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Integrated analysis and transcript abundance modelling of H3K4me3 and H3K27me3 in developing secondary xylem. Sci Rep 2017; 7:3370. [PMID: 28611454 PMCID: PMC5469831 DOI: 10.1038/s41598-017-03665-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/02/2017] [Indexed: 01/10/2023] Open
Abstract
Despite the considerable contribution of xylem development (xylogenesis) to plant biomass accumulation, its epigenetic regulation is poorly understood. Furthermore, the relative contributions of histone modifications to transcriptional regulation is not well studied in plants. We investigated the biological relevance of H3K4me3 and H3K27me3 in secondary xylem development using ChIP-seq and their association with transcript levels among other histone modifications in woody and herbaceous models. In developing secondary xylem of the woody model Eucalyptus grandis, H3K4me3 and H3K27me3 genomic spans were distinctly associated with xylogenesis-related processes, with (late) lignification pathways enriched for putative bivalent domains, but not early secondary cell wall polysaccharide deposition. H3K27me3-occupied genes, of which 753 (~31%) are novel targets, were enriched for transcriptional regulation and flower development and had significant preferential expression in roots. Linear regression models of the ChIP-seq profiles predicted ~50% of transcript abundance measured with strand-specific RNA-seq, confirmed in a parallel analysis in Arabidopsis where integration of seven additional histone modifications each contributed smaller proportions of unique information to the predictive models. This study uncovers the biological importance of histone modification antagonism and genomic span in xylogenesis and quantifies for the first time the relative correlations of histone modifications with transcript abundance in plants.
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102
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Xiao J, Jin R, Wagner D. Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants. Genome Biol 2017; 18:88. [PMID: 28490341 PMCID: PMC5425979 DOI: 10.1186/s13059-017-1228-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new organism. This developmental plasticity is thought to be an adaptation to the sessile lifestyle of plants. Recent discoveries have advanced our understanding of the orchestration of plant developmental switches by transcriptional master regulators, chromatin state changes, and hormone response pathways. Here, we review these recent advances with emphasis on the earliest stages of plant development and on the switch from pluripotency to differentiation in different plant organ systems.
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Affiliation(s)
- Jun Xiao
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Run Jin
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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103
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Kim DH, Sung S. Accelerated vernalization response by an altered PHD-finger protein in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2017; 12:e1308619. [PMID: 28498016 PMCID: PMC5501235 DOI: 10.1080/15592324.2017.1308619] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 03/15/2017] [Indexed: 05/23/2023]
Abstract
Vernalization is a response to the winter cold to acquire the competence to flower in next spring. VERNALIZATION INSENSITIVE 3 (VIN3) is a PHD-finger protein that binds to modified histones in vitro. VIN3 is induced by long-term cold and is necessary for Polycomb Repression Complex 2 (PRC2)-mediated tri-methylation of Histone H3 Lysine 27 (H3K27me3) at the FLC locus in Arabidopsis. An alteration in the PHD-finger domain of VIN3 changes the binding specificity of the PHD-finger domain of VIN3 in vitro and results in an accelerated vernalization response in vivo. The acceleration in vernalization response is achieved by increased enrichments of VIN3 and tri-methylation of Histone H3 Lysine 27 (H3K27me3) at the FLC locus without invoking the increased enrichment of Polycomb Repressive Complex 2. This result indicates that the binding specificity of the PHD-finger domain of VIN3 plays a role in mediating a proper vernalization response in Arabidopsis. Furthermore, this work shows a potential that the alteration of PHD-finger domains could be applied to alter various developmental processes in plants.
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Affiliation(s)
- Dong-Hwan Kim
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, TX, USA
| | - Sibum Sung
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, TX, USA
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104
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Macovei A, Pagano A, Leonetti P, Carbonera D, Balestrazzi A, Araújo SS. Systems biology and genome-wide approaches to unveil the molecular players involved in the pre-germinative metabolism: implications on seed technology traits. PLANT CELL REPORTS 2017; 36:669-688. [PMID: 27730302 DOI: 10.1007/s00299-016-2060-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 09/26/2016] [Indexed: 05/21/2023]
Abstract
The pre-germinative metabolism is among the most fascinating aspects of seed biology. The early seed germination phase, or pre-germination, is characterized by rapid water uptake (imbibition), which directs a series of dynamic biochemical events. Among those are enzyme activation, DNA damage and repair, and use of reserve storage compounds, such as lipids, carbohydrates and proteins. Industrial seedling production and intensive agricultural production systems require seed stocks with high rate of synchronized germination and low dormancy. Consequently, seed dormancy, a quantitative trait related to the activation of the pre-germinative metabolism, is probably the most studied seed trait in model species and crops. Single omics, systems biology, QTLs and GWAS mapping approaches have unveiled a list of molecules and regulatory mechanisms acting at transcriptional, post-transcriptional and post-translational levels. Most of the identified candidate genes encode for regulatory proteins targeting ROS, phytohormone and primary metabolisms, corroborating the data obtained from simple molecular biology approaches. Emerging evidences show that epigenetic regulation plays a crucial role in the regulation of these mentioned processes, constituting a still unexploited strategy to modulate seed traits. The present review will provide an up-date of the current knowledge on seed pre-germinative metabolism, gathering the most relevant results from physiological, genetics, and omics studies conducted in model and crop plants. The effects exerted by the biotic and abiotic stresses and priming are also addressed. The possible implications derived from the modulation of pre-germinative metabolism will be discussed from the point of view of seed quality and technology.
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Affiliation(s)
- Anca Macovei
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Andrea Pagano
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Paola Leonetti
- Institute for Sustainable Plant Protection, National Council of Research, via Amendola 122/D, 70126, Bari, Italy
| | - Daniela Carbonera
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Alma Balestrazzi
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Susana S Araújo
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, via Ferrata 9, 27100, Pavia, Italy.
- Plant Cell Biotechnology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Av. da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal.
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105
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Ctf4-related protein recruits LHP1-PRC2 to maintain H3K27me3 levels in dividing cells in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2017; 114:4833-4838. [PMID: 28428341 DOI: 10.1073/pnas.1620955114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Polycomb Repressive Complex (PRC) 2 catalyzes the H3K27me3 modification that warrants inheritance of a repressive chromatin structure during cell division, thereby assuring stable target gene repression in differentiated cells. It is still under investigation how H3K27me3 is passed on from maternal to filial strands during DNA replication; however, cell division can reinforce H3K27me3 coverage at target regions. To identify novel factors involved in the Polycomb pathway in plants, we performed a forward genetic screen for enhancers of the like heterochromatin protein 1 (lhp1) mutant, which shows relatively mild phenotypic alterations compared with other plant PRC mutants. We mapped enhancer of lhp1 (eol) 1 to a gene related to yeast Chromosome transmission fidelity 4 (Ctf4) based on phylogenetic analysis, structural similarities, physical interaction with the CMG helicase component SLD5, and an expression pattern confined to actively dividing cells. A combination of eol1 with the curly leaf (clf) allele, carrying a mutation in the catalytic core of PRC2, strongly enhanced the clf phenotype; furthermore, H3K27me3 coverage at target genes was strongly reduced in eol1 clf double mutants compared with clf single mutants. EOL1 physically interacted with CLF, its partially redundant paralog SWINGER (SWN), and LHP1. We propose that EOL1 interacts with LHP1-PRC2 complexes during replication and thereby participates in maintaining the H3K27me3 mark at target genes.
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106
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Berr A, Zhang X, Shen WH. [Reciprocity between active transcription and histone methylation]. Biol Aujourdhui 2017; 210:269-282. [PMID: 28327284 DOI: 10.1051/jbio/2017004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Indexed: 01/08/2023]
Abstract
In the nucleus of eukaryotic cells, the chromatin states dictated by the different combinations of histone post-translational modifications, such as the methylation of lysine residues, are an integral part of the multitude of epigenomes involved in the fine tuning of all genome functions, and in particular transcription. Over the last decade, an increasing number of factors have been identified as regulators involved in the establishment, reading or erasure of histone methylations. Their characterization in model organisms such as Arabidopsis has thus unraveled their fundamental roles in the control and regulation of essential developmental processes such as the floral transition, cell differentiation, gametogenesis, and/or the response/adaptation of plants to environmental stresses. In this review, we will focus on the methylation of histones functioning as a mark of activate transcription and we will try to highlight, based on recent findings, the more or less direct links between this mark and gene expression. Thus, we will discuss the different mechanisms allowing the dynamics and the integration of the chromatin states resulting from the different histone methylations in connection with the transcriptional machinery of the RNA polymerase II.
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107
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Yang X, Tong A, Yan B, Wang X. Governing the Silencing State of Chromatin: The Roles of Polycomb Repressive Complex 1 in Arabidopsis. PLANT & CELL PHYSIOLOGY 2017; 58:198-206. [PMID: 28069891 DOI: 10.1093/pcp/pcw209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
Polycomb group proteins form multiple protein complexes such as Polycomb Repressive Complex (PRC) 1 and PRC2, which repress the expression of thousands of genes. PRC1 and PRC2 are essential for normal development in Arabidopsis. Recently, significant progress has been made in understanding the functions and regulatory mechanisms of PRC1. In this review, we focus on the discovery of the composition of PRC1, functions of its components, the recruitment of PRC1 to target genes and the control of PRC1 function in Arabidopsis. Perspectives on dissecting the roles of PRC1 in plant gene expression and development are also given.
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Affiliation(s)
- Xianli Yang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Aizi Tong
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Bowen Yan
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Xiaoxue Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
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108
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Merini W, Romero-Campero FJ, Gomez-Zambrano A, Zhou Y, Turck F, Calonje M. The Arabidopsis Polycomb Repressive Complex 1 (PRC1) Components AtBMI1A, B, and C Impact Gene Networks throughout All Stages of Plant Development. PLANT PHYSIOLOGY 2017; 173:627-641. [PMID: 27837089 PMCID: PMC5210725 DOI: 10.1104/pp.16.01259] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/02/2016] [Indexed: 05/04/2023]
Abstract
Polycomb Group regulation in Arabidopsis (Arabidopsis thaliana) is required to maintain cell differentiation and allow developmental phase transitions. This is achieved by the activity of three PcG repressive complex 2s (PRC2s) and the participation of a yet poorly defined PRC1. Previous results showed that apparent PRC1 components perform discrete roles during plant development, suggesting the existence of PRC1 variants; however, it is not clear in how many processes these components participate. We show that AtBMI1 proteins are required to promote all developmental phase transitions and to control cell proliferation during organ growth and development, expanding their proposed range of action. While AtBMI1 function during germination is closely linked to B3 domain transcription factors VAL1/2 possibly in combination with GT-box binding factors, other AtBMI1 regulatory networks require participation of different factor combinations. Conversely, EMF1 and LHP1 bind many H3K27me3 positive genes up-regulated in atbmi1a/b/c mutants; however, loss of their function affects expression of a different subset, suggesting that even if EMF1, LHP1, and AtBMI1 exist in a common PRC1 variant, their role in repression depends on the functional context.
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Affiliation(s)
- Wiam Merini
- Institute of Plant Biochemistry and Photosynthesis, 41092 Seville, Spain (W.M., A.G.-Z., M.C.)
- Department of Computer Science and Artificial Intelligence, University of Seville, 41012 Seville, Spain (F.J.R.-C.); and
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, 50829 Cologne, Germany (F.T.)
| | - Francisco J Romero-Campero
- Institute of Plant Biochemistry and Photosynthesis, 41092 Seville, Spain (W.M., A.G.-Z., M.C.)
- Department of Computer Science and Artificial Intelligence, University of Seville, 41012 Seville, Spain (F.J.R.-C.); and
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, 50829 Cologne, Germany (F.T.)
| | - Angeles Gomez-Zambrano
- Institute of Plant Biochemistry and Photosynthesis, 41092 Seville, Spain (W.M., A.G.-Z., M.C.)
- Department of Computer Science and Artificial Intelligence, University of Seville, 41012 Seville, Spain (F.J.R.-C.); and
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, 50829 Cologne, Germany (F.T.)
| | - Yue Zhou
- Institute of Plant Biochemistry and Photosynthesis, 41092 Seville, Spain (W.M., A.G.-Z., M.C.)
- Department of Computer Science and Artificial Intelligence, University of Seville, 41012 Seville, Spain (F.J.R.-C.); and
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, 50829 Cologne, Germany (F.T.)
| | - Franziska Turck
- Institute of Plant Biochemistry and Photosynthesis, 41092 Seville, Spain (W.M., A.G.-Z., M.C.)
- Department of Computer Science and Artificial Intelligence, University of Seville, 41012 Seville, Spain (F.J.R.-C.); and
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, 50829 Cologne, Germany (F.T.)
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis, 41092 Seville, Spain (W.M., A.G.-Z., M.C.);
- Department of Computer Science and Artificial Intelligence, University of Seville, 41012 Seville, Spain (F.J.R.-C.); and
- Max Planck Institute for Plant Breeding Research, Department of Plant Developmental Biology, 50829 Cologne, Germany (F.T.)
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109
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110
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Feng J, Lu J. LHP1 Could Act as an Activator and a Repressor of Transcription in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:2041. [PMID: 29234344 PMCID: PMC5712405 DOI: 10.3389/fpls.2017.02041] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/14/2017] [Indexed: 05/19/2023]
Abstract
Polycomb group (PcG) proteins within the polycomb repressive complex 1 (PRC1) and PRC2 are significant epigenetic regulatory factors involved in important cellular and developmental processes in eukaryotes. In Arabidopsis, LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), also known as TERMINAL FLOWER 2, has been proposed as a plant specific subunit of PRC1 that could bind the trimethylated lysine 27 of histone H3 (H3K27me3), which is established by PRC2 and is required for a functional plant PcG system. LHP1 not only interacts with PRC1 to catalyze monoubiquitination at lysine 119 of histone H2A but also functions with PRC2 to establish H3K27me3. This review is about the interaction of LHP1 with PRC1 and PRC2, in which LHP1 may act as a bridge between the two. Meantime, this review highlights that LHP1 could act as an activator and a repressor of transcription.
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Affiliation(s)
- Jing Feng
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
- *Correspondence: Jiang Lu, Jing Feng,
| | - Jiang Lu
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning, China
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Jiang Lu, Jing Feng,
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111
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Li J, Wang Z, Hu Y, Cao Y, Ma L. Polycomb Group Proteins RING1A and RING1B Regulate the Vegetative Phase Transition in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2017; 8:867. [PMID: 28596781 PMCID: PMC5443144 DOI: 10.3389/fpls.2017.00867] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 05/09/2017] [Indexed: 05/18/2023]
Abstract
Polycomb group (PcG) protein-mediated gene silencing is a major regulatory mechanism in higher eukaryotes that affects gene expression at the transcriptional level. Here, we report that two conserved homologous PcG proteins, RING1A and RING1B (RING1A/B), are required for global H2A monoubiquitination (H2Aub) in Arabidopsis. The mutation of RING1A/B increased the expression of members of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) gene family and caused an early vegetative phase transition. The early vegetative phase transition observed in ring1a ring1b double mutant plants was dependent on an SPL family gene, and the H2Aub status of the chromatin at SPL locus was dependent on RING1A/B. Moreover, mutation in RING1A/B affected the miRNA156a-mediated vegetative phase transition, and RING1A/B and the AGO7-miR390-TAS3 pathway were found to additively regulate this transition in Arabidopsis. Together, our results demonstrate that RING1A/B regulates the vegetative phase transition in Arabidopsis through the repression of SPL family genes.
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112
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Chen D, Molitor AM, Xu L, Shen WH. Arabidopsis PRC1 core component AtRING1 regulates stem cell-determining carpel development mainly through repression of class I KNOX genes. BMC Biol 2016; 14:112. [PMID: 28007029 PMCID: PMC5178098 DOI: 10.1186/s12915-016-0336-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/25/2016] [Indexed: 11/27/2022] Open
Abstract
Background Polycomb repressive complex 2 (PRC2)-catalyzed H3K27me3 marks are tightly associated with the WUS-AG negative feedback loop to terminate floral stem cell fate to promote carpel development, but the roles of Polycomb repressive complex 1 (PRC1) in this event remain largely uncharacterized. Results Here we show conspicuous variability in the morphology and number of carpels among individual flowers in the absence of the PRC1 core components AtRING1a and AtRING1b, which contrasts with the wild-type floral meristem consumed by uniform carpel production in Arabidopsis thaliana. Promoter-driven GUS reporter analysis showed that AtRING1a and AtRING1b display a largely similar expression pattern, except in the case of the exclusively maternal-preferred expression of AtRING1b, but not AtRING1a, in the endosperm. Indeterminate carpel development in the atring1a;atring1b double mutant is due to replum/ovule-to-carpel conversion in association with ectopic expression of class I KNOX (KNOX-I) genes. Moreover, AtRING1a and AtRING1b also play a critical role in ovule development, mainly through promoting the degeneration of non-functional megaspores and proper integument formation. Genetic interaction analysis indicates that the AtRING1a/b-regulated KNOX-I pathway acts largely in a complementary manner with the WUS-AG pathway in controlling floral stem cell maintenance and proper carpel development. Conclusions Our study uncovers a novel mechanistic pathway through which AtRING1a and AtRING1b repress KNOX-I expression to terminate floral stem cell activities and establish carpel cell fate identities. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0336-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Donghong Chen
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 du CNRS, Université de Strasbourg, 12 rue du Général ZIMMER, 67084, Strasbourg, France. .,College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Hunan Agricultural University, Changsha, 410128, China.
| | - Anne M Molitor
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 du CNRS, Université de Strasbourg, 12 rue du Général ZIMMER, 67084, Strasbourg, France.,Present address: Institut de Genetique et de Biologie Moleculaire et Cellulaire, 1 rue Laurent Fries, 67404, Illkirch, France
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes (IBMP), UPR2357 du CNRS, Université de Strasbourg, 12 rue du Général ZIMMER, 67084, Strasbourg, France.
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113
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Xiao J, Lee US, Wagner D. Tug of war: adding and removing histone lysine methylation in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2016; 34:41-53. [PMID: 27614255 DOI: 10.1016/j.pbi.2016.08.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/11/2016] [Accepted: 08/24/2016] [Indexed: 05/17/2023]
Abstract
Histone lysine methylation plays a fundamental role in the epigenetic regulation of gene expression in multicellular eukaryotes, including plants. It shapes plant developmental and growth programs as well as responses to the environment. The methylation status of certain amino-acids, in particular of the histone 3 (H3) lysine tails, is dynamically controlled by opposite acting histone methyltransferase 'writers' and histone demethylase 'erasers'. The methylation status is interpreted by a third set of proteins, the histone modification 'readers', which specifically bind to a methylated amino-acid on the H3 tail. Histone methylation writers, readers, and erasers themselves are regulated by intrinsic or extrinsic stimuli; this forms a feedback loop that contributes to development and environmental adaptation in Arabidopsis and other plants. Recent studies have expanded our knowledge regarding the biological roles and dynamic regulation of histone methylation. In this review, we will discuss recent advances in understanding the regulation and roles of histone methylation in plants and animals.
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Affiliation(s)
- Jun Xiao
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Un-Sa Lee
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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114
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Wang Z, Chen F, Li X, Cao H, Ding M, Zhang C, Zuo J, Xu C, Xu J, Deng X, Xiang Y, Soppe WJJ, Liu Y. Arabidopsis seed germination speed is controlled by SNL histone deacetylase-binding factor-mediated regulation of AUX1. Nat Commun 2016; 7:13412. [PMID: 27834370 PMCID: PMC5114640 DOI: 10.1038/ncomms13412] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 09/30/2016] [Indexed: 12/22/2022] Open
Abstract
Histone acetylation is known to affect the speed of seed germination, but the molecular regulatory basis of this remains ambiguous. Here we report that loss of function of two histone deacetylase-binding factors, SWI-INDEPENDENT3 (SIN3)-LIKE1 (SNL1) and SNL2, results in accelerated radicle protrusion and growth during seed germination. AUXIN RESISTANT 1 (AUX1) is identified as a key factor in this process, enhancing germination speed downstream of SNL1 and SNL2. AUX1 expression and histone H3 acetylation at lysines 9 and 18 is regulated by SNL1 and SNL2. The D-type cyclins encoding genes CYCD1;1 and CYCD4;1 display increased expression in AUX1 over-expression lines and the snl1snl2 double mutant. Accordingly, knockout of CYCD4;1 reduces seed germination speed of AUX1 over-expression lines and snl1snl2 suggesting the importance of cell cycling for radicle protrusion during seed germination. Together, our work identifies AUX1 as a link between histone acetylation mediated by SNL1 and SNL2, and radicle growth promoted by CYCD1;1 and CYCD4;1 during seed germination. Histone acetylation influences the speed of seed germination. Here, Wang et al. show that loss of the SNL1/SNL2 histone deacetylase binding factors accelerates seed germination and provide evidence that they act by regulating the expression of AUX1 which in turn influences cell division.
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Affiliation(s)
- Zhi Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Fengying Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaoying Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Meng Ding
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cun Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinghong Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaonan Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jimei Xu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Deng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yong Xiang
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Wim J J Soppe
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany.,Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, 53115 Bonn, Germany
| | - Yongxiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Devic M, Roscoe T. Seed maturation: Simplification of control networks in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:335-346. [PMID: 27717470 DOI: 10.1016/j.plantsci.2016.08.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 08/05/2016] [Accepted: 08/21/2016] [Indexed: 05/09/2023]
Abstract
Networks controlling developmental or metabolic processes in plants are often complex as a consequence of the duplication and specialisation of the regulatory genes as well as the numerous levels of transcriptional and post-transcriptional controls added during evolution. Networks serve to accommodate multicellular complexity and increase robustness to environmental changes. Mathematical simplification by regrouping genes or pathways in a limited number of hubs has facilitated the construction of models for complex traits. In a complementary approach, a biological simplification can be achieved by using genetic modification to understand the core and singular ancestral function of the network, which is likely to be more prevalent within the plant kingdom rather than specific to a species. With this viewpoint, we review examples of simplification successfully undertaken in yeast and other organisms. A strategy of progressive complementation of single, double and triple mutants of seed maturation confirmed the fundamental role of the AFL sub-family of B3 transcription factors as master regulators of seed maturation, illustrating that biological simplification of complex networks could be more widely applied in plants. Defining minimal control networks will facilitate evolutionary comparisons of regulatory processes and the identification of an essential gene set for synthetic biology.
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Affiliation(s)
- Martine Devic
- Régulations Epigénétiques et Développement de la Graine, ERL 3500 CNRS-IRD UMR DIADE, Centre IRD de Montpellier, 911 avenue Agropolis BP64501, 34394, Montpellier, France.
| | - Thomas Roscoe
- Régulations Epigénétiques et Développement de la Graine, ERL 3500 CNRS-IRD UMR DIADE, Centre IRD de Montpellier, 911 avenue Agropolis BP64501, 34394, Montpellier, France
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Feng J, Chen D, Berr A, Shen WH. ZRF1 Chromatin Regulators Have Polycomb Silencing and Independent Roles in Development. PLANT PHYSIOLOGY 2016; 172:1746-1759. [PMID: 27630184 PMCID: PMC5100768 DOI: 10.1104/pp.16.00193] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 09/12/2016] [Indexed: 05/05/2023]
Abstract
Histone H2A monoubiquitination (H2Aub1), catalyzed by Polycomb-Repressive Complex1 (PRC1), is a key epigenetic mark in Polycomb silencing. However, little is known about how H2Aub1 is read to exert downstream physiological functions. The animal ZUOTIN-RELATED FACTOR1 (ZRF1) has been reported to bind H2Aub1 to promote or repress the expression of varied target genes. Here, we show that the Arabidopsis (Arabidopsis thaliana) ZRF1 homologs, AtZRF1a and AtZRF1b, are key regulators of multiple processes during plant growth and development. Loss of function of both AtZRF1a and AtZRF1b in atzrf1a atzrf1b mutants causes seed germination delay, small plant size, abnormal meristem activity, abnormal flower development, as well as gametophyte transmission and embryogenesis defects. Some of these defects overlap with those described previously in the PRC1-defective mutants atbmi1a atbmi1b and atring1a atring1b, but others are specific to atzrf1a atzrf1b In line with this, 4,519 genes (representing more than 14% of all genes) within the Arabidopsis genome are found differentially expressed in atzrf1a atzrf1b seedlings, and among them, 114 genes are commonly up-regulated in atring1a atring1b and atbmi1a atbmi1b Finally, we show that in both atzrf1a atzrf1b and atbmi1a atbmi1b seedlings, the seed developmental genes ABSCISIC ACID INSENSITIVE3, CRUCIFERIN3, and CHOTTO1 are derepressed, in association with the reduced levels of H2Aub1 and histone H3 lysine-27 trimethylation (H3K27me3). Collectively, our results indicate that AtZRF1a/b play both PRC1-related and PRC1-unrelated functions in regulating plant growth and development and that AtZRF1a/b promote H2Aub1 and H3K27me3 deposition in gene suppression. Our work provides novel insight into the mechanisms of function of this family of evolutionarily conserved chromatin regulators.
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Affiliation(s)
- Jing Feng
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357 Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (J.F., D.C., A.B., W.-H.S.); and
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China (D.C.)
| | - Donghong Chen
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357 Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (J.F., D.C., A.B., W.-H.S.); and
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China (D.C.)
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357 Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (J.F., D.C., A.B., W.-H.S.); and
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China (D.C.)
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357 Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France (J.F., D.C., A.B., W.-H.S.); and
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China (D.C.)
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Boccaccini A, Lorrai R, Ruta V, Frey A, Mercey-Boutet S, Marion-Poll A, Tarkowská D, Strnad M, Costantino P, Vittorioso P. The DAG1 transcription factor negatively regulates the seed-to-seedling transition in Arabidopsis acting on ABA and GA levels. BMC PLANT BIOLOGY 2016; 16:198. [PMID: 27613195 PMCID: PMC5016951 DOI: 10.1186/s12870-016-0890-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 09/04/2016] [Indexed: 05/05/2023]
Abstract
BACKGROUND In seeds, the transition from dormancy to germination is regulated by abscisic acid (ABA) and gibberellins (GAs), and involves chromatin remodelling. Particularly, the repressive mark H3K27 trimethylation (H3K27me3) has been shown to target many master regulators of this transition. DAG1 (DOF AFFECTING GERMINATION1), is a negative regulator of seed germination in Arabidopsis, and directly represses the GA biosynthetic gene GA3ox1 (gibberellin 3-β-dioxygenase 1). We set to investigate the role of DAG1 in seed dormancy and maturation with respect to epigenetic and hormonal control. RESULTS We show that DAG1 expression is controlled at the epigenetic level through the H3K27me3 mark during the seed-to-seedling transition, and that DAG1 directly represses also the ABA catabolic gene CYP707A2; consistently, the ABA level is lower while the GA level is higher in dag1 mutant seeds. Furthermore, both DAG1 expression and protein stability are controlled by GAs. CONCLUSIONS Our results point to DAG1 as a key player in the control of the developmental switch between seed dormancy and germination.
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Affiliation(s)
- Alessandra Boccaccini
- Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Riccardo Lorrai
- Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Veronica Ruta
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Anne Frey
- Institut Jean-Pierre Bourgin, UMR1318, INRA, AgroParisTech, Université Paris-Saclay, RD10, 78026 Versailles, Cedex France
| | - Stephanie Mercey-Boutet
- Institut Jean-Pierre Bourgin, UMR1318, INRA, AgroParisTech, Université Paris-Saclay, RD10, 78026 Versailles, Cedex France
| | - Annie Marion-Poll
- Institut Jean-Pierre Bourgin, UMR1318, INRA, AgroParisTech, Université Paris-Saclay, RD10, 78026 Versailles, Cedex France
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany ASCR & Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany ASCR & Palacký University, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
| | - Paolo Costantino
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Paola Vittorioso
- Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
- Dipartimento di Biologia e Biotecnologie “C. Darwin”, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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Fatihi A, Boulard C, Bouyer D, Baud S, Dubreucq B, Lepiniec L. Deciphering and modifying LAFL transcriptional regulatory network in seed for improving yield and quality of storage compounds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 250:198-204. [PMID: 27457996 DOI: 10.1016/j.plantsci.2016.06.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 06/16/2016] [Accepted: 06/18/2016] [Indexed: 05/11/2023]
Abstract
Increasing yield and quality of seed storage compounds in a sustainable way is a key challenge for our societies. Genome-wide analyses conducted in both monocot and dicot angiosperms emphasized drastic transcriptional switches that occur during seed development. In Arabidopsis thaliana, a reference species, genetic and molecular analyses have demonstrated the key role of LAFL (LEC1, ABI3, FUS3, and LEC2) transcription factors (TFs), in controlling gene expression programs essential to accomplish seed maturation and the accumulation of storage compounds. Here, we summarize recent progress obtained in the characterization of these LAFL proteins, their regulation, partners and target genes. Moreover, we illustrate how these evolutionary conserved TFs can be used to engineer new crops with altered seed compositions and point out the current limitations. Last, we discuss about the interest of investigating further the environmental and epigenetic regulation of this network for the coming years.
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Affiliation(s)
- Abdelhak Fatihi
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.
| | - Céline Boulard
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Daniel Bouyer
- Institut de Biologie de l'ENS, CNRS UMR8197, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris cedex 05, France
| | - Sébastien Baud
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Bertrand Dubreucq
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France
| | - Loïc Lepiniec
- IJPB, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles Cedex, France.
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119
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Brkljacic J, Grotewold E. Combinatorial control of plant gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:31-40. [PMID: 27427484 DOI: 10.1016/j.bbagrm.2016.07.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/05/2016] [Accepted: 07/07/2016] [Indexed: 01/02/2023]
Abstract
Combinatorial gene regulation provides a mechanism by which relatively small numbers of transcription factors can control the expression of a much larger number of genes with finely tuned temporal and spatial patterns. This is achieved by transcription factors assembling into complexes in a combinatorial fashion, exponentially increasing the number of genes that they can target. Such an arrangement also increases the specificity and affinity for the cis-regulatory sequences required for accurate target gene expression. Superimposed on this transcription factor combinatorial arrangement is the increasing realization that histone modification marks expand the regulatory information, which is interpreted by histone readers and writers that are part of the regulatory apparatus. Here, we review the progress in these areas from the perspective of plant combinatorial gene regulation, providing examples of different regulatory solutions and comparing them to other metazoans. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- Jelena Brkljacic
- Center for Applied Plant Sciences (CAPS),The Ohio State University, Columbus, OH 43210, USA
| | - Erich Grotewold
- Center for Applied Plant Sciences (CAPS),The Ohio State University, Columbus, OH 43210, USA; Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
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120
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Structure and function of histone methylation-binding proteins in plants. Biochem J 2016; 473:1663-80. [DOI: 10.1042/bcj20160123] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 02/29/2016] [Indexed: 12/28/2022]
Abstract
Post-translational modifications of histones play important roles in modulating many essential biological processes in both animals and plants. These covalent modifications, including methylation, acetylation, phosphorylation, ubiquitination, SUMOylation and so on, are laid out and erased by histone-modifying enzymes and read out by effector proteins. Recent studies have revealed that a number of developmental processes in plants are under the control of histone post-translational modifications, such as floral transition, seed germination, organogenesis and morphogenesis. Therefore, it is critical to identify those protein domains, which could specifically recognize these post-translational modifications to modulate chromatin structure and regulate gene expression. In the present review, we discuss the recent progress in understanding the structure and function of the histone methylation readers in plants, by focusing on Arabidopsis thaliana proteins.
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121
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Considine MJ, Considine JA. On the language and physiology of dormancy and quiescence in plants. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3189-203. [PMID: 27053719 DOI: 10.1093/jxb/erw138] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The language of dormancy is rich and poetic, as researchers spanning disciplines and decades have attempted to understand the spell that entranced 'Sleeping Beauty', and how she was gently awoken. The misleading use of 'dormancy', applied to annual axillary buds, for example, has confounded progress. Language is increasingly important as genetic and genomic approaches become more accessible to species of agricultural and ecological importance. Here we examine how terminology has been applied to different eco-physiological states in plants, and with pertinent reference to quiescent states described in other domains of life, in order to place plant quiescence and dormancy in a more complete context than previously described. The physiological consensus defines latency or quiescence as opportunistic avoidance states, where growth resumes in favourable conditions. In contrast, the dormant state in higher plants is entrained in the life history of the organism. Competence to resume growth requires quantitative and specific conditioning. This definition applies only to the embryo of seeds and specialized meristems in higher plants; however, mechanistic control of dormancy extends to mobile signals from peripheral tissues and organs, such as the endosperm of seed or subtending leaf of buds. The distinction between dormancy, quiescence, and stress-hardiness remains poorly delineated, most particularly in buds of winter perennials, which comprise multiple meristems of differing organogenic states. Studies in seeds have shown that dormancy is not a monogenic trait, and limited study has thus far failed to canalize dormancy as seen in seeds and buds. We argue that a common language, based on physiology, is central to enable further dissection of the quiescent and dormant states in plants. We direct the topic largely to woody species showing a single cycle of growth and reproduction per year, as these bear the majority of global timber, fruit, and nut production, as well being of great ecological value. However, for context and hypotheses, we draw on knowledge from annuals and other specialized plant conditions, from a perspective of the major physical, metabolic, and molecular cues that regulate cellular activity.
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Affiliation(s)
- Michael J Considine
- School of Plant Biology, and The Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia Department of Agriculture and Food Western Australia, South Perth, WA 6151 Australia Centre for Plant Sciences, University of Leeds, Leeds, Yorkshire LS2 9JT, UK
| | - John A Considine
- School of Plant Biology, and The Institute of Agriculture, The University of Western Australia, Perth, WA 6009 Australia
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122
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Chen DH, Huang Y, Ruan Y, Shen WH. The evolutionary landscape of PRC1 core components in green lineage. PLANTA 2016; 243:825-46. [PMID: 26729480 DOI: 10.1007/s00425-015-2451-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 12/16/2015] [Indexed: 05/20/2023]
Abstract
The origin and evolution of plant PRC1 core components. Polycomb repressive complex1 (PRC1) plays critical roles in epigenetic silencing of homeotic genes and determination of cell fate. Animal PRC1 has been well investigated for a long time, whereas plant PRC1 was just confirmed in recent years. It is enigmatic whether PRC1 core components in plants share a common ancestor with those in animals. We evaluated the origin of plant PRC1 RING-finger proteins (RING1 and BMI1) through comparing with the homologs in some representative unikonts and using BMI1- and RING1-like proteins as reciprocal outgroup, finding both PRC1 RING-finger proteins have the earliest origin in mosses, similar to LHP1. Additionally, the gene structure, copy number, and domain organization were analyzed to deeply understand the evolutionary history of plant PRC1 complex. In conclusion, PRC1 RING-finger proteins have independent origins in plants and animals, but convergent evolution might attribute to the conservation of PRC1 complex in plants and animals. Plant LHP1 as the homolog of non-PRC1 protein HP1 was recruited to fulfill the role of Pc counterpart. Gene duplication followed by functional divergence makes a great contribution to evolutionary progress of PRC1 in green plants.
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Affiliation(s)
- Dong-hong Chen
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China.
| | - Yong Huang
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China
| | - Ying Ruan
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China.
| | - Wen-Hui Shen
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
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Ramu VS, Swetha TN, Sheela SH, Babitha CK, Rohini S, Reddy MK, Tuteja N, Reddy CP, Prasad TG, Udayakumar M. Simultaneous expression of regulatory genes associated with specific drought-adaptive traits improves drought adaptation in peanut. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1008-20. [PMID: 26383697 DOI: 10.1111/pbi.12461] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 07/28/2015] [Accepted: 08/05/2015] [Indexed: 05/04/2023]
Abstract
Adaptation of crops to drought-prone rain-fed conditions can be achieved by improving plant traits such as efficient water mining (by superior root characters) and cellular-level tolerance mechanisms. Pyramiding these drought-adaptive traits by simultaneous expression of genes regulating drought-adaptive mechanisms has phenomenal relevance in improving stress tolerance. In this study, we provide evidence that peanut transgenic plants expressing Alfalfa zinc finger 1 (Alfin1), a root growth-associated transcription factor gene, Pennisetum glaucum heat-shock factor (PgHSF4) and Pea DNA helicase (PDH45) involved in protein turnover and protection showed improved tolerance, higher growth and productivity under drought stress conditions. Stable integration of all the transgenes was noticed in transgenic lines. The transgenic lines showed higher root growth, cooler crop canopy air temperature difference (less CCATD) and higher relative water content (RWC) under drought stress. Low proline levels in transgenic lines substantiate the maintenance of higher water status. The survival and recovery of transgenic lines was significantly higher under gradual moisture stress conditions with higher biomass. Transgenic lines also showed significant tolerance to ethrel-induced senescence and methyl viologen-induced oxidative stress. Several stress-responsive genes such as heat-shock proteins (HSPs), RING box protein-1 (RBX1), Aldose reductase, late embryogenesis abundant-5 (LEA5) and proline-rich protein-2 (PRP2), a gene involved in root growth, showed enhanced expression under stress in transgenic lines. Thus, the simultaneous expression of regulatory genes contributing for drought-adaptive traits can improve crop adaptation and productivity under water-limited conditions.
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Affiliation(s)
- Vemanna S Ramu
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, India
| | - Thavarekere N Swetha
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, India
| | - Shekarappa H Sheela
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, India
| | | | - Sreevathsa Rohini
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, India
- National Research Centre for Plant Biotechnology, New Delhi, India
| | - Malireddy K Reddy
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Chandrashekar P Reddy
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, India
| | - Trichi Ganesh Prasad
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, India
| | - Makarla Udayakumar
- Department of Crop Physiology, University of Agricultural Sciences, GKVK, Bangalore, India
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Boureau L, How-Kit A, Teyssier E, Drevensek S, Rainieri M, Joubès J, Stammitti L, Pribat A, Bowler C, Hong Y, Gallusci P. A CURLY LEAF homologue controls both vegetative and reproductive development of tomato plants. PLANT MOLECULAR BIOLOGY 2016; 90:485-501. [PMID: 26846417 DOI: 10.1007/s11103-016-0436-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 01/08/2016] [Indexed: 05/21/2023]
Abstract
The Enhancer of Zeste Polycomb group proteins, which are encoded by a small gene family in Arabidopsis thaliana, participate to the control of plant development. In the tomato (Solanum lycopersicum), these proteins are encoded by three genes (SlEZ1, SlEZ2 and SlEZ3) that display specific expression profiles. Using a gene specific RNAi strategy, we demonstrate that repression of SlEZ2 correlates with a general reduction of H3K27me3 levels, indicating that SlEZ2 is part of an active PRC2 complex. Reduction of SlEZ2 gene expression impacts the vegetative development of tomato plants, consistent with SlEZ2 having retained at least some of the functions of the Arabidopsis CURLY LEAF (CLF) protein. Notwithstanding, we observed significant differences between transgenic SlEZ2 RNAi tomato plants and Arabidopsis clf mutants. First, we found that reduced SlEZ2 expression has dramatic effects on tomato fruit development and ripening, functions not described in Arabidopsis for the CLF protein. In addition, repression of SlEZ2 has no significant effect on the flowering time or the control of flower organ identity, in contrast to the Arabidopsis clf mutation. Taken together, our results are consistent with a diversification of the function of CLF orthologues in plants, and indicate that although partly conserved amongst plants, the function of EZ proteins need to be newly investigated for non-model plants because they might have been recruited to specific developmental processes.
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Affiliation(s)
- L Boureau
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France
- Laboratory of Hematology, Centre Hospitalier Universitaire de Bordeaux - Hopital Haut Leveque, 5 Avenue Magellan, 33600, Pessac, France
| | - A How-Kit
- Laboratory for Functional Genomics, Foundation Jean Dausset - CEPH, 75010, Paris, France
| | - E Teyssier
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France
- Grape Ecophysiology and Functional Biology Laboratory, ISVV, University of Bordeaux, 210 Chemin de Leysotte, CS50008, 33882, Villenave d'Ornon Cédex, France
| | - S Drevensek
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure CNRS UMR 8197INSERM U1024, 46 rue d'Ulm, 75005, Paris, France
- Institute of Plant Sciences Paris-Saclay, INRA, CNRS, Université, Paris-Sud, Université d'Evry, Université Paris-Diderot, Bâtiment 630, 91405, Orsay, France
| | - M Rainieri
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure CNRS UMR 8197INSERM U1024, 46 rue d'Ulm, 75005, Paris, France
| | - J Joubès
- Laboratoire de Biogenèse Membranaire, UMR 5200, CNRS, Université de Bordeaux, Bâtiment A3, INRA, 71 Avenue Edouard Bourlaux, 33140, Villenave d'Ornon, France
- Laboratoire de Biogenèse Membranaire, UMR5200, CNRS, Bâtiment A3, INRA, 71 Avenue Edouard Bourlaux, 33140, Villenave d'Ornon, France
| | - L Stammitti
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France
- Grape Ecophysiology and Functional Biology Laboratory, ISVV, University of Bordeaux, 210 Chemin de Leysotte, CS50008, 33882, Villenave d'Ornon Cédex, France
| | - A Pribat
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France
| | - C Bowler
- Environmental and Evolutionary Genomics Section, Institut de Biologie de l'Ecole Normale Supérieure CNRS UMR 8197INSERM U1024, 46 rue d'Ulm, 75005, Paris, France
| | - Y Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, People's Republic of China.
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick, CV4 7AL, UK.
| | - P Gallusci
- UMR BFP, University of Bordeaux, 71 Avenue E Bourlaux, 33882, Villenave d'Ornon, France.
- Grape Ecophysiology and Functional Biology Laboratory, ISVV, University of Bordeaux, 210 Chemin de Leysotte, CS50008, 33882, Villenave d'Ornon Cédex, France.
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Wu T, Yang C, Ding B, Feng Z, Wang Q, He J, Tong J, Xiao L, Jiang L, Wan J. Microarray-based gene expression analysis of strong seed dormancy in rice cv. N22 and less dormant mutant derivatives. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 99:27-38. [PMID: 26713549 DOI: 10.1016/j.plaphy.2015.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 11/28/2015] [Accepted: 12/01/2015] [Indexed: 05/04/2023]
Abstract
Seed dormancy in rice is an important trait related to the pre-harvest sprouting resistance. In order to understand the molecular mechanisms of seed dormancy, gene expression was investigated by transcriptome analysis using seeds of the strongly dormant cultivar N22 and its less dormant mutants Q4359 and Q4646 at 24 days after heading (DAH). Microarray data revealed more differentially expressed genes in Q4359 than in Q4646 compared to N22. Most genes differing between Q4646 and N22 also differed between Q4359 and N22. GO analysis of genes differentially expressed in both Q4359 and Q4646 revealed that some genes such as those for starch biosynthesis were repressed, whereas metabolic genes such as those for carbohydrate metabolism were enhanced in Q4359 and Q4646 seeds relative to N22. Expression of some genes involved in cell redox homeostasis and chromatin remodeling differed significantly only between Q4359 and N22. The results suggested a close correlation between cell redox homeostasis, chromatin remodeling and seed dormancy. In addition, some genes involved in ABA signaling were down-regulated, and several genes involved in GA biosynthesis and signaling were up-regulated. These observations suggest that reduced seed dormancy in Q4359 was regulated by ABA-GA antagonism. A few differentially expressed genes were located in the regions containing qSdn-1 and qSdn-5 suggesting that they could be candidate genes underlying seed dormancy. Our work provides useful leads to further determine the underling mechanisms of seed dormancy and for cloning seed dormancy genes from N22.
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Affiliation(s)
- Tao Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunyan Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China
| | - Baoxu Ding
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiming Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qian Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128, China
| | - Ling Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Jianmin Wan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Förderer A, Zhou Y, Turck F. The age of multiplexity: recruitment and interactions of Polycomb complexes in plants. CURRENT OPINION IN PLANT BIOLOGY 2016; 29:169-78. [PMID: 26826786 DOI: 10.1016/j.pbi.2015.11.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 11/23/2015] [Accepted: 11/28/2015] [Indexed: 05/08/2023]
Abstract
Polycomb group (PcG) proteins form distinct complexes that modify chromatin by histone H3 methylation and H2A mono-ubiquitination leading to chromatin compaction and epigenetic repression of target genes. A network of PcG protein complexes, associated partners and antagonistically acting chromatin modifiers is essential to regulate developmental transitions and cell fate in all multicellular eukaryotes. In this review, we discuss insights on the subfunctionalization of PcG complexes and their modes of recruitment to target sites based on data from the model organism Arabidopsis thaliana.
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Affiliation(s)
- Alexander Förderer
- Max Planck Institute for Plant Breeding Research, Department Plant Developmental Biology, Carl von Linne Weg 10, 50829 Köln, Germany
| | - Yue Zhou
- Max Planck Institute for Plant Breeding Research, Department Plant Developmental Biology, Carl von Linne Weg 10, 50829 Köln, Germany
| | - Franziska Turck
- Max Planck Institute for Plant Breeding Research, Department Plant Developmental Biology, Carl von Linne Weg 10, 50829 Köln, Germany.
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127
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Wang H, Liu C, Cheng J, Liu J, Zhang L, He C, Shen WH, Jin H, Xu L, Zhang Y. Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements. PLoS Genet 2016; 12:e1005771. [PMID: 26760036 PMCID: PMC4711971 DOI: 10.1371/journal.pgen.1005771] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Accepted: 12/04/2015] [Indexed: 11/19/2022] Open
Abstract
Polycomb repressive complexes (PRCs) play crucial roles in transcriptional repression and developmental regulation in both plants and animals. In plants, depletion of different members of PRCs causes both overlapping and unique phenotypic defects. However, the underlying molecular mechanism determining the target specificity and functional diversity is not sufficiently characterized. Here, we quantitatively compared changes of tri-methylation at H3K27 in Arabidopsis mutants deprived of various key PRC components. We show that CURLY LEAF (CLF), a major catalytic subunit of PRC2, coordinates with different members of PRC1 in suppression of distinct plant developmental programs. We found that expression of flower development genes is repressed in seedlings preferentially via non-redundant role of CLF, which specifically associated with LIKE HETEROCHROMATIN PROTEIN1 (LHP1). In contrast, expression of embryo development genes is repressed by PRC1-catalytic core subunits AtBMI1 and AtRING1 in common with PRC2-catalytic enzymes CLF or SWINGER (SWN). This context-dependent role of CLF corresponds well with the change in H3K27me3 profiles, and is remarkably associated with differential co-occupancy of binding motifs of transcription factors (TFs), including MADS box and ABA-related factors. We propose that different combinations of PRC members distinctively regulate different developmental programs, and their target specificity is modulated by specific TFs. Polycomb group proteins (PcGs) are essential for development in both animals and plants. Studies in plants are advantageous for elucidation of specific effects of PcGs during development, since most PcG mutants are viable in plants but not in animals. Previous efforts in genetic study of plant PcGs revealed that different PcGs have both common and unique effects on plant development, but the mechanisms underlying the specific regulation of different developmental programs by PcGs are still far from clear. In this study, we quantitatively compared the change in H3K27me3 and gene expression profiles between mutants of key PcG members on a genome-wide scale in Arabidopsis seedlings, and successfully unraveled different developmental programs that are specifically regulated by different combinations of PcGs. This context specific effect of PcGs is closely associated with different sets of transcription factor binding motifs. Together, we revealed on a genome-wide scale that different combinations of PcGs, as well as their association with the binding sites of different TFs, serve to explain the specific regulation of different developmental programs by PcGs.
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Affiliation(s)
- Hua Wang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chunmei Liu
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jingfei Cheng
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jian Liu
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Zhang
- Department of Chemistry, Fudan University, Shanghai, China
| | - Chongsheng He
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
- Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS, Université de Strasbourg, Strasbourg, France
| | - Hong Jin
- Department of Chemistry, Fudan University, Shanghai, China
- Institute of Biomedical Science, Fudan University, Shanghai, China
- * E-mail: (HJ); (LX); (YZ)
| | - Lin Xu
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (HJ); (LX); (YZ)
| | - Yijing Zhang
- National Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (HJ); (LX); (YZ)
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Ye Y, Gong Z, Lu X, Miao D, Shi J, Lu J, Zhao Y. Germostatin resistance locus 1 encodes a PHD finger protein involved in auxin-mediated seed dormancy and germination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:3-15. [PMID: 26611158 DOI: 10.1111/tpj.13086] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/16/2015] [Accepted: 11/19/2015] [Indexed: 05/06/2023]
Abstract
Seed dormancy and germination are important physiological processes during the life cycle of a seed plant. Recently, auxin has been characterized as a positive regulator that functions during seed dormancy and as a negative regulator during germination. Through chemical genetic screenings, we have identified a small molecule, germostatin (GS), which effectively inhibits seed germination in Arabidopsis. GSR1 (germostatin resistance locus 1) encodes a tandem plant homeodomain (PHD) finger protein, identified by screening GS-resistant mutants. Certain PHD fingers of GSR1 are capable of binding unmethylated H3K4, which has been reported as an epigenetic mark of gene transcriptional repression. Biochemical studies show that GSR1 physically interacts with the transcriptional repressor ARF16 and attenuates the intensity of interaction of IAA17/ARF16 by directly interacting with IAA17 to release ARF16. Further results show that axr3-1, arf10 arf16 are hyposensitive to GS, and gsr1 not only resists auxin-mediated inhibition of seed germination but also displays decreased dormancy. We therefore propose that GSR1 may form a co-repressor with ARF16 to regulate seed germination. Besides promoting auxin biosynthesis via upregulating expression of YUCCA1, GS also enhances auxin responses by inducing degradation of DΙΙ-VENUS and upregulating expression of DR5-GFP. In summary, we identified GSR1 as a member of the auxin-mediated seed germination genetic network, and GS, a small non-auxin molecule that specifically acts on auxin-mediated seed germination.
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Affiliation(s)
- Yajin Ye
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
| | - Ziying Gong
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
| | - Xiao Lu
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
| | - Deyan Miao
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
| | - Jianmin Shi
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
| | - Juan Lu
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
| | - Yang Zhao
- Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, 200032, Shanghai, China
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 68 Wenchang Road, 650000, Yunnan, China
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Salvini M, Fambrini M, Giorgetti L, Pugliesi C. Molecular aspects of zygotic embryogenesis in sunflower (Helianthus annuus L.): correlation of positive histone marks with HaWUS expression and putative link HaWUS/HaL1L. PLANTA 2016; 243:199-215. [PMID: 26377219 DOI: 10.1007/s00425-015-2405-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 09/06/2015] [Indexed: 06/05/2023]
Abstract
The link HaWUS/ HaL1L , the opposite transcriptional behavior, and the decrease/increase in positive histone marks bond to both genes suggest an inhibitory effect of WUS on HaL1L in sunflower zygotic embryos. In Arabidopsis, a group of transcription factors implicated in the earliest events of embryogenesis is the WUSCHEL-RELATED HOMEOBOX (WOX) protein family including WUSCHEL (WUS) and other 14 WOX protein, some of which contain a conserved WUS-box domain in addition to the homeodomain. WUS transcripts appear very early in embryogenesis, at the 16-cell embryo stage, but gradually become restricted to the center of the developing shoot apical meristem (SAM) primordium and continues to be expressed in cells of the niche/organizing center of SAM and floral meristems to maintain stem cell population. Moreover, WUS has decisive roles in the embryonic program presumably promoting the vegetative-to-embryonic transition and/or maintaining the identity of the embryonic stem cells. However, data on the direct interaction between WUS and key genes for seed development (as LEC1 and L1L) are not collected. The novelty of this report consists in the characterization of Helianthus annuus WUS (HaWUS) gene and in its analysis regarding the pattern of the methylated lysine 4 (K4) of the Histone H3 and of the acetylated histone H3 during the zygotic embryo development. Also, a parallel investigation was performed for HaL1L gene since two copies of the WUS-binding site (WUSATA), previously identified on HaL1L nucleotide sequence, were able to be bound by the HaWUS recombinant protein suggesting a not described effect of HaWUS on HaL1L transcription.
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Affiliation(s)
- Mariangela Salvini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126, Pisa, Italy.
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Marco Fambrini
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Lucia Giorgetti
- Institute of Agricultural Biology and Biotechnology (IBBA), Italian National Research Council (CNR), Via Moruzzi 1, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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de la Paz Sanchez M, Aceves-García P, Petrone E, Steckenborn S, Vega-León R, Álvarez-Buylla ER, Garay-Arroyo A, García-Ponce B. The impact of Polycomb group (PcG) and Trithorax group (TrxG) epigenetic factors in plant plasticity. THE NEW PHYTOLOGIST 2015; 208:684-694. [PMID: 26037337 DOI: 10.1111/nph.13486] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/25/2015] [Indexed: 06/04/2023]
Abstract
Current advances indicate that epigenetic mechanisms play important roles in the regulatory networks involved in plant developmental responses to environmental conditions. Hence, understanding the role of such components becomes crucial to understanding the mechanisms underlying the plasticity and variability of plant traits, and thus the ecology and evolution of plant development. We now know that important components of phenotypic variation may result from heritable and reversible epigenetic mechanisms without genetic alterations. The epigenetic factors Polycomb group (PcG) and Trithorax group (TrxG) are involved in developmental processes that respond to environmental signals, playing important roles in plant plasticity. In this review, we discuss current knowledge of TrxG and PcG functions in different developmental processes in response to internal and environmental cues and we also integrate the emerging evidence concerning their function in plant plasticity. Many such plastic responses rely on meristematic cell behavior, including stem cell niche maintenance, cellular reprogramming, flowering and dormancy as well as stress memory. This information will help to determine how to integrate the role of epigenetic regulation into models of gene regulatory networks, which have mostly included transcriptional interactions underlying various aspects of plant development and its plastic response to environmental conditions.
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Affiliation(s)
- Maria de la Paz Sanchez
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Pamela Aceves-García
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Emilio Petrone
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Stefan Steckenborn
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Rosario Vega-León
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Elena R Álvarez-Buylla
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Epigenética, Desarrollo y Evolución de plantas, Instituto de Ecología, Universidad Nacional Autónoma de México (UNAM), 3er Circuito Ext Junto a J. Botánico, Ciudad Universitaria, México, DF 04510, Mexico
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131
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Zhou SF, Sun L, Valdés AE, Engström P, Song ZT, Lu SJ, Liu JX. Membrane-associated transcription factor peptidase, site-2 protease, antagonizes ABA signaling in Arabidopsis. THE NEW PHYTOLOGIST 2015; 208:188-97. [PMID: 25919792 DOI: 10.1111/nph.13436] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/29/2015] [Indexed: 05/23/2023]
Abstract
Abscisic acid plays important roles in maintaining seed dormancy while gibberellins (GA) and other phytohormones antagonize ABA to promote germination. However, how ABA signaling is desensitized during the transition from dormancy to germination is still poorly understood. We functionally characterized the role of membrane-associated transcription factor peptidase, site-2 protease (S2P), in ABA signaling during seed germination in Arabidopsis. Genetic analysis showed that loss-of-function of S2P conferred high ABA sensitivity during seed germination, and expression of the activated form of membrane-associated transcription factor bZIP17, in which the transmembrane domain and endoplasmic reticulum (ER) lumen-facing C-terminus were deleted, in the S2P mutant rescued its ABA-sensitive phenotype. MYC and green fluorescent protein (GFP)-tagged bZIP17 were processed and translocated from the ER to the nucleus in response to ABA treatment. Furthermore, genes encoding negative regulators of ABA signaling, such as the transcription factor ATHB7 and its target genes HAB1, HAB2, HAI1 and AHG3, were up-regulated in seeds of the wild-type upon ABA treatment; this up-regulation was impaired in seeds of S2P mutants. Our results suggest that S2P desensitizes ABA signaling during seed germination through regulating the activation of the membrane-associated transcription factor bZIP17 and therefore controlling the expression level of genes encoding negative regulators of ABA signaling.
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Affiliation(s)
- Shun-Fan Zhou
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Le Sun
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Ana Elisa Valdés
- Physiological Botany, Uppsala BioCenter, Uppsala University, Almas Allé 5, 75651, Uppsala, Sweden
- Linnean Centre for Plant Biology, Uppsala, Sweden
| | - Peter Engström
- Physiological Botany, Uppsala BioCenter, Uppsala University, Almas Allé 5, 75651, Uppsala, Sweden
- Linnean Centre for Plant Biology, Uppsala, Sweden
| | - Ze-Ting Song
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Sun-Jie Lu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jian-Xiang Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
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Jin J, Shi J, Liu B, Liu Y, Huang Y, Yu Y, Dong A. MORF-RELATED GENE702, a Reader Protein of Trimethylated Histone H3 Lysine 4 and Histone H3 Lysine 36, Is Involved in Brassinosteroid-Regulated Growth and Flowering Time Control in Rice. PLANT PHYSIOLOGY 2015; 168:1275-85. [PMID: 25855537 PMCID: PMC4528726 DOI: 10.1104/pp.114.255737] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/04/2015] [Indexed: 05/03/2023]
Abstract
The methylation of histone H3 lysine 36 (H3K36) plays critical roles in brassinosteroid (BR)-related processes and is involved in controlling flowering time in rice (Oryza sativa). Although enzymes that catalyze this methylation reaction have been described, little is known about the recognition mechanisms to decipher H3K36 methylation information in rice. In this study, biochemical characterizations showed that MORF-RELATED GENE702 (MRG702) binds to trimethylated H3K4 and H3K36 (H3K4me3 and H3K36me3) in vitro. Similar to the loss-of-function mutants of the rice H3K36 methyltransferase gene SET DOMAIN GROUP725 (SDG725), the MRG702 knockdown mutants displayed typical BR-deficient mutant and late-flowering phenotypes. Gene transcription analyses showed that MRG702 knockdown resulted in the down-regulation of BR-related genes, including DWARF11, BRASSINOSTEROD INSENSITIVE1, and BRASSINOSTEROID UPREGULATED1, and several flowering genes, including Early heading date1 (Ehd1), Ehd2, Ehd3, OsMADS50, Heading date 3a, and RICE FLOWERING LOCUS T1. A binding analysis showed that MRG702 directly binds to the chromatin at target gene loci. This binding is dependent on the level of trimethylated H3K36, which is mediated by SDG725. Together, our results demonstrate that MRG702 acts as a reader protein of H3K4me3 and H3K36me3 and deciphers the H3K36 methylation information set by SDG725. Therefore, the role of MRG702 in the BR pathway and in controlling flowering time in rice is to function as a reader protein to decipher methylation information.
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Affiliation(s)
- Jing Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (J.J., J.S., B.L., Y.Y., A.D.); andNational Center for Protein Science Shanghai, Graduate University of the Chinese Academy of Sciences, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China (Y.L., Y.H.)
| | - Jinlei Shi
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (J.J., J.S., B.L., Y.Y., A.D.); andNational Center for Protein Science Shanghai, Graduate University of the Chinese Academy of Sciences, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China (Y.L., Y.H.)
| | - Bing Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (J.J., J.S., B.L., Y.Y., A.D.); andNational Center for Protein Science Shanghai, Graduate University of the Chinese Academy of Sciences, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China (Y.L., Y.H.)
| | - Yanchao Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (J.J., J.S., B.L., Y.Y., A.D.); andNational Center for Protein Science Shanghai, Graduate University of the Chinese Academy of Sciences, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China (Y.L., Y.H.)
| | - Ying Huang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (J.J., J.S., B.L., Y.Y., A.D.); andNational Center for Protein Science Shanghai, Graduate University of the Chinese Academy of Sciences, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China (Y.L., Y.H.)
| | - Yu Yu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (J.J., J.S., B.L., Y.Y., A.D.); andNational Center for Protein Science Shanghai, Graduate University of the Chinese Academy of Sciences, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China (Y.L., Y.H.)
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China (J.J., J.S., B.L., Y.Y., A.D.); andNational Center for Protein Science Shanghai, Graduate University of the Chinese Academy of Sciences, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China (Y.L., Y.H.)
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Brusslan JA, Bonora G, Rus-Canterbury AM, Tariq F, Jaroszewicz A, Pellegrini M. A Genome-Wide Chronological Study of Gene Expression and Two Histone Modifications, H3K4me3 and H3K9ac, during Developmental Leaf Senescence. PLANT PHYSIOLOGY 2015; 168:1246-61. [PMID: 25802367 PMCID: PMC4528724 DOI: 10.1104/pp.114.252999] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 03/20/2015] [Indexed: 05/19/2023]
Abstract
The genome-wide abundance of two histone modifications, H3K4me3 and H3K9ac (both associated with actively expressed genes), was monitored in Arabidopsis (Arabidopsis thaliana) leaves at different time points during developmental senescence along with expression in the form of RNA sequencing data. H3K9ac and H3K4me3 marks were highly convergent at all stages of leaf aging, but H3K4me3 marks covered nearly 2 times the gene area as H3K9ac marks. Genes with the greatest fold change in expression displayed the largest positively correlated percentage change in coverage for both marks. Most senescence up-regulated genes were premarked by H3K4me3 and H3K9ac but at levels below the whole-genome average, and for these genes, gene expression increased without a significant increase in either histone mark. However, for a subset of genes showing increased or decreased expression, the respective gain or loss of H3K4me3 marks was found to closely match the temporal changes in mRNA abundance; 22% of genes that increased expression during senescence showed accompanying changes in H3K4me3 modification, and they include numerous regulatory genes, which may act as primary response genes.
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Affiliation(s)
- Judy A Brusslan
- Department of Biological Sciences, California State University, Long Beach, California 90840-9502 (J.A.B., A.M.R.-C., F.T.); andDepartment of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (G.B., A.J., M.P.)
| | - Giancarlo Bonora
- Department of Biological Sciences, California State University, Long Beach, California 90840-9502 (J.A.B., A.M.R.-C., F.T.); andDepartment of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (G.B., A.J., M.P.)
| | - Ana M Rus-Canterbury
- Department of Biological Sciences, California State University, Long Beach, California 90840-9502 (J.A.B., A.M.R.-C., F.T.); andDepartment of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (G.B., A.J., M.P.)
| | - Fayha Tariq
- Department of Biological Sciences, California State University, Long Beach, California 90840-9502 (J.A.B., A.M.R.-C., F.T.); andDepartment of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (G.B., A.J., M.P.)
| | - Artur Jaroszewicz
- Department of Biological Sciences, California State University, Long Beach, California 90840-9502 (J.A.B., A.M.R.-C., F.T.); andDepartment of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (G.B., A.J., M.P.)
| | - Matteo Pellegrini
- Department of Biological Sciences, California State University, Long Beach, California 90840-9502 (J.A.B., A.M.R.-C., F.T.); andDepartment of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California 90095 (G.B., A.J., M.P.)
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134
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Mozgova I, Köhler C, Hennig L. Keeping the gate closed: functions of the polycomb repressive complex PRC2 in development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:121-32. [PMID: 25762111 DOI: 10.1111/tpj.12828] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/09/2015] [Accepted: 03/10/2015] [Indexed: 05/08/2023]
Abstract
Plant ontogeny relies on the correct timing and sequence of transitions between individual developmental phases. These are specified by gene expression patterns that are established by the balanced action of activators and repressors. Polycomb repressive complexes (PRCs) represent an evolutionarily conserved system of epigenetic gene repression that governs the establishment and maintenance of cell, tissue and organ identity, contributing to the correct execution of the developmental programs. PRC2 is a four-subunit histone methyltransferase complex that catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3), which contributes to the change of chromatin structure and long-lasting gene repression. Here, we review the composition and molecular function of the different known PRC2 complexes in plants, and focus on the role of PRC2 in mediating the establishment of different developmental phases and transitions between them.
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Affiliation(s)
- Iva Mozgova
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
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135
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Merini W, Calonje M. PRC1 is taking the lead in PcG repression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:110-20. [PMID: 25754661 DOI: 10.1111/tpj.12818] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/17/2015] [Accepted: 03/02/2015] [Indexed: 05/28/2023]
Abstract
Polycomb group (PcG) proteins constitute a major epigenetic mechanism for gene repression throughout the plant life. For a long time, the PcG mechanism has been proposed to follow a hierarchical recruitment of PcG repressive complexes (PRCs) to target genes in which the binding of PRC2 and the incorporation of H3 lysine 27 trimethyl marks led to recruitment of PRC1, which in turn mediated H2A monoubiquitination. However, recent studies have turned this model upside-down by showing that PRC1 activity can be required for PRC2 recruitment and H3K27me3 marking. Here, we review the current knowledge on plant PRC1 composition and mechanisms of repression, as well as its role during plant development.
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Affiliation(s)
- Wiam Merini
- Institute of Plant Biochemistry and Photosynthesis, IBVF-CSIC-University of Seville, Avenida América Vespucio, 49, Isla de La Cartuja, 41092, Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis, IBVF-CSIC-University of Seville, Avenida América Vespucio, 49, Isla de La Cartuja, 41092, Seville, Spain
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136
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Basbouss-Serhal I, Soubigou-Taconnat L, Bailly C, Leymarie J. Germination Potential of Dormant and Nondormant Arabidopsis Seeds Is Driven by Distinct Recruitment of Messenger RNAs to Polysomes. PLANT PHYSIOLOGY 2015; 168:1049-65. [PMID: 26019300 PMCID: PMC4741348 DOI: 10.1104/pp.15.00510] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 05/21/2015] [Indexed: 05/19/2023]
Abstract
Dormancy is a complex evolutionary trait that temporally prevents seed germination, thus allowing seedling growth at a favorable season. High-throughput analyses of transcriptomes have led to significant progress in understanding the molecular regulation of this process, but the role of posttranscriptional mechanisms has received little attention. In this work, we have studied the dynamics of messenger RNA association with polysomes and compared the transcriptome with the translatome in dormant and nondormant seeds of Arabidopsis (Arabidopsis thaliana) during their imbibition at 25 °C in darkness, a temperature preventing germination of dormant seeds only. DNA microarray analysis revealed that 4,670 and 7,028 transcripts were differentially abundant in dormant and nondormant seeds in the transcriptome and the translatome, respectively. We show that there is no correlation between transcriptome and translatome and that germination regulation is also largely translational, implying a selective and dynamic recruitment of messenger RNAs to polysomes in both dormant and nondormant seeds. The study of 5' untranslated region features revealed that GC content and the number of upstream open reading frames could play a role in selective translation occurring during germination. Gene Ontology clustering showed that the functions of polysome-associated transcripts differed between dormant and nondormant seeds and revealed actors in seed dormancy and germination. In conclusion, our results demonstrate the essential role of selective polysome loading in this biological process.
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Affiliation(s)
- Isabelle Basbouss-Serhal
- Sorbonne Universités, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, F-75005 Paris, France (I.B.-S., C.B., J.L.);Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., C.B., J.L.); andUnité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165, Institut National de la Recherche Agronomique, 91057 Evry, France (L.S.-T.)
| | - Ludivine Soubigou-Taconnat
- Sorbonne Universités, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, F-75005 Paris, France (I.B.-S., C.B., J.L.);Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., C.B., J.L.); andUnité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165, Institut National de la Recherche Agronomique, 91057 Evry, France (L.S.-T.)
| | - Christophe Bailly
- Sorbonne Universités, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, F-75005 Paris, France (I.B.-S., C.B., J.L.);Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., C.B., J.L.); andUnité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165, Institut National de la Recherche Agronomique, 91057 Evry, France (L.S.-T.)
| | - Juliette Leymarie
- Sorbonne Universités, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, F-75005 Paris, France (I.B.-S., C.B., J.L.);Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Unité Mixte de Recherche 7622, Biologie du Développement, F-75005 Paris, France (I.B.-S., C.B., J.L.); andUnité de Recherche en Génomique Végétale, Unité Mixte de Recherche 1165, Institut National de la Recherche Agronomique, 91057 Evry, France (L.S.-T.)
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137
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Wei T, He Z, Tan X, Liu X, Yuan X, Luo Y, Hu S. An integrated RNA-Seq and network study reveals a complex regulation process of rice embryo during seed germination. Biochem Biophys Res Commun 2015; 464:176-81. [PMID: 26116530 DOI: 10.1016/j.bbrc.2015.06.110] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 06/17/2015] [Indexed: 01/08/2023]
Abstract
Seed germination is a crucial stage for plant development and agricultural production. To investigate its complex regulation process, the RNA-Seq study of rice embryo was conducted at three time points of 0, 12 and 48 h post imbibition (HPI). Dynamic transcriptional alterations were observed, especially in the early stage (0-12 HPI). Seed related genes, especially those encoding desiccation inducible proteins and storage reserves in embryo, decreased drastically after imbibition. The expression profiles of phytohormone related genes indicated distinct roles of abscisic acid (ABA), gibberellin (GA) and brassinosteroid (BR) in germination. Moreover, network analysis revealed the importance of protein phosphorylation in phytohormone interactions. Network and gene ontology (GO) analyses suggested that transcription factors (TFs) played a regulatory role in functional transitions during germination, and the enriched TF families at 0 HPI implied a regulation of epigenetic modification in dry seeds. In addition, 35 germination-specific TF genes in embryo were identified and seven genes were verified by qRT-PCR. Besides, enriched TF binding sites (TFBSs) supported physiological changes in germination. Overall, this study expands our comprehensive knowledge of multiple regulation factors underlying rice seed germination.
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Affiliation(s)
- Ting Wei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zilong He
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - XinYu Tan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xue Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao Yuan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingfeng Luo
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
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138
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PcG and trxG in plants - friends or foes. Trends Genet 2015; 31:252-62. [PMID: 25858128 DOI: 10.1016/j.tig.2015.03.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 03/07/2015] [Accepted: 03/09/2015] [Indexed: 01/07/2023]
Abstract
The highly-conserved Polycomb group (PcG) and trithorax group (trxG) proteins play major roles in regulating gene expression and maintaining developmental states in many organisms. However, neither the recruitment of Polycomb repressive complexes (PRC) nor the mechanisms of PcG and trxG-mediated gene silencing and activation are well understood. Recent progress in Arabidopsis research challenges the dominant model of PRC2-dependent recruitment of PRC1 to target genes. Moreover, evidence indicates that diverse forms of PRC1, with shared components, are a common theme in plants and mammals. Although trxG is known to antagonize PcG, emerging data reveal that trxG can also repress gene expression, acting cooperatively with PcG. We discuss these recent findings and highlight the employment of diverse epigenetic mechanisms during development in plants and animals.
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139
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Han C, Yang P. Studies on the molecular mechanisms of seed germination. Proteomics 2015; 15:1671-9. [PMID: 25597791 DOI: 10.1002/pmic.201400375] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 12/03/2014] [Accepted: 01/14/2015] [Indexed: 11/07/2022]
Abstract
Seed germination that begins with imbibition and ends with radicle emergence is the first step for plant growth. Successful germination is not only crucial for seedling establishment but also important for crop yield. After being dispersed from mother plant, seed undergoes continuous desiccation in ecosystem and selects proper environment to trigger germination. Owing to the contribution of transcriptomic, proteomic, and molecular biological studies, molecular aspect of seed germination is elucidated well in Arabidopsis. Recently, more and more proteomic and genetic studies concerning cereal seed germination were performed on rice (Oryza sativa) and barley (Hordeum vulgare), which possess completely different seed structure and domestication background with Arabidopsis. In this review, both the common features and the distinct mechanisms of seed germination are compared among different plant species including Arabidopsis, rice, and maize. These features include morphological changes, cell and its related structure recovery, metabolic activation, hormone behavior, and transcription and translation activation. This review will provide more comprehensive insights into the molecular mechanisms of seed germination.
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Affiliation(s)
- Chao Han
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China
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140
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The plant Polycomb repressive complex 1 (PRC1) existed in the ancestor of seed plants and has a complex duplication history. BMC Evol Biol 2015; 15:44. [PMID: 25881027 PMCID: PMC4397884 DOI: 10.1186/s12862-015-0319-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 02/24/2015] [Indexed: 12/31/2022] Open
Abstract
Background Polycomb repressive complex 1 (PRC1) is an essential protein complex for plant development. It catalyzes ubiquitination of histone H2A that is an important part of the transcription repression machinery. Absence of PRC1 subunits in Arabidopsis thaliana plants causes severe developmental defects. Many aspects of the plant PRC1 are elusive, including its origin and phylogenetic distribution. Results We established the evolutionary history of the plant PRC1 subunits (LHP1, Ring1a-b, Bmi1a-c, EMF1, and VRN1), enabled by sensitive phylogenetic methods and newly sequenced plant genomes from previously unsampled taxonomic groups. We showed that all PRC1 core subunits exist in gymnosperms, earlier than previously thought, and that VRN1 is a recent addition, found exclusively in eudicots. The retention of individual subunits in chlorophytes, mosses, lycophytes and monilophytes indicates that they can moonlight as part of other complexes or processes. Moreover, we showed that most PRC1 subunits underwent a complex, duplication-rich history that differs significantly between Brassicaceae and other eudicots. Conclusions PRC1 existed in the last common ancestor of seed plants where it likely played an important regulatory role, aiding their radiation. The presence of LHP1, Ring1 and Bmi1 in mosses, lycophytes and monilophytes also suggests the presence of a primitive yet functional PRC1. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0319-z) contains supplementary material, which is available to authorized users.
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141
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Wei W, Zhang YQ, Tao JJ, Chen HW, Li QT, Zhang WK, Ma B, Lin Q, Zhang JS, Chen SY. The Alfin-like homeodomain finger protein AL5 suppresses multiple negative factors to confer abiotic stress tolerance in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:871-883. [PMID: 25619813 DOI: 10.1111/tpj.12773] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/07/2015] [Accepted: 01/09/2015] [Indexed: 06/04/2023]
Abstract
Plant homeodomain (PHD) finger proteins affect processes of growth and development by changing transcription and reading epigenetic histone modifications, but their functions in abiotic stress responses remain largely unclear. Here we characterized seven Arabidopsis thaliana Alfin1-like PHD finger proteins (ALs) in terms of the responses to abiotic stresses. ALs localized to the nucleus and repressed transcription. Except AL6, all the ALs bound to G-rich elements. Mutations of the amino acids at positions 34 and 35 in AL6 caused loss of ability to bind to G-rich elements. Expression of the AL genes responded differentially to osmotic stress, salt, cold and abscisic acid treatments. AL5-over-expressing plants showed higher tolerance to salt, drought and freezing stress than Col-0. Consistently, al5 mutants showed reduced stress tolerance. We used ChIP-Seq assays to identify eight direct targets of AL5, and found that AL5 binds to the promoter regions of these genes. Knockout mutants of five of these target genes exhibited varying tolerances to stresses. These results indicate that AL5 inhibits multiple signaling pathways to confer stress tolerance. Our study sheds light on mechanisms of AL5-mediated signaling in abiotic stress responses, and provides tools for improvement of stress tolerance in crop plants.
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Affiliation(s)
- Wei Wei
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beichen West Road, Chaoyang District, Beijing, 100101, China
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142
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Xiao J, Wagner D. Polycomb repression in the regulation of growth and development in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2015; 23:15-24. [PMID: 25449722 DOI: 10.1016/j.pbi.2014.10.003] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/01/2014] [Accepted: 10/06/2014] [Indexed: 05/18/2023]
Abstract
Chromatin state is critical for cell identity and development in multicellular eukaryotes. Among the regulators of chromatin state, Polycomb group (PcG) proteins stand out because of their role in both establishment and maintenance of cell identity. PcG proteins act in two major complexes in metazoans and plants. These complexes function to epigenetically-in a mitotically heritable manner-prevent expression of important developmental regulators at the wrong stage of development or in the wrong tissue. In Arabidopsis, PcG function is required throughout the life cycle from seed germination to embryo formation. Recent studies have expanded our knowledge regarding the biological roles and the regulation of the activity of PcG complexes. In this review, we discuss novel functions of Polycomb repression in plant development as well as advances in understanding PcG complex recruitment, activity regulation and removal in Arabidopsis and other plant species.
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Affiliation(s)
- Jun Xiao
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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143
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Footitt S, Müller K, Kermode AR, Finch-Savage WE. Seed dormancy cycling in Arabidopsis: chromatin remodelling and regulation of DOG1 in response to seasonal environmental signals. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:413-25. [PMID: 25439058 PMCID: PMC4671266 DOI: 10.1111/tpj.12735] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 11/21/2014] [Accepted: 11/25/2014] [Indexed: 05/18/2023]
Abstract
The involvement of chromatin remodelling in dormancy cycling in the soil seed bank (SSB) is poorly understood. Natural variation between the winter and summer annual Arabidopsis ecotypes Cvi and Bur was exploited to investigate the expression of genes involved in chromatin remodelling via histone 2B (H2B) ubiquitination/de-ubiquitination and histone acetylation/deacetylation, the repressive histone methyl transferases CURLY LEAF (CLF) and SWINGER (SWN), and the gene silencing repressor ROS1 (REPRESSOR OF SILENCING1) and promoter of silencing KYP/SUVH4 (KRYPTONITE), during dormancy cycling in the SSB. ROS1 expression was positively correlated with dormancy while the reverse was observed for CLF and KYP/SUVH4. We propose ROS1 dependent repression of silencing and a sequential requirement of CLF and KYP/SUVH4 dependent gene repression and silencing for the maintenance and suppression of dormancy during dormancy cycling. Seasonal expression of H2B modifying genes was correlated negatively with temperature and positively with DOG1 expression, as were histone acetyltransferase genes, with histone deacetylases positively correlated with temperature. Changes in the histone marks H3K4me3 and H3K27me3 were seen on DOG1 (DELAY OF GERMINATION1) in Cvi during dormancy cycling. H3K4me3 activating marks remained stable along DOG1. During relief of dormancy, H3K27me3 repressive marks slowly accumulated and accelerated on exposure to light completing dormancy loss. We propose that these marks on DOG1 serve as a thermal sensing mechanism during dormancy cycling in preparation for light repression of dormancy. Overall, chromatin remodelling plays a vital role in temporal sensing through regulation of gene expression.
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Affiliation(s)
- Steven Footitt
- School of Life Sciences, Wellesbourne Campus, University of WarwickWarwickshire, CV35 9EF, UK
| | - Kerstin Müller
- Biological Sciences, Simon Fraser University8888 University Dr., Burnaby, BC, V5A 1S6, Canada
| | - Allison R Kermode
- Biological Sciences, Simon Fraser University8888 University Dr., Burnaby, BC, V5A 1S6, Canada
| | - William E Finch-Savage
- School of Life Sciences, Wellesbourne Campus, University of WarwickWarwickshire, CV35 9EF, UK
- * For correspondence (e-mail )
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144
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Abstract
Correct expression of specific sets of genes in time and space ensures the establishment and maintenance of cell identity, which is required for proper development of multicellular organisms. Polycomb and Trithorax group proteins form multisubunit complexes that antagonistically act in epigenetic gene repression and activation, respectively. The traditional view of Polycomb repressive complexes (PRCs) as executors of long-lasting and stable gene repression is being extended by evidence of flexible repression in response to developmental and environmental cues, increasing the complexity of mechanisms that ensure selective and properly timed PRC targeting and release of Polycomb repression. Here, we review advances in understanding of the composition, mechanisms of targeting, and function of plant PRCs and discuss the parallels and differences between plant and animal models.
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Affiliation(s)
- Iva Mozgova
- Department of Plant Biology, Uppsala BioCenter, and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden; ,
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145
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Mouriz A, López-González L, Jarillo JA, Piñeiro M. PHDs govern plant development. PLANT SIGNALING & BEHAVIOR 2015; 10:e993253. [PMID: 26156103 PMCID: PMC4622442 DOI: 10.4161/15592324.2014.993253] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 11/18/2014] [Indexed: 05/22/2023]
Abstract
Posttranslational modifications present in the amino-terminal tails of histones play a pivotal role in the chromatin-mediated regulation of gene expression patterns that control plant developmental transitions. Therefore, the function of protein domains that specifically recognize these histone covalent modifications and recruit chromatin remodeling complexes and the transcriptional machinery to modulate gene expression is essential for a proper control of plant development. Plant HomeoDomain (PHD) motifs act as effectors that can specifically bind a number of histone modifications and mediate the activation or repression of underlying genes. In this review we summarize recent findings that emphasize the crucial role of this versatile family of chromatin "reader" domains in the transcriptional regulation of plant developmental processes such as meiosis and postmeiotic events during pollen maturation, embryo meristem initiation and root development, germination as well as flowering time.
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Affiliation(s)
- Alfonso Mouriz
- Centro de Biotecnología y Genómica de Plantas; Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid; Madrid, Spain
| | - Leticia López-González
- Centro de Biotecnología y Genómica de Plantas; Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid; Madrid, Spain
| | - Jose A Jarillo
- Centro de Biotecnología y Genómica de Plantas; Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid; Madrid, Spain
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146
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Veerappan V, Chen N, Reichert AI, Allen RD. HSI2/VAL1 PHD-like domain promotes H3K27 trimethylation to repress the expression of seed maturation genes and complex transgenes in Arabidopsis seedlings. BMC PLANT BIOLOGY 2014; 14:293. [PMID: 25367506 PMCID: PMC4232687 DOI: 10.1186/s12870-014-0293-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/17/2014] [Indexed: 05/22/2023]
Abstract
BACKGROUND The novel mutant allele hsi2-4 was isolated in a genetic screen to identify Arabidopsis mutants with constitutively elevated expression of a glutathione S-transferase F8::luciferase (GSTF8::LUC) reporter gene in Arabidopsis. The hsi2-4 mutant harbors a point mutation that affects the plant homeodomain (PHD)-like domain in HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE GENE2 (HSI2)/VIVIPAROUS1/ABI3-LIKE1 (VAL1). In hsi2-4 seedlings, expression of this LUC transgene and certain endogenous seed-maturation genes is constitutively enhanced. The parental reporter line (WT LUC ) that was used for mutagenesis harbors two independent transgene loci, Kan R and Kan S . Both loci express luciferase whereas only the Kan R locus confers resistance to kanamycin. RESULTS Here we show that both transgene loci harbor multiple tandem insertions at single sites. Luciferase expression from these sites is regulated by the HSI2 PHD-like domain, which is required for the deposition of repressive histone methylation marks (H3K27me3) at both Kan R and Kan S loci. Expression of LUC and Neomycin Phosphotransferase II transgenes is associated with dynamic changes in H3K27me3 levels, and the activation marks H3K4me3 and H3K36me3 but does not appear to involve repressive H3K9me2 marks, DNA methylation or histone deacetylation. However, hsi2-2 and hsi2-4 mutants are partially resistant to growth inhibition associated with exposure to the DNA methylation inhibitor 5-aza-2'-deoxycytidine. HSI2 is also required for the repression of a subset of regulatory and structural seed maturation genes in vegetative tissues and H3K27me3 marks associated with most of these genes are also HSI2-dependent. CONCLUSIONS These data implicate HSI2 PHD-like domain in the regulation of gene expression involving histone modifications and DNA methylation-mediated epigenetic mechanisms.
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Affiliation(s)
- Vijaykumar Veerappan
- />Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401 USA
- />Current address: Department of Biological Sciences, University of North Texas, Denton, TX 76203-5017 USA
| | - Naichong Chen
- />Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401 USA
| | - Angelika I Reichert
- />Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401 USA
| | - Randy D Allen
- />Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401 USA
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147
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Callis J. The ubiquitination machinery of the ubiquitin system. THE ARABIDOPSIS BOOK 2014; 12:e0174. [PMID: 25320573 PMCID: PMC4196676 DOI: 10.1199/tab.0174] [Citation(s) in RCA: 216] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The protein ubiquitin is a covalent modifier of proteins, including itself. The ubiquitin system encompasses the enzymes required for catalysing attachment of ubiquitin to substrates as well as proteins that bind to ubiquitinated proteins leading them to their final fate. Also included are activities that remove ubiquitin independent of, or in concert with, proteolysis of the substrate, either by the proteasome or proteases in the vacuole. In addition to ubiquitin encoded by a family of fusion proteins, there are proteins with ubiquitin-like domains, likely forming ubiquitin's β-grasp fold, but incapable of covalent modification. However, they serve as protein-protein interaction platforms within the ubiquitin system. Multi-gene families encode all of these types of activities. Within the ubiquitination machinery "half" of the ubiquitin system are redundant, partially redundant, and unique components affecting diverse developmental and environmental responses in plants. Notably, multiple aspects of biotic and abiotic stress responses require, or are modulated by, ubiquitination. Finally, aspects of the ubiquitin system have broad utility: as components to enhance gene expression or to regulate protein abundance. This review focuses on the ubiquitination machinery: ubiquitin, unique aspects about the synthesis of ubiquitin and organization of its gene family, ubiquitin activating enzymes (E1), ubiquitin conjugating enzymes (E2) and ubiquitin ligases, or E3s. Given the large number of E3s in Arabidopsis this review covers the U box, HECT and RING type E3s, with the exception of the cullin-based E3s.
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Affiliation(s)
- Judy Callis
- Department of Molecular and Cellular Biology, University of California-Davis, Davis CA 95616
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148
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López-González L, Mouriz A, Narro-Diego L, Bustos R, Martínez-Zapater JM, Jarillo JA, Piñeiro M. Chromatin-dependent repression of the Arabidopsis floral integrator genes involves plant specific PHD-containing proteins. THE PLANT CELL 2014; 26:3922-38. [PMID: 25281686 PMCID: PMC4247585 DOI: 10.1105/tpc.114.130781] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The interplay among histone modifications modulates the expression of master regulatory genes in development. Chromatin effector proteins bind histone modifications and translate the epigenetic status into gene expression patterns that control development. Here, we show that two Arabidopsis thaliana paralogs encoding plant-specific proteins with a plant homeodomain (PHD) motif, SHORT LIFE (SHL) and EARLY BOLTING IN SHORT DAYS (EBS), function in the chromatin-mediated repression of floral initiation and play independent roles in the control of genes regulating flowering. Previous results showed that repression of the floral integrator FLOWERING LOCUS T (FT) requires EBS. We establish that SHL is necessary to negatively regulate the expression of SUPPRESSOR OF OVEREXPRESSION OF CO1 (SOC1), another floral integrator. SHL and EBS recognize di- and trimethylated histone H3 at lysine 4 and bind regulatory regions of SOC1 and FT, respectively. These PHD proteins maintain an inactive chromatin conformation in SOC1 and FT by preventing high levels of H3 acetylation, bind HISTONE DEACETYLASE6, and play a central role in regulating flowering time. SHL and EBS are widely conserved in plants but are absent in other eukaryotes, suggesting that the regulatory module mediated by these proteins could represent a distinct mechanism for gene expression control in plants.
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Affiliation(s)
- Leticia López-González
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid, 28223 Madrid, Spain
| | - Alfonso Mouriz
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid, 28223 Madrid, Spain
| | - Laura Narro-Diego
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid, 28223 Madrid, Spain
| | - Regla Bustos
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid, 28223 Madrid, Spain
| | - José Miguel Martínez-Zapater
- Instituto de Ciencias de la Vid y del Vino, Consejo Superior de Investigaciones Científicas, Universidad de La Rioja, Gobierno de La Rioja, 26006 Logroño, Spain
| | - Jose A Jarillo
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid, 28223 Madrid, Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigaciones Agrarias-Universidad Politécnica de Madrid, 28223 Madrid, Spain
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149
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Regulation of arabidopsis flowering by the histone mark readers MRG1/2 via interaction with CONSTANS to modulate FT expression. PLoS Genet 2014; 10:e1004617. [PMID: 25211338 PMCID: PMC4161306 DOI: 10.1371/journal.pgen.1004617] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 07/18/2014] [Indexed: 11/19/2022] Open
Abstract
Day-length is important for regulating the transition to reproductive development (flowering) in plants. In the model plant Arabidopsis thaliana, the transcription factor CONSTANS (CO) promotes expression of the florigen FLOWERING LOCUS T (FT), constituting a key flowering pathway under long-day photoperiods. Recent studies have revealed that FT expression is regulated by changes of histone modification marks of the FT chromatin, but the epigenetic regulators that directly interact with the CO protein have not been identified. Here, we show that the Arabidopsis Morf Related Gene (MRG) group proteins MRG1 and MRG2 act as H3K4me3/H3K36me3 readers and physically interact with CO to activate FT expression. In vitro binding analyses indicated that the chromodomains of MRG1 and MRG2 preferentially bind H3K4me3/H3K36me3 peptides. The mrg1 mrg2 double mutant exhibits reduced mRNA levels of FT, but not of CO, and shows a late-flowering phenotype under the long-day but not short-day photoperiod growth conditions. MRG2 associates with the chromatin of FT promoter in a way dependent of both CO and H3K4me3/H3K36me3. Vice versa, loss of MRG1 and MRG2 also impairs CO binding at the FT promoter. Crystal structure analyses of MRG2 bound with H3K4me3/H3K36me3 peptides together with mutagenesis analysis in planta further demonstrated that MRG2 function relies on its H3K4me3/H3K36me3-binding activity. Collectively, our results unravel a novel chromatin regulatory mechanism, linking functions of MRG1 and MRG2 proteins, H3K4/H3K36 methylations, and CO in FT activation in the photoperiodic regulation of flowering time in plants. The photoperiodic flowering in Arabidopsis requires the key regulator CO and its target gene FT. However, how CO regulates FT expression in the context of chromatin remains largely obscure. In this work, we present Arabidopsis MRG1/2 as novel chromatin effectors directly involved in the CO-FT photoperiodic flowering. Firstly, MRG1/2 proteins are identified as recognition factors of H3K4 and H3K36 methylation via their chromodomains. The mrg1 mrg2 double mutant shows a late-flowering phenotype only under long-day conditions through down-regulation of FT but not of CO. MRG2 can directly target in vivo the FT promoter chromatin in a H3K4me3/H3K36me3-level dependent manner. More importantly, MRG2 and CO physically interact and enhance each other's binding to the FT promoter in planta. Determination of co-crystal structures of MRG2 with H3K4me3/H3K36me3 peptides and mutagenesis of a key amino acid residue involved in structural interaction demonstrate that MRG2 reader activity is essential for in planta function. Taken together, our findings uncover a novel mechanism of FT activation in flowering promotion and provide a striking example of mutual interplay between a transcription factor and a histone methylation reader in transcription regulation.
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150
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Jarillo JA, Gaudin V, Hennig L, Köhler C, Piñeiro M. Plant chromatin warms up in Madrid: meeting summary of the 3rd European Workshop on Plant Chromatin 2013, Madrid, Spain. Epigenetics 2014; 9:644-52. [PMID: 24504145 DOI: 10.4161/epi.28094] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The 3rd European Workshop on Plant Chromatin (EWPC) was held on August 2013 in Madrid, Spain. A number of different topics on plant chromatin were presented during the meeting, including new factors mediating Polycomb Group protein function in plants, chromatin-mediated reprogramming in plant developmental transitions, the role of histone variants, and newly identified chromatin remodeling factors. The function of interactions between chromatin and transcription factors in the modulation of gene expression, the role of chromatin dynamics in the control of nuclear processes and the influence of environmental factors on chromatin organization were also reported. In this report, we highlight some of the new insights emerging in this growing area of research, presented at the 3rd EWPC.
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Affiliation(s)
- José A Jarillo
- Centro de Biotecnología y Genómica de Plantas (CBGP), INIA-UPM; INIA, Campus de Montegancedo; Madrid, Spain
| | - Valérie Gaudin
- NRA; AgroParis Tech; UMR1318; Insitut Jean Pierre Bourgin; Versailles, France
| | - Lars Hennig
- Swedish University of Agricultural Sciences; Uppsala BioCenter; Uppsala, Sweden
| | - Claudia Köhler
- Swedish University of Agricultural Sciences; Uppsala BioCenter; Uppsala, Sweden
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas (CBGP), INIA-UPM; INIA, Campus de Montegancedo; Madrid, Spain
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