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Elesawi IE, Hashem AM, Yao L, Maher M, Hassanin AA, Abd El-Moneim D, Safhi FA, Al Aboud NM, Alshamrani SM, Shehata WF, Chunli C. The role of DNA topoisomerase 1α (AtTOP1α) in regulating arabidopsis meiotic recombination and chromosome segregation. PeerJ 2024; 12:e17864. [PMID: 39221285 PMCID: PMC11365474 DOI: 10.7717/peerj.17864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/15/2024] [Indexed: 09/04/2024] Open
Abstract
Meiosis is a critical process in sexual reproduction, and errors during this cell division can significantly impact fertility. Successful meiosis relies on the coordinated action of numerous genes involved in DNA replication, strand breaks, and subsequent rejoining. DNA topoisomerase enzymes play a vital role by regulating DNA topology, alleviating tension during replication and transcription. To elucidate the specific function of DNA topoisomerase 1α ( A t T O P 1 α ) in male reproductive development of Arabidopsis thaliana, we investigated meiotic cell division in Arabidopsis flower buds. Combining cytological and biochemical techniques, we aimed to reveal the novel contribution of A t T O P 1 α to meiosis. Our results demonstrate that the absence of A t T O P 1 α leads to aberrant chromatin behavior during meiotic division. Specifically, the top1α1 mutant displayed altered heterochromatin distribution and clustered centromere signals at early meiotic stages. Additionally, this mutant exhibited disruptions in the distribution of 45s rDNA signals and a reduced frequency of chiasma formation during metaphase I, a crucial stage for genetic exchange. Furthermore, the atm-2×top1α1 double mutant displayed even more severe meiotic defects, including incomplete synapsis, DNA fragmentation, and the presence of polyads. These observations collectively suggest that A t T O P 1 α plays a critical role in ensuring accurate meiotic progression, promoting homologous chromosome crossover formation, and potentially functioning in a shared DNA repair pathway with ATAXIA TELANGIECTASIA MUTATED (ATM) in Arabidopsis microspore mother cells.
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Affiliation(s)
- Ibrahim Eid Elesawi
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Agricultural Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Ahmed M. Hashem
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Li Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mohamed Maher
- Agricultural Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | | | - Diaa Abd El-Moneim
- Department of Plant Production, (Genetic Branch), Faculty of Environmental and Agricultural Sciences, Arish University, El-Arish, El-Arish, Egypt
| | - Fatmah A. Safhi
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Nora M. Al Aboud
- Department of Biology Faculty of Science, Umm Al‐Qura University, Makkah, Saudi Arabia
| | - Salha Mesfer Alshamrani
- Department of Biological Science, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Wael F. Shehata
- College of Agriculture and Food Sciences, Department of Agricultural Biotechnology, King Faisal University, Al-Ahsa, Al-Ahsa, Saudi Arabia
- College of Environmental Agricultural Science, Plant Production Department, Arish University, Arish, North Sinai, Egypt
| | - Chen Chunli
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, China
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Peng X, Li H, Xu W, Yang Q, Li D, Fan T, Li B, Ding J, Ku W, Deng D, Zhu F, Xiao L, Wang R. The AtMINPP Gene, Encoding a Multiple Inositol Polyphosphate Phosphatase, Coordinates a Novel Crosstalk between Phytic Acid Metabolism and Ethylene Signal Transduction in Leaf Senescence. Int J Mol Sci 2024; 25:8969. [PMID: 39201658 PMCID: PMC11354338 DOI: 10.3390/ijms25168969] [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: 07/21/2024] [Revised: 08/13/2024] [Accepted: 08/15/2024] [Indexed: 09/02/2024] Open
Abstract
Plant senescence is a highly coordinated process that is intricately regulated by numerous endogenous and environmental signals. The involvement of phytic acid in various cell signaling and plant processes has been recognized, but the specific roles of phytic acid metabolism in Arabidopsis leaf senescence remain unclear. Here, we demonstrate that in Arabidopsis thaliana the multiple inositol phosphate phosphatase (AtMINPP) gene, encoding an enzyme with phytase activity, plays a crucial role in regulating leaf senescence by coordinating the ethylene signal transduction pathway. Through overexpressing AtMINPP (AtMINPP-OE), we observed early leaf senescence and reduced chlorophyll contents. Conversely, a loss-of-function heterozygous mutant (atminpp/+) exhibited the opposite phenotype. Correspondingly, the expression of senescence-associated genes (SAGs) was significantly upregulated in AtMINPP-OE but markedly decreased in atminpp/+. Yeast one-hybrid and chromatin immunoprecipitation assays indicated that the EIN3 transcription factor directly binds to the promoter of AtMINPP. Genetic analysis further revealed that AtMINPP-OE could accelerate the senescence of ein3-1eil1-3 mutants. These findings elucidate the mechanism by which AtMINPP regulates ethylene-induced leaf senescence in Arabidopsis, providing insights into the genetic manipulation of leaf senescence and plant growth.
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Affiliation(s)
- Xiaoyun Peng
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (X.P.); (Q.Y.); (T.F.); (J.D.); (W.K.); (F.Z.)
| | - Haiou Li
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (X.P.); (Q.Y.); (T.F.); (J.D.); (W.K.); (F.Z.)
| | - Wenzhong Xu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Qian Yang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (X.P.); (Q.Y.); (T.F.); (J.D.); (W.K.); (F.Z.)
| | - Dongming Li
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China;
| | - Tingting Fan
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (X.P.); (Q.Y.); (T.F.); (J.D.); (W.K.); (F.Z.)
| | - Bin Li
- Hunan Academy of Agricultural Sciences, Changsha 410125, China;
| | - Junhui Ding
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (X.P.); (Q.Y.); (T.F.); (J.D.); (W.K.); (F.Z.)
| | - Wenzhen Ku
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (X.P.); (Q.Y.); (T.F.); (J.D.); (W.K.); (F.Z.)
| | - Danyi Deng
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (X.P.); (Q.Y.); (T.F.); (J.D.); (W.K.); (F.Z.)
| | - Feiying Zhu
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (X.P.); (Q.Y.); (T.F.); (J.D.); (W.K.); (F.Z.)
- Hunan Academy of Agricultural Sciences, Changsha 410125, China;
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (X.P.); (Q.Y.); (T.F.); (J.D.); (W.K.); (F.Z.)
| | - Ruozhong Wang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China; (X.P.); (Q.Y.); (T.F.); (J.D.); (W.K.); (F.Z.)
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Bai Y, Zhou P, Ni Z, Iqbal S, Ouma KO, Huang X, Gao F, Ma C, Shi T, Gao Z. AGAMOUS-LIKE24 controls pistil number in Japanese apricot by targeting the KNOTTED1-LIKE gene KNAT2/6-a. PLANT PHYSIOLOGY 2024; 195:566-579. [PMID: 38345864 PMCID: PMC11060673 DOI: 10.1093/plphys/kiae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/25/2023] [Indexed: 05/02/2024]
Abstract
The formation of multi-pistil flowers reduces the yield and quality in Japanese apricot (Prunus mume). However, the molecular mechanism underlying the formation of multi-pistil flowers remains unknown. In the current study, overexpression of PmKNAT2/6-a, a class I KNOTTED1-like homeobox (KNOX) member, in Arabidopsis (Arabidopsis thaliana) resulted in a multi-pistil phenotype. Analysis of the upstream regulators of PmKNAT2/6-a showed that AGAMOUS-like 24 (PmAGL24) could directly bind to the PmKNAT2/6-a promoter and regulate its expression. PmAGL24 also interacted with Like Heterochromatin Protein 1 (PmLHP1) to recruit lysine trimethylation at position 27 on histone H3 (H3K27me3) to regulate PmKNAT2/6-a expression, which is indirectly involved in multiple pistils formation in Japanese apricot flowers. Our study reveals that the PmAGL24 transcription factor, an upstream regulator of PmKNAT2/6-a, regulates PmKNAT2/6-a expression via direct and indirect pathways and is involved in the formation of multiple pistils in Japanese apricot.
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Affiliation(s)
- Yang Bai
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Pengyu Zhou
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaojun Ni
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Shahid Iqbal
- Horticultural Science Department, North Florida Research and Education Center, University of Florida/IFAS, Quincy, FL 32351, USA
| | - Kenneth Omondi Ouma
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao Huang
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Feng Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chengdong Ma
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Shi
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihong Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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Lin X, Yuan T, Guo H, Guo Y, Yamaguchi N, Wang S, Zhang D, Qi D, Li J, Chen Q, Liu X, Zhao L, Xiao J, Wagner D, Cui S, Zhao H. The regulation of chromatin configuration at AGAMOUS locus by LFR-SYD-containing complex is critical for reproductive organ development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:478-496. [PMID: 37478313 DOI: 10.1111/tpj.16385] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 05/28/2023] [Accepted: 06/27/2023] [Indexed: 07/23/2023]
Abstract
Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes are evolutionarily conserved, multi-subunit machinery that play vital roles in the regulation of gene expression by controlling nucleosome positioning and occupancy. However, little is known about the subunit composition of SPLAYED (SYD)-containing SWI/SNF complexes in plants. Here, we show that the Arabidopsis thaliana Leaf and Flower Related (LFR) is a subunit of SYD-containing SWI/SNF complexes. LFR interacts directly with multiple SWI/SNF subunits, including the catalytic ATPase subunit SYD, in vitro and in vivo. Phenotypic analyses of lfr-2 mutant flowers revealed that LFR is important for proper filament and pistil development, resembling the function of SYD. Transcriptome profiling revealed that LFR and SYD shared a subset of co-regulated genes. We further demonstrate that the LFR and SYD interdependently activate the transcription of AGAMOUS (AG), a C-class floral organ identity gene, by regulating the occupation of nucleosome, chromatin loop, histone modification, and Pol II enrichment on the AG locus. Furthermore, the chromosome conformation capture (3C) assay revealed that the gene loop at AG locus is negatively correlated with the AG expression level, and LFR-SYD was functional to demolish the AG chromatin loop to promote its transcription. Collectively, these results provide insight into the molecular mechanism of the Arabidopsis SYD-SWI/SNF complex in the control of higher chromatin conformation of the floral identity gene essential to plant reproductive organ development.
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Affiliation(s)
- Xiaowei Lin
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
- School of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, 301617, China
| | - Tingting Yuan
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Hong Guo
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yi Guo
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Nobutoshi Yamaguchi
- Biological Science, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Shuge Wang
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Dongxia Zhang
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Dongmei Qi
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Jiayu Li
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Qiang Chen
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Xinye Liu
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Long Zhao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jun Xiao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, 19104-6084, Pennsylvania, USA
| | - Sujuan Cui
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Hongtao Zhao
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
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5
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Huang Z, Dinh TT, Luscher E, Li S, Liu X, Won SY, Chen X. Genetic Screens for Floral Mutants in Arabidopsis thaliana: Enhancers and Suppressors. Methods Mol Biol 2023; 2686:131-162. [PMID: 37540357 DOI: 10.1007/978-1-0716-3299-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The flower is a hallmark feature that has contributed to the evolutionary success of land plants. Diverse mutagenic agents have been employed as a tool to genetically perturb flower development and identify genes involved in floral patterning and morphogenesis. Since the initial studies to identify genes governing processes such as floral organ specification, mutagenesis in sensitized backgrounds has been used to isolate enhancers and suppressors to further probe the molecular basis of floral development. Here, we first describe two commonly employed methods for mutagenesis (using ethyl methanesulfonate (EMS) or T-DNAs as mutagens), and then describe three methods for identifying a mutation that leads to phenotypic alterations: traditional map-based cloning, modified high-efficiency thermal asymmetric interlaced PCR (mhiTAIL-PCR), and deep sequencing in the plant model Arabidopsis thaliana.
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Affiliation(s)
- Zhigang Huang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, China
| | - Thanh Theresa Dinh
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Elizabeth Luscher
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Shaofang Li
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Xigang Liu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - So Youn Won
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Xuemei Chen
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
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Zhang H, Tang Z, Zhang Y, Liu L, Zhao D, Liu X, Guo L, Dong J. TOP1α suppresses lateral root gravitropism in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2022; 17:2098646. [PMID: 35819101 PMCID: PMC9278425 DOI: 10.1080/15592324.2022.2098646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Root gravitropism is important for anchorage and exploration of soil for water and nutrients. It affects root architecture, which is one of the elements that influence crop yield. The mechanism of primary root gravitropism has been widely studied, but it is still not clear how lateral root gravitropism is regulated. Here, in this study, we found that Topoisomerase I α (TOP1α) repressed lateral root gravitropic growth, which was opposite to the previous report that TOP1α maintains primary root gravitropism, revealing a dual function of TOP1α in root gravitropism regulation. Further investigation showed that Target of Rapamycin (TOR) was suppressed in columella cells of lateral root to inhibit columella cell development, especially amyloplast biosynthesis. Our findings uncovered a new mechanism about lateral root gravitropism regulation, which might provide a theoretical support for improving agricultural production.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ziyan Tang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Ying Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Dan Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- College of Life Sciences, Hengshui University, Hengshui, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Lin Guo
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, China
- College of Plant Protection, Hebei Agricultural University, Baoding, China
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Lardon R, Trinh HK, Xu X, Vu LD, Van De Cotte B, Pernisová M, Vanneste S, De Smet I, Geelen D. Histidine kinase inhibitors impair shoot regeneration in Arabidopsis thaliana via cytokinin signaling and SAM patterning determinants. FRONTIERS IN PLANT SCIENCE 2022; 13:894208. [PMID: 36684719 PMCID: PMC9847488 DOI: 10.3389/fpls.2022.894208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/27/2022] [Indexed: 06/17/2023]
Abstract
Reversible protein phosphorylation is a post-translational modification involved in virtually all plant processes, as it mediates protein activity and signal transduction. Here, we probe dynamic protein phosphorylation during de novo shoot organogenesis in Arabidopsis thaliana. We find that application of three kinase inhibitors in various time intervals has different effects on root explants. Short exposures to the putative histidine (His) kinase inhibitor TCSA during the initial days on shoot induction medium (SIM) are detrimental for regeneration in seven natural accessions. Investigation of cytokinin signaling mutants, as well as reporter lines for hormone responses and shoot markers, suggests that TCSA impedes cytokinin signal transduction via AHK3, AHK4, AHP3, and AHP5. A mass spectrometry-based phosphoproteome analysis further reveals profound deregulation of Ser/Thr/Tyr phosphoproteins regulating protein modification, transcription, vesicle trafficking, organ morphogenesis, and cation transport. Among TCSA-responsive factors are prior candidates with a role in shoot apical meristem patterning, such as AGO1, BAM1, PLL5, FIP37, TOP1ALPHA, and RBR1, as well as proteins involved in polar auxin transport (e.g., PIN1) and brassinosteroid signaling (e.g., BIN2). Putative novel regeneration determinants regulated by TCSA include RD2, AT1G52780, PVA11, and AVT1C, while NAIP2, OPS, ARR1, QKY, and aquaporins exhibit differential phospholevels on control SIM. LC-MS/MS data are available via ProteomeXchange with identifier PXD030754.
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Affiliation(s)
- Robin Lardon
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Hoang Khai Trinh
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Biotechnology Research and Development Institute, Can Tho University, Can Tho, Vietnam
| | - Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Brigitte Van De Cotte
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Markéta Pernisová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Steffen Vanneste
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Lab of Plant Growth Analysis, Ghent University Global Campus, Incheon, South Korea
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Danny Geelen
- HortiCell, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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8
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Zhang H, Guo L, Li Y, Zhao D, Liu L, Chang W, Zhang K, Zheng Y, Hou J, Fu C, Zhang Y, Zhang B, Ma Y, Niu Y, Zhang K, Xing J, Cui S, Wang F, Tan K, Zheng S, Tang W, Dong J, Liu X. TOP1α fine-tunes TOR-PLT2 to maintain root tip homeostasis in response to sugars. NATURE PLANTS 2022; 8:792-801. [PMID: 35817819 DOI: 10.1038/s41477-022-01179-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Plant development is highly dependent on energy levels. TARGET OF RAPAMYCIN (TOR) activates the proximal root meristem to promote root development in response to photosynthesis-derived sugars during photomorphogenesis in Arabidopsis thaliana. However, the mechanisms of how root tip homeostasis is maintained to ensure proper root cap structure and gravitropism are unknown. PLETHORA (PLT) transcription factors are pivotal for the root apical meristem (RAM) identity by forming gradients, but how PLT gradients are established and maintained, and their roles in COL development are not well known. We demonstrate that endogenous sucrose induces TOPOISOMERASE1α (TOP1α) expression during the skotomorphogenesis-to-photomorphogenesis transition. TOP1α fine-tunes TOR expression in the root tip columella. TOR maintains columella stem cell identity correlating with reduced quiescent centre cell division in a WUSCHEL RELATED HOMEOBOX5-independent manner. Meanwhile, TOR promotes PLT2 expression and phosphorylates and stabilizes PLT2 to maintain its gradient consistent with TOR expression pattern. PLT2 controls cell division and amyloplast formation to regulate columella development and gravitropism. This elaborate mechanism helps maintain root tip homeostasis and gravitropism in response to energy changes during root development.
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Affiliation(s)
- Hao Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Lin Guo
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China.
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China.
| | - Yongpeng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
| | - Dan Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
- College of Life Sciences, Hengshui University, Hengshui, China
| | - Luping Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
| | - Wenwen Chang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China
| | - Ke Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Yichao Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Jiajie Hou
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Chenghao Fu
- Food Science College, Shenyang Agricultural University, ShenYang, China
| | - Ying Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Baowen Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Yuru Ma
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Yanxiao Niu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Kang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Jihong Xing
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Sujuan Cui
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Fengru Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Ke Tan
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Shuzhi Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Wenqiang Tang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Shijiazhuang, China.
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, China.
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9
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Pelayo MA, Yamaguchi N, Ito T. One factor, many systems: the floral homeotic protein AGAMOUS and its epigenetic regulatory mechanisms. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102009. [PMID: 33640614 DOI: 10.1016/j.pbi.2021.102009] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/10/2021] [Accepted: 01/13/2021] [Indexed: 05/15/2023]
Abstract
Tissue-specific transcription factors allow cells to specify new fates by exerting control over gene regulatory networks and the epigenetic landscape of a cell. However, our knowledge of the molecular mechanisms underlying cell fate decisions is limited. In Arabidopsis, the MADS-box transcription factor AGAMOUS (AG) plays a central role in regulating reproductive organ identity and meristem determinacy during flower development. During the vegetative phase, AG transcription is repressed by Polycomb complexes and intronic noncoding RNA. Once AG is transcribed in a spatiotemporally regulated manner during the reproductive phase, AG functions with chromatin regulators to change the chromatin structure at key target gene loci. The concerted actions of AG and the transcription factors functioning downstream of AG recruit general transcription machinery for proper cell fate decision. In this review, we describe progress in AG research that has provided important insights into the regulatory and epigenetic mechanisms underlying cell fate determination in plants.
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Affiliation(s)
- Margaret Anne Pelayo
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan
| | - Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.
| | - Toshiro Ito
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.
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10
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Tvorogova VE, Krasnoperova EY, Potsenkovskaia EA, Kudriashov AA, Dodueva IE, Lutova LA. What Does the WOX Say? Review of Regulators, Targets, Partners. Mol Biol 2021. [DOI: 10.1134/s002689332102031x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Zluhan-Martínez E, Pérez-Koldenkova V, Ponce-Castañeda MV, Sánchez MDLP, García-Ponce B, Miguel-Hernández S, Álvarez-Buylla ER, Garay-Arroyo A. Beyond What Your Retina Can See: Similarities of Retinoblastoma Function between Plants and Animals, from Developmental Processes to Epigenetic Regulation. Int J Mol Sci 2020; 21:E4925. [PMID: 32664691 PMCID: PMC7404004 DOI: 10.3390/ijms21144925] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/29/2020] [Accepted: 07/07/2020] [Indexed: 12/15/2022] Open
Abstract
The Retinoblastoma protein (pRb) is a key cell cycle regulator conserved in a wide variety of organisms. Experimental analysis of pRb's functions in animals and plants has revealed that this protein participates in cell proliferation and differentiation processes. In addition, pRb in animals and its orthologs in plants (RBR), are part of highly conserved protein complexes which suggest the possibility that analogies exist not only between functions carried out by pRb orthologs themselves, but also in the structure and roles of the protein networks where these proteins are involved. Here, we present examples of pRb/RBR participation in cell cycle control, cell differentiation, and in the regulation of epigenetic changes and chromatin remodeling machinery, highlighting the similarities that exist between the composition of such networks in plants and animals.
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Affiliation(s)
- Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
- Posgrado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Av. Universidad 3000, Coyoacán 04510, Mexico
| | - Vadim Pérez-Koldenkova
- Laboratorio Nacional de Microscopía Avanzada, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc, 330. Col. Doctores, Alc. Cuauhtémoc 06720, Mexico;
| | - Martha Verónica Ponce-Castañeda
- Unidad de Investigación Médica en Enfermedades Infecciosas, Centro Médico Nacional SXXI, Instituto Mexicano del Seguro Social, Mexico City 06720, Mexico;
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Sergio Miguel-Hernández
- Laboratorio de Citopatología Ambiental, Departamento de Morfología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Campus Zacatenco, Calle Wilfrido Massieu Esquina Cda, Manuel Stampa 07738, Mexico;
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de Plantas, Instituto de Ecología, Universidad Nacional Autónoma de Mexico, 3er Circuito Ext. Junto a J. Botánico, Ciudad Universitaria, UNAM 04510, Mexico; (E.Z.-M.); (M.d.l.P.S.); (B.G.-P.)
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12
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Zheng Y, Liu X. Review: Chromatin organization in plant and animal stem cell maintenance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:173-179. [PMID: 30824049 DOI: 10.1016/j.plantsci.2018.12.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/16/2018] [Accepted: 12/26/2018] [Indexed: 06/09/2023]
Abstract
Stem cells have self-renewal capacity and can differentiate into specialized cell types. Although the origin, form and differentiated destinations of stem cells differ between animals and plants, they are regulated by similar epigenetic mechanisms during differentiation. There is increasing evidence that the three-dimensional (3D) genome organization plays important roles in gene expression regulation during stem cell differentiation. In plant cells, however, studies related to chromatin interaction in gene expression regulation are just beginning and will be a hot topic in the future. In this review, we summarized the similarities of plant and animal stem cell niches and their function in stem cell maintenance, the roles of chromatin conformation changes in regulating gene expression and recent findings about chromatin organization in plant cells at genome-wide and loci-specific levels.
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Affiliation(s)
- Yan Zheng
- National Marine Data and Information Service, Tianjin 300100, China; Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Rd, Shijiazhuang, 050021 China
| | - Xigang Liu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Rd, Shijiazhuang, 050021 China.
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13
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Zhong P, Li J, Luo L, Zhao Z, Tian Z. TOP1α regulates FLOWERING LOCUS C expression by coupling histone modification and transcription machinery. Development 2019; 146:dev.167841. [PMID: 30705075 DOI: 10.1242/dev.167841] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 01/22/2019] [Indexed: 11/20/2022]
Abstract
The key steps of transcription are coupled with the opening of the DNA helical structure and establishment of active chromatin to facilitate the movement of the transcription machinery. Type I topoisomerases cleave one DNA strand and relax the supercoiled structure of transcribed templates. How topoisomerase-mediated DNA topological changes promote transcription and establish a permissive histone modification for transcription elongation is largely unknown. Here, we show that TOPOISOMERASE 1α in plants regulates FLOWERING LOCUS C transcription by coupling histone modification and transcription machinery. We demonstrate that TOP1α directly interacts with the methyltransferase SDG8 to establish high levels of H3K36 methylation downstream of FLC transcription start sites and recruits RNA polymerase II to facilitate transcription elongation. Our results provide a mechanistic framework for TOP1α control of the main steps of early transcription and demonstrate how topoisomerases couple RNA polymerase II and permissive histone modifications to initiate transcription elongation.
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Affiliation(s)
- Peiqiao Zhong
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| | - Jiaojiao Li
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| | - Linjie Luo
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| | - Zhong Zhao
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| | - Zhaoxia Tian
- CAS Center for Excellence in Molecular Plant Sciences, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
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14
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Cai H, Zhang M, Chai M, He Q, Huang X, Zhao L, Qin Y. Epigenetic regulation of anthocyanin biosynthesis by an antagonistic interaction between H2A.Z and H3K4me3. THE NEW PHYTOLOGIST 2019; 221:295-308. [PMID: 29959895 DOI: 10.1111/nph.15306] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/01/2018] [Indexed: 05/20/2023]
Abstract
The accumulation of anthocyanins in response to specific developmental cues or environmental conditions plays a vital role in plant development and protection against stresses. Extensive research has examined the regulation of anthocyanin biosynthetic genes at the transcriptional and post-transcriptional levels, but the role of chromatin in this regulation remains unknown. Chromatin immunoprecipitation and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analyses were performed. Genetic interactions between trimethylation of lysine 4 on histone H3 (H3K4me3) and the chromatin remodeling complex SWR1 in the control of anthocyanin biosynthesis were further studied. In this study, we provide evidence that a conserved histone H2 variant, H2A.Z, negatively regulates anthocyanin accumulation through deposition at a set of anthocyanin biosynthetic genes and consequently represses their expression in Arabidopsis thaliana. Our data indicate that the accumulation of anthocyanin in H2A.Z deposition-deficient mutants is associated with increased H3K4me3, which is required for promotion of the expression of anthocyanin biosynthetic genes. We further provide evidence that H3K4me3 in anthocyanin biosynthetic genes is negatively associated with the presence of H2A.Z. Our results reveal an antagonistic relationship between H2A.Z and H3K4me3 in the regulation of the expression of anthocyanin biosynthesis genes, adding another layer of regulation to anthocyanin biosynthesis genes and highlighting the role of chromatin in gene regulation.
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Affiliation(s)
- Hanyang Cai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Man Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mengnan Chai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qing He
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinyu Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lihua Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuan Qin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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15
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Guo L, Cao X, Liu Y, Li J, Li Y, Li D, Zhang K, Gao C, Dong A, Liu X. A chromatin loop represses WUSCHEL expression in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:1083-1097. [PMID: 29660180 DOI: 10.1111/tpj.13921] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 05/27/2023]
Abstract
WUSCHEL (WUS) is critical for plant meristem maintenance and determinacy in Arabidopsis, and the regulation of its spatiotemporal expression patterns is complex. We previously found that AGAMOUS (AG), a key MADS-domain transcription factor in floral organ identity and floral meristem determinacy, can directly suppress WUS expression through the recruitment of the Polycomb group (PcG) protein TERMINAL FLOWER 2 (TFL2, also known as LIKE HETEROCHROMATIN PROTEIN 1, LHP1) at the WUS locus; however, the mechanism by which WUS is repressed remains unclear. Here, using chromosome conformation capture (3C) and chromatin immunoprecipitation 3C, we found that two specific regions flanking the WUS gene body bound by AG and TFL2 form a chromatin loop that is directly promoted by AG during flower development in a manner independent of the physical distance and sequence content of the intervening region. Moreover, AG physically interacts with TFL2, and TFL2 binding to the chromatin loop is dependent on AG. Transgenic and CRISPR/Cas9-edited lines showed that the WUS chromatin loop represses gene expression by blocking the recruitment of RNA polymerase II at the locus. The findings uncover the WUS chromatin loop as another regulatory mechanism controlling WUS expression, and also shed light on the factors required for chromatin conformation change and their recruitment.
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Affiliation(s)
- Lin Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050021, China
| | - Xiuwei Cao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050021, 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
| | - Jun Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongpeng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050021, China
| | - Dongming Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050021, China
| | - Ke Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050021, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, 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
| | - Xigang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050021, China
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16
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Lin X, Gu D, Zhao H, Peng Y, Zhang G, Yuan T, Li M, Wang Z, Wang X, Cui S. LFR is functionally associated with AS2 to mediate leaf development in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:598-612. [PMID: 29775508 DOI: 10.1111/tpj.13973] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 06/08/2023]
Abstract
Leaves are essential organs for plants. We previously identified a functional gene possibly encoding a component of the SWI/SNF complex named Leaf and Flower Related (LFR) in Arabidopsis thaliana. Loss-of-function mutants of LFR displayed obvious defects in leaf morphogenesis, indicating its vital role in leaf development. Here an allelic null mutant of ASYMMETRIC LEAVES2 (AS2), as2-6, was isolated as an enhancer of lfr-1 in petiole length, vasculature pattern and leaf margin development. The lfr as2 double-mutants showed enhanced ectopic expression of BREVIPEDICELLUS (BP) compared with each of the single-mutants, which is consistent with their synergistic genetic enhancement in multiple BP-dependent development processes. Moreover, LFR and several putative subunits of the SWI/SNF complex interacted physically with AS2. LFR associated with BP chromatin in an AS1-AS2-dependent manner to promote the nucleosome occupancy for appropriate BP repression in leaves. Taken together, our findings reveal that LFR and the SWI/SNF complex play roles in leaf development at least partly by repressing BP transcription as interacting factors of AS2, which expounds our understanding of BP repression at the chromatin structure level in leaf development.
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Affiliation(s)
- Xiaowei Lin
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Dandan Gu
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Hongtao Zhao
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Yue Peng
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Guofang Zhang
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Tingting Yuan
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Mengge Li
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Zhijuan Wang
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Xiutang Wang
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
| | - Sujuan Cui
- Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Hebei, 050024, China
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Normal University, Hebei, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Hebei Normal University, Hebei, 050024, China
- College of Life Science, Hebei Normal University, Hebei, 050024, China
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17
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Chen DH, Huang Y, Jiang C, Si JP. Chromatin-Based Regulation of Plant Root Development. FRONTIERS IN PLANT SCIENCE 2018; 9:1509. [PMID: 30386363 PMCID: PMC6198463 DOI: 10.3389/fpls.2018.01509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/26/2018] [Indexed: 05/10/2023]
Abstract
Plant is endowed with sessile habit and nutrient acquisition mainly through the root organ, which also provides an excellent model to study stem cell fate and asymmetric division due to well-organized cell layers and relatively simple cell types in root meristem. Besides genetic material DNA wrapped around histone octamer, chromatin structure determined by chromatin modification including DNA methylation, histone modification and chromatin remodeling also contributes greatly to the regulation of gene expression. In this review, we summarize the current progresses on the molecular mechanisms of chromatin modification in regulating root development.
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Affiliation(s)
- Dong-Hong Chen
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium Catenatum, Zhejiang A&F University, Hangzhou, China
- *Correspondence: Dong-Hong Chen
| | - Yong Huang
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, China
| | | | - Jin-Ping Si
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium Catenatum, Zhejiang A&F University, Hangzhou, China
- Jin-Ping Si
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18
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Abstract
Our understanding of the epigenetic mechanisms that regulate gene expression has been largely increased in recent years by the development and refinement of different techniques. This has revealed that gene transcription is highly influenced by epigenetic mechanisms, i.e., those that do not involve changes in the genome sequence, but rather in nuclear architecture, chromosome conformation and histone and DNA modifications. Our understanding of how these different levels of epigenetic regulation interact with each other and with classical transcription-factor based gene regulation to influence gene transcription has just started to emerge. This review discusses the latest advances in unraveling the complex interactions between different types of epigenetic regulation and transcription factor activity, with special attention to the approaches that can be used to study these interactions.
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Affiliation(s)
- Marian Bemer
- Department of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands.
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19
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van der Knaap E, Østergaard L. Shaping a fruit: Developmental pathways that impact growth patterns. Semin Cell Dev Biol 2017; 79:27-36. [PMID: 29092788 DOI: 10.1016/j.semcdb.2017.10.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 10/20/2017] [Accepted: 10/26/2017] [Indexed: 12/27/2022]
Abstract
Angiosperms produce seeds as their progeny enclosed in maternally-derived structures called fruits. Evolutionarily, fruits have contributed enormously to the success of the Angiosperms phylum by providing protection and nutrition to the developing seeds, while ensuring the efficient dispersal upon maturity. Fruits vary massively in both size and shape and certain species have been targeted for domestication due to their nutritional value and delicious taste. Among the vast array of 3D fruit shapes that exist in nature, the mechanism by which growth is oriented and coordinated to generate this diversity of forms is unclear. In this review, we discuss the latest results in identifying components that control fruit morphology and their effect on isotropic and anisotropic growth. Moreover, we will compare the current knowledge on the mechanisms that control fruit growth, size and shape between the domesticated Solanaceae species, tomato and members of the large family of Brassicaceae.
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Affiliation(s)
- Esther van der Knaap
- Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA, 30602, USA.
| | - Lars Østergaard
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom.
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20
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Huang Z, Shi T, Zheng B, Yumul RE, Liu X, You C, Gao Z, Xiao L, Chen X. APETALA2 antagonizes the transcriptional activity of AGAMOUS in regulating floral stem cells in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2017; 215:1197-1209. [PMID: 27604611 PMCID: PMC5342953 DOI: 10.1111/nph.14151] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 07/18/2016] [Indexed: 05/19/2023]
Abstract
APETALA2 (AP2) is best known for its function in the outer two floral whorls, where it specifies the identities of sepals and petals by restricting the expression of AGAMOUS (AG) to the inner two whorls in Arabidopsis thaliana. Here, we describe a role of AP2 in promoting the maintenance of floral stem cell fate, not by repressing AG transcription, but by antagonizing AG activity in the center of the flower. We performed a genetic screen with ag-10 plants, which exhibit a weak floral determinacy defect, and isolated a mutant with a strong floral determinacy defect. This mutant was found to harbor another mutation in AG and was named ag-11. We performed a genetic screen in the ag-11 background to isolate mutations that suppress the floral determinacy defect. Two suppressor mutants were found to harbor mutations in AP2. While AG is known to shut down the expression of the stem cell maintenance gene WUSCHEL (WUS) to terminate floral stem cell fate, AP2 promotes the expression of WUS. AP2 does not repress the transcription of AG in the inner two whorls, but instead counteracts AG activity.
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Affiliation(s)
- Zhigang Huang
- Hunan Provincial Key Laboratory of Phytohormones and Growth DevelopmentHunan Provincial Key Laboratory for Crop Germplasm Innovation and UtilizationHunan Agricultural UniversityChangsha410128China
- Department of Botany and Plant SciencesInstitute of Integrative Genome BiologyUniversity of CaliforniaRiversideCA92521USA
| | - Ting Shi
- Department of Botany and Plant SciencesInstitute of Integrative Genome BiologyUniversity of CaliforniaRiversideCA92521USA
- College of HorticultureNanjing Agricultural UniversityNo. 1 WeigangNanjing210095China
| | - Binglian Zheng
- State Key Laboratory of Genetic EngineeringCollaborative Innovation Center for Genetics and DevelopmentInstitute of Plant BiologySchool of Life SciencesFudan UniversityShanghai200438China
| | - Rae Eden Yumul
- Department of Botany and Plant SciencesInstitute of Integrative Genome BiologyUniversity of CaliforniaRiversideCA92521USA
| | - Xigang Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringCenter for Agricultural Resources ResearchInstitute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuang050021China
| | - Chenjiang You
- Department of Botany and Plant SciencesInstitute of Integrative Genome BiologyUniversity of CaliforniaRiversideCA92521USA
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhen518060China
| | - Zhihong Gao
- College of HorticultureNanjing Agricultural UniversityNo. 1 WeigangNanjing210095China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth DevelopmentHunan Provincial Key Laboratory for Crop Germplasm Innovation and UtilizationHunan Agricultural UniversityChangsha410128China
| | - Xuemei Chen
- Department of Botany and Plant SciencesInstitute of Integrative Genome BiologyUniversity of CaliforniaRiversideCA92521USA
- Howard Hughes Medical InstituteUniversity of CaliforniaRiversideCA92521USA
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21
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Kupriyanova EV, Albert EV, Bliznina AI, Mamoshina PO, Ezhova TA. Arabidopsis DNA topoisomerase I alpha is required for adaptive response to light and flower development. Biol Open 2017; 6:832-843. [PMID: 28495963 PMCID: PMC5483022 DOI: 10.1242/bio.024422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA topoisomerase I alpha (TOP1α) plays a specific role in Arabidopsis thaliana development and is required for stem cell regulation in shoot and floral meristems. Recently, a new role independent of meristem functioning has been described for TOP1α, namely flowering time regulation. The same feature had been detected by us earlier for fas5, a mutant allele of TOP1α. In this study we clarify the effects of fas5 on bolting initiation and analyze the molecular basis of its role on flowering time regulation. We show that fas5 mutation leads to a constitutive shade avoidance syndrome, accompanied by leaf hyponasty, petiole elongation, lighter leaf color and early bolting. Other alleles of TOP1α demonstrate the same shade avoidance response. RNA sequencing confirmed the activation of shade avoidance gene pathways in fas5 mutant plants. It also revealed the repression of many genes controlling floral meristem identity and organ morphogenesis. Our research further expands the knowledge of TOP1α function in plant development and reveals that besides stem cell maintenance TOP1α plays an important new role in regulating the adaptive plant response to light stimulus and flower development. Summary: This study expands upon the existing knowledge of Arabidopsis DNA topoisomerase gene TOP1α function in plant development and demonstrates its important new role in regulating shade response and flower development.
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Affiliation(s)
- Evgenia V Kupriyanova
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
| | - Evgeniy V Albert
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
| | - Aleksandra I Bliznina
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
| | - Polina O Mamoshina
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
| | - Tatiana A Ezhova
- Department of Genetics, Faculty of Biology, Lomonosov Moscow State University, 119234, Leninskiye Gory 1/12, Moscow 119234, Russia
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22
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Shafiq S, Chen C, Yang J, Cheng L, Ma F, Widemann E, Sun Q. DNA Topoisomerase 1 Prevents R-loop Accumulation to Modulate Auxin-Regulated Root Development in Rice. MOLECULAR PLANT 2017; 10:821-833. [PMID: 28412545 DOI: 10.1016/j.molp.2017.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/02/2017] [Accepted: 04/03/2017] [Indexed: 05/21/2023]
Abstract
R-loop structures (RNA:DNA hybrids) have important functions in many biological processes, including transcriptional regulation and genome instability among diverse organisms. DNA topoisomerase 1 (TOP1), an essential manipulator of DNA topology during RNA transcription and DNA replication processes, can prevent R-loop accumulation by removing the positive and negative DNA supercoiling that is made by RNA polymerases during transcription. TOP1 is required for plant development, but little is known about its function in preventing co-transcriptional R-loop accumulation in various biological processes in plants. Here we show that knockdown of OsTOP1 strongly affects rice development, causing defects in root architecture and gravitropism, which are the consequences of misregulation of auxin signaling and transporter genes. We found that R-loops are naturally formed at rice auxin-related gene loci, and overaccumulate when OsTOP1 is knocked down or OsTOP1 protein activity is inhibited. OsTOP1 therefore sets the accurate expression levels of auxin-related genes by preventing the overaccumulation of inherent R-loops. Our data reveal R-loops as important factors in polar auxin transport and plant root development, and highlight that OsTOP1 functions as a key to link transcriptional R-loops with plant hormone signaling, provide new insights into transcriptional regulation of hormone signaling in plants.
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Affiliation(s)
- Sarfraz Shafiq
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China; Permanent affiliation: Department of Environmental Sciences, COMSATS Institute of Information Technology, Abbottabad 22060, Pakistan
| | - Chunli Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jing Yang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lingling Cheng
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fei Ma
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Emilie Widemann
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qianwen Sun
- Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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23
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Gao C, Qi S, Liu K, Li D, Jin C, Duan S, Zhang M, Chen M. Functional characterization of Brassica napus DNA topoisomerase Iα-1 and its effect on flowering time when expressed in Arabidopsis thaliana. Biochem Biophys Res Commun 2017; 486:124-129. [PMID: 28283390 DOI: 10.1016/j.bbrc.2017.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 03/06/2017] [Indexed: 01/17/2023]
Abstract
Previous studies have shown that DNA topoisomerase Iα (AtTOP1α) has specific developmental functions during growth and development in Arabidopsis thaliana. However, little is known about the roles of DNA topoisomerases in the closely related and commercially important plant, rapeseed (Brassica napus). Here, the full-length BnTOP1α-1 coding sequence was cloned from the A2 subgenome of the Brassica napus inbred line L111. We determine that all BnTOP1α paralogs showed differing patterns of expression in different organs of L111, and that when expressed in tobacco leaves as a fusion protein with green fluorescent protein, BnTOP1α-1 localized to the nucleus. We further showed that ectopic expression of BnTOP1α-1 in the A. thaliana top1α-7 mutant fully complemented the early flowering phenotype of the mutant. Moreover, altered expression levels in top1α-7 seedlings of several key genes controlling flowering time were restored to wild type levels by ectopic expression of BnTOP1α-1. These results provide valuable insights into the roles of rapeseed DNA topoisomerases in flowering time, and provide a promising target for genetic manipulation of this commercially significant process in rapeseed.
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Affiliation(s)
- Chenhao Gao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuanghui Qi
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Kaige Liu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dong Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Changyu Jin
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shaowei Duan
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Meng Zhang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingxun Chen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
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24
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Gong X, Shen L, Peng YZ, Gan Y, Yu H. DNA Topoisomerase Iα Affects the Floral Transition. PLANT PHYSIOLOGY 2017; 173:642-654. [PMID: 27837087 PMCID: PMC5210759 DOI: 10.1104/pp.16.01603] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/08/2016] [Indexed: 05/16/2023]
Abstract
DNA topoisomerases modulate DNA topology to maintain chromosome superstructure and genome integrity, which is indispensable for DNA replication and RNA transcription. Their function in plant development still remains largely unknown. Here, we report a hitherto unidentified role of Topoisomerase Iα (TOP1α) in controlling flowering time in Arabidopsis (Arabidopsis thaliana). Loss of function of TOP1α results in early flowering under both long and short days. This is attributed mainly to a decrease in the expression of a central flowering repressor, FLOWERING LOCUS C (FLC), and its close homologs, MADS AFFECTING FLOWERING4 (MAF4) and MAF5, during the floral transition. TOP1α physically binds to the genomic regions of FLC, MAF4, and MAF5 and promotes the association of RNA polymerase II complexes to their transcriptional start sites. These correlate with the changes in histone modifications but do not directly affect nucleosome occupancy at these loci. Our results suggest that TOP1α mediates DNA topology to facilitate the recruitment of RNA polymerase II at FLC, MAF4, and MAF5 in conjunction with histone modifications, thus facilitating the expression of these key flowering repressors to prevent precocious flowering in Arabidopsis.
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Affiliation(s)
- Ximing Gong
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Lisha Shen
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Ya Zhi Peng
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Yinbo Gan
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
| | - Hao Yu
- Department of Biological Sciences and Temasek Life Sciences Laboratory, National University of Singapore, 117543, Singapore (X.G., L.S., Y.Z.P., H.Y.); and
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China (Y.G.)
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25
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Xiao J, Lee US, Wagner D. Tug of war: adding and removing histone lysine methylation in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2016; 34:41-53. [PMID: 27614255 DOI: 10.1016/j.pbi.2016.08.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/11/2016] [Accepted: 08/24/2016] [Indexed: 05/17/2023]
Abstract
Histone lysine methylation plays a fundamental role in the epigenetic regulation of gene expression in multicellular eukaryotes, including plants. It shapes plant developmental and growth programs as well as responses to the environment. The methylation status of certain amino-acids, in particular of the histone 3 (H3) lysine tails, is dynamically controlled by opposite acting histone methyltransferase 'writers' and histone demethylase 'erasers'. The methylation status is interpreted by a third set of proteins, the histone modification 'readers', which specifically bind to a methylated amino-acid on the H3 tail. Histone methylation writers, readers, and erasers themselves are regulated by intrinsic or extrinsic stimuli; this forms a feedback loop that contributes to development and environmental adaptation in Arabidopsis and other plants. Recent studies have expanded our knowledge regarding the biological roles and dynamic regulation of histone methylation. In this review, we will discuss recent advances in understanding the regulation and roles of histone methylation in plants and animals.
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Affiliation(s)
- Jun Xiao
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Un-Sa Lee
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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26
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Gutierrez C. 25 Years of Cell Cycle Research: What's Ahead? TRENDS IN PLANT SCIENCE 2016; 21:823-833. [PMID: 27401252 DOI: 10.1016/j.tplants.2016.06.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/13/2016] [Accepted: 06/21/2016] [Indexed: 05/27/2023]
Abstract
We have reached 25 years since the first molecular approaches to plant cell cycle. Fortunately, we have witnessed an enormous advance in this field that has benefited from using complementary approaches including molecular, cellular, genetic and genomic resources. These studies have also branched and demonstrated the functional relevance of cell cycle regulators for virtually every aspect of plant life. The question is - where are we heading? I review here the latest developments in the field and briefly elaborate on how new technological advances should contribute to novel approaches that will benefit the plant cell cycle field. Understanding how the cell division cycle is integrated at the organismal level is perhaps one of the major challenges.
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Affiliation(s)
- Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC), Universidad Autónoma de Madrid (UAM), Nicolas Cabrera 1, 28049 Madrid, Spain.
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27
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Brzezinka K, Altmann S, Czesnick H, Nicolas P, Gorka M, Benke E, Kabelitz T, Jähne F, Graf A, Kappel C, Bäurle I. Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling. eLife 2016; 5:e17061. [PMID: 27680998 DOI: 10.7554/elife.17061.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/25/2016] [Indexed: 05/21/2023] Open
Abstract
Plants as sessile organisms can adapt to environmental stress to mitigate its adverse effects. As part of such adaptation they maintain an active memory of heat stress for several days that promotes a more efficient response to recurring stress. We show that this heat stress memory requires the activity of the FORGETTER1 (FGT1) locus, with fgt1 mutants displaying reduced maintenance of heat-induced gene expression. FGT1 encodes the Arabidopsis thaliana orthologue of Strawberry notch (Sno), and the protein globally associates with the promoter regions of actively expressed genes in a heat-dependent fashion. FGT1 interacts with chromatin remodelers of the SWI/SNF and ISWI families, which also display reduced heat stress memory. Genomic targets of the BRM remodeler overlap significantly with FGT1 targets. Accordingly, nucleosome dynamics at loci with altered maintenance of heat-induced expression are affected in fgt1. Together, our results suggest that by modulating nucleosome occupancy, FGT1 mediates stress-induced chromatin memory.
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Affiliation(s)
- Krzysztof Brzezinka
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Simone Altmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Hjördis Czesnick
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Philippe Nicolas
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michal Gorka
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Eileen Benke
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Tina Kabelitz
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Felix Jähne
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Alexander Graf
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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28
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Brzezinka K, Altmann S, Czesnick H, Nicolas P, Gorka M, Benke E, Kabelitz T, Jähne F, Graf A, Kappel C, Bäurle I. Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling. eLife 2016; 5:e17061. [PMID: 27680998 DOI: 10.7554/elife.17061.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/25/2016] [Indexed: 05/24/2023] Open
Abstract
Plants as sessile organisms can adapt to environmental stress to mitigate its adverse effects. As part of such adaptation they maintain an active memory of heat stress for several days that promotes a more efficient response to recurring stress. We show that this heat stress memory requires the activity of the FORGETTER1 (FGT1) locus, with fgt1 mutants displaying reduced maintenance of heat-induced gene expression. FGT1 encodes the Arabidopsis thaliana orthologue of Strawberry notch (Sno), and the protein globally associates with the promoter regions of actively expressed genes in a heat-dependent fashion. FGT1 interacts with chromatin remodelers of the SWI/SNF and ISWI families, which also display reduced heat stress memory. Genomic targets of the BRM remodeler overlap significantly with FGT1 targets. Accordingly, nucleosome dynamics at loci with altered maintenance of heat-induced expression are affected in fgt1. Together, our results suggest that by modulating nucleosome occupancy, FGT1 mediates stress-induced chromatin memory.
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Affiliation(s)
- Krzysztof Brzezinka
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Simone Altmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Hjördis Czesnick
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Philippe Nicolas
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michal Gorka
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Eileen Benke
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Tina Kabelitz
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Felix Jähne
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Alexander Graf
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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29
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Brzezinka K, Altmann S, Czesnick H, Nicolas P, Gorka M, Benke E, Kabelitz T, Jähne F, Graf A, Kappel C, Bäurle I. Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling. eLife 2016; 5. [PMID: 27680998 PMCID: PMC5040591 DOI: 10.7554/elife.17061] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/25/2016] [Indexed: 12/28/2022] Open
Abstract
Plants as sessile organisms can adapt to environmental stress to mitigate its adverse effects. As part of such adaptation they maintain an active memory of heat stress for several days that promotes a more efficient response to recurring stress. We show that this heat stress memory requires the activity of the FORGETTER1 (FGT1) locus, with fgt1 mutants displaying reduced maintenance of heat-induced gene expression. FGT1 encodes the Arabidopsis thaliana orthologue of Strawberry notch (Sno), and the protein globally associates with the promoter regions of actively expressed genes in a heat-dependent fashion. FGT1 interacts with chromatin remodelers of the SWI/SNF and ISWI families, which also display reduced heat stress memory. Genomic targets of the BRM remodeler overlap significantly with FGT1 targets. Accordingly, nucleosome dynamics at loci with altered maintenance of heat-induced expression are affected in fgt1. Together, our results suggest that by modulating nucleosome occupancy, FGT1 mediates stress-induced chromatin memory. DOI:http://dx.doi.org/10.7554/eLife.17061.001 In nature, plant growth is often limited by unfavourable conditions or disease. Plants have thus evolved sophisticated mechanisms to adapt to such stresses. In fact, brief exposure to stress can prime plants to be better prepared for a future stress following a period without stress. However, the molecular basis of this memory-like phenomenon is poorly understood. Now, Brzezinka, Altmann et al. have used priming by heat stress as a model to dissect the memory of environmental stresses in thale cress, Arabidopsis thaliana. First, a library of mutant plants were tested to identify a gene that is specifically required for heat stress memory but not for the initial responses to heat. Brzezinka, Altmann et al. identified one such gene and termed it FORGETTER1 (or FGT1 for short). Further experiments then revealed that the FGT1 protein binds directly to a specific class of heat-inducible genes that are relevant for heat stress memory. Brzezinka, Altmann et al. propose that the FGT1 protein makes sure that the heat-inducible genes are always accessible and active by modifying the way the DNA containing these genes is packaged. DNA is wrapped around protein complexes called nucleosomes and depending on how tightly the DNA of a gene is wrapped makes it more or less easy to activate the gene. In agreement with this model, FGT1 does interact with proteins that can reposition nucleosomes and leave the DNA more loosely packaged. Also, the fact that plants that lack a working FGT1 gene repackage the DNA of memory-related genes too early after experiencing heat stress provides further support for the model. Together these findings could lead to new approaches for breeding programmes to improve stress tolerance in crop plants. One future challenge will be to find out whether memories involving nucleosomes are also made in response to other stressful conditions, such as attack by pests and disease. DOI:http://dx.doi.org/10.7554/eLife.17061.002
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Affiliation(s)
- Krzysztof Brzezinka
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Simone Altmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Hjördis Czesnick
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Philippe Nicolas
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michal Gorka
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Eileen Benke
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Tina Kabelitz
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Felix Jähne
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Alexander Graf
- Max-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Gene-regulatory networks controlling inflorescence and flower development in Arabidopsis thaliana. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:95-105. [PMID: 27487457 DOI: 10.1016/j.bbagrm.2016.07.014] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 07/21/2016] [Accepted: 07/22/2016] [Indexed: 11/23/2022]
Abstract
Reproductive development in plants is controlled by complex and intricate gene-regulatory networks of transcription factors. These networks integrate the information from endogenous, hormonal and environmental regulatory pathways. Many of the key players have been identified in Arabidopsis and other flowering plant species, and their interactions and molecular modes of action are being elucidated. An emerging theme is that there is extensive crosstalk between different pathways, which can be accomplished at the molecular level by modulation of transcription factor activity or of their downstream targets. In this review, we aim to summarize current knowledge on transcription factors and epigenetic regulators that control basic developmental programs during inflorescence and flower morphogenesis in the model plant Arabidopsis thaliana. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Zhang Y, Zheng L, Hong JH, Gong X, Zhou C, Pérez-Pérez JM, Xu J. TOPOISOMERASE1α Acts through Two Distinct Mechanisms to Regulate Stele and Columella Stem Cell Maintenance. PLANT PHYSIOLOGY 2016; 171:483-93. [PMID: 26969721 PMCID: PMC4854680 DOI: 10.1104/pp.15.01754] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/10/2016] [Indexed: 05/11/2023]
Abstract
TOPOISOMERASE1 (TOP1), which releases DNA torsional stress generated during replication through its DNA relaxation activity, plays vital roles in animal and plant development. In Arabidopsis (Arabidopsis thaliana), TOP1 is encoded by two paralogous genes (TOP1α and TOP1β), of which TOP1α displays specific developmental functions that are critical for the maintenance of shoot and floral stem cells. Here, we show that maintenance of two different populations of root stem cells is also dependent on TOP1α-specific developmental functions, which are exerted through two distinct novel mechanisms. In the proximal root meristem, the DNA relaxation activity of TOP1α is critical to ensure genome integrity and survival of stele stem cells (SSCs). Loss of TOP1α function triggers DNA double-strand breaks in S-phase SSCs and results in their death, which can be partially reversed by the replenishment of SSCs mediated by ETHYLENE RESPONSE FACTOR115 In the quiescent center and root cap meristem, TOP1α is epistatic to RETINOBLASTOMA-RELATED (RBR) in the maintenance of undifferentiated state and the number of columella stem cells (CSCs). Loss of TOP1α function in either wild-type or RBR RNAi plants leads to differentiation of CSCs, whereas overexpression of TOP1α mimics and further enhances the effect of RBR reduction that increases the number of CSCs Taken together, these findings provide important mechanistic insights into understanding stem cell maintenance in plants.
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Affiliation(s)
- Yonghong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Lanlan Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Jing Han Hong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Ximing Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Chun Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - José Manuel Pérez-Pérez
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
| | - Jian Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China (Y.Z., L.Z., C.Z.);Department of Biological Sciences and NUS Centre for BioImaging Sciences, National University of Singapore, Singapore 117543 (J.H.H., X.G., J.X.); andInstituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain (J.M.P.-P.)
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Abstract
Auxin is arguably the most important signaling molecule in plants, and the last few decades have seen remarkable breakthroughs in understanding its production, transport, and perception. Recent investigations have focused on transcriptional responses to auxin, providing novel insight into the functions of the domains of key transcription regulators in responses to the hormonal cue and prominently implicating chromatin regulation in these responses. In addition, studies are beginning to identify direct targets of the auxin-responsive transcription factors that underlie auxin modulation of development. Mechanisms to tune the response to different auxin levels are emerging, as are first insights into how this single hormone can trigger diverse responses. Key unanswered questions center on the mechanism for auxin-directed transcriptional repression and the identity of additional determinants of auxin response specificity. Much of what has been learned in model plants holds true in other species, including the earliest land plants.
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Affiliation(s)
- Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
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Iglesias FM, Cerdán PD. Maintaining Epigenetic Inheritance During DNA Replication in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:38. [PMID: 26870059 PMCID: PMC4735446 DOI: 10.3389/fpls.2016.00038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 01/11/2016] [Indexed: 05/18/2023]
Abstract
Biotic and abiotic stresses alter the pattern of gene expression in plants. Depending on the frequency and duration of stress events, the effects on the transcriptional state of genes are "remembered" temporally or transmitted to daughter cells and, in some instances, even to offspring (transgenerational epigenetic inheritance). This "memory" effect, which can be found even in the absence of the original stress, has an epigenetic basis, through molecular mechanisms that take place at the chromatin and DNA level but do not imply changes in the DNA sequence. Many epigenetic mechanisms have been described and involve covalent modifications on the DNA and histones, such as DNA methylation, histone acetylation and methylation, and RNAi dependent silencing mechanisms. Some of these chromatin modifications need to be stable through cell division in order to be truly epigenetic. During DNA replication, histones are recycled during the formation of the new nucleosomes and this process is tightly regulated. Perturbations to the DNA replication process and/or the recycling of histones lead to epigenetic changes. In this mini-review, we discuss recent evidence aimed at linking DNA replication process to epigenetic inheritance in plants.
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Affiliation(s)
| | - Pablo D. Cerdán
- Fundación Instituto Leloir, IIBBA-CONICET Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires Buenos Aires, Argentina
- *Correspondence: Pablo D. Cerdán,
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34
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Gaillochet C, Lohmann JU. The never-ending story: from pluripotency to plant developmental plasticity. Development 2015; 142:2237-49. [PMID: 26130755 PMCID: PMC4510588 DOI: 10.1242/dev.117614] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Plants are sessile organisms, some of which can live for over a thousand years. Unlike most animals, plants employ a post-embryonic mode of development driven by the continuous activity of pluripotent stem cells. Consequently, plants are able to initiate new organs over extended periods of time, and many species can readily replace lost body structures by de novo organogenesis. Classical studies have also shown that plant tissues have a remarkable capacity to undergo de-differentiation and proliferation in vitro, highlighting the fact that plant cell fate is highly plastic. This suggests that the mechanisms regulating fate transitions must be continuously active in most plant cells and that the control of cellular pluripotency lies at the core of diverse developmental programs. Here, we review how pluripotency is established in plant stem cell systems, how it is maintained during development and growth and re-initiated during regeneration, and how these mechanisms eventually contribute to the amazing developmental plasticity of plants.
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Affiliation(s)
- Christophe Gaillochet
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, University of Heidelberg, Heidelberg, 69120, Germany
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35
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Cao X, He Z, Guo L, Liu X. Epigenetic Mechanisms Are Critical for the Regulation of WUSCHEL Expression in Floral Meristems. PLANT PHYSIOLOGY 2015; 168:1189-96. [PMID: 25829464 PMCID: PMC4528737 DOI: 10.1104/pp.15.00230] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/25/2015] [Indexed: 05/04/2023]
Abstract
The floral meristem (FM), which develops from the inflorescence meristem upon completion of the floral transition, terminates after producing a defined number of floral organs. This is in contrast to the shoot apical meristem, which is active throughout the entire life span of plants. WUSCHEL (WUS) encodes a homeodomain-containing protein and plays a critical role in shoot apical meristem, inflorescence meristem, and FM establishment and maintenance as well as FM determinacy. Although many genes have been implicated in FM determinacy through the regulation of WUS expression, precisely how these genes are coordinated to regulate WUS and consequently dictate FM fate remains unclear. Emerging lines of evidence indicate that epigenetic mechanisms, such as histone modification, chromatin remodeling, noncoding RNAs, and DNA methylation, play vital roles in meristem maintenance and termination. Here, recent findings demonstrating the involvement of the epigenetic network in the regulation of WUS expression in the context of FM determinacy are summarized and discussed.
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Affiliation(s)
- Xiuwei Cao
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China (X.C., Z.H., L.G., X.L.); andCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (X.C., Z.H.)
| | - Zishan He
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China (X.C., Z.H., L.G., X.L.); andCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (X.C., Z.H.)
| | - Lin Guo
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China (X.C., Z.H., L.G., X.L.); andCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (X.C., Z.H.)
| | - Xigang Liu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China (X.C., Z.H., L.G., X.L.); andCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (X.C., Z.H.)
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36
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Ashour ME, Atteya R, El-Khamisy SF. Topoisomerase-mediated chromosomal break repair: an emerging player in many games. Nat Rev Cancer 2015; 15:137-51. [PMID: 25693836 DOI: 10.1038/nrc3892] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The mammalian genome is constantly challenged by exogenous and endogenous threats. Although much is known about the mechanisms that maintain DNA and RNA integrity, we know surprisingly little about the mechanisms that underpin the pathology and tissue specificity of many disorders caused by defective responses to DNA or RNA damage. Of the different types of endogenous damage, protein-linked DNA breaks (PDBs) are emerging as an important player in cancer development and therapy. PDBs can arise during the abortive activity of DNA topoisomerases, a class of enzymes that modulate DNA topology during several chromosomal transactions, such as gene transcription and DNA replication, recombination and repair. In this Review, we discuss the mechanisms underpinning topoisomerase-induced PDB formation and repair with a focus on their role during gene transcription and the development of tissue-specific cancers.
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Affiliation(s)
- Mohamed E Ashour
- 1] Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK. [2] Center for Genomics, Helmy Institute, Zewail City of Science and Technology, Giza 12588, Egypt
| | - Reham Atteya
- Center for Genomics, Helmy Institute, Zewail City of Science and Technology, Giza 12588, Egypt
| | - Sherif F El-Khamisy
- 1] Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK. [2] Center for Genomics, Helmy Institute, Zewail City of Science and Technology, Giza 12588, Egypt
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37
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Sun B, Ito T. Regulation of floral stem cell termination in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2015; 6:17. [PMID: 25699061 PMCID: PMC4313600 DOI: 10.3389/fpls.2015.00017] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 01/08/2015] [Indexed: 05/06/2023]
Abstract
In Arabidopsis, floral stem cells are maintained only at the initial stages of flower development, and they are terminated at a specific time to ensure proper development of the reproductive organs. Floral stem cell termination is a dynamic and multi-step process involving many transcription factors, chromatin remodeling factors and signaling pathways. In this review, we discuss the mechanisms involved in floral stem cell maintenance and termination, highlighting the interplay between transcriptional regulation and epigenetic machinery in the control of specific floral developmental genes. In addition, we discuss additional factors involved in floral stem cell regulation, with the goal of untangling the complexity of the floral stem cell regulatory network.
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Affiliation(s)
- Bo Sun
- Temasek Life Sciences Laboratory, 1 Research Link, National University of SingaporeSingapore
| | - Toshiro Ito
- Temasek Life Sciences Laboratory, 1 Research Link, National University of SingaporeSingapore
- Department of Biological Sciences, National University of SingaporeSingapore
- *Correspondence: Toshiro Ito, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore; Department of Biological Sciences, National University of Singapore, Singapore 117543, Republic of Singapore e-mail:
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