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Huang R, Feng Y, Gao Z, Ahmed A, Zhang W. The Epigenomic Features and Potential Functions of PEG- and PDS-Favorable DNA G-Quadruplexes in Rice. Int J Mol Sci 2024; 25:634. [PMID: 38203805 PMCID: PMC10779103 DOI: 10.3390/ijms25010634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
A G-quadruplex (G4) is a typical non-B DNA structure and involved in various DNA-templated events in eukaryotic genomes. PEG and PDS chemicals have been widely applied for promoting the folding of in vivo or in vitro G4s. However, how PEG and PDS preferentially affect a subset of G4 formation genome-wide is still largely unknown. We here conducted a BG4-based IP-seq in vitro under K++PEG or K++PDS conditions in the rice genome. We found that PEG-favored IP-G4s+ have distinct sequence features, distinct genomic distributions and distinct associations with TEGs, non-TEGs and subtypes of TEs compared to PDS-favored ones. Strikingly, PEG-specific IP-G4s+ are associated with euchromatin with less enrichment levels of DNA methylation but with more enriched active histone marks, while PDS-specific IP-G4s+ are associated with heterochromatin with higher enrichment levels of DNA methylation and repressive marks. Moreover, we found that genes with PEG-specific IP-G4s+ are more expressed than those with PDS-specific IP-G4s+, suggesting that PEG/PDS-specific IP-G4s+ alone or coordinating with epigenetic marks are involved in the regulation of the differential expression of related genes, therefore functioning in distinct biological processes. Thus, our study provides new insights into differential impacts of PEG and PDS on G4 formation, thereby advancing our understanding of G4 biology.
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Affiliation(s)
| | | | | | | | - Wenli Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, CIC-MCP, Nanjing Agricultural University, No.1 Weigang, Nanjing 210095, China; (R.H.); (Y.F.); (Z.G.); (A.A.)
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2
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Volná A, Bartas M, Nezval J, Pech R, Pečinka P, Špunda V, Červeň J. Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the Regulations of Plant Growth and Stress Responses. Methods Mol Biol 2023; 2642:331-361. [PMID: 36944887 DOI: 10.1007/978-1-0716-3044-0_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Epigenetics deals with changes in gene expression that are not caused by modifications in the primary sequence of nucleic acids. These changes beyond primary structures of nucleic acids not only include DNA/RNA methylation, but also other reversible conversions, together with histone modifications or RNA interference. In addition, under particular conditions (such as specific ion concentrations or protein-induced stabilization), the right-handed double-stranded DNA helix (B-DNA) can form noncanonical structures commonly described as "non-B DNA" structures. These structures comprise, for example, cruciforms, i-motifs, triplexes, and G-quadruplexes. Their formation often leads to significant differences in replication and transcription rates. Noncanonical RNA structures have also been documented to play important roles in translation regulation and the biology of noncoding RNAs. In human and animal studies, the frequency and dynamics of noncanonical DNA and RNA structures are intensively investigated, especially in the field of cancer research and neurodegenerative diseases. In contrast, noncanonical DNA and RNA structures in plants have been on the fringes of interest for a long time and only a few studies deal with their formation, regulation, and physiological importance for plant stress responses. Herein, we present a review focused on the main fields of epigenetics in plants and their possible roles in stress responses and signaling, with special attention dedicated to noncanonical DNA and RNA structures.
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Affiliation(s)
- Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jakub Nezval
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Radomír Pech
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Vladimír Špunda
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
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3
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Falanga AP, Terracciano M, Oliviero G, Roviello GN, Borbone N. Exploring the Relationship between G-Quadruplex Nucleic Acids and Plants: From Plant G-Quadruplex Function to Phytochemical G4 Ligands with Pharmaceutic Potential. Pharmaceutics 2022; 14:2377. [PMID: 36365194 PMCID: PMC9698481 DOI: 10.3390/pharmaceutics14112377] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/19/2022] [Accepted: 11/01/2022] [Indexed: 10/31/2023] Open
Abstract
G-quadruplex (G4) oligonucleotides are higher-order DNA and RNA secondary structures of enormous relevance due to their implication in several biological processes and pathological states in different organisms. Strategies aiming at modulating human G4 structures and their interrelated functions are first-line approaches in modern research aiming at finding new potential anticancer treatments or G4-based aptamers for various biomedical and biotechnological applications. Plants offer a cornucopia of phytocompounds that, in many cases, are effective in binding and modulating the thermal stability of G4s and, on the other hand, contain almost unexplored G4 motifs in their genome that could inspire new biotechnological strategies. Herein, we describe some G4 structures found in plants, summarizing the existing knowledge of their functions and biological role. Moreover, we review some of the most promising G4 ligands isolated from vegetal sources and report on the known relationships between such phytochemicals and G4-mediated biological processes that make them potential leads in the pharmaceutical sector.
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Affiliation(s)
- Andrea P. Falanga
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Monica Terracciano
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies, Via Sergio Pansini 5, 80131 Naples, Italy
| | - Giovanni N. Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Nicola Borbone
- Department of Pharmacy, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
- Institute of Applied Sciences and Intelligent Systems, Italian National Council of Research (ISASI-CNR), Via Pietro Castellino 111, 80131 Napoli, Italy
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4
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Dobrovolná M, Bohálová N, Peška V, Wang J, Luo Y, Bartas M, Volná A, Mergny JL, Brázda V. The Newly Sequenced Genome of Pisum sativum Is Replete with Potential G-Quadruplex-Forming Sequences-Implications for Evolution and Biological Regulation. Int J Mol Sci 2022; 23:8482. [PMID: 35955617 PMCID: PMC9369095 DOI: 10.3390/ijms23158482] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/25/2022] [Accepted: 07/28/2022] [Indexed: 11/20/2022] Open
Abstract
G-quadruplexes (G4s) have been long considered rare and physiologically unimportant in vitro curiosities, but recent methodological advances have proved their presence and functions in vivo. Moreover, in addition to their functional relevance in bacteria and animals, including humans, their importance has been recently demonstrated in evolutionarily distinct plant species. In this study, we analyzed the genome of Pisum sativum (garden pea, or the so-called green pea), a unique member of the Fabaceae family. Our results showed that this genome contained putative G4 sequences (PQSs). Interestingly, these PQSs were located nonrandomly in the nuclear genome. We also found PQSs in mitochondrial (mt) and chloroplast (cp) DNA, and we experimentally confirmed G4 formation for sequences found in these two organelles. The frequency of PQSs for nuclear DNA was 0.42 PQSs per thousand base pairs (kbp), in the same range as for cpDNA (0.53/kbp), but significantly lower than what was found for mitochondrial DNA (1.58/kbp). In the nuclear genome, PQSs were mainly associated with regulatory regions, including 5'UTRs, and upstream of the rRNA region. In contrast to genomic DNA, PQSs were located around RNA genes in cpDNA and mtDNA. Interestingly, PQSs were also associated with specific transposable elements such as TIR and LTR and around them, pointing to their role in their spreading in nuclear DNA. The nonrandom localization of PQSs uncovered their evolutionary and functional significance in the Pisum sativum genome.
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Affiliation(s)
- Michaela Dobrovolná
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
| | - Natália Bohálová
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Vratislav Peška
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
| | - Jiawei Wang
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
| | - Yu Luo
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, CEDEX, 91405 Orsay, France
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic;
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Laboratoire d’Optique et Biosciences (LOB), Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, CEDEX, 91128 Palaiseau, France; (J.W.); (Y.L.)
| | - Václav Brázda
- Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic; (M.D.); (N.B.); (V.P.)
- Faculty of Chemistry, Brno University of Technology, Purkyňova 118, 612 00 Brno, Czech Republic
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5
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Feng Y, Tao S, Zhang P, Sperti FR, Liu G, Cheng X, Zhang T, Yu H, Wang XE, Chen C, Monchaud D, Zhang W. Epigenomic features of DNA G-quadruplexes and their roles in regulating rice gene transcription. PLANT PHYSIOLOGY 2022; 188:1632-1648. [PMID: 34893906 PMCID: PMC8896617 DOI: 10.1093/plphys/kiab566] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/04/2021] [Indexed: 06/01/2023]
Abstract
A DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure involved in many biological processes in mammals. The current knowledge on plant DNA G4s, however, is limited; whether and how DNA G4s impact gene expression in plants is still largely unknown. Here, we applied a protocol referred to as BG4-DNA-IP-seq followed by a comprehensive characterization of DNA G4s in rice (Oryza sativa L.); we next integrated dG4s (experimentally detectable G4s) with existing omics data and found that dG4s exhibited differential DNA methylation between transposable element (TE) and non-TE genes. dG4 regions displayed genic-dependent enrichment of epigenomic signatures; finally, we showed that these sites displayed a positive association with expression of DNA G4-containing genes when located at promoters, and a negative association when located in the gene body, suggesting localization-dependent promotional/repressive roles of DNA G4s in regulating gene transcription. This study reveals interrelations between DNA G4s and epigenomic signatures, as well as implicates DNA G4s in modulating gene transcription in rice. Our study provides valuable resources for the functional characterization or bioengineering of some of key DNA G4s in rice.
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Affiliation(s)
- Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Pengyue Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Francesco Rota Sperti
- Institut de Chimie Moleculaire, ICMUB, CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Guanqing Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology and Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Tao Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology and Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hengxiu Yu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Xiu-e Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Caiyan Chen
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB, CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
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6
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Cagirici HB, Budak H, Sen TZ. Genome-wide discovery of G-quadruplexes in barley. Sci Rep 2021; 11:7876. [PMID: 33846409 PMCID: PMC8041835 DOI: 10.1038/s41598-021-86838-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/19/2021] [Indexed: 12/04/2022] Open
Abstract
G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome-wide identification of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5′ untranslated region (5′ UTR), the first coding domain sequence, and the first intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs.
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Affiliation(s)
- H Busra Cagirici
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, U.S. Department of Agriculture - Agricultural Research Service, 800 Buchanan St, Albany, CA, 94710, USA
| | - Hikmet Budak
- Montana BioAg Inc., Missoula, MT, USA.,Agrogen, LLC., Omaha, NE, USA
| | - Taner Z Sen
- Crop Improvement and Genetics Research Unit, Western Regional Research Center, U.S. Department of Agriculture - Agricultural Research Service, 800 Buchanan St, Albany, CA, 94710, USA.
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7
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Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles. G3-GENES GENOMES GENETICS 2020; 10:2021-2032. [PMID: 32295768 PMCID: PMC7263691 DOI: 10.1534/g3.120.401288] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
G-quadruplexes are nucleic acid secondary structures formed by a stack of square planar G-quartets. G-quadruplexes were implicated in many biological functions including telomere maintenance, replication, transcription, and translation, in many species including humans and plants. For wheat, however, though it is one of the world's most important staple food, no G-quadruplex studies have been reported to date. Here, we computationally identify putative G4 structures (G4s) in wheat genome for the first time and compare its distribution across the genome against five other genomes (human, maize, Arabidopsis, rice, and sorghum). We identified close to 1 million G4 motifs with a density of 76 G4s/Mb across the whole genome and 93 G4s/Mb over genic regions. Remarkably, G4s were enriched around three regions, two located on the antisense and one on the sense strand at the following positions: 1) the transcription start site (TSS) (antisense), 2) the first coding domain sequence (CDS) (antisense), and 3) the start codon (sense). Functional enrichment analysis revealed that the gene models containing G4 motifs within these peaks were associated with specific gene ontology (GO) terms, such as developmental process, localization, and cellular component organization or biogenesis. We investigated genes encoding MADS-box transcription factors and showed examples of G4 motifs within critical regulatory regions in the VRN-1 genes in wheat. Furthermore, comparison with other plants showed that monocots share a similar distribution of G4s, but Arabidopsis shows a unique G4 distribution. Our study shows for the first time the prevalence and possible functional roles of G4s in wheat.
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Shimada TL, Yamaguchi K, Shigenobu S, Takahashi H, Murase M, Fukuyoshi S, Hara-Nishimura I. Excess sterols disrupt plant cellular activity by inducing stress-responsive gene expression. JOURNAL OF PLANT RESEARCH 2020; 133:383-392. [PMID: 32185672 DOI: 10.1007/s10265-020-01181-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/10/2020] [Indexed: 06/10/2023]
Abstract
Sterols are important lipid constituents of cellular membranes in plants and other organisms. Sterol homeostasis is under strict regulation in plants because excess sterols negatively impact plant growth. HIGH STEROL ESTER 1 (HISE1) functions as a negative regulator of sterol accumulation. If sterol production exceeds a certain threshold, excess sterols are detoxified via conversion to sterol esters by PHOSPHOLIPID STEROL ACYL TRANSFERASE 1 (PSAT1). We previously reported that the Arabidopsis thaliana double mutant hise1-3 psat1-2 shows 1.5-fold higher sterol content than the wild type and consequently a severe growth defect. However, the specific defects caused by excess sterol accumulation in plants remain unknown. In this study, we investigated the effects of excess sterols on plants by analyzing the phenotypes and transcriptomes of the hise1-3 psat1-2 double mutant. Transcriptomic analysis revealed that 435 genes were up-regulated in hise1-3 psat1-2 leaves compared with wild-type leaves. Gene ontology (GO) enrichment analysis revealed that abiotic and biotic stress-responsive genes including RESPONSIVE TO DESICCATION 29B/LOW-TEMPERATURE-INDUCED 65 (RD29B/LTI65) and COLD-REGULATED 15A (COR15A) were up-regulated in hise1-3 psat1-2 leaves compared with wild-type leaves. Expression levels of senescence-related genes were also much higher in hise1-3 psat1-2 leaves than in wild-type leaves. hise1-3 psat1-2 leaves showed early senescence, suggesting that excess sterols induce senescence of leaves. In the absence of sucrose, hise1-3 psat1-2 exhibited defects in seedling growth and root elongation. Together, our data suggest that excess sterol accumulation disrupts cellular activities of vegetative organs including leaves and roots, resulting in multiple damages to plants.
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Affiliation(s)
- Takashi L Shimada
- Graduate School of Horticulture, Chiba University, Matsudo648, Matsudo, Chiba, 271-8510, Japan.
- Plant Molecular Science Center, Chiba University, Chiba, Chiba, 260-8675, Japan.
| | - Katsushi Yamaguchi
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Aichi, 444-8585, Japan
| | - Hiro Takahashi
- Graduate School of Horticulture, Chiba University, Matsudo648, Matsudo, Chiba, 271-8510, Japan
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, 920-1192, Japan
| | - Masataka Murase
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Ishikawa, 920-1192, Japan
| | - Shuichi Fukuyoshi
- Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa, 920-1192, Japan
| | - Ikuko Hara-Nishimura
- Faculty of Science and Engineering, Konan University, Kobe, Hyogo, 658-8501, Japan
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9
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Sjakste T, Leonova E, Petrovs R, Trapina I, Röder MS, Sjakste N. Tight DNA-protein complexes isolated from barley seedlings are rich in potential guanine quadruplex sequences. PeerJ 2020; 8:e8569. [PMID: 32110488 PMCID: PMC7034378 DOI: 10.7717/peerj.8569] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/15/2020] [Indexed: 11/20/2022] Open
Abstract
Background The concept of chromatin domains attached to the nuclear matrix is being revisited, with nucleus described as a set of topologically associating domains. The significance of the tightly bound to DNA proteins (TBP), a protein group that remains attached to DNA after its deproteinization should be also revisited, as the existence of these interactions is in good agreement with the concept of the topologically associating domain. The work aimed to characterize the DNA component of TBP isolated from barley seedlings. Methods The tight DNA-protein complexes from the first leaves, coleoptiles, and roots of barley seedlings were isolated by purification with chromatography on nitrocellulose or exhaustive digestion of DNA with DNase I. Cloning and transformation were performed using pMOSBBlue Blunt Ended Cloning Kit. Inserts were amplified by PCR, and sequencing was performed on the MegaBace 1000 Sequencing System. The BLAST search was performed using sequence databases at NCBI, CR-EST, and TREP and Ensembl Plants databases. Comparison to MAR/SAR sequences was performed using http://smartdb.bioinf.med.uni-goettingen.de/cgi-bin/SMARtDB/smar.cgi database. The prediction of G quadruplexes (GQ) was performed with the aid of R-studio library pqsfinder. CD spectra were recorded on a Chirascan CS/3D spectrometer. Results Although the barley genome is AT-rich (43% of GC pairs), most DNA fragments associated with TBP were GC-rich (up to 70% in some fractions). Both fractionation procedures yielded a high proportion of CT-motif sequences presented predominantly by the 16-bp CC(TCTCCC)2 TC fragment present in clones derived from the TBP-bound DNA and absent in free DNA. BLAST analysis revealed alignment with different barley repeats. Some clones, however, aligned with both nuclear and chloroplast structural genes. Alignments with MAR/SAR motifs were very few. The analysis produced by the pqsfinder program revealed numerous potential quadruplex-forming sites in the TBP-bound sequences. A set of oligonucleotides containing sites of possible GQs were designed and ordered. Three of them represented the minus strand of the CT-repeat. Two were derived from sequences of two clones of nitrocellulose retained fraction from leaves and contained GC-rich motifs different from the CT motif. Circular dichroism spectroscopy revealed profound changes in spectra when oligonucleotides were incubated with 100 mM KCl. There was either an increase of positive band in the area of 260 nm or the formation of a positive band at 290 nm. In the former case, changes are typical for parallel G-quadruplexes and, in the latter, 3 + 1 structures. Discussion The G-quadruplexes anchor proteins are probably involved in the maintenance of the topologically associated domain structure.
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Affiliation(s)
- Tatjana Sjakste
- Genomics and Bioinformatics Group, Institute of Biology, University of Latvia, Riga, Latvia
| | - Elina Leonova
- Faculty of Medicine, University of Latvia, Riga, Latvia
| | | | - Ilva Trapina
- Genomics and Bioinformatics Group, Institute of Biology, University of Latvia, Riga, Latvia
| | - Marion S Röder
- Leibniz Institute for Plant Genetics and Crop Research, Gatersleben, Germany
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10
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Stefos GC, Theodorou G, Politis I. DNA G-quadruplexes: functional significance in plant and farm animal science. Anim Biotechnol 2019; 32:262-271. [PMID: 31642375 DOI: 10.1080/10495398.2019.1679823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
G-quadruplexes (G4s) are non-canonical structures that can be formed in DNA and RNA sequences which carry four short runs of guanines. They are distributed in the whole genome but are enriched in gene promoter regions, gene UTRs and chromosome telomeres. The whole array of their functional roles is not fully explored yet but there is solid evidence supporting their implication in a number of processes like regulation of transcription, replication and telomere organization, among others. During the last decade, there is an increased research interest for G4s that has resulted in a better understanding of their role in several physiological and pathological conditions. On the other hand, these structures are poorly studied in plant species and animals of agricultural interest. Here, we summarize the current methods that are used for studying G4s, we review the studies concerning plants and farm animals and we discuss the advantages of a more thorough inclusion of G4s research in the agricultural sciences.
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Affiliation(s)
- Georgios C Stefos
- Independent researcher, Agricultural University of Athens, Athens, Greece
| | - Georgios Theodorou
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Athens, Greece
| | - Ioannis Politis
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Athens, Greece
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11
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Kopec PM, Karlowski WM. Sequence Dynamics of Pre-mRNA G-Quadruplexes in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:812. [PMID: 31316532 PMCID: PMC6610454 DOI: 10.3389/fpls.2019.00812] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 06/05/2019] [Indexed: 06/01/2023]
Abstract
Intramolecular G-quadruplexes (G4s) are secondary structures that may form within G-rich stretches of nucleic acids. Although their presence has been associated with genomic instability and mutagenicity, recent reports suggest their involvement in regulation of diverse cellular events, including transcription and translation. The majority of data regarding G4s stems from mammalian and yeast studies, leaving the plant G4s almost unexplored. Using the publicly available Arabidopsis thaliana and Oryza sativa WGS data, we examined the single nucleotide variability of sequences predicted to form G4s (pG4s) structures. We focused our analysis on protein coding transcripts and compared the results to well-characterized Homo sapiens data. We demonstrate that the overall high variability of pG4s is not uniform and differs between gene structural elements. Specifically, plant AUG-containing pG4s, located within 5'UTR/CDS junctions, are abundant and appear not to be affected by a higher frequency of sequence change, indicating their functional relevance. Furthermore, we show that substitutions lowering the probability of G4s' formation are preferred over neutral or stabilizing modifications.
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Affiliation(s)
| | - Wojciech M. Karlowski
- Department of Computational Biology, Faculty of Biology, Mickiewicz University in Poznań, Poznań, Poland
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Ding Y, Fleming AM, Burrows CJ. Case studies on potential G-quadruplex-forming sequences from the bacterial orders Deinococcales and Thermales derived from a survey of published genomes. Sci Rep 2018; 8:15679. [PMID: 30356061 PMCID: PMC6200779 DOI: 10.1038/s41598-018-33944-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/06/2018] [Indexed: 12/13/2022] Open
Abstract
Genomes provide a platform for storage of chemical information that must be stable under the context in which an organism thrives. The 2'-deoxyguanosine (G) nucleotide has the potential to provide additional chemical information beyond its Watson-Crick base-pairing capacity. Sequences with four or more runs of three G nucleotides each are potential G-quadruplex forming sequences (PQSs) that can adopt G-quadruplex folds. Herein, we analyzed sequenced genomes from the NCBI database to determine the PQS densities of the genome sequences. First, we found organisms with large genomes, including humans, alligators, and maize, have similar densities of PQSs (~300 PQSs/Mbp), and the genomes are significantly enriched in PQSs with more than four G tracks. Analysis of microorganism genomes found a greater diversity of PQS densities. In general, PQS densities positively tracked with the GC% of the genome. Exceptions to this observation were the genomes from thermophiles that had many more PQSs than expected by random chance. Analysis of the location of these PQSs in annotated genomes from the order Thermales showed these G-rich sequences to be randomly distributed; in contrast, in the order Deinococcales the PQSs were enriched and biased around transcription start sites of genes. Four representative PQSs, two each from the Thermales and Deinococcales, were studied by biophysical methods to establish the ability of them to fold to G-quadruplexes. The experiments found the two PQSs in the Thermales did not adopt G-quadruplex folds, while the two most common in the Deinococcales adopted stable parallel-stranded G-quadruplexes. The findings lead to a hypothesis that thermophilic organisms are enriched with PQSs as an unavoidable consequence to stabilize thermally their genomes to live at high temperature; in contrast, the genomes from stress-resistant bacteria found in the Deinococcales may utilize PQSs for gene regulatory purposes.
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Affiliation(s)
- Yun Ding
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112-0850, United States.
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112-0850, United States.
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Griffin BD, Bass HW. Review: Plant G-quadruplex (G4) motifs in DNA and RNA; abundant, intriguing sequences of unknown function. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 269:143-147. [PMID: 29606212 DOI: 10.1016/j.plantsci.2018.01.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/12/2018] [Accepted: 01/20/2018] [Indexed: 06/08/2023]
Abstract
DNA sequences capable of forming G-quadruplex (G4) structures can be predicted and mapped in plant genomes using computerized pattern search programs. Non-telomeric G4 motifs have recently been found to number in the thousands across many plant species and enriched around gene promoters, prompting speculation that they may represent a newly uncovered and ubiquitous family of cis-acting elements. Comparative analysis shows that monocots exhibit five to ten times higher G4 motif density than eudicots, but the significance of this difference has not been determined. The vast scale and complexity of G4 functions, actual or theoretical, are reviewed in relation to the multiple modes of action and myriad genetic functions for which G4s have been implicated in DNA and RNA. Future experimental strategies and opportunities include identifying plant G4-interactomes, resolving the structures of G4s with and without their binding partners, and defining molecular mechanisms through reporter gene, genetic, or genome editing approaches. Given the global importance of plants for food, clothing, medicine, and energy, together with the potential role of G4 motifs as a widely conserved set of DNA sequences that could coordinate gene regulation, future plant G4 research holds great potential for use in plant improvement strategies.
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Affiliation(s)
- Brianna D Griffin
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, FL, 32306-4295, USA.
| | - Hank W Bass
- Department of Biological Science, 319 Stadium Drive, Florida State University, Tallahassee, FL, 32306-4295, USA.
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Garg R, Aggarwal J, Thakkar B. Genome-wide discovery of G-quadruplex forming sequences and their functional relevance in plants. Sci Rep 2016; 6:28211. [PMID: 27324275 PMCID: PMC4914980 DOI: 10.1038/srep28211] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 05/18/2016] [Indexed: 11/22/2022] Open
Abstract
DNA, in addition to the canonical B-form, can acquire a variety of alternate structures, such as G-quadruplexes. These structures have been implicated in several cellular processes in animals. In this study, we identified different types of G-quadruplex forming sequences (GQSes) in 15 sequenced plants and analyzed their distribution in various genomic features, including gene body, coding, intergenic and promoter regions. G2-type GQSes were most abundant in all the plant species analyzed. A strong association of G3-type GQSes with intergenic, promoter and intronic regions was found. However, G2-type GQSes were enriched in genic, CDS, exonic and untranslated regions. Further, we identified GQSes present in the conserved genes among monocots and dicots. The genes involved in development, cell growth and size, transmembrane transporter, and regulation of gene expression were found to be significantly enriched. In the promoter region, we detected strong co-occurrence of Telobox, ERF, MYB, RAV1B and E2F motifs with GQSes. Further, we validated the structure formation of several plant GQSes, demonstrated their effect on stalling in-vitro replication and revealed their interaction with plant nuclear proteins. Our data provide insights into the prevalence of GQSes in plants, establish their association with different genomic features and functional relevance.
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Affiliation(s)
- Rohini Garg
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Jyoti Aggarwal
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Bijal Thakkar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
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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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Liu JQ, Xiao S, Hao YH, Tan Z. Strand-Biased Formation of G-Quadruplexes in DNA Duplexes Transcribed with T7 RNA Polymerase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Liu JQ, Xiao S, Hao YH, Tan Z. Strand-Biased Formation of G-Quadruplexes in DNA Duplexes Transcribed with T7 RNA Polymerase. Angew Chem Int Ed Engl 2015; 54:8992-6. [PMID: 26074352 DOI: 10.1002/anie.201503648] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Indexed: 11/07/2022]
Abstract
G-quadruplex-forming sequences are enriched near transcription start sites (TSSs) in animal genes. They readily form G-quadruplexes in transcription, which in turn regulate transcription. Therefore, the control of G-quadruplex formation is important for their functionality. It is now shown that G-quadruplexes form efficiently on the non-template, but hardly on the template DNA strand in the downstream vicinity of TSSs in DNA duplexes when they are transcribed by the T7 RNA polymerase (RNAP). Structural analysis reveals that the T7 RNAP causes distortion in a DNA duplex both inside and in front of the enzyme. This structural distortion leads to strand-biased G-quadruplex formation when a G-quadruplex-forming sequence is partially fed into the T7 RNAP to a position about seven nucleotides away from the front of RNA synthesis. Based on these facts, we propose a model for the strand-biased formation of G-quadruplexes in transcribed DNA duplexes.
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Affiliation(s)
- Jia-quan Liu
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 (P. R. China)
| | - Shan Xiao
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 (P. R. China).,Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515 (P. R. China)
| | - Yu-hua Hao
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 (P. R. China)
| | - Zheng Tan
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 (P. R. China).
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Wang Y, Zhao M, Zhang Q, Zhu GF, Li FF, Du LF. Genomic distribution and possible functional roles of putative G-quadruplex motifs in two subspecies of Oryza sativa. Comput Biol Chem 2015; 56:122-30. [DOI: 10.1016/j.compbiolchem.2015.04.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 04/16/2015] [Accepted: 04/18/2015] [Indexed: 12/13/2022]
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19
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Yang M, Wu Y, Jin S, Hou J, Mao Y, Liu W, Shen Y, Wu L. Flower bud transcriptome analysis of Sapium sebiferum (Linn.) Roxb. and primary investigation of drought induced flowering: pathway construction and G-quadruplex prediction based on transcriptome. PLoS One 2015; 10:e0118479. [PMID: 25738565 PMCID: PMC4349590 DOI: 10.1371/journal.pone.0118479] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 01/17/2015] [Indexed: 11/27/2022] Open
Abstract
Sapium sebiferum (Linn.) Roxb. (Chinese Tallow Tree) is a perennial woody tree and its seeds are rich in oil which hold great potential for biodiesel production. Despite a traditional woody oil plant, our understanding on S. sebiferum genetics and molecular biology remains scant. In this study, the first comprehensive transcriptome of S. sebiferum flower has been generated by sequencing and de novo assembly. A total of 149,342 unigenes were generated from raw reads, of which 24,289 unigenes were successfully matched to public database. A total of 61 MADS box genes and putative pathways involved in S. sebiferum flower development have been identified. Abiotic stress response network was also constructed in this work, where 2,686 unigenes are involved in the pathway. As for lipid biosynthesis, 161 unigenes have been identified in fatty acid (FA) and triacylglycerol (TAG) biosynthesis. Besides, the G-Quadruplexes in RNA of S. sebiferum also have been predicted. An interesting finding is that the stress-induced flowering was observed in S. sebiferum for the first time. According to the results of semi-quantitative PCR, expression tendencies of flowering-related genes, GA1, AP2 and CRY2, accorded with stress-related genes, such as GRX50435 and PRXⅡ39562. This transcriptome provides functional genomic information for further research of S. sebiferum, especially for the genetic engineering to shorten the juvenile period and improve yield by regulating flower development. It also offers a useful database for the research of other Euphorbiaceae family plants.
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Affiliation(s)
- Minglei Yang
- Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People’s Republic of China
| | - Ying Wu
- Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People’s Republic of China
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, Henan, People’s Republic of China
| | - Shan Jin
- Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People’s Republic of China
| | - Jinyan Hou
- Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People’s Republic of China
| | - Yingji Mao
- Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People’s Republic of China
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Wenbo Liu
- Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People’s Republic of China
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Yangcheng Shen
- Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People’s Republic of China
- School of Life Science, Anhui University, Hefei, Anhui, People’s Republic of China
| | - Lifang Wu
- Key Laboratory of Ion Beam Bioengineering and Bioenergy Forest Research Center of State Forestry Administration, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, People’s Republic of China
- School of Life Science, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
- * E-mail:
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20
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Andorf CM, Kopylov M, Dobbs D, Koch KE, Stroupe ME, Lawrence CJ, Bass HW. G-Quadruplex (G4) Motifs in the Maize (Zea mays L.) Genome Are Enriched at Specific Locations in Thousands of Genes Coupled to Energy Status, Hypoxia, Low Sugar, and Nutrient Deprivation. J Genet Genomics 2014; 41:627-47. [DOI: 10.1016/j.jgg.2014.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 10/16/2014] [Accepted: 10/24/2014] [Indexed: 02/07/2023]
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21
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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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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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23
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Xiao S, Zhang JY, Zheng KW, Hao YH, Tan Z. Bioinformatic analysis reveals an evolutional selection for DNA:RNA hybrid G-quadruplex structures as putative transcription regulatory elements in warm-blooded animals. Nucleic Acids Res 2013; 41:10379-90. [PMID: 23999096 PMCID: PMC3905843 DOI: 10.1093/nar/gkt781] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Recently, we reported the co-transcriptional formation of DNA:RNA hybrid G-quadruplex (HQ) structure by the non-template DNA strand and nascent RNA transcript, which in turn modulates transcription under both in vitro and in vivo conditions. Here we present bioinformatic analysis on putative HQ-forming sequences (PHQS) in the genomes of eukaryotic organisms. Starting from amphibian, PHQS motifs are concentrated in the immediate 1000-nt region downstream of transcription start sites, implying their potential role in transcription regulation. Moreover, their occurrence shows a strong bias toward the non-template versus the template strand. PHQS has become constitutional in genes in warm-blooded animals, and the magnitude of the strand bias correlates with the ability of PHQS to form HQ, suggesting a selection based on HQ formation. This strand bias is reversed in lower species, implying that the selection of PHQS/HQ depended on the living temperature of the organisms. In comparison with the putative intramolecular G-quadruplex-forming sequences (PQS), PHQS motifs are far more prevalent and abundant in the transcribed regions, making them the dominant candidates in the formation of G-quadruplexes in transcription. Collectively, these results suggest that the HQ structures are evolutionally selected to function in transcription and other transcription-mediated processes that involve guanine-rich non-template strand.
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Affiliation(s)
- Shan Xiao
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
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24
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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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25
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Iwasaki M, Takahashi H, Iwakawa H, Nakagawa A, Ishikawa T, Tanaka H, Matsumura Y, Pekker I, Eshed Y, Vial-Pradel S, Ito T, Watanabe Y, Ueno Y, Fukazawa H, Kojima S, Machida Y, Machida C. Dual regulation of ETTIN (ARF3) gene expression by AS1-AS2, which maintains the DNA methylation level, is involved in stabilization of leaf adaxial-abaxial partitioning in Arabidopsis. Development 2013; 140:1958-69. [PMID: 23571218 DOI: 10.1242/dev.085365] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Leaf primordia are generated at the periphery of the shoot apex, developing into flat symmetric organs with adaxial-abaxial polarity, in which the indeterminate state is repressed. Despite the crucial role of the ASYMMETRIC LEAVES1 (AS1)-AS2 nuclear-protein complex in leaf adaxial-abaxial polarity specification, information on mechanisms controlling their downstream genes has remained elusive. We systematically analyzed transcripts by microarray and chromatin immunoprecipitation assays and performed genetic rescue of as1 and as2 phenotypic abnormalities, which identified a new target gene, ETTIN (ETT)/AUXIN RESPONSE FACTOR3 (ARF3), which encodes an abaxial factor acting downstream of the AS1-AS2 complex. While the AS1-AS2 complex represses ETT by direct binding of AS1 to the ETT promoter, it also indirectly activates miR390- and RDR6-dependent post-transcriptional gene silencing to negatively regulate both ETT and ARF4 activities. Furthermore, AS1-AS2 maintains the status of DNA methylation in the ETT coding region. In agreement, filamentous leaves formed in as1 and as2 plants treated with a DNA methylation inhibitor were rescued by loss of ETT and ARF4 activities. We suggest that negative transcriptional, post-transcriptional and epigenetic regulation of the ARFs by AS1-AS2 is important for stabilizing early leaf partitioning into abaxial and adaxial domains.
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Affiliation(s)
- Mayumi Iwasaki
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, Japan
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26
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Nakagawa A, Takahashi H, Kojima S, Sato N, Ohga K, Cha BY, Woo JT, Nagai K, Horiguchi G, Tsukaya H, Machida Y, Machida C. Berberine enhances defects in the establishment of leaf polarity in asymmetric leaves1 and asymmetric leaves2 of Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2012; 79:569-81. [PMID: 22684430 PMCID: PMC3402677 DOI: 10.1007/s11103-012-9929-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 05/13/2012] [Indexed: 05/09/2023]
Abstract
Leaves develop as flat lateral organs from the indeterminate shoot apical meristem. The establishment of polarity along three-dimensional axes, proximal-distal, medial-lateral, and adaxial-abaxial axes, is crucial for the growth of normal leaves. The mutations of ASYMMETRIC LEAVES1 (AS1) and AS2 of Arabidopsis thaliana cause defects in repression of the indeterminate state and the establishment of axis formation in leaves. Although many mutations have been identified that enhance the adaxial-abaxial polarity defects of as1 and as2 mutants, the roles of the causative genes in leaf development are still unknown. In this study, we found that wild-type plants treated with berberine produced pointed leaves, which are often observed in the single mutants that enhance phenotypes of as1 and as2 mutants. The berberine-treated as1 and as2 mutants formed abaxialized filamentous leaves. Berberine, an isoquinoline alkaloid compound naturally produced in various plant sources, has a growth inhibitory effect on plants that do not produce berberine. We further showed that transcript levels of meristem-specific class 1 KNOX homeobox genes and abaxial determinant genes were increased in berberine-treated as1 and as2. Berberine treated plants carrying double mutations of AS2 and the large subunit ribosomal protein gene RPL5B showed more severe defects in polarity than did the as2 single mutant plants. We suggest that berberine inhibits (a) factor(s) that might be required for leaf adaxial cell differentiation through a pathway independent of AS1 and AS2. Multiple pathways might play important roles in the formation of flat symmetric leaves.
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Affiliation(s)
- Ayami Nakagawa
- 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
| | - Hiro Takahashi
- 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
| | - 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
| | - Nobuo Sato
- Plant Biology Research Center, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501 Japan
| | - Kazuomi Ohga
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501 Japan
| | - Byung Yoon Cha
- Research Institute for Biological Functions, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501 Japan
| | - Je-Tae Woo
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501 Japan
- Research Institute for Biological Functions, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501 Japan
| | - Kazuo Nagai
- Graduate School of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501 Japan
- Research Institute for Biological Functions, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501 Japan
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501 Japan
| | - Hirokazu Tsukaya
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033 Japan
| | - Yasunori Machida
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602 Japan
| | - 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
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