemotherapeutic response through a combination of knowledge-based algorithm and hypothesis-free genomic data. J Biosci Bioeng 2013; 116:768-73. [PMID: 23816762 DOI: 10.1016/j.jbiosc.2013.05.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/02/2013] [Accepted: 05/13/2013] [Indexed: 01/06/2023]
Abstract
Inter-individual variations in drug responses among patients are known to cause serious problems in medicine. Genome-wide association study (GWAS) is powerful for examining single-nucleotide polymorphisms (SNPs) and their relationships with drug response variations. However, no significant SNP has been identified using GWAS due to multiple testing problems. Therefore, we propose a combination method consisting of knowledge-based algorithm, two stages of screening, and permutation test for identifying SNPs in the present study. We applied this method to a genome-wide pharmacogenomics study for which 109,365 SNPs had been genotyped using Illumina Human-1 BeadChip for 119 gastric cancer patients treated with fluoropyrimidine. We identified rs2293347 in epidermal growth factor receptor (EGFR) is as a candidate SNP related to chemotherapeutic response. The p value for the rs2293347 was 2.19 × 10(-5) for Fisher's exact test, and the p value was 0.00360 for the permutation test (multiple testing problems are corrected). Additionally, rs2293347 was clearly superior to clinical parameters and showed a sensitivity value of 55.0% and specificity value of 94.4% in the evaluation by using multiple regression models. Recent studies have shown that combination chemotherapy of fluoropyrimidine and EGFR-targeting agents is effective for gastric cancer patients highly expressing EGFR. These results suggest that rs2293347 is a potential predictive factor for selecting chemotherapies, such as fluoropyrimidine alone or combination chemotherapies.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan; Plant Biology Research Center, Chubu University, Matsumoto-cho 1200, Kasugai, Aichi 487-8501, Japan; Division of Genetics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan.
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77
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Takahashi H, Iwakawa H, Ishibashi N, Kojima S, Matsumura Y, Prananingrum P, Iwasaki M, Takahashi A, Ikezaki M, Luo L, Kobayashi T, Machida Y, Machida C. 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. PLANT & CELL PHYSIOLOGY 2013; 54:418-31. [PMID: 23396601 PMCID: PMC3589830 DOI: 10.1093/pcp/pct027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 02/01/2013] [Indexed: 05/22/2023]
Abstract
It is necessary to use algorithms to analyze gene expression data from DNA microarrays, such as in clustering and machine learning. Previously, we developed the knowledge-based fuzzy adaptive resonance theory (KB-FuzzyART), a clustering algorithm suitable for analyzing gene expression data, to find clues for identifying gene networks. Leaf primordia form around the shoot apical meristem (SAM), which consists of indeterminate stem cells. Upon initiation of leaf development, adaxial-abaxial patterning is crucial for lateral expansion, via cellular proliferation, and the formation of flat symmetric leaves. Many regulatory genes that specify such patterning have been identified. Analysis by the KB-FuzzyART and subsequent molecular and genetic analyses previously showed that ASYMMETRIC LEAVES1 (AS1) and AS2 repress the expression of some abaxial-determinant genes, such as AUXIN RESPONSE FACTOR3 (ARF3)/ETTIN (ETT) and ARF4, which are responsible for defects in leaf adaxial-abaxial polarity in as1 and as2. In the present study, genetic analysis revealed that ARF3/ETT and ARF4 were regulated by modifier genes, BOBBER1 (BOB1) and ELONGATA3 (ELO3), together with AS1-AS2. We analyzed expression arrays with as2 elo3 and as2 bob1, and extracted genes downstream of ARF3/ETT by using KB-FuzzyART and molecular analyses. The results showed that expression of Kip-related protein (KRP) (for inhibitors of cyclin-dependent protein kinases) and Isopentenyltransferase (IPT) (for biosynthesis of cytokinin) genes were controlled by AS1-AS2 through ARF3/ETT and ARF4 functions, which suggests that the AS1-AS2-ETT pathway plays a critical role in controlling the cell division cycle and the biosynthesis of cytokinin around SAM to stabilize leaf development in Arabidopsis thaliana.
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Affiliation(s)
- Hiro Takahashi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo-shi, Chiba, 271-8510 Japan
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- These authors contributed equally to this work
| | - Hidekazu Iwakawa
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- These authors contributed equally to this work
- Present address: Department of Biological Sciences, Purdue University, West, Lafayette, IN 47907-1392, USA
| | - Nanako Ishibashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- These authors contributed equally to this work
| | - Shoko Kojima
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Yoko Matsumura
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Pratiwi Prananingrum
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Mayumi Iwasaki
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Present address: Department of Plant Biology, University of Geneva, CH-1211 Geneva 4, Switzerland
| | - Anna Takahashi
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Masaya Ikezaki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Lilan Luo
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Takeshi Kobayashi
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
| | - Yasunori Machida
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- *Corresponding authors: Chiyoko Machida, Email, ; Fax, +81-568-51-6276; Yasunori Machida, Email, ; Fax, +81-52-789-2502
| | - Chiyoko Machida
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 487-8501 Japan
- *Corresponding authors: Chiyoko Machida, Email, ; Fax, +81-568-51-6276; Yasunori Machida, Email, ; Fax, +81-52-789-2502
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