51
|
Ojolo SP, Cao S, Priyadarshani SVGN, Li W, Yan M, Aslam M, Zhao H, Qin Y. Regulation of Plant Growth and Development: A Review From a Chromatin Remodeling Perspective. FRONTIERS IN PLANT SCIENCE 2018; 9:1232. [PMID: 30186301 PMCID: PMC6113404 DOI: 10.3389/fpls.2018.01232] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 08/03/2018] [Indexed: 05/04/2023]
Abstract
In eukaryotes, genetic material is packaged into a dynamic but stable nucleoprotein structure called chromatin. Post-translational modification of chromatin domains affects the expression of underlying genes and subsequently the identity of cells by conveying epigenetic information from mother to daughter cells. SWI/SNF chromatin remodelers are ATP-dependent complexes that modulate core histone protein polypeptides, incorporate variant histone species and modify nucleotides in DNA strands within the nucleosome. The present review discusses the SWI/SNF chromatin remodeler family, its classification and recent advancements. We also address the involvement of SWI/SNF remodelers in regulating vital plant growth and development processes such as meristem establishment and maintenance, cell differentiation, organ initiation, flower morphogenesis and flowering time regulation. Moreover, the role of chromatin remodelers in key phytohormone signaling pathways is also reviewed. The information provided in this review may prompt further debate and investigations aimed at understanding plant-specific epigenetic regulation mediated by chromatin remodeling under continuously varying plant growth conditions and global climate change.
Collapse
Affiliation(s)
- Simon P. Ojolo
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shijiang Cao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - S. V. G. N. Priyadarshani
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weimin Li
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Maokai Yan
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mohammad Aslam
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Heming Zhao
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Qin
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Yuan Qin, ;
| |
Collapse
|
52
|
Chen DH, Huang Y, Jiang C, Si JP. Chromatin-Based Regulation of Plant Root Development. FRONTIERS IN PLANT SCIENCE 2018; 9:1509. [PMID: 30386363 PMCID: PMC6198463 DOI: 10.3389/fpls.2018.01509] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/26/2018] [Indexed: 05/10/2023]
Abstract
Plant is endowed with sessile habit and nutrient acquisition mainly through the root organ, which also provides an excellent model to study stem cell fate and asymmetric division due to well-organized cell layers and relatively simple cell types in root meristem. Besides genetic material DNA wrapped around histone octamer, chromatin structure determined by chromatin modification including DNA methylation, histone modification and chromatin remodeling also contributes greatly to the regulation of gene expression. In this review, we summarize the current progresses on the molecular mechanisms of chromatin modification in regulating root development.
Collapse
Affiliation(s)
- Dong-Hong Chen
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium Catenatum, Zhejiang A&F University, Hangzhou, China
- *Correspondence: Dong-Hong Chen
| | - Yong Huang
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, China
| | | | - Jin-Ping Si
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium Catenatum, Zhejiang A&F University, Hangzhou, China
- Jin-Ping Si
| |
Collapse
|
53
|
Yamaguchi N, Huang J, Xu Y, Tanoi K, Ito T. Fine-tuning of auxin homeostasis governs the transition from floral stem cell maintenance to gynoecium formation. Nat Commun 2017; 8:1125. [PMID: 29066759 PMCID: PMC5654772 DOI: 10.1038/s41467-017-01252-6] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 09/01/2017] [Indexed: 11/23/2022] Open
Abstract
To ensure successful plant reproduction and crop production, the spatial and temporal control of the termination of the floral meristem must be coordinated. In Arabidopsis, the timing of this termination is determined by AGAMOUS (AG). Following its termination, the floral meristem underdoes gynoecium formation. A direct target of AG, CRABS CLAW (CRC), is involved in both floral meristem determinacy and gynoecium development. However, how floral meristem termination is coordinated with gynoecium formation is not understood. Here, we identify a mechanistic link between floral meristem termination and gynoecium development through fine-tuning of auxin homeostasis by CRC. CRC controls auxin homeostasis in the medial region of the developing gynoecium to generate proper auxin maxima. This regulation partially occurs via direct transcriptional repression of TORNADO2 (TRN2) by CRC. Plasma membrane-localized TRN2 modulates auxin homeostasis. We propose a model describing how regulation of auxin homeostasis mediates the transition from floral meristem termination to gynoecium development. In Arabidopsis, the timing of floral meristem termination is determined by AGAMOUS. Here, the authors show that the CRC transcription factor, itself a direct target of AGAMOUS, coordinates meristem termination with subsequent gynoecium formation partly by repressing TRN2 expression and regulating auxin homeostasis.
Collapse
Affiliation(s)
- Nobutoshi Yamaguchi
- Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.,Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi-shi, Saitama, 332-0012, Japan
| | - Jiangbo Huang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore
| | - Yifeng Xu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Keitaro Tanoi
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi-shi, Saitama, 332-0012, Japan.,Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Toshiro Ito
- Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan. .,Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. .,Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
| |
Collapse
|
54
|
Zha P, Jing Y, Xu G, Lin R. PICKLE chromatin-remodeling factor controls thermosensory hypocotyl growth of Arabidopsis. PLANT, CELL & ENVIRONMENT 2017; 40:2426-2436. [PMID: 28771755 DOI: 10.1111/pce.13049] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 07/28/2017] [Accepted: 07/29/2017] [Indexed: 05/25/2023]
Abstract
Temperature is a major signal that governs plant distribution and shapes plant growth. High ambient temperature promotes plant thermomorphogenesis without significant induction of heat-stress responses. Although much progress of warm temperature-mediated plant growth has been made during recent years, the thermomorphogenic signalling pathway is not well understood. We previously revealed that PICKLE (PKL), an ATP-dependent chromatin remodelling factor, negatively controls photomorphogenesis in Arabidopsis thaliana. Here, we show that mutations in PKL lead to reduced sensitivity in hypocotyl elongation to warm temperature (28 °C). We demonstrate that CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1) directly binds to the specific promoter regions of PKL and its expression is reduced in the cca1 mutants. We find that the cca1 seedlings are also less sensitive to temperature-mediated growth than the wild-type plants. Furthermore, PKL affects the level of trimethylation of histone H3 Lys 27 associated with INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19) and IAA29 and regulates their expression. We also identify 6 additional transcription factors as the upstream regulators of PKL. Our study thus reveals PKL and CCA1 as 2 novel factors in controlling plant growth in response to the elevated temperature environment and provides new insight into the integration of light and temperature signals through chromatin regulation.
Collapse
Affiliation(s)
- Ping Zha
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanjun Jing
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Gang Xu
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
55
|
Campos-Rivero G, Osorio-Montalvo P, Sánchez-Borges R, Us-Camas R, Duarte-Aké F, De-la-Peña C. Plant hormone signaling in flowering: An epigenetic point of view. JOURNAL OF PLANT PHYSIOLOGY 2017; 214:16-27. [PMID: 28419906 DOI: 10.1016/j.jplph.2017.03.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/06/2017] [Accepted: 03/29/2017] [Indexed: 05/19/2023]
Abstract
Reproduction is one of the most important phases in an organism's lifecycle. In the case of angiosperm plants, flowering provides the major developmental transition from the vegetative to the reproductive stage, and requires genetic and epigenetic reprogramming to ensure the success of seed production. Flowering is regulated by a complex network of genes that integrate multiple environmental cues and endogenous signals so that flowering occurs at the right time; hormone regulation, signaling and homeostasis are very important in this process. Working alone or in combination, hormones are able to promote flowering by epigenetic regulation. Some plant hormones, such as gibberellins, jasmonic acid, abscisic acid and auxins, have important effects on chromatin compaction mediated by DNA methylation and histone posttranslational modifications, which hints at the role that epigenetic regulation may play in flowering through hormone action. miRNAs have been viewed as acting independently from DNA methylation and histone modification, ignoring their potential to interact with hormone signaling - including the signaling of auxins, gibberellins, ethylene, jasmonic acid, salicylic acid and others - to regulate flowering. Therefore, in this review we examine new findings about interactions between epigenetic mechanisms and key players in hormone signaling to coordinate flowering.
Collapse
Affiliation(s)
| | | | | | - Rosa Us-Camas
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mexico.
| | - Fátima Duarte-Aké
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mexico.
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mexico.
| |
Collapse
|
56
|
Jégu T, Veluchamy A, Ramirez-Prado JS, Rizzi-Paillet C, Perez M, Lhomme A, Latrasse D, Coleno E, Vicaire S, Legras S, Jost B, Rougée M, Barneche F, Bergounioux C, Crespi M, Mahfouz MM, Hirt H, Raynaud C, Benhamed M. The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility. Genome Biol 2017; 18:114. [PMID: 28619072 PMCID: PMC5471679 DOI: 10.1186/s13059-017-1246-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/26/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Plant adaptive responses to changing environments involve complex molecular interplays between intrinsic and external signals. Whilst much is known on the signaling components mediating diurnal, light, and temperature controls on plant development, their influence on chromatin-based transcriptional controls remains poorly explored. RESULTS In this study we show that a SWI/SNF chromatin remodeler subunit, BAF60, represses seedling growth by modulating DNA accessibility of hypocotyl cell size regulatory genes. BAF60 binds nucleosome-free regions of multiple G box-containing genes, opposing in cis the promoting effect of the photomorphogenic and thermomorphogenic regulator Phytochrome Interacting Factor 4 (PIF4) on hypocotyl elongation. Furthermore, BAF60 expression level is regulated in response to light and daily rhythms. CONCLUSIONS These results unveil a short path between a chromatin remodeler and a signaling component to fine-tune plant morphogenesis in response to environmental conditions.
Collapse
Affiliation(s)
- Teddy Jégu
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
- Present address: Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Present address: Department of Genetics, Harvard Medical School, Boston, MA, 02114, USA
| | - Alaguraj Veluchamy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Juan S Ramirez-Prado
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Charley Rizzi-Paillet
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Magalie Perez
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Anaïs Lhomme
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - David Latrasse
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Emeline Coleno
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Serge Vicaire
- Plateforme Biopuces et séquençage, IGBMC, 1 rue Laurent Fries Parc d'Innovation, 67400, Illkirch, France
| | - Stéphanie Legras
- Plateforme Biopuces et séquençage, IGBMC, 1 rue Laurent Fries Parc d'Innovation, 67400, Illkirch, France
| | - Bernard Jost
- Plateforme Biopuces et séquençage, IGBMC, 1 rue Laurent Fries Parc d'Innovation, 67400, Illkirch, France
| | - Martin Rougée
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Fredy Barneche
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Catherine Bergounioux
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Martin Crespi
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Magdy M Mahfouz
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Heribert Hirt
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia
| | - Cécile Raynaud
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France
| | - Moussa Benhamed
- Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405, Orsay, France.
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.
| |
Collapse
|
57
|
Qiu Y, Liu SL, Adams KL. Concerted Divergence after Gene Duplication in Polycomb Repressive Complexes. PLANT PHYSIOLOGY 2017; 174:1192-1204. [PMID: 28455403 PMCID: PMC5462007 DOI: 10.1104/pp.16.01983] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 04/24/2017] [Indexed: 05/29/2023]
Abstract
Duplicated genes are a major contributor to genome evolution and phenotypic novelty. There are multiple possible evolutionary fates of duplicated genes. Here, we provide an example of concerted divergence of simultaneously duplicated genes whose products function in the same complex. We studied POLYCOMB REPRESSIVE COMPLEX2 (PRC2) in Brassicaceae. The VERNALIZATION (VRN)-PRC2 complex contains VRN2 and SWINGER (SWN), and both genes were duplicated during a whole-genome duplication to generate FERTILIZATION INDEPENDENT SEED2 (FIS2) and MEDEA (MEA), which function in the Brassicaceae-specific FIS-PRC2 complex that regulates seed development. We examined the expression of FIS2, MEA, and their paralogs, compared their cytosine and histone methylation patterns, and analyzed the sequence evolution of the genes. We found that FIS2 and MEA have reproductive-specific expression patterns that are correlated and derived from the broadly expressed VRN2 and SWN in outgroup species. In vegetative tissues of Arabidopsis (Arabidopsis thaliana), repressive methylation marks are enriched in FIS2 and MEA, whereas active marks are associated with their paralogs. We detected comparable accelerated amino acid substitution rates in FIS2 and MEA but not in their paralogs. We also show divergence patterns of the PRC2-associated VERNALIZATION5/VIN3-LIKE2 that are similar to FIS2 and MEA These lines of evidence indicate that FIS2 and MEA have diverged in concert, resulting in functional divergence of the PRC2 complexes in Brassicaceae. This type of concerted divergence is a previously unreported fate of duplicated genes. In addition, the Brassicaceae-specific FIS-PRC2 complex modified the regulatory pathways in female gametophyte and seed development.
Collapse
Affiliation(s)
- Yichun Qiu
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (Y.Q., K.L.A.); and
- Department of Life Science, Tunghai University, Taichung, Taiwan 40704 (S.-L.L.)
| | - Shao-Lun Liu
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (Y.Q., K.L.A.); and
- Department of Life Science, Tunghai University, Taichung, Taiwan 40704 (S.-L.L.)
| | - Keith L Adams
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4 (Y.Q., K.L.A.); and
- Department of Life Science, Tunghai University, Taichung, Taiwan 40704 (S.-L.L.)
| |
Collapse
|
58
|
Yang R, Zheng Z, Chen Q, Yang L, Huang H, Miki D, Wu W, Zeng L, Liu J, Zhou JX, Ogas J, Zhu JK, He XJ, Zhang H. The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci. Genome Biol 2017; 18:103. [PMID: 28569170 PMCID: PMC5452414 DOI: 10.1186/s13059-017-1226-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/03/2017] [Indexed: 11/27/2022] Open
Abstract
Background The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in non-coding RNA-directed DNA methylation in Arabidopsis thaliana. Results Through forward genetic screens we identified PKL, a gene required for developmental regulation in plants, as a factor promoting transcriptional silencing at the transgenic RD29A promoter. Mutation of PKL results in DNA methylation changes at more than half of the loci that are targeted by RNA-directed DNA methylation (RdDM). A small number of transposable elements and genes had reduced DNA methylation correlated with derepression in the pkl mutant, though for the majority, decreases in DNA methylation are not sufficient to cause release of silencing. The changes in DNA methylation in the pkl mutant are positively correlated with changes in 24-nt siRNA levels. In addition, PKL is required for the accumulation of Pol V-dependent transcripts and for the positioning of Pol V-stabilized nucleosomes at several tested loci, indicating that RNA polymerase V-related functions are impaired in the pkl mutant. Conclusions PKL is required for transcriptional silencing and has significant effects on RdDM in plants. The changes in DNA methylation in the pkl mutant are correlated with changes in the non-coding RNAs produced by Pol IV and Pol V. We propose that at RdDM target regions, PKL may be required to create a chromatin environment that influences non-coding RNA production, DNA methylation, and transcriptional silencing. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1226-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rong Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Zhimin Zheng
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Qing Chen
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Lan Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Huan Huang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Wenwu Wu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Liang Zeng
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Jun Liu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Jin-Xing Zhou
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Joe Ogas
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China.,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China.
| |
Collapse
|
59
|
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.
Collapse
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.
| |
Collapse
|
60
|
Huang F, Zhu QH, Zhu A, Wu X, Xie L, Wu X, Helliwell C, Chaudhury A, Finnegan EJ, Luo M. Mutants in the imprinted PICKLE RELATED 2 gene suppress seed abortion of fertilization independent seed class mutants and paternal excess interploidy crosses in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:383-395. [PMID: 28155248 DOI: 10.1111/tpj.13500] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/23/2017] [Accepted: 01/25/2017] [Indexed: 05/26/2023]
Abstract
Endosperm cellularization is essential for embryo development and viable seed formation. Loss of function of the FERTILIZATION INDEPENDENT SEED (FIS) class Polycomb genes, which mediate trimethylation of histone H3 lysine27 (H3K27me3), as well as imbalanced contributions of parental genomes interrupt this process. The causes of the failure of cellularization are poorly understood. In this study we identified PICKLE RELATED 2 (PKR2) mutations which suppress seed abortion in fis1/mea by restoring endosperm cellularization. PKR2, a paternally expressed imprinted gene (PEG), encodes a CHD3 chromatin remodeler. PKR2 is specifically expressed in syncytial endosperm and its maternal copy is repressed by FIS1. Seed abortion in a paternal genome excess interploidy cross was also partly suppressed by pkr2. Simultaneous mutations in PKR2 and another PEG, ADMETOS (ADM), additively rescue the seed abortion in fis1 and in the interploidy cross, suggesting that PKR2 and ADM modulate endosperm cellularization independently and reproductive isolation between plants of different ploidy is established by imprinted genes. Genes upregulated in fis1 and downregulated in the presence of pkr2 are enriched in glycosyl-hydrolyzing activity, while genes downregulated in fis1 and upregulated in the presence of pkr2 are enriched with microtubule motor activity, consistent with the cellularization patterns in fis1 and the suppressor line. The antagonistic functions of FIS1 and PKR2 in modulating endosperm development are similar to those of PICKLE (PKL) and CURLY LEAF (CLF), which antagonistically regulate root meristem activity. Our results provide further insights into the function of imprinted genes in endosperm development and reproductive isolation.
Collapse
Affiliation(s)
- Fang Huang
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Qian-Hao Zhu
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, PO Box 1700, ACT, 2601, Australia
| | - Anyu Zhu
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, PO Box 1700, ACT, 2601, Australia
| | - Xiaoba Wu
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, PO Box 1700, ACT, 2601, Australia
| | - Liqiong Xie
- School of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Xianjun Wu
- Rice Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, 611130, China
| | - Chris Helliwell
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, PO Box 1700, ACT, 2601, Australia
| | | | - E Jean Finnegan
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, PO Box 1700, ACT, 2601, Australia
| | - Ming Luo
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, PO Box 1700, ACT, 2601, Australia
| |
Collapse
|
61
|
Park J, Oh DH, Dassanayake M, Nguyen KT, Ogas J, Choi G, Sun TP. Gibberellin Signaling Requires Chromatin Remodeler PICKLE to Promote Vegetative Growth and Phase Transitions. PLANT PHYSIOLOGY 2017; 173:1463-1474. [PMID: 28057895 PMCID: PMC5291033 DOI: 10.1104/pp.16.01471] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/27/2016] [Indexed: 05/20/2023]
Abstract
PICKLE (PKL) is an ATP-dependent chromodomain-helicase-DNA-binding domain (CHD3) chromatin remodeling enzyme in Arabidopsis (Arabidopsis thaliana). Previous studies showed that PKL promotes embryonic-to-vegetative transition by inhibiting expression of seed-specific genes during seed germination. The pkl mutants display a low penetrance of the "pickle root" phenotype, with a thick and green primary root that retains embryonic characteristics. The penetrance of this pickle root phenotype in pkl is dramatically increased in gibberellin (GA)-deficient conditions. At adult stages, the pkl mutants are semidwarfs with delayed flowering time, which resemble reduced GA-signaling mutants. These findings suggest that PKL may play a positive role in regulating GA signaling. A recent biochemical analysis further showed that PKL and GA signaling repressors DELLAs antagonistically regulate hypocotyl cell elongation genes by direct protein-protein interaction. To elucidate further the role of PKL in GA signaling and plant development, we studied the genetic interaction between PKL and DELLAs using the hextuple mutant containing pkl and della pentuple (dP) mutations. Here, we show that PKL is required for most of GA-promoted developmental processes, including vegetative growth such as hypocotyl, leaf, and inflorescence stem elongation, and phase transitions such as juvenile-to-adult leaf and vegetative-to-reproductive phase. The removal of all DELLA functions (in the dP background) cannot rescue these phenotypes in pkl RNA-sequencing analysis using the ga1 (a GA-deficient mutant), pkl, and the ga1 pkl double mutant further shows that expression of 80% of GA-responsive genes in seedlings is PKL dependent, including genes that function in cell elongation, cell division, and phase transitions. These results indicate that the CHD3 chromatin remodeler PKL is required for regulating gene expression during most of GA-regulated developmental processes.
Collapse
Affiliation(s)
- Jeongmoo Park
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Dong-Ha Oh
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Maheshi Dassanayake
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Khoa Thi Nguyen
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Joe Ogas
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Giltsu Choi
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.)
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.)
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| | - Tai-Ping Sun
- Department of Biology, Duke University, Durham, North Carolina 27708 (J.P., T.-p.S.);
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea (J.P., K.T.N., G.C.);
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803 (D.-H.O., M.D.); and
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47906 (J.O)
| |
Collapse
|
62
|
|
63
|
Yamada M. Functions of long intergenic non-coding (linc) RNAs in plants. JOURNAL OF PLANT RESEARCH 2017; 130:67-73. [PMID: 27999969 DOI: 10.1007/s10265-016-0894-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/28/2016] [Indexed: 05/08/2023]
Abstract
Whole transcriptome analyses in many organisms have revealed that most transcribed RNAs do not encode proteins. These non-coding RNAs likely contribute to the regulation of gene expression during the development of multicellular organisms. In eukaryotes, the roles of small RNAs, one class of non-coding RNAs, in transcriptional and post-transcriptional regulation have been well characterized. However, the functions of a second class of non-coding RNAs, long intergenic noncoding (linc) RNAs, are relatively unknown, especially in plants. Recent advances in RNA-seq and tiling microarray technologies have revealed the presence of many lincRNAs across plant species. This review focuses on the functions of lincRNAs that have been recently reported in plants. One of the most well characterized functions of lincRNAs is to epigenetically regulate gene expression by recruiting proteins for chromosome modification to specific loci. Second, lincRNAs are known to inhibit the physical interaction between microRNAs (miRNAs) and their target mRNAs thus controling protein levels of the target mRNAs. Lastly, lincRNAs control alternative splicing by binding and sequestering the proteins required for alternative splicing.
Collapse
Affiliation(s)
- Masashi Yamada
- Department of Biology and HHMI, Duke University, Durham, NC, 27710, USA.
| |
Collapse
|
64
|
Fletcher JC. State of the Art: trxG Factor Regulation of Post-embryonic Plant Development. FRONTIERS IN PLANT SCIENCE 2017; 8:1925. [PMID: 29184559 PMCID: PMC5694493 DOI: 10.3389/fpls.2017.01925] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 10/24/2017] [Indexed: 05/07/2023]
Abstract
Multicellular organisms rely on the precise and consistent regulation of gene expression to direct their development in tissue- and cell-type specific patterns. This regulatory activity involves arrays of DNA-binding transcription factors and epigenetic factors that modify chromatin structure. Among the chromatin modifiers, trithorax (trxG) and Polycomb (PcG) group proteins play important roles in orchestrating the stable activation and repression of gene expression, respectively. These proteins have generally antagonistic functions in maintaining cell and tissue homeostasis as well as in mediating widespread transcriptional reprogramming during developmental transitions. Plants utilize multiple trxG factors to regulate gene transcription as they modulate their development in response to both endogenous and environmental cues. Here, I will discuss the roles of trxG factors and their associated proteins in post-embryonic plant development.
Collapse
Affiliation(s)
- Jennifer C. Fletcher
- Plant Gene Expression Center, United States Department of Agriculture – Agricultural Research Service, Albany, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: Jennifer C. Fletcher,
| |
Collapse
|
65
|
Abstract
Diverse environmental stimuli largely affect the ionic balance of soil, which have a direct effect on growth and crop yield. Details are fast emerging on the genetic/molecular regulators, at whole-genome levels, of plant responses to mineral deficiencies in model and crop plants. These genetic regulators determine the root architecture and physiological adaptations for better uptake and utilization of minerals from soil. Recent evidence also shows the potential roles of epigenetic mechanisms in gene regulation, driven by minerals imbalance. Mineral deficiency or sufficiency leads to developmental plasticity in plants for adaptation, which is preceded by a change in the pattern of gene expression. Notably, such changes at molecular levels are also influenced by altered chromatin structure and methylation patterns, or involvement of other epigenetic components. Interestingly, many of the changes induced by mineral deficiency are also inheritable in the form of epigenetic memory. Unravelling these mechanisms in response to mineral deficiency would further advance our understanding of this complex plant response. Further studies on such approaches may serve as an exciting interaction model of epigenetic and genetic regulations of mineral homeostasis in plants and designing strategies for crop improvement.
Collapse
|
66
|
de Lucas M, Pu L, Turco G, Gaudinier A, Morao AK, Harashima H, Kim D, Ron M, Sugimoto K, Roudier F, Brady SM. Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation. THE PLANT CELL 2016; 28:2616-2631. [PMID: 27650334 PMCID: PMC5134969 DOI: 10.1105/tpc.15.00744] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 08/29/2016] [Accepted: 09/14/2016] [Indexed: 05/21/2023]
Abstract
Spatiotemporal regulation of transcription is fine-tuned at multiple levels, including chromatin compaction. Polycomb Repressive Complex 2 (PRC2) catalyzes the trimethylation of Histone 3 at lysine 27 (H3K27me3), which is the hallmark of a repressive chromatin state. Multiple PRC2 complexes have been reported in Arabidopsis thaliana to control the expression of genes involved in developmental transitions and maintenance of organ identity. Here, we show that PRC2 member genes display complex spatiotemporal gene expression patterns and function in root meristem and vascular cell proliferation and specification. Furthermore, PRC2 gene expression patterns correspond with vascular and nonvascular tissue-specific H3K27me3-marked genes. This tissue-specific repression via H3K27me3 regulates the balance between cell proliferation and differentiation. Using enhanced yeast one-hybrid analysis, upstream regulators of the PRC2 member genes are identified, and genetic analysis demonstrates that transcriptional regulation of some PRC2 genes plays an important role in determining PRC2 spatiotemporal activity within a developing organ.
Collapse
Affiliation(s)
- Miguel de Lucas
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Li Pu
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Gina Turco
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Ana Karina Morao
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, Institut National de la Santé et de la Recherche Médicale, U1024 Paris, France
| | - Hirofumi Harashima
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Dahae Kim
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Mily Ron
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Keiko Sugimoto
- RIKEN Center for Sustainable Resource Science, Tsurumi, Yokohama 230-0045, Japan
| | - Francois Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8197, Institut National de la Santé et de la Recherche Médicale, U1024 Paris, France
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| |
Collapse
|
67
|
Abstract
Reversible histone acetylation and deacetylation at the N-terminus of histone tails play a crucial role in regulation of gene activity. Hyperacetylation of histones relaxes chromatin structure and is associated with transcriptional activation, whereas hypoacetylation of histones induces chromatin compaction and gene repression. Histone acetylation and deacetylation are catalyzed by histone acetyltransferases (HATs) and histone deacetylases (HDACs), respectively. Emerging evidences revealed that plant HATs and HDACs play essential roles in regulation of gene expression in plant development and plant responses to environmental stresses. Furthermore, HATs and HDACs were shown to interact with various chromatin-remodeling factors and transcription factors involved in transcriptional regulation of multiple developmental processes.
Collapse
Affiliation(s)
- X Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - S Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - C-W Yu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - C-Y Chen
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - K Wu
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
68
|
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.
Collapse
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.
| |
Collapse
|
69
|
Wang Y, Wang D, Gan T, Liu L, Long W, Wang Y, Niu M, Li X, Zheng M, Jiang L, Wan J. CRL6, a member of the CHD protein family, is required for crown root development in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 105:185-194. [PMID: 27108205 DOI: 10.1016/j.plaphy.2016.04.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/29/2016] [Accepted: 04/12/2016] [Indexed: 05/25/2023]
Abstract
The root system in monocotyledonous plants is largely composed of postembryonic shoot-borne roots named crown roots, which are important for nutrients and water uptake. The molecular mechanism underlying regulation of crown root development is not fully explored. In this study, we characterized a rice (Oryza sativa) mutant defective in crown root formation, designated as crown rootless6 (crl6). Histological analysis showed that CRL6 influences crown root formation by regulating primordial initiation and development. Map-based cloning and subsequent complementation tests verified that the CRL6 gene encodes a member of the large chromodomain, helicase/ATPase, and DNA-binding domain (CHD) family protein. Realtime RT-PCR analysis showed that CRL6 was most highly expressed in the stem base region where crown roots initiated. In addition, auxin-action inhibited phenotype was observed during crl6 development. The expressions of OsIAA genes were down-regulated in crl6. Our results provide evidence that CRL6 plays an important role in crown root development in rice via auxin-related signaling pathway.
Collapse
Affiliation(s)
- Yihua Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Di Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Gan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Linglong Liu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Wuhua Long
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunlong Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Mei Niu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaohui Li
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Ming Zheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China; National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
70
|
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.
Collapse
|
71
|
Liu J, Deng S, Wang H, Ye J, Wu HW, Sun HX, Chua NH. CURLY LEAF Regulates Gene Sets Coordinating Seed Size and Lipid Biosynthesis. PLANT PHYSIOLOGY 2016; 171:424-36. [PMID: 26945048 PMCID: PMC4854673 DOI: 10.1104/pp.15.01335] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 03/03/2016] [Indexed: 05/05/2023]
Abstract
CURLY LEAF (CLF), a histone methyltransferase of Polycomb Repressive Complex 2 (PRC2) for trimethylation of histone H3 Lys 27 (H3K27me3), has been thought as a negative regulator controlling mainly postgermination growth in Arabidopsis (Arabidopsis thaliana). Approximately 14% to 29% of genic regions are decorated by H3K27me3 in the Arabidopsis genome; however, transcriptional repression activities of PRC2 on a majority of these regions remain unclear. Here, by analysis of transcriptome profiles, we found that approximately 11.6% genes in the Arabidopsis genome were repressed by CLF in various organs. Unexpectedly, approximately 54% of these genes were preferentially repressed in siliques. Further analyses of 118 transcriptome datasets uncovered a group of genes that was preferentially expressed and repressed by CLF in embryos at the mature-green stage. This observation suggests that CLF mediates a large-scale H3K27me3 programming/reprogramming event during embryonic development. Plants of clf-28 produced bigger and heavier seeds with higher oil content, larger oil bodies, and altered long-chain fatty acid composition compared with wild type. Around 46% of CLF-repressed genes were associated with H3K27me3 marks; moreover, we verified histone modification and transcriptional repression by CLF on regulatory genes. Our results suggest that CLF silences specific gene expression modules. Genes operating within a module have various molecular functions, but they cooperate to regulate a similar physiological function during embryo development.
Collapse
Affiliation(s)
- Jun Liu
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065;National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; andTemasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Shulin Deng
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065;National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; andTemasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Huan Wang
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065;National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; andTemasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Jian Ye
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065;National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; andTemasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Hui-Wen Wu
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065;National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; andTemasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Hai-Xi Sun
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065;National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; andTemasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065;National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; andTemasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore
| |
Collapse
|
72
|
Cross-Talk Between Sporophyte and Gametophyte Generations Is Promoted by CHD3 Chromatin Remodelers in Arabidopsis thaliana. Genetics 2016; 203:817-29. [PMID: 27075727 DOI: 10.1534/genetics.115.180141] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 03/27/2016] [Indexed: 11/18/2022] Open
Abstract
Angiosperm reproduction requires the integrated development of multiple tissues with different genotypes. To achieve successful fertilization, the haploid female gametophytes and diploid ovary must coordinate their development, after which the male gametes must navigate through the maternal sporophytic tissues to reach the female gametes. After fertilization, seed development requires coordinated development of the maternal diploid integuments, the triploid endosperm, and the diploid zygote. Transcription and signaling factors contribute to communication between these tissues, and roles for epigenetic regulation have been described for some of these processes. Here we identify a broad role for CHD3 chromatin remodelers in Arabidopsis thaliana reproductive development. Plants lacking the CHD3 remodeler, PICKLE, exhibit various reproductive defects including abnormal development of the integuments, female gametophyte, and pollen tube, as well as delayed progression of ovule and embryo development. Genetic analyses demonstrate that these phenotypes result from loss of PICKLE in the maternal sporophyte. The paralogous gene PICKLE RELATED 2 is preferentially expressed in the endosperm and acts antagonistically with respect to PICKLE in the seed: loss of PICKLE RELATED 2 suppresses the large seed phenotype of pickle seeds. Surprisingly, the alteration of seed size in pickle plants is sufficient to determine the expression of embryonic traits in the seedling primary root. These findings establish an important role for CHD3 remodelers in plant reproduction and highlight how the epigenetic status of one tissue can impact the development of genetically distinct tissues.
Collapse
|
73
|
Vialette-Guiraud ACM, Andres-Robin A, Chambrier P, Tavares R, Scutt CP. The analysis of Gene Regulatory Networks in plant evo-devo. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2549-63. [PMID: 27006484 DOI: 10.1093/jxb/erw119] [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] [Indexed: 05/09/2023]
Abstract
We provide an overview of methods and workflows that can be used to investigate the topologies of Gene Regulatory Networks (GRNs) in the context of plant evolutionary-developmental (evo-devo) biology. Many of the species that occupy key positions in plant phylogeny are poorly adapted as laboratory models and so we focus here on techniques that can be efficiently applied to both model and non-model species of interest to plant evo-devo. We outline methods that can be used to describe gene expression patterns and also to elucidate the transcriptional, post-transcriptional, and epigenetic regulatory mechanisms underlying these patterns, in any plant species with a sequenced genome. We furthermore describe how the technique of Protein Resurrection can be used to confirm inferences on ancestral GRNs and also to provide otherwise-inaccessible points of reference in evolutionary histories by exploiting paralogues generated in gene and whole genome duplication events. Finally, we argue for the better integration of molecular data with information from paleobotanical, paleoecological, and paleogeographical studies to provide the fullest possible picture of the processes that have shaped the evolution of plant development.
Collapse
Affiliation(s)
- Aurélie C M Vialette-Guiraud
- Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Amélie Andres-Robin
- Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Pierre Chambrier
- Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Raquel Tavares
- Laboratoire de Biométrie et Biologie Évolutive (UMR 5558 - CNRS/université Lyon 1/université de Lyon), Bâtiment Gregor Mendel, 43 bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Charles P Scutt
- Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| |
Collapse
|
74
|
Zhou Y, Hartwig B, James GV, Schneeberger K, Turck F. Complementary Activities of TELOMERE REPEAT BINDING Proteins and Polycomb Group Complexes in Transcriptional Regulation of Target Genes. THE PLANT CELL 2016; 28:87-101. [PMID: 26721861 PMCID: PMC4746681 DOI: 10.1105/tpc.15.00787] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/11/2015] [Accepted: 12/25/2015] [Indexed: 05/19/2023]
Abstract
In multicellular organisms, Polycomb Repressive Complex 1 (PRC1) and PRC2 repress target genes through histone modification and chromatin compaction. Arabidopsis thaliana mutants strongly compromised in the pathway cannot develop differentiated organs. LIKE HETEROCHROMATIN PROTEIN1 (LHP1) is so far the only known plant PRC1 component that directly binds to H3K27me3, the histone modification set by PRC2, and also associates genome-wide with trimethylation of lysine 27 of histone H3 (H3K27me3). Surprisingly, lhp1 mutants show relatively mild phenotypic alterations. To explain this paradox, we screened for genetic enhancers of lhp1 mutants to identify novel components repressing target genes together with, or in parallel to, LHP1. Two enhancing mutations were mapped to TELOMERE REPEAT BINDING PROTEIN1 (TRB1) and its paralog TRB3. We show that TRB1 binds to thousands of genomic sites containing telobox or related cis-elements with a significant increase of sites and strength of binding in the lhp1 background. Furthermore, in combination with lhp1, but not alone, trb1 mutants show increased transcription of LHP1 targets, such as floral meristem identity genes, which are more likely to be bound by TRB1 in the lhp1 background. By contrast, expression of a subset of LHP1-independent TRB1 target genes, many involved in primary metabolism, is decreased in the absence of TRB1 alone. Thus, TRB1 is a bivalent transcriptional modulator that maintains downregulation of Polycomb Group (PcG) target genes in lhp1 mutants, while it sustains high expression of targets that are regulated independently of PcG.
Collapse
Affiliation(s)
- Yue Zhou
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Benjamin Hartwig
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Geo Velikkakam James
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Korbinian Schneeberger
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Franziska Turck
- Department Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| |
Collapse
|
75
|
Xu M, Hu T, Smith MR, Poethig RS. Epigenetic Regulation of Vegetative Phase Change in Arabidopsis. THE PLANT CELL 2016; 28:28-41. [PMID: 26704382 PMCID: PMC4746683 DOI: 10.1105/tpc.15.00854] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 12/09/2015] [Accepted: 12/18/2015] [Indexed: 05/18/2023]
Abstract
Vegetative phase change in flowering plants is regulated by a decrease in the level of miR156. The molecular mechanism of this temporally regulated decrease in miR156 expression is still unknown. Most of the miR156 in Arabidopsis thaliana shoots is produced by MIR156A and MIR156C. We found that the downregulation of these genes during vegetative phase change is associated with an increase in their level of histone H3 lysine 27 trimethylation (H3K27me3) and requires this chromatin modification. The increase in H3K27me3 at MIR156A/MIR156C is associated with an increase in the binding of PRC2 to these genes and is mediated redundantly by the E(z) homologs SWINGER and CURLY LEAF. The CHD3 chromatin remodeler PICKLE (PKL) promotes the addition of H3K27me3 to MIR156A/MIR156C but is not responsible for the temporal increase in this chromatin mark. PKL is bound to the promoters of MIR156A/MIR156C, where it promotes low levels of H3K27ac early in shoot development and stabilizes the nucleosome at the +1 position. These results suggest a molecular mechanism for the initiation and maintenance of vegetative phase change in plants.
Collapse
Affiliation(s)
- Mingli Xu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Tieqiang Hu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Michael R Smith
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - R Scott Poethig
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| |
Collapse
|
76
|
Takatsuka H, Umeda M. Epigenetic Control of Cell Division and Cell Differentiation in the Root Apex. FRONTIERS IN PLANT SCIENCE 2015; 6:1178. [PMID: 26734056 PMCID: PMC4689806 DOI: 10.3389/fpls.2015.01178] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/09/2015] [Indexed: 05/25/2023]
Abstract
Epigenetics is defined as heritable changes in gene expression and genome integrity that are accompanied by no alteration in DNA sequence. Throughout plant life cycle, many processes, including genome imprinting, stress responses, and cellular differentiation, are known to be determined by epigenetic regulation. The root apex is also considered to be under the control of epigenetic regulation for optimal growth under variable environments. Recent reports reveal that epigenetic control is especially important in the stem cell niche and the meristematic zone where both cell production and cell specification occur. DNA methylation, histone methylation, and histone acetylation are well-known epigenetic modifications, and each epigenetic modification has distinct roles in roots. Here, we review the updated findings that demonstrate the significance of epigenetic regulation in root apex of Arabidopsis.
Collapse
Affiliation(s)
- Hirotomo Takatsuka
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyNara, Japan
| | - Masaaki Umeda
- Graduate School of Biological Sciences, Nara Institute of Science and TechnologyNara, Japan
- Japan Science and Technology, Core Research for Evolutional Science and Technology AgencyIkoma, Japan
| |
Collapse
|
77
|
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.
Collapse
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
| |
Collapse
|
78
|
Ma X, Ma J, Zhai H, Xin P, Chu J, Qiao Y, Han L. CHR729 Is a CHD3 Protein That Controls Seedling Development in Rice. PLoS One 2015; 10:e0138934. [PMID: 26398683 PMCID: PMC4580627 DOI: 10.1371/journal.pone.0138934] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/05/2015] [Indexed: 12/22/2022] Open
Abstract
CHD3 is one of the chromatin-remodeling factors that contribute to controlling the expression of genes associated with plant development. Loss-of-function mutants display morphological and growth defects. However, the molecular mechanisms underlying CHD3 regulation of plant development remain unclear. In this study, a rice CHD3 protein, CHR729, was identified. The corresponding mutant line (t483) exhibited late seed germination, low germination rate, dwarfism, low tiller number, root growth inhibition, adaxial albino leaves, and short and narrow leaves. CHR729 encoded a nuclear protein and was expressed in almost all organs. RNA-sequencing analysis showed that several plant hormone-related genes were up- or down-regulated in t483 compared to wild type. In particular, expression of the gibberellin synthetase gibberellin 20 oxidase 4 gene was elevated in the mutant. Endogenous gibberellin assays demonstrated that the content of bioactive GA3 was reduced in t483 compared to wild type. Moreover, the seedling dwarfism, late seed germination, and short root length phenotypes of t483 were partially rescued by treatment with exogenous GA3. These results suggest that the rice CHD3 protein CHR729 plays an important role in many aspects of seedling development and controls this development via the gibberellin pathway.
Collapse
Affiliation(s)
- Xiaoding Ma
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Ma
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Honghong Zhai
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Peiyong Xin
- National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jinfang Chu
- National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yongli Qiao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Longzhi Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail:
| |
Collapse
|
79
|
Han SK, Wu MF, Cui S, Wagner D. Roles and activities of chromatin remodeling ATPases in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:62-77. [PMID: 25977075 DOI: 10.1111/tpj.12877] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/04/2015] [Accepted: 05/06/2015] [Indexed: 05/18/2023]
Abstract
Chromatin remodeling ATPases and their associated complexes can alter the accessibility of the genome in the context of chromatin by using energy derived from the hydrolysis of ATP to change the positioning, occupancy and composition of nucleosomes. In animals and plants, these remodelers have been implicated in diverse processes ranging from stem cell maintenance and differentiation to developmental phase transitions and stress responses. Detailed investigation of their roles in individual processes has suggested a higher level of selectivity of chromatin remodeling ATPase activity than previously anticipated, and diverse mechanisms have been uncovered that can contribute to the selectivity. This review summarizes recent advances in understanding the roles and activities of chromatin remodeling ATPases in plants.
Collapse
Affiliation(s)
- Soon-Ki Han
- Howard Hughes Medical Institute and Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Miin-Feng Wu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sujuan Cui
- Hebei Key Laboratory of Molecular Cell Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| |
Collapse
|
80
|
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.
Collapse
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
| |
Collapse
|
81
|
Ikeuchi M, Iwase A, Rymen B, Harashima H, Shibata M, Ohnuma M, Breuer C, Morao AK, de Lucas M, De Veylder L, Goodrich J, Brady SM, Roudier F, Sugimoto K. PRC2 represses dedifferentiation of mature somatic cells in Arabidopsis. NATURE PLANTS 2015; 1:15089. [PMID: 27250255 DOI: 10.1038/nplants.2015.89] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 05/29/2015] [Indexed: 05/18/2023]
Abstract
Plant somatic cells are generally acknowledged to retain totipotency, the potential to develop into any cell type within an organism. This astonishing plasticity may contribute to a high regenerative capacity on severe damage, but how plants control this potential during normal post-embryonic development remains largely unknown(1,2). Here we show that POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a chromatin regulator that maintains gene repression through histone modification, prevents dedifferentiation of mature somatic cells in Arabidopsis thaliana roots. Loss-of-function mutants in PRC2 subunits initially develop unicellular root hairs indistinguishable from those in wild type but fail to retain the differentiated state, ultimately resulting in the generation of an unorganized cell mass and somatic embryos from a single root hair. Strikingly, mutant root hairs complete the normal endoreduplication programme, increasing their nuclear ploidy, but subsequently reinitiate mitotic division coupled with successive DNA replication. Our data show that the WOUND INDUCED DEDIFFERENTIATION3 (WIND3) and LEAFY COTYLEDON2 (LEC2) genes are among the PRC2 targets involved in this reprogramming, as their ectopic overexpression partly phenocopies the dedifferentiation phenotype of PRC2 mutants. These findings unveil the pivotal role of PRC2-mediated gene repression in preventing unscheduled reprogramming of fully differentiated plant cells.
Collapse
Affiliation(s)
- Momoko Ikeuchi
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Iwase
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Bart Rymen
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Hirofumi Harashima
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Michitaro Shibata
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Mariko Ohnuma
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Christian Breuer
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Ana Karina Morao
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, Paris Cedex 05 75230, France
| | - Miguel de Lucas
- Department of Plant Biology and Genome Center, University of California, Davis, 1002 Life Sciences, One Shields Avenue, Davis, California 95616, USA
| | - Lieven De Veylder
- Department of Plant Systems Biology, VIB, Gent B-9052, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent B-9052, Belgium
| | - Justin Goodrich
- Institute of Molecular Plant Sciences, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, 1002 Life Sciences, One Shields Avenue, Davis, California 95616, USA
| | - François Roudier
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS UMR8197, INSERM U1024, 46 rue d'Ulm, Paris Cedex 05 75230, France
| | - Keiko Sugimoto
- RIKEN Centre for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| |
Collapse
|
82
|
Guo S, Sun B, Looi LS, Xu Y, Gan ES, Huang J, Ito T. Co-ordination of Flower Development Through Epigenetic Regulation in Two Model Species: Rice and Arabidopsis. PLANT & CELL PHYSIOLOGY 2015; 56:830-42. [PMID: 25746984 DOI: 10.1093/pcp/pcv037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/24/2015] [Indexed: 05/21/2023]
Abstract
Angiosperms produce flowers for reproduction. Flower development is a multistep developmental process, beginning with the initiation of the floral meristems, followed by floral meristem identity specification and maintenance, organ primordia initiation, floral organ identity specification, floral stem cell termination and finally floral organ maturation. During flower development, each of a large number of genes is expressed in a spatiotemporally regulated manner. Underlying these molecular and phenotypic events are various genetic and epigenetic pathways, consisting of diverse transcription factors, chromatin-remodeling factors and signaling molecules. Over the past 30 years, genetic, biochemical and genomic assays have revealed the underlying genetic frameworks that control flower development. Here, we will review the transcriptional regulation of flower development in two model species: Arabidopsis thaliana and rice (Oryza sativa). We focus on epigenetic regulation that functions to co-ordinate transcription pathways in flower development.
Collapse
Affiliation(s)
- Siyi Guo
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Republic of Singapore These authors contributed equally to this work
| | - Bo Sun
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Republic of Singapore These authors contributed equally to this work
| | - Liang-Sheng Looi
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Republic of Singapore Department of Biological Sciences, National University of Singapore, 117604, Republic of Singapore
| | - Yifeng Xu
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Republic of Singapore
| | - Eng-Seng Gan
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Republic of Singapore Department of Biological Sciences, National University of Singapore, 117604, Republic of Singapore
| | - Jiangbo Huang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Republic of Singapore Department of Biological Sciences, National University of Singapore, 117604, Republic of Singapore
| | - Toshiro Ito
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604, Republic of Singapore Department of Biological Sciences, National University of Singapore, 117604, Republic of Singapore
| |
Collapse
|
83
|
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.
Collapse
|
84
|
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.
Collapse
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.
| |
Collapse
|
85
|
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.
Collapse
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; ,
| | | |
Collapse
|
86
|
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.
Collapse
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
| | | |
Collapse
|
87
|
Napsucialy-Mendivil S, Alvarez-Venegas R, Shishkova S, Dubrovsky JG. Arabidopsis homolog of trithorax1 (ATX1) is required for cell production, patterning, and morphogenesis in root development. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:6373-84. [PMID: 25205583 PMCID: PMC4246177 DOI: 10.1093/jxb/eru355] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Arabidopsis homolog of trithorax1 (ATX1/SDG27), a known regulator of flower development, encodes a H3K4histone methyltransferase that maintains a number of genes in an active state. In this study, the role of ATX1 in root development was evaluated. The loss-of-function mutant atx1-1 was impaired in primary root growth. The data suggest that ATX1 controls root growth by regulating cell cycle duration, cell production, and the transition from cell proliferation in the root apical meristem (RAM) to cell elongation. In atx1-1, the quiescent centre (QC) cells were irregular in shape and more expanded than those of the wild type. This feature, together with the atypical distribution of T-divisions, the presence of oblique divisions, and the abnormal cell patterning in the RAM, suggests a lack of coordination between cell division and cell growth in the mutant. The expression domain of QC-specific markers was expanded both in the primary RAM and in the developing lateral root primordia of atx1-1 plants. These abnormalities were independent of auxin-response gradients. ATX1 was also found to be required for lateral root initiation, morphogenesis, and emergence. The time from lateral root initiation to emergence was significantly extended in the atx1-1 mutant. Overall, these data suggest that ATX1 is involved in the timing of root development, stem cell niche maintenance, and cell patterning during primary and lateral root development. Thus, ATX1 emerges as an important player in root system architecture.
Collapse
Affiliation(s)
- Selene Napsucialy-Mendivil
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México
| | - Raúl Alvarez-Venegas
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados, Unidad Irapuato, Irapuato, Gto., CP 36821, México
| | - Svetlana Shishkova
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México
| | - Joseph G Dubrovsky
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apartado Postal 510-3, 62250 Cuernavaca, Morelos, México
| |
Collapse
|
88
|
Engelhorn J, Blanvillain R, Carles CC. Gene activation and cell fate control in plants: a chromatin perspective. Cell Mol Life Sci 2014; 71:3119-37. [PMID: 24714879 PMCID: PMC11113918 DOI: 10.1007/s00018-014-1609-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Revised: 03/10/2014] [Accepted: 03/12/2014] [Indexed: 01/02/2023]
Abstract
In plants, environment-adaptable organogenesis extends throughout the lifespan, and iterative development requires repetitive rounds of activation and repression of several sets of genes. Eukaryotic genome compaction into chromatin forms a physical barrier for transcription; therefore, induction of gene expression requires alteration in chromatin structure. One of the present great challenges in molecular and developmental biology is to understand how chromatin is brought from a repressive to permissive state on specific loci and in a very specific cluster of cells, as well as how this state is further maintained and propagated through time and cell division in a cell lineage. In this review, we report recent discoveries implementing our knowledge on chromatin dynamics that modulate developmental gene expression. We also discuss how new data sets highlight plant specificities, likely reflecting requirement for a highly dynamic chromatin.
Collapse
Affiliation(s)
- Julia Engelhorn
- Université Grenoble Alpes, UMR5168, 38041, Grenoble, France,
| | | | | |
Collapse
|
89
|
Stress induces cell dedifferentiation in plants. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:378-84. [PMID: 25086338 DOI: 10.1016/j.bbagrm.2014.07.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 07/20/2014] [Accepted: 07/22/2014] [Indexed: 12/14/2022]
Abstract
Accumulating evidence lends support to the proposal that a major theme in plant responses to stresses is dedifferentiation, whereby mature cells acquire stem cell features (e.g. open chromatin conformation) prior to acquisition of a new cell fate. In this review, we discuss data addressing plant cell plasticity and provide evidence linking stress, dedifferentiation and a switch in cell fate. We emphasize the epigenetic modifications associated with stress-induced global changes in chromatin structure and conclude with the implications for genetic variation and for induced pluripotent stem cells in animals. It appears that stress is perceived as a signal that directs plant cells to undergo reprogramming (dedifferentiation) as a means for adaptation and in preparation for a stimulus-based acquisition of a new cell fate. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
Collapse
|
90
|
Somatic embryogenesis - Stress-induced remodeling of plant cell fate. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:385-402. [PMID: 25038583 DOI: 10.1016/j.bbagrm.2014.07.005] [Citation(s) in RCA: 211] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/08/2014] [Accepted: 07/10/2014] [Indexed: 01/13/2023]
Abstract
Plants as sessile organisms have remarkable developmental plasticity ensuring heir continuous adaptation to the environment. An extreme example is somatic embryogenesis, the initiation of autonomous embryo development in somatic cells in response to exogenous and/or endogenous signals. In this review I briefly overview the various pathways that can lead to embryo development in plants in addition to the fertilization of the egg cell and highlight the importance of the interaction of stress- and hormone-regulated pathways during the induction of somatic embryogenesis. Somatic embryogenesis can be initiated in planta or in vitro, directly or indirectly, and the requirement for dedifferentiation as well as the way to achieve developmental totipotency in the various systems is discussed in light of our present knowledge. The initiation of all forms of the stress/hormone-induced in vitro as well as the genetically provoked in planta somatic embryogenesis requires extensive and coordinated genetic reprogramming that has to take place at the chromatin level, as the embryogenic program is under strong epigenetic repression in vegetative plant cells. Our present knowledge on chromatin-based mechanisms potentially involved in the somatic-to-embryogenic developmental transition is summarized emphasizing the potential role of the chromatin to integrate stress, hormonal, and developmental pathways leading to the activation of the embryogenic program. The role of stress-related chromatin reorganization in the genetic instability of in vitro cultures is also discussed. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
Collapse
|
91
|
Abstract
The astonishingly long lives of plants and their regeneration capacity depend on the activity of plant stem cells. As in animals, stem cells reside in stem cell niches, which produce signals that regulate the balance between self-renewal and the generation of daughter cells that differentiate into new tissues. Plant stem cell niches are located within the meristems, which are organized structures that are responsible for most post-embryonic development. The continuous organ production that is characteristic of plant growth requires a robust regulatory network to keep the balance between pluripotent stem cells and differentiating progeny. Components of this network have now been elucidated and provide a unique opportunity for comparing strategies that were developed in the animal and plant kingdoms, which underlie the logic of stem cell behaviour.
Collapse
|
92
|
Gu X, Xu T, He Y. A histone H3 lysine-27 methyltransferase complex represses lateral root formation in Arabidopsis thaliana. MOLECULAR PLANT 2014; 7:977-988. [PMID: 24711289 DOI: 10.1093/mp/ssu035] [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] [Indexed: 05/09/2023]
Abstract
Root branching or lateral root formation is crucial to maximize a root system acquiring nutrients and water from soil. A lateral root (LR) arises from asymmetric cell division of founder cells (FCs) in a pre-branch site of the primary root, and FC establishment is essential for lateral root formation. FCs are known to be specified from xylem pole pericycle cells, but the molecular genetic mechanisms underlying FC establishment are unclear. Here, we report that, in Arabidopsis thaliana, a PRC2 (for Polycomb repressive complex 2) histone H3 lysine-27 (H3K27) methyltransferase complex, functions to inhibit FC establishment during LR initiation. We found that functional loss of the PRC2 subunits EMF2 (for EMBRYONIC FLOWER 2) or CLF (for CURLY LEAF) leads to a great increase in the number of LRs formed in the primary root. The CLF H3K27 methyltransferase binds to chromatin of the auxin efflux carrier gene PIN FORMED 1 (PIN1), deposits the repressive mark H3K27me3 to repress its expression, and functions to down-regulate auxin maxima in root tissues and inhibit FC establishment. Our findings collectively suggest that EMF2-CLF PRC2 acts to down-regulate root auxin maxima and show that this complex represses LR formation in Arabidopsis.
Collapse
Affiliation(s)
- Xiaofeng Gu
- Department of Biological Sciences, National University of Singapore, Singapore; Temasek Life Sciences Laboratory, Singapore
| | - Tongda Xu
- Temasek Life Sciences Laboratory, Singapore; Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yuehui He
- Department of Biological Sciences, National University of Singapore, Singapore; Temasek Life Sciences Laboratory, Singapore; Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| |
Collapse
|
93
|
Raynaud C, Mallory AC, Latrasse D, Jégu T, Bruggeman Q, Delarue M, Bergounioux C, Benhamed M. Chromatin meets the cell cycle. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2677-89. [PMID: 24497647 DOI: 10.1093/jxb/ert433] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The cell cycle is one of the most comprehensively studied biological processes, due primarily to its significance in growth and development, and its deregulation in many human disorders. Studies using a diverse set of model organisms, including yeast, worms, flies, frogs, mammals, and plants, have greatly expanded our knowledge of the cell cycle and have contributed to the universally accepted view of how the basic cell cycle machinery is regulated. In addition to the oscillating activity of various cyclin-dependent kinase (CDK)-cyclin complexes, a plethora of proteins affecting various aspects of chromatin dynamics has been shown to be essential for cell proliferation during plant development. Furthermore, it was reported recently that core cell cycle regulators control gene expression by modifying histone patterns. This review focuses on the intimate relationship between the cell cycle and chromatin. It describes the dynamics and functions of chromatin structures throughout cell cycle progression and discusses the role of heterochromatin as a barrier against re-replication and endoreduplication. It also proposes that core plant cell cycle regulators control gene expression in a manner similar to that described in mammals. At present, our challenge in plants is to define the complete set of effectors and actors that coordinate cell cycle progression and chromatin structure and to understand better the functional interplay between these two processes.
Collapse
Affiliation(s)
- Cécile Raynaud
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Allison C Mallory
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - David Latrasse
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Teddy Jégu
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Quentin Bruggeman
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Marianne Delarue
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Catherine Bergounioux
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, 91405 Orsay, France
| |
Collapse
|
94
|
Zhang D, Jing Y, Jiang Z, Lin R. The Chromatin-Remodeling Factor PICKLE Integrates Brassinosteroid and Gibberellin Signaling during Skotomorphogenic Growth in Arabidopsis. THE PLANT CELL 2014; 26:2472-2485. [PMID: 24920333 PMCID: PMC4114946 DOI: 10.1105/tpc.113.121848] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 05/05/2014] [Accepted: 05/21/2014] [Indexed: 05/20/2023]
Abstract
Plant cell elongation is controlled by endogenous hormones, including brassinosteroid (BR) and gibberellin (GA), and by environmental factors, such as light/darkness. The molecular mechanisms underlying the convergence of these signals that govern cell growth remain largely unknown. We previously showed that the chromatin-remodeling factor PICKLE/ENHANCED PHOTOMORPHOGENIC1 (PKL/EPP1) represses photomorphogenesis in Arabidopsis thaliana. Here, we demonstrated that PKL physically interacted with PHYTOCHROME-INTERACTING FACTOR3 (PIF3) and BRASSINAZOLE-RESISTANT1 (BZR1), key components of the light and BR signaling pathways, respectively. Also, this interaction promoted the association of PKL with cell elongation-related genes. We found that PKL, PIF3, and BZR1 coregulate skotomorphogenesis by repressing the trimethylation of histone H3 Lys-27 (H3K27me3) on target promoters. Moreover, DELLA proteins interacted with PKL and attenuated its binding ability. Strikingly, brassinolide and GA3 inhibited H3K27me3 modification of histones associated with cell elongation-related loci in a BZR1- and DELLA-mediated manner, respectively. Our findings reveal that the PKL chromatin-remodeling factor acts as a critical node that integrates light/darkness, BR, and GA signals to epigenetically regulate plant growth and development. This work also provides a molecular framework by which hormone signals regulate histone modification in concert with light/dark environmental cues.
Collapse
Affiliation(s)
- Dong Zhang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zhimin Jiang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China National Center for Plant Gene Research, Beijing 100093, China
| |
Collapse
|
95
|
Chen N, Zhou WB, Wang YX, Dong AW, Yu Y. Polycomb-group histone methyltransferase CLF is required for proper somatic recombination in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:550-558. [PMID: 24393343 DOI: 10.1111/jipb.12157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 12/30/2013] [Indexed: 06/03/2023]
Abstract
Homologous recombination (HR) is a key process during meiosis in reproductive cells and the DNA damage repair process in somatic cells. Although chromatin structure is thought to be crucial for HR, only a small number of chromatin modifiers have been studied in HR regulation so far. Here, we investigated the function of CURLY LEAF (CLF), a Polycomb-group (PcG) gene responsible for histone3 lysine 27 trimethylation (H3K27me3), in somatic and meiotic HR in Arabidopsis thaliana. Although fluorescent protein reporter assays in pollen and seeds showed that the frequency of meiotic cross-over in the loss-of-function mutant clf-29 was not significantly different from that in wild type, there was a lower frequency of HR in clf-29 than in wild type under normal conditions and under bleomycin treatment. The DNA damage levels were comparable between clf-29 and wild type, even though several DNA damage repair genes (e.g. ATM, BRCA2a, RAD50, RAD51, RAD54, and PARP2) were expressed at lower levels in clf-29. Under bleomycin treatment, the expression levels of DNA repair genes were similar in clf-29 and wild type, thus CLF may also regulate HR via other mechanisms. These findings expand the current knowledge of PcG function and contribute to general interests of epigenetic regulation in genome stability regulation.
Collapse
Affiliation(s)
- Na Chen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | | | | | | | | |
Collapse
|
96
|
Ühlken C, Horvath B, Stadler R, Sauer N, Weingartner M. MAIN-LIKE1 is a crucial factor for correct cell division and differentiation in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:107-20. [PMID: 24635680 DOI: 10.1111/tpj.12455] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 12/04/2013] [Accepted: 01/17/2014] [Indexed: 05/10/2023]
Abstract
Plant development requires accurate coordination of gene expression, both in actively dividing meristematic cells and differentiated cells. Cell fate establishment and maintenance, among others, are mediated by chromatin organization complexes that determine the stable transcriptional states of specific cell types. Here, we focus on MAIN-LIKE1 (MAIL1), one of three homologs of MAINTENANCE OF MERISTEMS (MAIN), which form a plant-specific gene family in Arabidopsis thaliana. We show that MAIL1 encodes a ubiquitously expressed nuclear protein. A mail1 loss-of-function mutant developed short primary roots, in which the meristematic cells accumulated DNA double-strand breaks and underwent massive cell death. In addition, mail1 mutant showed also cell differentiation defects in root and shoot tissues, and developed disorganized callus-like structures. The genetic interaction between main and mail1 mutants suggests that they act in the same pathway, and that both are essential for maintaining correct cell division acitivity in meristematic cells, while MAIL1 has an additional function in differentiating cells.
Collapse
Affiliation(s)
- Christine Ühlken
- Molekulare Pflanzenphysiologie and Erlangen Center of Plant Science, Friedrich-Alexander Universität Erlangen-Nürnberg, D-91058, Erlangen, Germany
| | | | | | | | | |
Collapse
|
97
|
Folta A, Severing EI, Krauskopf J, van de Geest H, Verver J, Nap JP, Mlynarova L. Over-expression of Arabidopsis AtCHR23 chromatin remodeling ATPase results in increased variability of growth and gene expression. BMC PLANT BIOLOGY 2014; 14:76. [PMID: 24666886 PMCID: PMC3987066 DOI: 10.1186/1471-2229-14-76] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/17/2014] [Indexed: 05/05/2023]
Abstract
BACKGROUND Plants are sessile organisms that deal with their -sometimes adverse- environment in well-regulated ways. Chromatin remodeling involving SWI/SNF2-type ATPases is thought to be an important epigenetic mechanism for the regulation of gene expression in different developmental programs and for integrating these programs with the response to environmental signals. In this study, we report on the role of chromatin remodeling in Arabidopsis with respect to the variability of growth and gene expression in relationship to environmental conditions. RESULTS Already modest (2-fold) over-expression of the AtCHR23 ATPase gene in Arabidopsis results in overall reduced growth compared to the wild-type. Detailed analyses show that in the root, the reduction of growth is due to reduced cell elongation. The reduced-growth phenotype requires sufficient light and is magnified by applying deliberate abiotic (salt, osmotic) stress. In contrast, the knockout mutation of AtCHR23 does not lead to such visible phenotypic effects. In addition, we show that over-expression of AtCHR23 increases the variability of growth in populations of genetically identical plants. These data indicate that accurate and controlled expression of AtCHR23 contributes to the stability or robustness of growth. Detailed RNAseq analyses demonstrate that upon AtCHR23 over-expression also the variation of gene expression is increased in a subset of genes that associate with environmental stress. The larger variation of gene expression is confirmed in individual plants with the help of independent qRT-PCR analysis. CONCLUSIONS Over-expression of AtCHR23 gives Arabidopsis a phenotype that is markedly different from the growth arrest phenotype observed upon over-expression of AtCHR12, the paralog of AtCHR23, in response to abiotic stress. This demonstrates functional sub-specialization of highly similar ATPases in Arabidopsis. Over-expression of AtCHR23 increases the variability of growth among genetically identical individuals in a way that is consistent with increased variability of expression of a distinct subset of genes that associate with environmental stress. We propose that ATCHR23-mediated chromatin remodeling is a potential component of a buffer system in plants that protects against environmentally-induced phenotypic and transcriptional variation.
Collapse
Affiliation(s)
- Adam Folta
- Laboratory of Molecular Biology, Plant Sciences Group, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Edouard I Severing
- Laboratory of Genetics, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Julian Krauskopf
- Applied Bioinformatics, Bioscience, Plant Research International, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- Present address: Department of Toxigenomics, Maastricht University, Maastricht, The Netherlands
| | - Henri van de Geest
- Applied Bioinformatics, Bioscience, Plant Research International, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Jan Verver
- Laboratory of Molecular Biology, Plant Sciences Group, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Jan-Peter Nap
- Applied Bioinformatics, Bioscience, Plant Research International, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- Expertise Centre ALIFE, Institute for Life Science & Technology, Hanze University of Applied Sciences, Groningen, The Netherlands
| | - Ludmila Mlynarova
- Laboratory of Molecular Biology, Plant Sciences Group, Wageningen University and Research Centre, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| |
Collapse
|
98
|
Horstman A, Willemsen V, Boutilier K, Heidstra R. AINTEGUMENTA-LIKE proteins: hubs in a plethora of networks. TRENDS IN PLANT SCIENCE 2014; 19:146-57. [PMID: 24280109 DOI: 10.1016/j.tplants.2013.10.010] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/24/2013] [Accepted: 10/27/2013] [Indexed: 05/18/2023]
Abstract
Members of the AINTEGUMENTA-LIKE (AIL) family of APETALA 2/ETHYLENE RESPONSE FACTOR (AP2/ERF) domain transcription factors are expressed in all dividing tissues in the plant, where they have central roles in developmental processes such as embryogenesis, stem cell niche specification, meristem maintenance, organ positioning, and growth. When overexpressed, AIL proteins induce adventitious growth, including somatic embryogenesis and ectopic organ formation. The Arabidopsis (Arabidopsis thaliana) genome contains eight AIL genes, including AINTEGUMENTA, BABY BOOM, and the PLETHORA genes. Studies on these transcription factors have revealed their intricate relationship with auxin as well as their involvement in an increasing number of gene regulatory networks, in which extensive crosstalk and feedback loops have a major role.
Collapse
Affiliation(s)
- Anneke Horstman
- Plant Research International, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Viola Willemsen
- Plant Developmental Biology, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Kim Boutilier
- Plant Research International, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Renze Heidstra
- Plant Developmental Biology, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
| |
Collapse
|
99
|
Choi SC, Lee S, Kim SR, Lee YS, Liu C, Cao X, An G. Trithorax group protein Oryza sativa Trithorax1 controls flowering time in rice via interaction with early heading date3. PLANT PHYSIOLOGY 2014; 164:1326-37. [PMID: 24420930 PMCID: PMC3938623 DOI: 10.1104/pp.113.228049] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Trithorax group proteins are chromatin-remodeling factors that activate target gene expression by antagonistically functioning against the Polycomb group. In Arabidopsis (Arabidopsis thaliana), Arabidopsis Trithorax protein1 (ATX1) regulates flowering time and floral organ identity. Here, we observed that suppression of Oryza sativa Trithorax1 (OsTrx1), an ortholog of ATX1, delayed flowering time in rice (Oryza sativa). Because the delay occurred only under long-day conditions, we evaluated the flowering signal pathways that specifically function under long-day conditions. Among them, the OsMADS50 and Heading date1 pathways were not affected by the mutation. However, the Grain number, plant height, and heading date7 (Ghd7) pathway was altered in ostrx1. Transcript levels of OsGI, phytochrome genes, and Early heading date3 (Ehd3), which function upstream of Ghd7, were unchanged in the mutant. Because Trx group proteins form a complex with other proteins to modify the chromatin structure of target genes, we investigated whether OsTrx1 interacts with a previously identified protein that functions upstream of Ghd7. We demonstrated that the plant homeodomain motif of OsTrx1 binds to native histone H3 from the calf thymus and that OsTrx1 binds to Ehd3 through the region between the plant homeodomain and SET domains. Finally, we showed that the SET domain at the C-terminal end of OsTrx1 has histone H3 methyltransferase activity when incubated with oligonucleosomes. Our results suggest that OsTrx1 plays an important role in regulating flowering time in rice by modulating chromatin structure.
Collapse
|
100
|
Perrot-Rechenmann C. Auxin Signaling in Plants. Mol Biol 2014. [DOI: 10.1007/978-1-4614-7570-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|