101
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Xu C, Tian J, Mo B. siRNA-mediated DNA methylation and H3K9 dimethylation in plants. Protein Cell 2013; 4:656-63. [PMID: 23943321 DOI: 10.1007/s13238-013-3052-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 07/04/2013] [Indexed: 12/25/2022] Open
Abstract
Heterochromatic siRNAs regulate transcriptional gene silencing by inducing DNA methylation and histone H3K9 dimethylation. Recent advances have revealed the distinct phases involved in siRNA mediated silencing pathway, although the precise functions of a number of factors remain undesignated, putative mechanisms for the connection between DNA and histone methylation have been investigated, and much effort has been invested to understand the biological functions of siRNA-mediated epigenetic modification. In this review, we summarize the mechanism of siRNA-mediated epigenetic modification, which involves the production of siRNA and the recruitments of DNA and histone methytransferases to the target sequences assisted by complementary pairing between 24-nt siRNAs and nascent scaffold RNAs, the roles of siRNA-mediated epigenetic modification in maintaining genome stability and regulating gene expression have been discussed, newly identified players of the siRNA mediated silencing pathway have also been introduced.
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Affiliation(s)
- Chi Xu
- College of Life Science, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Jing Tian
- College of Life Science, Shenzhen Key Laboratory of Marine Biological Resources and Ecological Environment, Shenzhen University, Shenzhen, 518060, China
| | - Beixin Mo
- College of Life Science, Shenzhen Key Laboratory of Microbial Genetic Engineering, Shenzhen University, Shenzhen, 518060, China.
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102
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Sani E, Herzyk P, Perrella G, Colot V, Amtmann A. Hyperosmotic priming of Arabidopsis seedlings establishes a long-term somatic memory accompanied by specific changes of the epigenome. Genome Biol 2013; 14:R59. [PMID: 23767915 PMCID: PMC3707022 DOI: 10.1186/gb-2013-14-6-r59] [Citation(s) in RCA: 210] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 06/14/2013] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND In arid and semi-arid environments, drought and soil salinity usually occur at the beginning and end of a plant's life cycle, offering a natural opportunity for the priming of young plants to enhance stress tolerance in mature plants. Chromatin marks, such as histone modifications, provide a potential molecular mechanism for priming plants to environmental stresses, but whether transient exposure of seedlings to hyperosmotic stress leads to chromatin changes that are maintained throughout vegetative growth remains unclear. RESULTS We have established an effective protocol for hyperosmotic priming in the model plant Arabidopsis, which includes a transient mild salt treatment of seedlings followed by an extensive period of growth in control conditions. Primed plants are identical to non-primed plants in growth and development, yet they display reduced salt uptake and enhanced drought tolerance after a second stress exposure. ChIP-seq analysis of four histone modifications revealed that the priming treatment altered the epigenomic landscape; the changes were small but they were specific for the treated tissue, varied in number and direction depending on the modification, and preferentially targeted transcription factors. Notably, priming leads to shortening and fractionation of H3K27me3 islands. This effect fades over time, but is still apparent after a ten day growth period in control conditions. Several genes with priming-induced differences in H3K27me3 showed altered transcriptional responsiveness to the second stress treatment. CONCLUSION Experience of transient hyperosmotic stress by young plants is stored in a long-term somatic memory comprising differences of chromatin status, transcriptional responsiveness and whole plant physiology.
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103
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Lu Z, Huang X, Ouyang Y, Yao J. Genome-wide identification, phylogenetic and co-expression analysis of OsSET gene family in rice. PLoS One 2013; 8:e65426. [PMID: 23762371 PMCID: PMC3676427 DOI: 10.1371/journal.pone.0065426] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 04/23/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND SET domain is responsible for the catalytic activity of histone lysine methyltransferases (HKMTs) during developmental process. Histone lysine methylation plays a crucial and diverse regulatory function in chromatin organization and genome function. Although several SET genes have been identified and characterized in plants, the understanding of OsSET gene family in rice is still very limited. METHODOLOGY/PRINCIPAL FINDINGS In this study, a systematic analysis was performed and revealed the presence of at least 43 SET genes in rice genome. Phylogenetic and structural analysis grouped SET proteins into five classes, and supposed that the domains out of SET domain were significant for the specific of histone lysine methylation, as well as the recognition of methylated histone lysine. Based on the global microarray, gene expression profile revealed that the transcripts of OsSET genes were accumulated differentially during vegetative and reproductive developmental stages and preferentially up or down-regulated in different tissues. Cis-elements identification, co-expression analysis and GO analysis of expression correlation of 12 OsSET genes suggested that OsSET genes might be involved in cell cycle regulation and feedback. CONCLUSIONS/SIGNIFICANCE This study will facilitate further studies on OsSET family and provide useful clues for functional validation of OsSETs.
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Affiliation(s)
- Zhanhua Lu
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, PR China
| | - Xiaolong Huang
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, PR China
| | - Yidan Ouyang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, PR China
| | - Jialing Yao
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, PR China
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104
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Yao X, Feng H, Yu Y, Dong A, Shen WH. SDG2-mediated H3K4 methylation is required for proper Arabidopsis root growth and development. PLoS One 2013; 8:e56537. [PMID: 23483879 PMCID: PMC3585709 DOI: 10.1371/journal.pone.0056537] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 01/10/2013] [Indexed: 01/25/2023] Open
Abstract
Trithorax group (TrxG) proteins are evolutionarily conserved in eukaryotes and play critical roles in transcriptional activation via deposition of histone H3 lysine 4 trimethylation (H3K4me3) in chromatin. Several Arabidopsis TrxG members have been characterized, and among them SET DOMAIN GROUP 2 (SDG2) has been shown to be necessary for global genome-wide H3K4me3 deposition. Although pleiotropic phenotypes have been uncovered in the sdg2 mutants, SDG2 function in the regulation of stem cell activity has remained largely unclear. Here, we investigate the sdg2 mutant root phenotype and demonstrate that SDG2 is required for primary root stem cell niche (SCN) maintenance as well as for lateral root SCN establishment. Loss of SDG2 results in drastically reduced H3K4me3 levels in root SCN and differentiated cells and causes the loss of auxin gradient maximum in the root quiescent centre. Elevated DNA damage is detected in the sdg2 mutant, suggesting that impaired genome integrity may also have challenged the stem cell activity. Genetic interaction analysis reveals that SDG2 and CHROMATIN ASSEMBLY FACTOR-1 act synergistically in root SCN and genome integrity maintenance but not in telomere length maintenance. We conclude that SDG2-mediated H3K4me3 plays a distinctive role in the regulation of chromatin structure and genome integrity, which are key features in pluripotency of stem cells and crucial for root growth and development.
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Affiliation(s)
- Xiaozhen Yao
- State Key Laboratory of Genetic Engineering, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Haiyang Feng
- State Key Laboratory of Genetic Engineering, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Yu Yu
- State Key Laboratory of Genetic Engineering, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Fudan University, Shanghai, PR China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, School of Life Sciences, Fudan University, Shanghai, PR China
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg Cedex, France
- * E-mail:
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105
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Gan ES, Huang J, Ito T. Functional Roles of Histone Modification, Chromatin Remodeling and MicroRNAs in Arabidopsis Flower Development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 305:115-61. [DOI: 10.1016/b978-0-12-407695-2.00003-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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106
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Zografou T, Turck F. Epigenetic Control of Flowering Time. EPIGENETIC MEMORY AND CONTROL IN PLANTS 2013. [DOI: 10.1007/978-3-642-35227-0_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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107
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Choi SM, Song HR, Han SK, Han M, Kim CY, Park J, Lee YH, Jeon JS, Noh YS, Noh B. HDA19 is required for the repression of salicylic acid biosynthesis and salicylic acid-mediated defense responses in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:135-46. [PMID: 22381007 DOI: 10.1111/j.1365-313x.2012.04977.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
To cope with a lifetime of exposure to a variety of pathogens, plants have developed exquisite and refined defense mechanisms that vary depending on the type of attacking pathogen. Defense-associated transcriptional reprogramming is a central part of plant defense mechanisms. Chromatin modification has recently been shown to be another layer of regulation for plant defense mechanisms. Here, we show that the RPD3/HDA1-class histone deacetylase HDA19 is involved in the repression of salicylic acid (SA)-mediated defense responses in Arabidopsis. Loss of HDA19 activity increased SA content and increased the expression of a group of genes required for accumulation of SA as well as pathogenesis related (PR) genes, resulting in enhanced resistance to Pseudomonas syringae. We found that HDA19 directly associates with and deacetylates histones at the PR1 and PR2 promoters. Thus, our study shows that HDA19, by modifying chromatin to a repressive state, ensures low basal expression of defense genes, such as PR1, under unchallenged conditions, as well as their proper induction without overstimulation during defense responses to pathogen attacks. Thus, the role of HDA19 might be critical in preventing unnecessary activation and self-destructive overstimulation of defense responses, allowing successful growth and development.
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Affiliation(s)
- Sun-Mee Choi
- School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
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108
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Alvarez-Venegas R, Avramova Z. Evolution of the PWWP-domain encoding genes in the plant and animal lineages. BMC Evol Biol 2012; 12:101. [PMID: 22734652 PMCID: PMC3457860 DOI: 10.1186/1471-2148-12-101] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Accepted: 06/06/2012] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Conserved domains are recognized as the building blocks of eukaryotic proteins. Domains showing a tendency to occur in diverse combinations ('promiscuous' domains) are involved in versatile architectures in proteins with different functions. Current models, based on global-level analyses of domain combinations in multiple genomes, have suggested that the propensity of some domains to associate with other domains in high-level architectures increases with organismal complexity. Alternative models using domain-based phylogenetic trees propose that domains have become promiscuous independently in different lineages through convergent evolution and are, thus, random with no functional or structural preferences. Here we test whether complex protein architectures have occurred by accretion from simpler systems and whether the appearance of multidomain combinations parallels organismal complexity. As a model, we analyze the modular evolution of the PWWP domain and ask whether its appearance in combinations with other domains into multidomain architectures is linked with the occurrence of more complex life-forms. Whether high-level combinations of domains are conserved and transmitted as stable units (cassettes) through evolution is examined in the genomes of plant or metazoan species selected for their established position in the evolution of the respective lineages. RESULTS Using the domain-tree approach, we analyze the evolutionary origins and distribution patterns of the promiscuous PWWP domain to understand the principles of its modular evolution and its existence in combination with other domains in higher-level protein architectures. We found that as a single module the PWWP domain occurs only in proteins with a limited, mainly, species-specific distribution. Earlier, it was suggested that domain promiscuity is a fast-changing (volatile) feature shaped by natural selection and that only a few domains retain their promiscuity status throughout evolution. In contrast, our data show that most of the multidomain PWWP combinations in extant multicellular organisms (humans or land plants) are present in their unicellular ancestral relatives suggesting they have been transmitted through evolution as conserved linear arrangements ('cassettes'). Among the most interesting biologically relevant results is the finding that the genes of the two plant Trithorax family subgroups (ATX1/2 and ATX3/4/5) have different phylogenetic origins. The two subgroups occur together in the earliest land plants Physcomitrella patens and Selaginella moellendorffii. CONCLUSION Gain/loss of a single PWWP domain is observed throughout evolution reflecting dynamic lineage- or species-specific events. In contrast, higher-level protein architectures involving the PWWP domain have survived as stable arrangements driven by evolutionary descent. The association of PWWP domains with the DNA methyltransferases in O. tauri and in the metazoan lineage seems to have occurred independently consistent with convergent evolution. Our results do not support models wherein more complex protein architectures involving the PWWP domain occur with the appearance of more evolutionarily advanced life forms.
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Affiliation(s)
- Raúl Alvarez-Venegas
- Department of Genetic Engineering, Centro de Investigación y de Estudios Avanzados, Unidad Irapuato, Irapuato Gto., 36821, Mexico
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109
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Yun JY, Tamada Y, Kang YE, Amasino RM. Arabidopsis trithorax-related3/SET domain GROUP2 is required for the winter-annual habit of Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2012; 53:834-46. [PMID: 22378382 PMCID: PMC3345368 DOI: 10.1093/pcp/pcs021] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 02/21/2012] [Indexed: 05/18/2023]
Abstract
The winter-annual habit of Arabidopsis thaliana requires active alleles of flowering locus C (FLC), which encodes a potent flowering repressor, and FRIGIDA (FRI), an activator of FLC. FLC activation by FRI is accompanied by an increase in specific histone modifications, such as tri-methylation of histone H3 at lysine 4 (H3K4me3), and requires three H3K4 methyltransferases, the Drosophila Trithorax-class Arabidopsis trithorax1 (ATX1) and ATX2, and yeast Set1-class ATX-related7/set domain group25 (ATXR7/SDG25). However, lesions in all of these genes failed to suppress the enhanced FLC expression caused by FRI completely, suggesting that another H3K4 methyltransferase may participate in the FLC activation. Here, we show that ATXR3/SDG2, which is a member of a novel class of H3K4 methyltransferases, also contributes to FLC activation. An ATXR3 lesion suppressed the enhanced FLC expression and delayed flowering caused by an active allele of FRI in non-vernalized plants. The decrease in FLC expression in atxr3 mutants was accompanied by reduced H3K4me3 levels at FLC chromatin. We also found that the rapid flowering of atxr3 was epistatic to that of atxr7, suggesting that ATXR3 functions in FLC activation in sequence with ATXR7. Our results indicate that the novel-class H3K4 methyltransferase, ATXR3, is a transcriptional activator that plays a role in the FLC activation and establishing the winter-annual habit. In addition, ATXR3 also contributes to the activation of other FLC clade members, such as flowering locus M/MADS affecting flowering1 (FLM/MAF1) and MAF5, at least partially explaining the ATXR3 function in delayed flowering caused by non-inductive photoperiods.
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Affiliation(s)
- Jae-Young Yun
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706-1544, USA
- These authors contributed equally to this work
| | - Yosuke Tamada
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706-1544, USA
- National Institute for Basic Biology, Okazaki, Aichi, 444-8585 Japan
- School of Life Science, Graduate University of Advanced Studies, Okazaki, Aichi, 444-8585 Japan
- These authors contributed equally to this work
| | - Ye Eun Kang
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706-1544, USA
| | - Richard M. Amasino
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706-1544, USA
- *Corresponding author: E-mail, ; Fax, +1-608-262-3453
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110
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Buzas DM, Tamada Y, Kurata T. FLC: a hidden polycomb response element shows up in silence. PLANT & CELL PHYSIOLOGY 2012; 53:785-793. [PMID: 22107881 DOI: 10.1093/pcp/pcr163] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A sizeable fraction of eukaryotic genomes is regulated by Polycomb group (PcG) and trithorax group (trxG) proteins, which play key roles in epigenetic repression and activation, respectively. In Drosophila melanogaster, homeotic genes are well-documented PcG targets; they are known to contain cis-acting elements termed Polycomb response elements (PREs), which bind PcG proteins and satisfy three defined criteria, and also often contain binding sites for the trithorax (trx) protein. However, the presence of PREs, or an alternative mode for PcG/trxG interaction with the genome, has not been well documented outside Drosophila. In Arabidopsis thaliana, PcG/trxG regulation has been studied extensively for the flowering repressor gene FLOWERING LOCUS C (FLC). Here we evaluate how PRE-like activities that reside within the FLC locus may satisfy the defined Drosophila criteria, by analyzing four FLC transcription states. When the FLC locus is not transcribed, the intrinsic PcG recruitment ability of the coding region can be attributed to two redundant cis-acting elements (Modules IIA and IIB). When FLC is highly expressed, trxG recruitment is to a region overlapping the transcription start site (Module I). Exposure to prolonged cold converts the active FLC state into a repressed state that is maintained after the cold period finishes. These two additional transcriptional states also rely on the same three modules for PcG/trxG regulation. We conclude that each of Modules I, IIA and IIB partially fulfills the PRE function criteria, and that together they represent the functional FLC PRE, which differs structurally from canonical PREs in Drosophila.
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Affiliation(s)
- Diana Mihaela Buzas
- Plant Reproductive Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192 Japan.
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111
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Hayot CM, Forouzesh E, Goel A, Avramova Z, Turner JA. Viscoelastic properties of cell walls of single living plant cells determined by dynamic nanoindentation. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:2525-40. [PMID: 22291130 PMCID: PMC3346220 DOI: 10.1093/jxb/err428] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 11/29/2011] [Accepted: 12/05/2011] [Indexed: 05/18/2023]
Abstract
Plant development results from controlled cell divisions, structural modifications, and reorganizations of the cell wall. Thereby, regulation of cell wall behaviour takes place at multiple length scales involving compositional and architectural aspects in addition to various developmental and/or environmental factors. The physical properties of the primary wall are largely determined by the nature of the complex polymer network, which exhibits time-dependent behaviour representative of viscoelastic materials. Here, a dynamic nanoindentation technique is used to measure the time-dependent response and the viscoelastic behaviour of the cell wall in single living cells at a micron or sub-micron scale. With this approach, significant changes in storage (stiffness) and loss (loss of energy) moduli are captured among the tested cells. The results reveal hitherto unknown differences in the viscoelastic parameters of the walls of same-age similarly positioned cells of the Arabidopsis ecotypes (Col 0 and Ws 2). The technique is also shown to be sensitive enough to detect changes in cell wall properties in cells deficient in the activity of the chromatin modifier ATX1. Extensive computational modelling of the experimental measurements (i.e. modelling the cell as a viscoelastic pressure vessel) is used to analyse the influence of the wall thickness, as well as the turgor pressure, at the positions of our measurements. By combining the nanoDMA technique with finite element simulations quantifiable measurements of the viscoelastic properties of plant cell walls are achieved. Such techniques are expected to find broader applications in quantifying the influence of genetic, biological, and environmental factors on the nanoscale mechanical properties of the cell wall.
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Affiliation(s)
- Céline M. Hayot
- Mechanical and Materials Engineering, University of Nebraska-Lincoln, W342 Nebraska Hall, Lincoln, Nebraska 68588-0526, USA
| | - Elham Forouzesh
- Mechanical and Materials Engineering, University of Nebraska-Lincoln, W342 Nebraska Hall, Lincoln, Nebraska 68588-0526, USA
| | - Ashwani Goel
- Mechanical and Materials Engineering, University of Nebraska-Lincoln, W342 Nebraska Hall, Lincoln, Nebraska 68588-0526, USA
| | - Zoya Avramova
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-2118, USA
| | - Joseph A. Turner
- Mechanical and Materials Engineering, University of Nebraska-Lincoln, W342 Nebraska Hall, Lincoln, Nebraska 68588-0526, USA
- To whom correspondence should be addressed. E-mail
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112
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Zhu X, Chen C, Wang B. Phylogenetics and evolution of Trx SET genes in fully sequenced land plants. Genome 2012; 55:269-80. [PMID: 22417073 DOI: 10.1139/g2012-012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Plant Trx SET proteins are involved in H3K4 methylation and play a key role in plant floral development. Genes encoding Trx SET proteins constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. To investigate the evolutionary history of the Trx SET gene family, we made a comprehensive evolutionary analysis on this gene family from 13 major representatives of green plants. A novel clustering (here named as cpTrx clade), which included the III-1, III-2, and III-4 orthologous groups, previously resolved was identified. Our analysis showed that plant Trx proteins possessed a variety of domain organizations and gene structures among paralogs. Additional domains such as PHD, PWWP, and FYR were early integrated into primordial SET-PostSET domain organization of cpTrx clade. We suggested that the PostSET domain was lost in some members of III-4 orthologous group during the evolution of land plants. At least four classes of gene structures had been formed at the early evolutionary stage of land plants. Three intronless orphan Trx SET genes from the Physcomitrella patens (moss) were identified, and supposedly, their parental genes have been eliminated from the genome. The structural differences among evolutionary groups of plant Trx SET genes with different functions were described, contributing to the design of further experimental studies.
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Affiliation(s)
- Xinyu Zhu
- School of Life Sciences, Nantong University, Nantong, China.
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113
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Kim DH, Sung S. Environmentally coordinated epigenetic silencing of FLC by protein and long noncoding RNA components. CURRENT OPINION IN PLANT BIOLOGY 2012; 15:51-6. [PMID: 22078062 DOI: 10.1016/j.pbi.2011.10.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 10/17/2011] [Accepted: 10/19/2011] [Indexed: 05/18/2023]
Abstract
In Arabidopsis, the role of the vernalization pathway is to repress expression of a potent floral repressor, FLOWERING LOCUS C (FLC), after a sufficient period of winter cold has been perceived. Following winter, the lack of FLC expression allows unimpeded operation of the photoperiod pathway and hence rapid flowering of vernalized plants in spring via the activation of floral integrator genes. Molecular studies revealed that regulation of the key floral repressor, FLC, is under the control of the interplay between Trithorax group (TrxG)-mediated activation and Polycomb group (PcG)-mediated repression. On-off switch of genes by TrxG and PcG is an evolutionarily conserved mechanism to coordinate cellular identity in eukaryotes. Regulation of FLC by external cues provides an excellent model system to study mechanisms in which cell identity is influenced by environment. In this review, we discuss coordinated contributions by protein and long noncoding RNA components to this environmentally induced epigenetic switch of a developmental program in plants.
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Affiliation(s)
- Dong-Hwan Kim
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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114
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Tang X, Lim MH, Pelletier J, Tang M, Nguyen V, Keller WA, Tsang EWT, Wang A, Rothstein SJ, Harada JJ, Cui Y. Synergistic repression of the embryonic programme by SET DOMAIN GROUP 8 and EMBRYONIC FLOWER 2 in Arabidopsis seedlings. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:1391-404. [PMID: 22162868 PMCID: PMC3276103 DOI: 10.1093/jxb/err383] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 07/19/2011] [Accepted: 10/25/2011] [Indexed: 05/18/2023]
Abstract
The seed maturation programme occurs only during the late phase of embryo development, and repression of the maturation genes is pivotal for seedling development. However, mechanisms that repress the expression of this programme in vegetative tissues are not well understood. A genetic screen was performed for mutants that express maturation genes in leaves. Here, it is shown that mutations affecting SDG8 (SET DOMAIN GROUP 8), a putative histone methyltransferase, cause ectopic expression of a subset of maturation genes in leaves. Further, to investigate the relationship between SDG8 and the Polycomb Group (PcG) proteins, which are known to repress many developmentally important genes including seed maturation genes, double mutants were made and formation of somatic embryos was observed on mutant seedlings with mutations in both SDG8 and EMF2 (EMBRYONIC FLOWER 2). Analysis of histone methylation status at the chromatin sites of a number of maturation loci revealed a synergistic effect of emf2 and sdg8 on the deposition of the active histone mark which is the trimethylation of Lys4 on histone 3 (H3K4me3). This is consistent with high expression of these genes and formation of somatic embryos in the emf2 sdg8 double mutants. Interestingly, a double mutant of sdg8 and vrn2 (vernalization2), a paralogue of EMF2, grew and developed normally to maturity. These observations demonstrate a functional cooperative interplay between SDG8 and an EMF2-containing PcG complex in maintaining vegetative cell identity by repressing seed genes to promote seedling development. The work also indicates the functional specificities of PcG complexes in Arabidopsis.
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Affiliation(s)
- Xurong Tang
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario N5V 4T3, Canada
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Myung-Ho Lim
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario N5V 4T3, Canada
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, 150 Suin-ro, Gwonseon-gu, Suwon 441-707, Korea
| | - Julie Pelletier
- Section of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Mingjuan Tang
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario N5V 4T3, Canada
| | - Vi Nguyen
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario N5V 4T3, Canada
| | - Wilfred A. Keller
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Edward W. T. Tsang
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Aiming Wang
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario N5V 4T3, Canada
| | - Steven J. Rothstein
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - John J. Harada
- Section of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616, USA
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, Southern Crop Protection and Food Research Centre, London, Ontario N5V 4T3, Canada
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Rodríguez JL, Pascual J, Viejo M, Valledor L, Meijón M, Hasbún R, Yrei NY, Santamaría ME, Pérez M, Fernández Fraga M, Berdasco M, Rodríguez Fernández R, Cañal MJ. Basic procedures for epigenetic analysis in plant cell and tissue culture. Methods Mol Biol 2012; 877:325-341. [PMID: 22610639 DOI: 10.1007/978-1-61779-818-4_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In vitro culture is one of the most studied techniques, and it is used to study many developmental processes, especially in forestry species, because of growth timing and easy manipulation. Epigenetics has been shown as an important influence on many research analyses such as cancer in mammals and developmental processes in plants such as flowering, but regarding in vitro culture, techniques to study DNA methylation or chromatin modifications were mainly limited to identify somaclonal variation of the micropropagated material. Because in vitro culture is not only a way to generate plant material but also a bunch of differentially induced developmental processes, an approach of techniques and some research carried out to study the different changes regarding DNA methylation and chromatin and translational modifications that take place during these processes is reviewed.
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Affiliation(s)
- José L Rodríguez
- Área de Fisiología Vegetal, Departamento BOS, Facultad de Biología, Universidad de Oviedo, Oviedo, Spain.
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Kim ED, Sung S. Long noncoding RNA: unveiling hidden layer of gene regulatory networks. TRENDS IN PLANT SCIENCE 2012; 17:16-21. [PMID: 22104407 DOI: 10.1016/j.tplants.2011.10.008] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 10/24/2011] [Accepted: 10/25/2011] [Indexed: 05/19/2023]
Abstract
Long noncoding RNAs (lncRNAs) are increasingly recognized as functional regulatory components in eukaryotic gene regulation. Distinct classes of lncRNAs have been identified in eukaryotes and they play roles in various regulatory networks. Previously characterized lncRNAs include primary transcripts for small regulatory RNAs. In the era of deep sequencing, new classes of lncRNAs have emerged as potent regulatory components in gene regulation. Recent studies showed that many lncRNAs are potent cis- and trans-regulators of gene activity and they can function as scaffolds for chromatin-modifying complexes. Furthermore, differential expressions of lncRNAs suggest that transcription of lncRNAs can modulate gene activity during development and in response to external stimuli. Here, we summarize our current understanding on potential roles of lncRNAs in plants.
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Affiliation(s)
- Eun-Deok Kim
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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117
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Huang Y, Liu C, Shen WH, Ruan Y. Phylogenetic analysis and classification of the Brassica rapa SET-domain protein family. BMC PLANT BIOLOGY 2011; 11:175. [PMID: 22168908 PMCID: PMC3264562 DOI: 10.1186/1471-2229-11-175] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Accepted: 12/14/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND The SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain is an evolutionarily conserved sequence of approximately 130-150 amino acids, and constitutes the catalytic site of lysine methyltransferases (KMTs). KMTs perform many crucial biological functions via histone methylation of chromatin. Histone methylation marks are interpreted differently depending on the histone type (i.e. H3 or H4), the lysine position (e.g. H3K4, H3K9, H3K27, H3K36 or H4K20) and the number of added methyl groups (i.e. me1, me2 or me3). For example, H3K4me3 and H3K36me3 are associated with transcriptional activation, but H3K9me2 and H3K27me3 are associated with gene silencing. The substrate specificity and activity of KMTs are determined by sequences within the SET domain and other regions of the protein. RESULTS Here we identified 49 SET-domain proteins from the recently sequenced Brassica rapa genome. We performed sequence similarity and protein domain organization analysis of these proteins, along with the SET-domain proteins from the dicot Arabidopsis thaliana, the monocots Oryza sativa and Brachypodium distachyon, and the green alga Ostreococcus tauri. We showed that plant SET-domain proteins can be grouped into 6 distinct classes, namely KMT1, KMT2, KMT3, KMT6, KMT7 and S-ET. Apart from the S-ET class, which has an interrupted SET domain and may be involved in methylation of nonhistone proteins, the other classes have characteristics of histone methyltransferases exhibiting different substrate specificities: KMT1 for H3K9, KMT2 for H3K4, KMT3 for H3K36, KMT6 for H3K27 and KMT7 also for H3K4. We also propose a coherent and rational nomenclature for plant SET-domain proteins. Comparisons of sequence similarity and synteny of B. rapa and A. thaliana SET-domain proteins revealed recent gene duplication events for some KMTs. CONCLUSION This study provides the first characterization of the SET-domain KMT proteins of B. rapa. Phylogenetic analysis data allowed the development of a coherent and rational nomenclature of this important family of proteins in plants, as in animals. The results obtained in this study will provide a base for nomenclature of KMTs in other plant species and facilitate the functional characterization of these important epigenetic regulatory genes in Brassica crops.
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Affiliation(s)
- Yong Huang
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Chunlin Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg Cedex, France
| | - Ying Ruan
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
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118
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119
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Valluru R, Van den Ende W. Myo-inositol and beyond--emerging networks under stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:387-400. [PMID: 21889044 DOI: 10.1016/j.plantsci.2011.07.009] [Citation(s) in RCA: 192] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 07/18/2011] [Accepted: 07/19/2011] [Indexed: 05/18/2023]
Abstract
Myo-inositol is a versatile compound that generates diversified derivatives upon phosphorylation by lipid-dependent and -independent pathways. Phosphatidylinositols form one such group of myo-inositol derivatives that act both as membrane structural lipid molecules and as signals. The significance of these compounds lies in their dual functions as signals as well as key metabolites under stress. Several stress- and non-stress related pathways regulated by phosphatidylinositol isoforms and associated enzymes, kinases and phosphatases, appear to function in parallel to coordinatively adapt growth and stress responses in plants. Recent evidence also postulates their crucial roles in nuclear functions as they interact with the key players of chromatin structure, yet other nuclear functions remain largely unknown. Phosphatidylinositol monophosphate 5-kinase interacts with and represses a cytosolic neutral invertase, a key enzyme of sugar metabolism suggesting a crosstalk between lipid and sugar signaling. Besides phosphatidylinositol, myo-inositol derived galactinol and associated raffinose-family oligosaccharides are emerging as antioxidants and putative signaling compounds too. Importantly, myo-inositol polyphosphate 5-phosphatase (5PTase) acts, depending on sugar status, as a positive or negative regulator of a global energy sensor, SnRK1. This implies that both myo-inositol- and sugar-derived (e.g. trehalose 6-phosphate) molecules form part of a broad regulatory network with SnRK1 as the central regulator. Recently, it was shown that the transcription factor bZIP11 also takes part in this network. Moreover, a functional coordination between neutral invertase and hexokinase is emerging as a sweet network that contributes to oxidative stress homeostasis in plants. In this review, we focus on myo-inositol, its direct and more downstream derivatives (galactinol, raffinose), and the contribution of their associated networks to plant stress tolerance.
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Affiliation(s)
- Ravi Valluru
- Ecophysiology of Plants Under Environmental Stress, INRA-SUPAGRO, Institute of Integrative Plant Biology, 2 Place Viala, Montpellier, France
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120
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Berr A, Shafiq S, Shen WH. Histone modifications in transcriptional activation during plant development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:567-76. [PMID: 21777708 DOI: 10.1016/j.bbagrm.2011.07.001] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 06/30/2011] [Accepted: 07/06/2011] [Indexed: 12/24/2022]
Abstract
In eukaryotic cell nuclei, chromatin states dictated by different combinations of post-translational modifications of histones, such as acetylation, methylation and monoubiquitination of lysine residues, are part of the multitude of epigenomes involved in the fine-tuning of all genetic functions and in particular transcription. During the past decade, an increasing number of 'writers', 'readers' and 'erasers' of histone modifications have been identified. Characterization of these factors in Arabidopsis has unraveled their pivotal roles in the regulation of essential processes, such as floral transition, cell differentiation, gametogenesis, and plant response/adaptation to environmental stresses. In this review we focus on histone modification marks associated with transcriptional activation to highlight current knowledge on Arabidopsis 'writers', 'readers' and 'erasers' of histone modifications and to discuss recent findings on molecular mechanisms of integration of histone modifications with the RNA polymerase II transcriptional machinery during transcription of the flowering repressor gene FLC.
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Affiliation(s)
- Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg CEDEX, France
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121
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Thorstensen T, Grini PE, Aalen RB. SET domain proteins in plant development. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:407-20. [PMID: 21664308 DOI: 10.1016/j.bbagrm.2011.05.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 05/08/2011] [Accepted: 05/10/2011] [Indexed: 10/18/2022]
Abstract
Post-translational methylation of lysine residues on histone tails is an epigenetic modification crucial for regulation of chromatin structure and gene expression in eukaryotes. The majority of the histone lysine methyltransferases (HKMTases) conferring such modifications are proteins with a conserved SET domain responsible for the enzymatic activity. The SET domain proteins in the model plant Arabidopsis thaliana can be assigned to evolutionarily conserved classes with different specificities allowing for different outcomes on chromatin structure. Here we review the present knowledge of the biochemical and biological functions of plant SET domain proteins in developmental processes. This article is part of a Special Issue entitled: Epigenetic control of cellular and developmental processes in plants.
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Affiliation(s)
- Tage Thorstensen
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
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122
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Xia H, Yandeau-Nelson M, Thompson DB, Guiltinan MJ. Deficiency of maize starch-branching enzyme I results in altered starch fine structure, decreased digestibility and reduced coleoptile growth during germination. BMC PLANT BIOLOGY 2011; 11:95. [PMID: 21599988 PMCID: PMC3245629 DOI: 10.1186/1471-2229-11-95] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 05/21/2011] [Indexed: 05/17/2023]
Abstract
BACKGROUND Two distinct starch branching enzyme (SBE) isoforms predate the divergence of monocots and dicots and have been conserved in plants since then. This strongly suggests that both SBEI and SBEII provide unique selective advantages to plants. However, no phenotype for the SBEI mutation, sbe1a, had been previously observed. To explore this incongruity the objective of the present work was to characterize functional and molecular phenotypes of both sbe1a and wild-type (Wt) in the W64A maize inbred line. RESULTS Endosperm starch granules from the sbe1a mutant were more resistant to digestion by pancreatic α-amylase, and the sbe1a mutant starch had an altered branching pattern for amylopectin and amylose. When kernels were germinated, the sbe1a mutant was associated with shorter coleoptile length and higher residual starch content, suggesting that less efficient starch utilization may have impaired growth during germination. CONCLUSIONS The present report documents for the first time a molecular phenotype due to the absence of SBEI, and suggests strongly that it is associated with altered physiological function of the starch in vivo. We believe that these results provide a plausible rationale for the conservation of SBEI in plants in both monocots and dicots, as greater seedling vigor would provide an important survival advantage when resources are limited.
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Affiliation(s)
- Huan Xia
- MARS Petcare US, 315 Cool Springs Boulevard, Franklin, Tennessee 37067, USA
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania 16802-2504, USA
| | - Marna Yandeau-Nelson
- Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011-3260, USA
- Department of Horticulture, The Pennsylvania State University, University Park, Pennsylvania 16802-5807, USA
| | - Donald B Thompson
- Department of Food Science, The Pennsylvania State University, University Park, Pennsylvania 16802-2504, USA
| | - Mark J Guiltinan
- Department of Horticulture, The Pennsylvania State University, University Park, Pennsylvania 16802-5807, USA
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123
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Feng S, Jacobsen SE. Epigenetic modifications in plants: an evolutionary perspective. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:179-86. [PMID: 21233005 PMCID: PMC3097131 DOI: 10.1016/j.pbi.2010.12.002] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 12/04/2010] [Accepted: 12/15/2010] [Indexed: 05/21/2023]
Abstract
Plant genomes are modified by an array of epigenetic marks that help regulate plant growth and reproduction. Although plants share many epigenetic features with animals and fungi, some epigenetic marks are unique to plants. In different organisms, the same epigenetic mark can play different roles and/or similar functions can be carried out by different epigenetic marks. Furthermore, while the enzymatic systems responsible for generating or eliminating epigenetic marks are often conserved, there are also cases where they are quite divergent between plants and other organisms. DNA methylation and methylation of histone tails on the lysine 4, 9, and 27 positions are among the best characterized epigenetic marks in both plants and animals. Recent studies have greatly enhanced our knowledge about the pattern of these marks in various genomes and provided insights into how they are established and maintained and how they function. This review focuses on the conservation and divergence of the pathways that mediate these four types of epigenetic marks.
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Affiliation(s)
- Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
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124
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Deal RB, Henikoff S. Histone variants and modifications in plant gene regulation. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:116-22. [PMID: 21159547 PMCID: PMC3093162 DOI: 10.1016/j.pbi.2010.11.005] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 11/17/2010] [Indexed: 05/19/2023]
Abstract
Genomes are packaged by complexing DNA with histone proteins, which provides an opportunity to regulate gene expression by dynamically impeding access of transcriptional regulatory proteins and RNA polymerases to DNA. The incorporation of histone variants into nucleosomes and addition of post-translational modifications to histones can alter the physical properties of nucleosomes and thereby serve as a mechanism for regulating DNA exposure. Chromatin-based gene regulation has profound effects on developmental processes including regulation of the vegetative to reproductive transition, as well as responses to pathogens and abiotic factors. Incorporation of the histone variant H2A.Z and methylation of histone H3 lysine residues 4 and 27 have emerged as key elements in the regulation of genes involved in each of these processes.
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Affiliation(s)
- Roger B. Deal
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA 98109, USA
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125
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Chen X, Hu Y, Zhou DX. Epigenetic gene regulation by plant Jumonji group of histone demethylase. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1809:421-6. [PMID: 21419882 DOI: 10.1016/j.bbagrm.2011.03.004] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 03/07/2011] [Accepted: 03/10/2011] [Indexed: 12/22/2022]
Abstract
Histone methylation plays an important role in epigenetic regulation of gene expression. Reversible methylation/demethylation of several histone lysine residues is mediated by distinct histone methyltransferases and histone demethylases. Jumonji proteins have been characterized to be involved in histone demethylation. Plant Jumonji homologues are found to have important functions in epigenetic processes, gene expression and plant development and to play an essential role in interplay between histone modifications and DNA methylation. This article is part of a Special Issue entitled: Epigenetic Control of cellular and developmental processes in plants.
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Affiliation(s)
- Xiangsong Chen
- National Key Laboratory for Crop genetic Improvement, Huazhong Agricultural University, Wuhan, China
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126
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Crevillén P, Dean C. Regulation of the floral repressor gene FLC: the complexity of transcription in a chromatin context. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:38-44. [PMID: 20884277 DOI: 10.1016/j.pbi.2010.08.015] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 08/30/2010] [Indexed: 05/20/2023]
Abstract
The genetic pathways regulating the floral transition in Arabidopsis are becoming increasingly well understood. The ease with which mutant phenotypes can be quantified has led to many suppressor screens and the molecular identification of the underlying genes. One focus has been on the pathways that regulate the gene encoding the floral repressor FLC. This has revealed a set of antagonistic pathways comprising evolutionary conserved activities that link chromatin regulation, transcription level and co-transcriptional RNA metabolism. Here we discuss our current understanding of the transcriptional activation of FLC, how different activities are integrated at this one locus and why FLC regulation seems so sensitive to mutation in these conserved gene regulatory pathways.
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Affiliation(s)
- Pedro Crevillén
- Department of Cell & Developmental Biology, John Innes Centre, Norwich NR4 7UH, UK
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127
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Ndamukong I, Lapko H, Cerny RL, Avramova Z. A cytoplasm-specific activity encoded by the Trithorax-like ATX1 gene. Nucleic Acids Res 2011; 39:4709-18. [PMID: 21245040 PMCID: PMC3113559 DOI: 10.1093/nar/gkq1300] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Eukaryotes produce multiple products from a single gene locus by alternative splicing, translation or promoter usage as mechanisms expanding the complexity of their proteome. Trithorax proteins, including the Arabidopsis Trithorax-like protein ATX1, are histone modifiers regulating gene activity. Here, we report that a novel member of the Trithorax family has a role unrelated to chromatin. It is encoded from an internal promoter in the ATX1 locus as an isoform containing only the SET domain (soloSET). It is located exclusively in the cytoplasm and its substrate is the elongation factor 1A (EF1A). Loss of SET, but not of the histone modifying ATX1-SET activity, affects cytoskeletal actin bundling illustrating that the two isoforms have distinct functions in Arabidopsis cells.
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Affiliation(s)
- Ivan Ndamukong
- School of Biological Sciences, University of Nebraska, Lincoln, Nebraska, USA
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128
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Ding Y, Avramova Z, Fromm M. Two distinct roles of ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1) at promoters and within transcribed regions of ATX1-regulated genes. THE PLANT CELL 2011; 23:350-63. [PMID: 21266657 PMCID: PMC3051232 DOI: 10.1105/tpc.110.080150] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Revised: 12/15/2010] [Accepted: 12/22/2010] [Indexed: 05/18/2023]
Abstract
The Arabidopsis thaliana trithorax-like protein, ATX1, shares common structural domains, has similar histone methyltransferase (HMT) activity, and belongs in the same phylogenetic subgroup as its animal counterparts. Most of our knowledge of the role of HMTs in trimethylating lysine 4 of histone H3 (H3K4me3) in transcriptional regulation comes from studies of yeast and mammalian homologs. Little is known about the mechanism by which ATX1, or any other HMT of plant origin, affects transcription. Here, we provide insights into how ATX1 influences transcription at regulated genes, playing two distinct roles. At promoters, ATX1 is required for TATA binding protein (TBP) and RNA Polymerase II (Pol II) recruitment. In a subsequent event, ATX1 is recruited by a phosphorylated form of Pol II to the +300-bp region of transcribed sequences, where it trimethylates nucleosomes. In support of this model, inhibition of phosphorylation of the C-terminal domain of Pol II reduced the amounts of H3K4me3 and ATX1 bound at the +300-nucleotide region. Importantly, these changes did not reduce the occupancy of ATX1, TBP, or Pol II at promoters. Our results indicate that ATX1 affects transcription at target genes by a mechanism distinct from its ability to trimethylate H3K4 within genes.
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Affiliation(s)
- Yong Ding
- University of Nebraska Center for Biotechnology and Center for Plant Science Innovation, Lincoln, Nebraska 68588
- University of Nebraska School of Biological Sciences, Lincoln, Nebraska 68588
| | - Zoya Avramova
- University of Nebraska School of Biological Sciences, Lincoln, Nebraska 68588
| | - Michael Fromm
- University of Nebraska Center for Biotechnology and Center for Plant Science Innovation, Lincoln, Nebraska 68588
- Address correspondence to
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129
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Kaufmann K, Pajoro A, Angenent GC. Regulation of transcription in plants: mechanisms controlling developmental switches. Nat Rev Genet 2010; 11:830-42. [PMID: 21063441 DOI: 10.1038/nrg2885] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Unlike animals, plants produce new organs throughout their life cycle using pools of stem cells that are organized in meristems. Although many key regulators of meristem and organ identities have been identified, it is still not well understood how they function at the molecular level and how they can switch an entire developmental programme in which thousands of genes are involved. Recent advances in the genome-wide identification of target genes controlled by key plant transcriptional regulators and their interactions with epigenetic factors provide new insights into general transcriptional regulatory mechanisms that control switches of developmental programmes and cell fates in complex organisms.
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130
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SET DOMAIN GROUP2 is the major histone H3 lysine [corrected] 4 trimethyltransferase in Arabidopsis. Proc Natl Acad Sci U S A 2010; 107:18557-62. [PMID: 20937886 DOI: 10.1073/pnas.1010478107] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Posttranslational modifications of histones play important roles in modulating chromatin structure and regulating gene expression. We have previously shown that more than two thirds of Arabidopsis genes contain histone H3 methylation at lysine 4 (H3K4me) and that trimethylation of H3K4 (H3K4me3) is preferentially located at actively transcribed genes. In addition, several Arabidopsis mutants with locus-specific loss of H3K4me have been found to display various developmental abnormalities. These findings suggest that H3K4me3 may play important roles in maintaining the normal expression of a large number of genes. However, the major enzyme(s) responsible for H3K4me3 has yet to be identified in plants, making it difficult to address questions regarding the mechanisms and functions of H3K4me3. Here we described the characterization of SET DOMAIN GROUP 2 (SDG2), a large Arabidopsis protein containing a histone lysine methyltransferase domain. We found that SDG2 homologs are highly conserved in plants and that the Arabidopsis SDG2 gene is broadly expressed during development. In addition, the loss of SDG2 leads to severe and pleiotropic phenotypes, as well as the misregulation of a large number of genes. Consistent with our finding that SDG2 is a robust and specific H3K4 methyltransferase in vitro, the loss of SDG2 leads to a drastic decrease in H3K4me3 in vivo. Taken together, these results suggest that SDG2 is the major enzyme responsible for H3K4me3 in Arabidopsis and that SDG2-dependent H3K4m3 is critical for regulating gene expression and plant development.
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131
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Kim DH, Zografos BR, Sung S. Vernalization-mediated VIN3 Induction Overcomes the LIKE-HETEROCHROMATIN PROTEIN1/POLYCOMB REPRESSION COMPLEX2-mediated epigenetic repression. PLANT PHYSIOLOGY 2010; 154:949-57. [PMID: 20671111 PMCID: PMC2948996 DOI: 10.1104/pp.110.161083] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 07/28/2010] [Indexed: 05/20/2023]
Abstract
VERNALIZATION INSENSITIVE3 (VIN3) induction by vernalization is one of the earliest events in the vernalization response of Arabidopsis (Arabidopsis thaliana). However, the mechanism responsible for vernalization-mediated VIN3 induction is poorly understood. Here, we show that the constitutive repression of VIN3 in the absence of the cold is due to multiple repressive components, including a transposable element-derived sequence, LIKE-HETEROCHROMATIN PROTEIN1 and POLYCOMB REPRESSION COMPLEX2. Furthermore, the full extent of VIN3 induction by vernalization requires activating complex components, including EARLY FLOWERING7 and EARLY FLOWERING IN SHORT DAYS. In addition, we observed dynamic changes in the histone modifications present at VIN3 chromatin during the course of vernalization. Our results show that the induction of VIN3 includes dynamic changes at the level of chromatin triggered by long-term cold exposure.
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Affiliation(s)
- Dong-Hwan Kim
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA
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132
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Berr A, McCallum EJ, Ménard R, Meyer D, Fuchs J, Dong A, Shen WH. Arabidopsis SET DOMAIN GROUP2 is required for H3K4 trimethylation and is crucial for both sporophyte and gametophyte development. THE PLANT CELL 2010; 22:3232-48. [PMID: 20810545 PMCID: PMC2990135 DOI: 10.1105/tpc.110.079962] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 09/28/2010] [Accepted: 10/13/2010] [Indexed: 05/18/2023]
Abstract
Histone H3 lysine 4 trimethylation (H3K4me3) is abundant in euchromatin and is in general associated with transcriptional activation in eukaryotes. Although some Arabidopsis thaliana SET DOMAIN GROUP (SDG) genes have been previously shown to be involved in H3K4 methylation, they are unlikely to be responsible for global genome-wide deposition of H3K4me3. Most strikingly, sparse knowledge is currently available about the role of histone methylation in gametophyte development. In this study, we show that the previously uncharacterized SDG2 is required for global H3K4me3 deposition and its loss of function causes wide-ranging defects in both sporophyte and gametophyte development. Transcriptome analyses of young flower buds have identified 452 genes downregulated by more than twofold in the sdg2-1 mutant; among them, 11 genes, including SPOROCYTELESS/NOZZLE (SPL/NZZ) and MALE STERILITY1 (MS1), have been previously shown to be essential for male and/or female gametophyte development. We show that both SPL/NZZ and MS1 contain bivalent chromatin domains enriched simultaneously with the transcriptionally active mark H3K4me3 and the transcriptionally repressive mark H3K27me3 and that SDG2 is specifically required for the H3K4me3 deposition. Our data suggest that SDG2-mediated H3K4me3 deposition poises SPL/NZZ and MS1 for transcriptional activation, forming a key regulatory mechanism in the gene networks responsible for gametophyte development.
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Affiliation(s)
- Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg Cedex, France
| | - Emily J. McCallum
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg Cedex, France
| | - Rozenn Ménard
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg Cedex, France
| | - Denise Meyer
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg Cedex, France
| | - Jörg Fuchs
- Leibniz-Institute of Plant Genetics and Crop Plant Research, D-06466 Gatersleben, Germany
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, PR China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes du Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg Cedex, France
- Address correspondence to
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133
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Yu X, Michaels SD. The Arabidopsis Paf1c complex component CDC73 participates in the modification of FLOWERING LOCUS C chromatin. PLANT PHYSIOLOGY 2010; 153:1074-84. [PMID: 20463090 PMCID: PMC2899897 DOI: 10.1104/pp.110.158386] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 05/11/2010] [Indexed: 05/18/2023]
Abstract
FLOWERING LOCUS C (FLC) is a key repressor of flowering in Arabidopsis (Arabidopsis thaliana) and is regulated, both positively and negatively, by posttranslational histone modifications. For example, vernalization (the promotion of flowering by cold temperatures) epigenetically silences FLC expression through repressive histone modifications such as histone H3 lysine-9 dimethylation (H3K9me2) and H3K27me3. In contrast, an RNA polymerase II-associated complex (Paf1c) activates FLC expression through increased H3K4 and H3K36 methylation. As a result of this regulation, FLC has become a useful model for the study of chromatin structure in Arabidopsis. Here we show that At3g22590 is the Arabidopsis homolog of the yeast (Saccharomyces cerevisiae) Paf1c component CDC73 and is enriched at FLC chromatin. In contrast to other Paf1c component mutants that exhibit pleiotropic developmental phenotypes, the effects of cdc73 mutations are primarily limited to flowering time, suggesting that CDC73 may only be required for Paf1c function at a subset of target genes. In rapid-cycling strains, cdc73 mutants showed reduced FLC mRNA levels and decreased H3K4me3 at the FLC locus. Interestingly, in late-flowering autonomous-pathway mutants, which contain higher levels of FLC, cdc73 mutations only suppressed FLC in a subset of mutants. H3K4me3 was uniformly reduced in all autonomous-pathway cdc73 double mutants tested; however, those showing reduced FLC expression also showed an increase in H3K27me3. Thus, CDC73 is required for high levels of FLC expression in a subset of autonomous-pathway-mutant backgrounds and functions both to promote activating histone modifications (H3K4me3) as well as preventing repressive ones (e.g. H3K27me3).
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134
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Kim DH, Doyle MR, Sung S, Amasino RM. Vernalization: winter and the timing of flowering in plants. Annu Rev Cell Dev Biol 2010; 25:277-99. [PMID: 19575660 DOI: 10.1146/annurev.cellbio.042308.113411] [Citation(s) in RCA: 338] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plants have evolved many systems to sense their environment and to modify their growth and development accordingly. One example is vernalization, the process by which flowering is promoted as plants sense exposure to the cold temperatures of winter. A requirement for vernalization is an adaptive trait that helps prevent flowering before winter and permits flowering in the favorable conditions of spring. In Arabidopsis and cereals, vernalization results in the suppression of genes that repress flowering. We describe recent progress in understanding the molecular basis of this suppression. In Arabidopsis, vernalization involves the recruitment of chromatin-modifying complexes to a clade of flowering repressors that are silenced epigenetically via histone modifications. We also discuss the similarities and differences in vernalization between Arabidopsis and cereals.
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Affiliation(s)
- Dong-Hwan Kim
- Section of Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.
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135
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Alvarez-Venegas R. Regulation by polycomb and trithorax group proteins in Arabidopsis. THE ARABIDOPSIS BOOK 2010; 8:e0128. [PMID: 22303254 PMCID: PMC3244960 DOI: 10.1199/tab.0128] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polycomb group (PcG) and trithorax group (trxG) proteins are key regulators of homeotic genes and have crucial roles in cell proliferation, growth and development. PcG and trxG proteins form higher order protein complexes that contain SET domain proteins, with a histone methyltransferase (HMTase) activity, responsible for the different types of lysine methylation at the N-terminal tails of the core histone proteins. In recent years, genetic studies along with biochemical and cell biological analyses in Arabidopsis have enabled researchers to begin to understand how PcG and trxG proteins are recruited to chromatin and how they regulate their target genes and to elucidate their functions. This review focuses on the advances in our understanding of the biological roles of PcG and trxG proteins, their molecular mechanisms of action and further examines the role of histone marks in PcG and trxG regulation in Arabidopsis.
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Affiliation(s)
- Raúl Alvarez-Venegas
- Department of Genetic Engineering, Center for Research and Advanced Studies, CINVESTAV-IPN Unidad lrapuato, C.P. 36821 lrapuato, Guanajuato, México
- Address correspondence to
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136
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Abstract
Histone methylation plays a fundamental role in regulating diverse developmental processes and is also involved in silencing repetitive sequences in order to maintain genome stability. The methylation marks are written on lysine or arginine by distinct enzymes, namely, histone lysine methyltransferases (HKMTs) or protein arginine methyltransferases (PRMTs). Once established, the methylation marks are specifically recognized by the proteins that act as readers and are interpreted into specific biological outcomes. Histone methylation status is dynamic; methylation marks can be removed by eraser enzymes, the histone demethylases (HDMs). The proteins responsible for writing, reading, and erasing the methylation marks are known mostly in animals. During the past several years, a growing body of literature has demonstrated the impact of histone methylation on genome management, transcriptional regulation, and development in plants. The aim of this review is to summarize the biochemical, genetic, and molecular action of histone methylation in two plants, the dicot Arabidopsis and the monocot rice.
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Affiliation(s)
- Chunyan Liu
- National Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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137
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PONTVIANNE FRÉDÉRIC, BLEVINS TODD, PIKAARD CRAIGS. Arabidopsis Histone Lysine Methyltransferases. ADVANCES IN BOTANICAL RESEARCH 2010; 53:1-22. [PMID: 20703330 PMCID: PMC2918895 DOI: 10.1016/s0065-2296(10)53001-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
In eukaryotes, changes in chromatin structure regulate the access of gene regulatory sequences to the transcriptional machinery and play important roles in the repression of transposable elements, thereby protecting genome integrity. Chromatin dynamics and gene expression states are highly correlated, with DNA methylation and histone post-translational modifications playing important roles in the establishment or maintenance of chromatin states in plants. Histones can be covalently modified in a variety of ways, thereby affecting nucleosome spacing and/or higher-order nucleosome interactions directly or via the recruitment of histone-binding proteins. An extremely important group of chromatin modifying enzymes are the histone lysine methyltransferases (HKMTs). These enzymes are involved in the establishment and/or maintenance of euchromatic or heterochromatic states of active or transcriptionally repressed sequences, respectively. The vast majority of HKMTs possess a SET domain named for the three Drosophila proteins that are the founding members of the family: Suppressor of variegation, Enhancer of zeste and Trithorax. It is the SET domain that is responsible for HKMT enzymatic activity. Mutation of Arabidopsis HKMT genes can result in phenotypic abnormalities due to the improper regulation of important developmental genes. Here, we review the different classes of HKMTs present in the model plant Arabidopsis thaliana and discuss what is known about their biochemical and biological functions.
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138
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Lafos M, Schubert D. Balance of power--dynamic regulation of chromatin in plant development. Biol Chem 2009; 390:1113-23. [PMID: 19747083 DOI: 10.1515/bc.2009.129] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Chromatin states profoundly determine and maintain gene activity and gene repression in eukaryotic organisms. Regulation of chromatin involves chromatin remodeling, chromatin modifications and exchange of chromatin components and is linked to DNA methylation in some cases. In plants and other organisms, chromatin proteins control many developmental pathways, integrate changes in the environment and can confer a cellular memory of these cues. Here, we review the molecular mechanisms that provide a dynamic regulation of chromatin in a cell. In addition, we discuss how chromatin needs to be flexibly regulated during plant growth to confer stable expression states that can occasionally be reset, e.g., owing to changes in the environment and progression of development.
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Affiliation(s)
- Marcel Lafos
- Institute of Genetics, Heinrich Heine University Düsseldorf, D-40225 Düsseldorf, Germany
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139
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Sang Y, Wu MF, Wagner D. The stem cell--chromatin connection. Semin Cell Dev Biol 2009; 20:1143-8. [PMID: 19765665 PMCID: PMC3407560 DOI: 10.1016/j.semcdb.2009.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 08/26/2009] [Accepted: 09/08/2009] [Indexed: 11/30/2022]
Abstract
Stem cells self-renew and give rise to all differentiated cell types of the adult body. They are classified as toti-, pluri- or multi-potent based on the number of different cell types they can give rise to. Recently it has become apparent that chromatin regulation plays a critical role in determining the fate of stem cells and their descendants. In this review we will discuss the role of chromatin regulators in maintenance of stem cells and their ability to give rise to differentiating cells in both the animal and plant kingdom. We will highlight similarities and differences in chromatin-mediated control of stem cell fate in plants and animals. We will consider possible reasons why chromatin regulators play a central role in pluripotency in both kingdoms given that multicellularity evolved independently in each.
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Affiliation(s)
| | | | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104
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140
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Berr A, Xu L, Gao J, Cognat V, Steinmetz A, Dong A, Shen WH. SET DOMAIN GROUP25 encodes a histone methyltransferase and is involved in FLOWERING LOCUS C activation and repression of flowering. PLANT PHYSIOLOGY 2009; 151:1476-85. [PMID: 19726574 PMCID: PMC2773071 DOI: 10.1104/pp.109.143941] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 08/26/2009] [Indexed: 05/18/2023]
Abstract
Covalent modifications of histone lysine residues by methylation play key roles in the regulation of chromatin structure and function. In contrast to H3K9 and H3K27 methylations that mark repressive states of transcription and are absent in some lower eukaryotes, H3K4 and H3K36 methylations are considered as active marks of transcription and are highly conserved in all eukaryotes from yeast (Saccharomyces cerevisiae) to Homo sapiens. Paradoxically, protein complexes catalyzing H3K4 and H3K36 methylations are less-extensively characterized in higher eukaryotes, particularly in plants. Arabidopsis (Arabidopsis thaliana) contains 12 SET DOMAIN GROUP (SDG) proteins phylogenetic classified to Trithorax Group (TrxG) and thus potentially involved in H3K4 and H3K36 methylations. So far only some genes of this family had been functionally characterized. Here we report on the genetic and molecular characterization of SDG25, a previously uncharacterized member of the Arabidopsis TrxG family. We show that the loss-of-function mutant sdg25-1 has an early flowering phenotype associated with suppression of FLOWERING LOCUS C (FLC) expression. Recombinant SDG25 proteins could methylate histone H3 from oligonucleosomes and mutant sdg25-1 plants showed weakly reduced levels of H3K36 dimethylation at FLC chromatin. Interestingly, sdg25-1 transcriptome shared a highly significant number of differentially expressed genes with that of sdg26-1, a previously characterized mutant exhibiting late-flowering phenotype and elevated FLC expression. Taken together, our results provide, to our knowledge, the first demonstration for a biological function of SDG25 and reveal additional layers of complexity of overlap and nonoverlap functions of the TrxG family genes in Arabidopsis.
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141
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Ding Y, Lapko H, Ndamukong I, Xia Y, Al-Abdallat A, Lalithambika S, Sadder M, Saleh A, Fromm M, Riethoven JJ, Lu G, Avramova Z. The Arabidopsis chromatin modifier ATX1, the myotubularin-like AtMTM and the response to drought. PLANT SIGNALING & BEHAVIOR 2009; 4:1049-58. [PMID: 19901554 PMCID: PMC2819512 DOI: 10.4161/psb.4.11.10103] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 09/15/2009] [Indexed: 05/19/2023]
Abstract
Plants respond to environmental stresses by altering transcription of genes involved in the response. The chromatin modifier ATX1 regulates expression of a large number of genes; consequently, factors that affect ATX1 activity would also influence expression from ATX1-regulated genes. Here, we demonstrate that dehydration is such a factor implicating ATX1 in the plant's response to drought. In addition, we report that a hitherto unknown Arabidopsis gene, At3g10550, encodes a phosphoinositide 3'-phosphatase related to the animal myotubularins (AtMTM1). Myotubularin activities in plants have not been described and herein, we identify an overlapping set of genes co-regulated by ATX1 and AtMTM under drought conditions. We propose that these shared genes represent the ultimate targets of partially overlapping branches of the pathways of the nuclear ATX1 and the cytoplasmic AtMTM1. Our analyses offer first genome-wide insights into the relationship of an epigenetic factor and a lipid phosphatase from the other end of a shared drought responding pathway in Arabidopsis.
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Affiliation(s)
- Yong Ding
- UNL Center for Biotechnology and Plant Science Initiative; UNL; Lincoln, NE USA
| | - Hanna Lapko
- School of Biological Sciences; UNL; Lincoln, NE USA
| | | | - Yuannan Xia
- Genomics Core Research Facility; Center for Biotechnology UNL; Lincoln, NE USA
| | - Ayed Al-Abdallat
- UNL Center for Biotechnology and Plant Science Initiative; UNL; Lincoln, NE USA
- Faculty of Agriculture; University of Jordan; Amman, Jordan
| | | | - Monther Sadder
- School of Biological Sciences; UNL; Lincoln, NE USA
- Faculty of Agriculture; University of Jordan; Amman, Jordan
| | | | - Michael Fromm
- UNL Center for Biotechnology and Plant Science Initiative; UNL; Lincoln, NE USA
| | - Jean-Jack Riethoven
- Bioinformatics Core Research Facility; Center for Biotechnology UNL; Lincoln, NE USA
| | - Guoqing Lu
- Department of Biology; University of Nebraska at Omaha; Omaha, NE USA
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142
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Tamada Y, Yun JY, Woo SC, Amasino RM. ARABIDOPSIS TRITHORAX-RELATED7 is required for methylation of lysine 4 of histone H3 and for transcriptional activation of FLOWERING LOCUS C. THE PLANT CELL 2009; 21:3257-69. [PMID: 19855050 PMCID: PMC2782277 DOI: 10.1105/tpc.109.070060] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2009] [Revised: 09/04/2009] [Accepted: 09/16/2009] [Indexed: 05/18/2023]
Abstract
In the winter-annual accessions of Arabidopsis thaliana, presence of an active allele of FRIGIDA (FRI) elevates expression of FLOWERING LOCUS C (FLC), a repressor of flowering, and thus confers a vernalization requirement. FLC activation by FRI involves methylation of Lys 4 of histone H3 (H3K4) at FLC chromatin. Many multicellular organisms that have been examined contain two classes of H3K4 methylases, a yeast (Saccharomyces cerevisiae) Set1 class and a class related to Drosophila melanogaster Trithorax. In this work, we demonstrate that ARABIDOPSIS TRITHORAX-RELATED7 (ATXR7), a putative Set1 class H3K4 methylase, is required for proper FLC expression. The atxr7 mutation partially suppresses the delayed flowering of a FRI-containing line. The rapid flowering of atxr7 is associated with reduced FLC expression and is accompanied by decreased H3K4 methylation and increased H3K27 methylation at FLC. Thus, ATXR7 is required for the proper levels of these histone modifications that set the level of FLC expression to create a vernalization requirement in winter-annual accessions. Previously, it has been reported that lesions in ATX1, which encodes a Trithorax class H3K4 methylase, partially suppress the delayed flowering of winter-annual Arabidopsis. We show that the flowering phenotype of atx1 atxr7 double mutants is additive relative to those of single mutants. Therefore, both classes of H3K4 methylases appear to be required for proper regulation of FLC expression.
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143
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Sablowski R. Genes and functions controlled by floral organ identity genes. Semin Cell Dev Biol 2009; 21:94-9. [PMID: 19733677 DOI: 10.1016/j.semcdb.2009.08.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 08/28/2009] [Indexed: 12/13/2022]
Abstract
Floral organ identity genes specify the identity of floral organs in a manner analogous to the specification of body segments by Hox genes in animals. Different combinations of organ identity genes co-ordinate the expression of genes required for the development of each type of floral organ, from organ initiation until final differentiation. Here, I review what is known about the genes and functions subordinate to the organ identity genes. The sets of target genes change as organ development progresses and ultimately organ identity genes modify the expression of thousands of genes with a multitude of predicted functions, particularly in reproductive organs. However, genes involved in transcriptional control and hormone functions feature prominently among the early and direct targets. Functional analysis showed that control of organ-specific tissues and structures can be delegated to specialised intermediate regulators, but organ identity genes also fine-tune genes with general roles in shoot organ development, consistent with the notion that organ identity genes modify a core leaf-like developmental program. Future challenges include obtaining data with cellular resolution, predictive modelling of the regulatory network, and quantitative analysis of how organ identity genes and their targets control cell behaviour and ultimately organ shape.
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Affiliation(s)
- Robert Sablowski
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom.
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144
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Adrian J, Torti S, Turck F. From decision to commitment: the molecular memory of flowering. MOLECULAR PLANT 2009; 2:628-642. [PMID: 19825644 DOI: 10.1093/mp/ssp031] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
During the floral transition the shoot apical meristem changes its identity from a vegetative to an inflorescence state. This change in identity can be promoted by external signals, such as inductive photoperiod conditions or vernalization, and is accompanied by changes in expression of key developmental genes. The change in meristem identity is usually not reversible, even if the inductive signal occurs only transiently. This implies that at least some of the key genes must possess an intrinsic memory of the newly acquired expression state that ensures irreversibility of the process. In this review, we discuss different molecular scenarios that may underlie a molecular memory of gene expression.
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Affiliation(s)
- Jessika Adrian
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829 Köln, Germany
| | - Stefano Torti
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829 Köln, Germany
| | - Franziska Turck
- Max Planck Institute for Plant Breeding Research, Carl von Linné Weg 10, 50829 Köln, Germany.
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145
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Shen WH, Xu L. Chromatin remodeling in stem cell maintenance in Arabidopsis thaliana. MOLECULAR PLANT 2009; 2:600-609. [PMID: 19825642 DOI: 10.1093/mp/ssp022] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Pluripotent stem cells are able to both self-renew and generate undifferentiated cells for the formation of new tissues and organs. In higher plants, stem cells found in the shoot apical meristem (SAM) and the root apical meristem (RAM) are origins of organogenesis occurring post-embryonically. It is important to understand how the regulation of stem cell fate is coordinated to enable the meristem to constantly generate different types of lateral organs. Much knowledge has accumulated on specific transcription factors controlling SAM and RAM activity. Here, we review recent evidences for a role of chromatin remodeling in the maintenance of stable expression states of transcription factor genes and the control of stem cell activity in Arabidopsis.
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Affiliation(s)
- Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes (IBMP) du CNRS, Université de Strasbourg (UdS), 12 rue du Général Zimmer, 67084 Strasbourg Cédex, France.
| | - Lin Xu
- Institut de Biologie Moléculaire des Plantes (IBMP) du CNRS, Université de Strasbourg (UdS), 12 rue du Général Zimmer, 67084 Strasbourg Cédex, France; National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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146
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Zhang X, Bernatavichute YV, Cokus S, Pellegrini M, Jacobsen SE. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol 2009; 10:R62. [PMID: 19508735 PMCID: PMC2718496 DOI: 10.1186/gb-2009-10-6-r62] [Citation(s) in RCA: 413] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Revised: 02/03/2009] [Accepted: 06/09/2009] [Indexed: 11/25/2022] Open
Abstract
Analysis of the genome-wide distribution patterns of histone H3 lysine4 methylation in Arabidopsis thaliana seedlings shows that it has widespread roles in regulating gene expression. Background Post-translational modifications of histones play important roles in maintaining normal transcription patterns by directly or indirectly affecting the structural properties of the chromatin. In plants, methylation of histone H3 lysine 4 (H3K4me) is associated with genes and required for normal plant development. Results We have characterized the genome-wide distribution patterns of mono-, di- and trimethylation of H3K4 (H3K4me1, H3K4me2 and H3K4me3, respectively) in Arabidopsis thaliana seedlings using chromatin immunoprecipitation and high-resolution whole-genome tiling microarrays (ChIP-chip). All three types of H3K4me are found to be almost exclusively genic, and two-thirds of Arabidopsis genes contain at least one type of H3K4me. H3K4me2 and H3K4me3 accumulate predominantly in promoters and 5' genic regions, whereas H3K4me1 is distributed within transcribed regions. In addition, H3K4me3-containing genes are highly expressed with low levels of tissue specificity, but H3K4me1 or H3K4me2 may not be directly involved in transcriptional activation. Furthermore, the preferential co-localization of H3K4me3 and H3K27me3 found in mammals does not appear to occur in plants at a genome-wide level, but H3K4me2 and H3K27me3 co-localize at a higher-than-expected frequency. Finally, we found that H3K4me2/3 and DNA methylation appear to be mutually exclusive, but surprisingly, H3K4me1 is highly correlated with CG DNA methylation in the transcribed regions of genes. Conclusions H3K4me plays widespread roles in regulating gene expression in plants. Although many aspects of the mechanisms and functions of H3K4me appear to be conserved among all three kingdoms, we observed significant differences in the relationship between H3K4me and transcription or other epigenetic pathways in plants and mammals.
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Affiliation(s)
- Xiaoyu Zhang
- Department of Plant Biology, University of Georgia, Green Street, Athens, GA 30602, USA.
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147
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Jiang D, Gu X, He Y. Establishment of the winter-annual growth habit via FRIGIDA-mediated histone methylation at FLOWERING LOCUS C in Arabidopsis. THE PLANT CELL 2009; 21:1733-46. [PMID: 19567704 PMCID: PMC2714927 DOI: 10.1105/tpc.109.067967] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Revised: 05/17/2009] [Accepted: 06/04/2009] [Indexed: 05/19/2023]
Abstract
In Arabidopsis thaliana, flowering-time variation exists among accessions, and the winter-annual (late-flowering without vernalization) versus rapid-cycling (early flowering) growth habit is typically determined by allelic variation at FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). FRI upregulates the expression of FLC, a central floral repressor, to levels that inhibit flowering, resulting in the winter-annual habit. Here, we show that FRI promotes histone H3 lysine-4 trimethylation (H3K4me3) in FLC to upregulate its expression. We identified an Arabidopsis homolog of the human WDR5, namely, WDR5a, which is a conserved core component of the human H3K4 methyltransferase complexes called COMPASS-like. We found that recombinant WDR5a binds H3K4-methylated peptides and that WDR5a also directly interacts with an H3K4 methyltransferase, ARABIDOPSIS TRITHORAX1. FRI mediates WDR5a enrichment at the FLC locus, leading to increased H3K4me3 and FLC upregulation. WDR5a enrichment is not required for elevated H3K4me3 in FLC upon loss of function of an FLC repressor, suggesting that two distinct mechanisms underlie elevated H3K4me3 in FLC. Our findings suggest that FRI is involved in the enrichment of a WDR5a-containing COMPASS-like complex at FLC chromatin that methylates H3K4, leading to FLC upregulation and thus the establishment of the winter-annual growth habit.
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Affiliation(s)
- Danhua Jiang
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Republic of Singapore
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Cazzonelli CI, Millar T, Finnegan EJ, Pogson BJ. Promoting gene expression in plants by permissive histone lysine methylation. PLANT SIGNALING & BEHAVIOR 2009; 4:484-8. [PMID: 19816124 PMCID: PMC2688292 DOI: 10.4161/psb.4.6.8316] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2009] [Accepted: 03/02/2009] [Indexed: 05/23/2023]
Abstract
Plants utilize sophisticated epigenetic regulatory mechanisms to coordinate changes in gene expression during development and in response to environmental stimuli. Epigenetics refers to the modification of DNA and chromatin associated proteins, which affect gene expression and cell function, without changing the DNA sequence. Such modifications are inherited through mitosis, and in rare instances through meiosis, although it can be reversible and thus regulatory. Epigenetic modifications are controlled by groups of proteins, such as the family of histone lysine methytransferases (HKMTs). The catalytic core known as the SET domain encodes HKMT activity and either promotes or represses gene expression. A large family of SET domain proteins is present in Arabidopsis where there is growing evidence that two classes of these genes are involved in promoting gene expression in a diverse range of developmental processes. This review will focus on the function of these two classes and the processes that they control, highlighting the huge potential this regulatory mechanism has in plants.
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Affiliation(s)
- Christopher I Cazzonelli
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Biochemistry and Molecular Biology, The Australian National University, Canberra, Australia.
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149
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Lee WY, Lee D, Chung WI, Kwon CS. Arabidopsis ING and Alfin1-like protein families localize to the nucleus and bind to H3K4me3/2 via plant homeodomain fingers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 58:511-24. [PMID: 19154204 DOI: 10.1111/j.1365-313x.2009.03795.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
In yeast and animals, tri- and dimethylation of histone H3 at lysine 4 (H3K4me3/2) are markers of transcriptionally active genes that have recently been shown to be primary ligands for the plant homeodomain (PHD) finger. However, PHD fingers able to bind to H3K4me3/2 have not been identified in plants. Here, we identify 83 canonical PHD fingers in the Arabidopsis proteome database that are supported by both SMART and Pfam prediction. Among these, we focus on PHD fingers in ING (inhibitor of growth) homologues (AtING) and Alfin1-like (AL) proteins, which are highly similar to those in human ING2 and bromodomain PHD finger transcription factor (BPTF), based on predicted tertiary structures. ING proteins are found in yeast, animals and plants, whereas AL proteins exist only in plants. In vitro binding experiments indicated that PHD fingers in AtING and AL proteins in Arabidopsis can bind to H3K4me3, and, to a lesser extent, to H3K4me2. In addition, mutational analysis confirmed that a predicted aromatic cage and a specific conserved acidic residue are both crucial for binding to H3K4me3/2. Finally, we demonstrate that AtING and AL proteins are nuclear proteins that are expressed in various tissues of the Arabidopsis plant. Thus, we propose that ING and AL proteins are nuclear proteins that are involved in chromatin regulation by binding to H3K4me3/2, the active histone markers, in plants.
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Affiliation(s)
- Woo Yong Lee
- Department of Biological Sciences, KAIST, Daejeon 305-701, Korea
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150
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Ndamukong I, Chetram A, Saleh A, Avramova Z. Wall-modifying genes regulated by the Arabidopsis homolog of trithorax, ATX1: repression of the XTH33 gene as a test case. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 58:541-53. [PMID: 19154201 DOI: 10.1111/j.1365-313x.2009.03798.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The plant cell wall is a dynamic structure playing important roles in the control of plant cell growth and differentiation. These processes involve global reprogramming of the genome driven by dynamic changes in chromatin structure. The chromatin modifier ARABIDOPSIS HOMOLOG OF TRITHORAX (ATX1) methylates lysine residue 4 on histone H3 (H3K4me), acting as an epigenetic mark on associated genes. The remarkable overrepresentation in the ATX1-regulated gene fraction of genes encoding plasma membrane and cell wall-remodeling activities suggested a link between two separate factors affecting growth, development and adaptation in Arabidopsis: the wall-modifying activities regulating cell extension, growth and fate, and the epigenetic mechanisms regulating chromatin structure and gene expression. A co-regulated fraction of specific wall-modifying proteins suggests that they may function together. Here, we study the ATX1-dependent expression of the gene encoding the wall-loosening factor XTH33 as a test case for development- and tissue-specific effects displayed by the chromatin modifier. In addition, we show that XTH33 is, most likely, an integral plasma membrane protein. A putative transmembrane domain is conserved in some, but not all, XTH family members, suggesting that they may be differently positioned when functioning as wall modifiers.
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