51
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Hernández-Verdeja T, Strand Å. Retrograde Signals Navigate the Path to Chloroplast Development. PLANT PHYSIOLOGY 2018; 176:967-976. [PMID: 29254985 PMCID: PMC5813530 DOI: 10.1104/pp.17.01299] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/12/2017] [Indexed: 05/18/2023]
Abstract
Complex signaling networks between the chloroplast and the nucleus mediate the emergence of the seedling into the light and the establishment of photosynthesis.
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Affiliation(s)
- Tamara Hernández-Verdeja
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Åsa Strand
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
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52
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Automated 3D Gene Position Analysis Using a Customized Imaris Plugin: XTFISHInsideNucleus. Methods Mol Biol 2018; 1675:591-613. [PMID: 29052213 DOI: 10.1007/978-1-4939-7318-7_32] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Fluorescence in situ hybridization (FISH) is commonly used to visualize chromosomal regions or genomic loci within the nucleus, and can largely contribute to unraveling the link between structure and function in the nucleus. Three-dimensional (3D) analyses are required to best capture the nucleus' organizing principles, but the experimental setup and computational analyses are far from trivial. Here, we present a robust workflow for 3D FISH against repeats and single copy loci in embedded intact nuclei from Arabidopsis leaves. We then describe in detail the image acquisition, subsequent image deconvolution before 3D image processing, and the image reconstruction. We developed an automated batch image processing pipeline using a customized, open source plugin implemented in the Imaris environment.
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53
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Groves NR, Biel AM, Newman-Griffis AH, Meier I. Dynamic Changes in Plant Nuclear Organization in Response to Environmental and Developmental Signals. PLANT PHYSIOLOGY 2018; 176:230-241. [PMID: 28739821 PMCID: PMC5761808 DOI: 10.1104/pp.17.00788] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 07/17/2017] [Indexed: 05/19/2023]
Abstract
The functional organization of the plant nuclear pore, nuclear envelope, and nucleoplasm marks dynamically changing environmental cues and developmental programs.
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Affiliation(s)
- Norman R Groves
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Alecia M Biel
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
| | - Anna H Newman-Griffis
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
| | - Iris Meier
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210
- Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210
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54
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Abstract
Our understanding of the epigenetic mechanisms that regulate gene expression has been largely increased in recent years by the development and refinement of different techniques. This has revealed that gene transcription is highly influenced by epigenetic mechanisms, i.e., those that do not involve changes in the genome sequence, but rather in nuclear architecture, chromosome conformation and histone and DNA modifications. Our understanding of how these different levels of epigenetic regulation interact with each other and with classical transcription-factor based gene regulation to influence gene transcription has just started to emerge. This review discusses the latest advances in unraveling the complex interactions between different types of epigenetic regulation and transcription factor activity, with special attention to the approaches that can be used to study these interactions.
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Affiliation(s)
- Marian Bemer
- Department of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands.
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55
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Bräutigam K, Cronk Q. DNA Methylation and the Evolution of Developmental Complexity in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:1447. [PMID: 30349550 PMCID: PMC6186995 DOI: 10.3389/fpls.2018.01447] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/12/2018] [Indexed: 05/20/2023]
Abstract
All land plants so far examined use DNA methylation to silence transposons (TEs). DNA methylation therefore appears to have been co-opted in evolution from an original function in TE management to a developmental function (gene regulation) in both phenotypic plasticity and in normal development. The significance of DNA methylation to the evolution of developmental complexity in plants lies in its role in the management of developmental pathways. As such it is more important in fine tuning the presence, absence, and placement of organs rather than having a central role in the evolution of new organs. Nevertheless, its importance should not be underestimated as it contributes considerably to the range of phenotypic expression and complexity available to plants: the subject of the emerging field of epi-evodevo. Furthermore, changes in DNA methylation can function as a "soft" mutation that may be important in the early stages of major evolutionary novelty.
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Affiliation(s)
- Katharina Bräutigam
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Quentin Cronk
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Quentin Cronk,
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56
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Wang Q, Liu Q, Wang X, Zuo Z, Oka Y, Lin C. New insights into the mechanisms of phytochrome-cryptochrome coaction. THE NEW PHYTOLOGIST 2018; 217:547-551. [PMID: 29139123 PMCID: PMC6677561 DOI: 10.1111/nph.14886] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 10/02/2017] [Indexed: 05/18/2023]
Abstract
Contents Summary 547 I. Introduction 547 II. Phytochromes mediate light-induced transcription of BICs to inactivate cryptochromes 548 III. PPKs phosphorylate light-signaling proteins and histones to affect plant development 548 IV. Prospect 550 Acknowledgements 550 References 550 SUMMARY: Plants perceive and respond to light signals by multiple sensory photoreceptors, including phytochromes and cryptochromes, which absorb different wavelengths of light to regulate genome expression and plant development. Photophysiological analyses have long revealed the coordinated actions of different photoreceptors, a phenomenon referred to as the photoreceptor coaction. The mechanistic explanations of photoreceptor coactions are not fully understood. The function of direct protein-protein interaction of phytochromes and cryptochromes and common signaling molecules of these photoreceptors, such as SPA1/COP1 E3 ubiquitin ligase complex and bHLH transcription factors PIFs, would partially explain phytochrome-cryptochrome coactions. In addition, newly discovered proteins that block cryptochrome photodimerization or catalyze cryptochrome phosphorylation may also participate in the phytochrome and cryptochrome coaction. This Tansley insight, which is not intended to make a comprehensive review of the studies of photoreceptor coactions, attempts to highlight those recent findings and their possible roles in the photoreceptor coaction.
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Affiliation(s)
- Qin Wang
- Basic Forestry and Proteomics Research Center, UCLA-FAFU Joint Research Center on Plant Proteomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Qing Liu
- Basic Forestry and Proteomics Research Center, UCLA-FAFU Joint Research Center on Plant Proteomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xu Wang
- Basic Forestry and Proteomics Research Center, UCLA-FAFU Joint Research Center on Plant Proteomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Zecheng Zuo
- Basic Forestry and Proteomics Research Center, UCLA-FAFU Joint Research Center on Plant Proteomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yoshito Oka
- Basic Forestry and Proteomics Research Center, UCLA-FAFU Joint Research Center on Plant Proteomics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chentao Lin
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA
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57
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She W, Baroux C, Grossniklaus U. Cell-Type Specific Chromatin Analysis in Whole-Mount Plant Tissues by Immunostaining. Methods Mol Biol 2018; 1675:443-454. [PMID: 29052206 DOI: 10.1007/978-1-4939-7318-7_25] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Chromatin organization in eukaryotes is highly dynamic, playing fundamental roles in regulating diverse nuclear processes including DNA replication, transcription, and repair. Thus, the analysis of chromatin organization is of great importance for the elucidation of chromatin-mediated biological processes. Immunostaining coupled with imaging is one of the most powerful tools for chromatin analysis at the cellular level. However, in plants, it is sometimes technically challenging to apply this method due to the inaccessibility of certain cell types and/or poor penetration of the reagents into plant tissues and cells. To circumvent these limitations, we developed a highly efficient protocol enabling the analysis of chromatin modifications and nuclear organization at the single-cell level with high resolution in whole-mount plant tissues. The main procedure consists of five steps: (1) tissue fixation; (2) dissection and embedding; (3) tissue processing; (4) antibody incubation; and (5) imaging. This protocol has been simplified for the processing of multiple samples without the need for laborious tissue sectioning. Additionally, it preserves cellular morphology and chromatin organization, allowing comparative analyses of chromatin organization between different cell types or developmental stages. This protocol was successfully used for various tissues of different plant species, including Arabidopsis thaliana, Oryza sativa (rice), and Zea mays (maize). Importantly, this method is very useful to analyze poorly accessible tissues, such as female meiocytes, gametophytes, and embryos.
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Affiliation(s)
- Wenjing She
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
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58
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Molinier J. Genome and Epigenome Surveillance Processes Underlying UV Exposure in Plants. Genes (Basel) 2017; 8:genes8110316. [PMID: 29120372 PMCID: PMC5704229 DOI: 10.3390/genes8110316] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 11/03/2017] [Accepted: 11/03/2017] [Indexed: 02/07/2023] Open
Abstract
Land plants and other photosynthetic organisms (algae, bacteria) use the beneficial effect of sunlight as a source of energy for the photosynthesis and as a major source of information from the environment. However, the ultraviolet component of sunlight also produces several types of damage, which can affect cellular and integrity, interfering with growth and development. In order to reduce the deleterious effects of UV, photosynthetic organisms combine physiological adaptation and several types of DNA repair pathways to avoid dramatic changes in the structure. Therefore, plants may have obtained an evolutionary benefit from combining genome and surveillance processes, to efficiently deal with the deleterious effects of UV radiation. This review will present the different mechanisms activated upon UV exposure that contribute to maintain genome and integrity.
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Affiliation(s)
- Jean Molinier
- Institut de Biologie Moléculaire des Plantes, UPR2357-CNRS, 12 rue du Général Zimmer, 67000 Strasbourg, France.
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59
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Seluzicki A, Burko Y, Chory J. Dancing in the dark: darkness as a signal in plants. PLANT, CELL & ENVIRONMENT 2017; 40:2487-2501. [PMID: 28044340 PMCID: PMC6110299 DOI: 10.1111/pce.12900] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 05/21/2023]
Abstract
Daily cycles of light and dark provide an organizing principle and temporal constraints under which life on Earth evolved. While light is often the focus of plant studies, it is only half the story. Plants continuously adjust to their surroundings, taking both dawn and dusk as cues to organize their growth, development and metabolism to appropriate times of day. In this review, we examine the effects of darkness on plant physiology and growth. We describe the similarities and differences between seedlings grown in the dark versus those grown in light-dark cycles, and the evolution of etiolated growth. We discuss the integration of the circadian clock into other processes, looking carefully at the points of contact between clock genes and growth-promoting gene-regulatory networks in temporal gating of growth. We also examine daily starch accumulation and degradation, and the possible contribution of dark-specific metabolic controls in regulating energy and growth. Examining these studies together reveals a complex and continuous balancing act, with many signals, dark included, contributing information and guiding the plant through its life cycle. The extraordinary interconnection between light and dark is manifest during cycles of day and night and during seedling emergence above versus below the soil surface.
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Affiliation(s)
- Adam Seluzicki
- Salk Institute for Biological Studies, Plant Biology Laboratory, La Jolla, CA, 92037, USA
| | - Yogev Burko
- Salk Institute for Biological Studies, Plant Biology Laboratory, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Joanne Chory
- Salk Institute for Biological Studies, Plant Biology Laboratory, La Jolla, CA, 92037, USA
- Howard Hughes Medical Institute Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
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60
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Abstract
Dynamic reshuffling of the chromatin landscape is a recurrent theme orchestrated in many, if not all, plant developmental transitions and adaptive responses. Spatiotemporal variations of the chromatin properties on regulatory genes and on structural genomic elements trigger the establishment of distinct transcriptional contexts, which in some instances can epigenetically be inherited. Studies on plant cell plasticity during the differentiation of stem cells, including gametogenesis, or the specialization of vegetative cells in various organs, as well as the investigation of allele-specific gene regulation have long been impaired by technical challenges in generating specific chromatin profiles in complex or hardly accessible cell populations. Recent advances in increasing the sensitivity of genome-enabled technologies and in the isolation of specific cell types have allowed for overcoming such limitations. These developments hint at multilevel regulatory events ranging from nucleosome accessibility and composition to higher order chromatin organization and genome topology. Uncovering the large extent to which chromatin dynamics and epigenetic processes influence gene expression is therefore not surprisingly revolutionizing current views on plant molecular genetics and (epi)genomics as well as their perspectives in eco-evolutionary biology. Here, we introduce current methodologies to probe genome-wide chromatin variations for which protocols are detailed in this book chapter, with an emphasis on the plant model species Arabidopsis.
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61
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Narsai R, Gouil Q, Secco D, Srivastava A, Karpievitch YV, Liew LC, Lister R, Lewsey MG, Whelan J. Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination. Genome Biol 2017; 18:172. [PMID: 28911330 PMCID: PMC5599894 DOI: 10.1186/s13059-017-1302-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 08/16/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene expression and the dynamic changes in the epigenome and small RNAs during germination is limited. The interactions between genome, transcriptome and epigenome must be revealed in order to identify the regulatory mechanisms that control seed germination. RESULTS We present an integrated analysis of high-resolution RNA sequencing, small RNA sequencing and MethylC sequencing over ten developmental time points in Arabidopsis thaliana seeds, finding extensive transcriptomic and epigenomic transformations associated with seed germination. We identify previously unannotated loci from which messenger RNAs are expressed transiently during germination and find widespread alternative splicing and divergent isoform abundance of genes involved in RNA processing and splicing. We generate the first dynamic transcription factor network model of germination, identifying known and novel regulatory factors. Expression of both microRNA and short interfering RNA loci changes significantly during germination, particularly between the seed and the post-germinative seedling. These are associated with changes in gene expression and large-scale demethylation observed towards the end of germination, as the epigenome transitions from an embryo-like to a vegetative seedling state. CONCLUSIONS This study reveals the complex dynamics and interactions of the transcriptome and epigenome during seed germination, including the extensive remodelling of the seed DNA methylome from an embryo-like to vegetative-like state during the seed-to-seedling transition. Data are available for exploration in a user-friendly browser at https://jbrowse.latrobe.edu.au/germination_epigenome .
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Affiliation(s)
- Reena Narsai
- ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Quentin Gouil
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
| | - David Secco
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Akanksha Srivastava
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
| | - Yuliya V Karpievitch
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Lim Chee Liew
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Ryan Lister
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia
- Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Mathew G Lewsey
- Centre for AgriBioscience, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - James Whelan
- ARC Centre of Excellence in Plant Energy Biology, Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
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62
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Snoek BL, Pavlova P, Tessadori F, Peeters AJM, Bourbousse C, Barneche F, de Jong H, Fransz PF, van Zanten M. Genetic Dissection of Morphometric Traits Reveals That Phytochrome B Affects Nucleus Size and Heterochromatin Organization in Arabidopsis thaliana. G3 (BETHESDA, MD.) 2017; 7:2519-2531. [PMID: 28592555 PMCID: PMC5555459 DOI: 10.1534/g3.117.043539] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/31/2017] [Indexed: 02/05/2023]
Abstract
Microscopically visible chromatin is partitioned into two major components in Arabidopsis thaliana nuclei. On one hand, chromocenters are conspicuous foci of highly condensed "heterochromatic" domains that contain mostly repeated sequences. On the other hand, less condensed and gene-rich "euchromatin" emanates from these chromocenters. This differentiation, together with the dynamic nature of chromatin compaction in response to developmental and environmental stimuli, makes Arabidopsis a powerful system for studying chromatin organization and dynamics. Heterochromatin dynamics can be monitored by measuring the Heterochromatin Index, i.e., the proportion of nuclei displaying well-defined chromocenters, or the DNA fraction of chromocenters (relative heterochromatin fraction). Both measures are composite traits, thus their values represent the sum of effects of various underlying morphometric properties. We exploited genetic variation between natural occurring accessions to determine the genetic basis of individual nucleus and chromocenter morphometric parameters (area, perimeter, density, roundness, and heterogeneity) that together determine chromatin compaction. Our novel reductionist genetic approach revealed quantitative trait loci (QTL) for all measured traits. Genomic colocalization among QTL was limited, which suggests a complex genetic regulation of chromatin compaction. Yet genomic intervals of QTL for nucleus size (area and perimeter) both overlap with a known QTL for heterochromatin compaction that is explained by natural polymorphism in the red/far-red light and temperature receptor Phytochrome B. Mutant analyses and genetic complementation assays show that Phytochrome B is a negative regulator of nucleus size, revealing that perception of climatic conditions by a Phytochrome-mediated hub is a major determinant for coordinating nucleus size and heterochromatin compaction.
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Affiliation(s)
- Basten L Snoek
- Laboratory of Nematology, Wageningen University, 6708 PB, The Netherlands
- Theoretical Biology and Bioinformatics, Institute of Biodynamics and Biocomplexity
| | - Penka Pavlova
- Laboratory of Genetics, Wageningen University, 6708 PB, The Netherlands
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 SM, The Netherlands
| | - Federico Tessadori
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 SM, The Netherlands
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, University Medical Center Utrecht, 3584 CT, The Netherlands
| | - Anton J M Peeters
- Department of Biology, Institute of Education, Utrecht University, 3584 CH, The Netherlands
| | - Clara Bourbousse
- 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, Ecole Normale Supérieure, Paris Sciences et Lettres Research University, F-75005, France
| | - Fredy Barneche
- 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, Ecole Normale Supérieure, Paris Sciences et Lettres Research University, F-75005, France
| | - Hans de Jong
- Laboratory of Genetics, Wageningen University, 6708 PB, The Netherlands
| | - Paul F Fransz
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 SM, The Netherlands
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, 3584 CH, The Netherlands
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63
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Liu Y, Zhang W, Zhang K, You Q, Yan H, Jiao Y, Jiang J, Xu W, Su Z. Genome-wide mapping of DNase I hypersensitive sites reveals chromatin accessibility changes in Arabidopsis euchromatin and heterochromatin regions under extended darkness. Sci Rep 2017. [PMID: 28642500 PMCID: PMC5481438 DOI: 10.1038/s41598-017-04524-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Light, as the energy source in photosynthesis, is essential for plant growth and development. Extended darkness causes dramatic gene expression changes. In this study, we applied DNase-seq (DNase I hypersensitive site sequencing) to study changes of chromatin accessibility in euchromatic and heterochromatic regions under extended darkness in Arabidopsis. We generated 27 Gb DNase-seq and 67.6 Gb RNA-seq data to investigate chromatin accessibility changes and global gene expression under extended darkness and control condition in Arabidopsis. We found that ~40% DHSs (DNaseI hypersensitive sites) were diminished under darkness. In non-TE regions, the majority of DHS-changed genes were DHS-diminished under darkness. A total of 519 down-regulated genes were associated with diminished DHSs under darkness, mainly involved in photosynthesis process and retrograde signaling, and were regulated by chloroplast maintenance master regulators such as GLK1. In TE regions, approximately half of the DHS-changed TEs were DHS-increased under darkness and were primarily associated with the LTR/Gypsy retrotransposons in the heterochromatin flanking the centromeres. In contrast, DHS-diminished TEs under darkness were enriched in Copia, LINE, and MuDR dispersed across chromosomes. Together, our results indicated that extended darkness resulted in more increased chromatin compaction in euchromatin and decompaction in heterochromatin, thus further leading to gene expression changes in Arabidopsis.
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Affiliation(s)
- Yue Liu
- College of Biological Sciences, China Agricultural University, State key Laboratory of Plant Physiology and Biochemistry, Beijing, China
| | - Wenli Zhang
- Nanjing Agricultural University, State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, Nanjing, China
| | - Kang Zhang
- College of Biological Sciences, China Agricultural University, State key Laboratory of Plant Physiology and Biochemistry, Beijing, China
| | - Qi You
- College of Biological Sciences, China Agricultural University, State key Laboratory of Plant Physiology and Biochemistry, Beijing, China
| | - Hengyu Yan
- College of Biological Sciences, China Agricultural University, State key Laboratory of Plant Physiology and Biochemistry, Beijing, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Jiming Jiang
- University of Wisconsin-Madison, Department of Horticulture, Madison, WI, USA
| | - Wenying Xu
- College of Biological Sciences, China Agricultural University, State key Laboratory of Plant Physiology and Biochemistry, Beijing, China
| | - Zhen Su
- College of Biological Sciences, China Agricultural University, State key Laboratory of Plant Physiology and Biochemistry, Beijing, China.
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64
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Vergara Z, Gutierrez C. Emerging roles of chromatin in the maintenance of genome organization and function in plants. Genome Biol 2017; 18:96. [PMID: 28535770 PMCID: PMC5440935 DOI: 10.1186/s13059-017-1236-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chromatin is not a uniform macromolecular entity; it contains different domains characterized by complex signatures of DNA and histone modifications. Such domains are organized both at a linear scale along the genome and spatially within the nucleus. We discuss recent discoveries regarding mechanisms that establish boundaries between chromatin states and nuclear territories. Chromatin organization is crucial for genome replication, transcriptional silencing, and DNA repair and recombination. The replication machinery is relevant for the maintenance of chromatin states, influencing DNA replication origin specification and accessibility. Current studies reinforce the idea of intimate crosstalk between chromatin features and processes involving DNA transactions.
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Affiliation(s)
- Zaida Vergara
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049, Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049, Madrid, Spain.
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65
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Xiao J, Jin R, Wagner D. Developmental transitions: integrating environmental cues with hormonal signaling in the chromatin landscape in plants. Genome Biol 2017; 18:88. [PMID: 28490341 PMCID: PMC5425979 DOI: 10.1186/s13059-017-1228-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Plant development is predominantly postembryonic and tuned in to respond to environmental cues. All living plant cells can be triggered to de-differentiate, assume different cell identities, or form a new organism. This developmental plasticity is thought to be an adaptation to the sessile lifestyle of plants. Recent discoveries have advanced our understanding of the orchestration of plant developmental switches by transcriptional master regulators, chromatin state changes, and hormone response pathways. Here, we review these recent advances with emphasis on the earliest stages of plant development and on the switch from pluripotency to differentiation in different plant organ systems.
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Affiliation(s)
- Jun Xiao
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Run Jin
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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66
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Bi X, Cheng YJ, Hu B, Ma X, Wu R, Wang JW, Liu C. Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery. Genome Res 2017; 27:1162-1173. [PMID: 28385710 PMCID: PMC5495068 DOI: 10.1101/gr.215186.116] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 04/05/2017] [Indexed: 12/12/2022]
Abstract
The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonrandom positioning of chromatin at the nuclear periphery and its biological relevance have been studied extensively in animals. However, it remains unknown whether comparable chromatin organizations exist in plants. Here, using a strategy using restriction enzyme-mediated chromatin immunoprecipitation, we present genome-wide identification of nonrandom domain organization of chromatin at the peripheral zone of Arabidopsis thaliana nuclei. We show that in various tissues, 10%-20% of the regions on the chromosome arms are anchored at the nuclear periphery, and these regions largely overlap between different tissues. Unlike LADs in animals, the identified domains in plants are not gene-poor or A/T-rich. These domains are enriched with silenced protein-coding genes, transposable element genes, and heterochromatic marks, which collectively define a repressed environment. In addition, these domains strongly correlate with our genome-wide chromatin interaction data set (Hi-C) by largely explaining the patterns of chromatin compartments, revealed on Hi-C maps. Moreover, our results reveal a spatial compartment of different DNA methylation pathways that regulate silencing of transposable elements, where the CHH methylation of transposable elements located at the nuclear periphery and in the interior are preferentially mediated by CMT2 and DRM methyltransferases, respectively. Taken together, the results demonstrate functional partitioning of the Arabidopsis genome in the nuclear space.
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Affiliation(s)
- Xiuli Bi
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen 72076, Germany
| | - Ying-Juan Cheng
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Shanghai Institutes for Biological Sciences (SIBS), Shanghai 200032, People's Republic of China.,University of Chinese Academy of Sciences, Shanghai 200032, People's Republic of China
| | - Bo Hu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen 72076, Germany
| | - Xiaoli Ma
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen 72076, Germany
| | - Rui Wu
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Shanghai Institutes for Biological Sciences (SIBS), Shanghai 200032, People's Republic of China
| | - Chang Liu
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen 72076, Germany
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67
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Brown SC, Bourge M, Maunoury N, Wong M, Wolfe Bianchi M, Lepers-Andrzejewski S, Besse P, Siljak-Yakovlev S, Dron M, Satiat-Jeunemaître B. DNA Remodeling by Strict Partial Endoreplication in Orchids, an Original Process in the Plant Kingdom. Genome Biol Evol 2017; 9:1051-1071. [PMID: 28419219 PMCID: PMC5546068 DOI: 10.1093/gbe/evx063] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2017] [Indexed: 12/12/2022] Open
Abstract
DNA remodeling during endoreplication appears to be a strong developmental characteristic in orchids. In this study, we analyzed DNA content and nuclei in 41 species of orchids to further map the genome evolution in this plant family. We demonstrate that the DNA remodeling observed in 36 out of 41 orchids studied corresponds to strict partial endoreplication. Such process is developmentally regulated in each wild species studied. Cytometry data analyses allowed us to propose a model where nuclear states 2C, 4E, 8E, etc. form a series comprising a fixed proportion, the euploid genome 2C, plus 2-32 additional copies of a complementary part of the genome. The fixed proportion ranged from 89% of the genome in Vanilla mexicana down to 19% in V. pompona, the lowest value for all 148 orchids reported. Insterspecific hybridization did not suppress this phenomenon. Interestingly, this process was not observed in mass-produced epiphytes. Nucleolar volumes grow with the number of endocopies present, coherent with high transcription activity in endoreplicated nuclei. Our analyses suggest species-specific chromatin rearrangement. Towards understanding endoreplication, V. planifolia constitutes a tractable system for isolating the genomic sequences that confer an advantage via endoreplication from those that apparently suffice at diploid level.
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Affiliation(s)
- Spencer C. Brown
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Mickaël Bourge
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Nicolas Maunoury
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | - Maurice Wong
- Service du Développement Rural, Papeete Tahiti, French Polynesia,
France
| | - Michele Wolfe Bianchi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
| | | | - Pascale Besse
- UMR 53, PVBMT Université de la Réunion – Cirad, Pôle de Protection des
Plantes, St Pierre, France
| | - Sonja Siljak-Yakovlev
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech,
Université Paris-Saclay, Orsay Cedex, France
| | - Michel Dron
- Institute of Plant Sciences Paris Saclay IPS2, Université Paris-Sud, CNRS,
INRA, Université Evry, Université Paris Diderot, Sorbonne Paris-Cité, Université
Paris-Saclay, Orsay, France
| | - Béatrice Satiat-Jeunemaître
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université
Paris‐Sud, Université Paris‐Saclay, Gif‐sur‐Yvette Cedex, France
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68
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Poulet A, Duc C, Voisin M, Desset S, Tutois S, Vanrobays E, Benoit M, Evans DE, Probst AV, Tatout C. The LINC complex contributes to heterochromatin organisation and transcriptional gene silencing in plants. J Cell Sci 2017; 130:590-601. [PMID: 28049722 DOI: 10.1242/jcs.194712] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 12/04/2016] [Indexed: 12/20/2022] Open
Abstract
The linker of nucleoskeleton and cytoskeleton (LINC) complex is an evolutionarily well-conserved protein bridge connecting the cytoplasmic and nuclear compartments across the nuclear membrane. While recent data support its function in nuclear morphology and meiosis, its involvement in chromatin organisation has not been studied in plants. Here, 3D imaging methods have been used to investigate nuclear morphology and chromatin organisation in interphase nuclei of the model plant Arabidopsis thaliana in which heterochromatin clusters in conspicuous chromatin domains called chromocentres. Chromocentres form a repressive chromatin environment contributing to transcriptional silencing of repeated sequences, a general mechanism needed for genome stability. Quantitative measurements of the 3D position of chromocentres indicate their close proximity to the nuclear periphery but that their position varies with nuclear volume and can be altered in specific mutants affecting the LINC complex. Finally, we propose that the plant LINC complex contributes to proper heterochromatin organisation and positioning at the nuclear periphery, since its alteration is associated with the release of transcriptional silencing as well as decompaction of heterochromatic sequences.
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Affiliation(s)
- Axel Poulet
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France.,Sainsbury Laboratory Cambridge, University of Cambridge, Cambridge CB2 1LR, UK
| | - Céline Duc
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Maxime Voisin
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Sophie Desset
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Sylvie Tutois
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Emmanuel Vanrobays
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Matthias Benoit
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK
| | - David E Evans
- Sainsbury Laboratory Cambridge, University of Cambridge, Cambridge CB2 1LR, UK
| | - Aline V Probst
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
| | - Christophe Tatout
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France
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69
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Perrella G, Kaiserli E. Light behind the curtain: photoregulation of nuclear architecture and chromatin dynamics in plants. THE NEW PHYTOLOGIST 2016; 212:908-919. [PMID: 27813089 PMCID: PMC5111779 DOI: 10.1111/nph.14269] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/14/2016] [Indexed: 05/24/2023]
Abstract
Light is a powerful stimulus regulating many aspects of plant development and phenotypic plasticity. Plants sense light through the action of specialized photoreceptor protein families that absorb different wavelengths and intensities of light. Recent discoveries in the area of photobiology have uncovered photoreversible changes in nuclear organization correlated with transcriptional regulation patterns that lead to de-etiolation and photoacclimation. Novel signalling components bridging photoreceptor activation with chromatin remodelling and regulation of gene expression have been discovered. Moreover, coregulated gene loci have been shown to relocate to the nuclear periphery in response to light. The study of photoinduced changes in nuclear architecture is a flourishing area leading to major discoveries that will allow us to better understand how highly conserved mechanisms underlying genomic reprogramming are triggered by environmental and endogenous stimuli. This review aims to discuss fundamental and innovative reports demonstrating how light triggers changes in chromatin and nuclear architecture during photomorphogenesis.
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Affiliation(s)
- Giorgio Perrella
- Institute of Molecular, Cell and Systems BiologyCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems BiologyCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
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70
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Velanis CN, Herzyk P, Jenkins GI. Regulation of transcription by the Arabidopsis UVR8 photoreceptor involves a specific histone modification. PLANT MOLECULAR BIOLOGY 2016; 92:425-443. [PMID: 27534420 PMCID: PMC5080334 DOI: 10.1007/s11103-016-0522-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 08/02/2016] [Indexed: 05/21/2023]
Abstract
The photoreceptor UV RESISTANCE LOCUS 8 (UVR8) specifically mediates photomorphogenic responses to UV-B wavelengths. UVR8 acts by regulating transcription of a set of genes, but the underlying mechanisms are unknown. Previous research indicated that UVR8 can associate with chromatin, but the specificity and functional significance of this interaction are not clear. Here we show, by chromatin immunoprecipitation, that UV-B exposure of Arabidopsis increases acetylation of lysines K9 and/or K14 of histone H3 at UVR8-regulated gene loci in a UVR8-dependent manner. The transcription factors HY5 and/or HYH, which mediate UVR8-regulated transcription, are also required for this chromatin modification, at least for the ELIP1 gene. Furthermore, sequencing of the immunoprecipitated DNA revealed that all UV-B-induced enrichments in H3K9,14diacetylation across the genome are UVR8-dependent, and approximately 40 % of the enriched loci contain known UVR8-regulated genes. In addition, inhibition of histone acetylation by anacardic acid reduces the UV-B induced, UVR8 mediated expression of ELIP1 and CHS. No evidence was obtained in yeast 2-hybrid assays for a direct interaction between either UVR8 or HY5 and several proteins involved in light-regulated histone modification, nor for the involvement of these proteins in UVR8-mediated responses in plants, although functional redundancy between proteins could influence the results. In summary, this study shows that UVR8 regulates a specific chromatin modification associated with transcriptional regulation of a set of UVR8-target genes.
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Affiliation(s)
- Christos N Velanis
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK
| | - Pawel Herzyk
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, G61 1QH, UK
| | - Gareth I Jenkins
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Bower Building, Glasgow, G12 8QQ, UK.
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71
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Zhu A, Greaves IK, Liu PC, Wu L, Dennis ES, Peacock WJ. Early changes of gene activity in developing seedlings of Arabidopsis hybrids relative to parents may contribute to hybrid vigour. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:597-607. [PMID: 27460790 DOI: 10.1111/tpj.13285] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/19/2016] [Accepted: 07/21/2016] [Indexed: 05/15/2023]
Abstract
Hybrid vigour (heterosis) has been used for decades in crop industries, especially in the production of maize and rice. Hybrid varieties usually exceed their parents in plant biomass and seed yield. But the molecular basis of hybrid vigour is not fully understood. In this project, we studied heterosis at early stages of seedling development in Arabidopsis hybrids derived from crossing Ler and C24 accessions. We found that early heterosis is associated with non-additive gene expression that resulted from earlier changes in gene expression in the hybrids relative to the parents. The non-additively expressed genes are involved in metabolic pathways, including photosynthesis, critical for plant growth. The early increased expression levels of genes involved in energy production in hybrids is associated with heterosis in the young seedlings that could be essential for biomass heterosis at later developmental stages of the plant.
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Affiliation(s)
- Anyu Zhu
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, 2600, Australia
- University of Technology, Sydney, NSW, 2007, Australia
| | - Ian K Greaves
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, 2600, Australia
| | - Pei-Chuan Liu
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, 2600, Australia
- University of Technology, Sydney, NSW, 2007, Australia
| | - Limin Wu
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, 2600, Australia
| | - Elizabeth S Dennis
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, 2600, Australia
- University of Technology, Sydney, NSW, 2007, Australia
| | - W James Peacock
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, 2600, Australia
- University of Technology, Sydney, NSW, 2007, Australia
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72
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Bo K, Wang H, Pan Y, Behera TK, Pandey S, Wen C, Wang Y, Simon PW, Li Y, Chen J, Weng Y. SHORT HYPOCOTYL1 Encodes a SMARCA3-Like Chromatin Remodeling Factor Regulating Elongation. PLANT PHYSIOLOGY 2016; 172:1273-1292. [PMID: 27559036 PMCID: PMC5047076 DOI: 10.1104/pp.16.00501] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 08/22/2016] [Indexed: 05/18/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), the UVR8-mediated signaling pathway is employed to attain UVB protection and acclimation to deal with low-dosage UVB (LDUVB)-induced stresses. Here, we identified SHORT HYPOCOTYL1 (SH1) in cucumber (Cucumis sativus), which regulates LDUVB-dependent hypocotyl elongation by modulating the UVR8 signaling pathway. We showed that hypocotyl elongation in cucumbers carrying the recessive sh1 allele was LDUVB insensitive and that Sh1 encoded a human SMARCA3-like chromatin remodeling factor. The allele frequency and distribution pattern at this locus among natural populations supported the wild cucumber origin of sh1 for local adaptation, which was under selection during domestication. The cultivated cucumber carries predominantly the Sh1 allele; the sh1 allele is nearly fixed in the semiwild Xishuangbanna cucumber, and the wild cucumber population is largely at Hardy-Weinberg equilibrium for the two alleles. The SH1 protein sequence was highly conserved among eukaryotic organisms, but its regulation of hypocotyl elongation in cucumber seems to be a novel function. While Sh1 expression was inhibited by LDUVB, its transcript abundance was highly correlated with hypocotyl elongation rate and the expression level of cell-elongation-related genes. Expression profiling of key regulators in the UVR8 signaling pathway revealed significant differential expression of CsHY5 between two near isogenic lines of Sh1 Sh1 and CsHY5 acted antagonistically at transcriptional level. A working model was proposed in which Sh1 regulates LDUVB-dependent hypocotyl elongation in cucumber through changing the chromatin states and thus the accessibility of CsHY5 in the UVR8 signaling pathway to promoters of LDUVB-responsive genes for hypocotyl elongation.
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Affiliation(s)
- Kailiang Bo
- Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.)
| | - Hui Wang
- Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.)
| | - Yupeng Pan
- Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.)
| | - Tusar K Behera
- Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.)
| | - Sudhakar Pandey
- Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.)
| | - Changlong Wen
- Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.)
| | - Yuhui Wang
- Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.)
| | - Philipp W Simon
- Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.)
| | - Yuhong Li
- Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.)
| | - Jinfeng Chen
- Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.)
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, Wisconsin 53706 (K.B., Y.P., Y.Wa., P.W.S., Y.We.); Horticulture College, Nanjing Agricultural University, Nanjing 210095, China (K.B., J.C.);Horticulture College, Northwest A&F University, Yangling 712100, China (H.W., Y.P., Y.L.);Division of Vegetable Science, Indian Agricultural Research Institute, New Delhi 10012, India (T.K.B.);Division of Crop Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh 221305, India (S.P.);Beijing Vegetable Research Center and National Engineering Research Center for Vegetables, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China (C.W.); andVegetable Crops Research Unit, United States Department of Agriculture Agricultural Research Service, Madison, Wisconsin 53706 (P.W.S., Y.We.)
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73
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Bey T, Jamge S, Klemme S, Komar DN, Le Gall S, Mikulski P, Schmidt M, Zicola J, Berr A. Chromatin and epigenetics in all their states: Meeting report of the first conference on Epigenetic and Chromatin Regulation of Plant Traits - January 14 - 15, 2016 - Strasbourg, France. Epigenetics 2016; 11:625-34. [PMID: 27184433 DOI: 10.1080/15592294.2016.1185580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
In January 2016, the first Epigenetic and Chromatin Regulation of Plant Traits conference was held in Strasbourg, France. An all-star lineup of speakers, a packed audience of 130 participants from over 20 countries, and a friendly scientific atmosphere contributed to make this conference a meeting to remember. In this article we summarize some of the new insights into chromatin, epigenetics, and epigenomics research and highlight nascent ideas and emerging concepts in this exciting area of research.
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Affiliation(s)
- Till Bey
- a Swammerdam Institute for Life Sciences , University of Amsterdam , Amsterdam , The Netherlands
| | - Suraj Jamge
- b Plant Research International , Bioscience , Wageningen , The Netherlands.,c Laboratory of Molecular Biology , Wageningen University , Wageningen , The Netherlands
| | - Sonja Klemme
- d Crop Science Division , Bayer CropScience SA-NV , Zwijnaarde , Belgium
| | - Dorota Natalia Komar
- e Centro de Biotecnología y Genómica de Plantas (CBGP) , Instituto Nacional de Investigación y TecnologíaAgraria y Alimentaria (INIA)-Universidad Politécnica de Madrid , Madrid , Spain
| | - Sabine Le Gall
- f VIB Department of Plant Systems Biology , Ghent , Belgium.,g Department of Plant Biotechnology and Bioinformatics , Ghent University , Ghent , Belgium
| | - Pawel Mikulski
- h Institute for Biology, Freie Universität Berlin , Berlin , Germany
| | - Martin Schmidt
- f VIB Department of Plant Systems Biology , Ghent , Belgium.,g Department of Plant Biotechnology and Bioinformatics , Ghent University , Ghent , Belgium
| | - Johan Zicola
- i Max Planck Institute for Plant Breeding Research , Cologne , Germany
| | - Alexandre Berr
- j Institut de Biologie Moléculaire des Plantes (IBMP) du CNRS, Université de Strasbourg , Strasbourg Cedex , France
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Rodriguez-Granados NY, Ramirez-Prado JS, Veluchamy A, Latrasse D, Raynaud C, Crespi M, Ariel F, Benhamed M. Put your 3D glasses on: plant chromatin is on show. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3205-21. [PMID: 27129951 DOI: 10.1093/jxb/erw168] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The three-dimensional organization of the eukaryotic nucleus and its chromosomal conformation have emerged as important features in the complex network of mechanisms behind gene activity and genome connectivity dynamics, which can be evidenced in the regionalized chromosomal spatial distribution and the clustering of diverse genomic regions with similar expression patterns. The development of chromatin conformation capture (3C) techniques has permitted the elucidation of commonalities between the eukaryotic phyla, as well as important differences among them. The growing number of studies in the field performed in plants has shed light on the structural and regulatory features of these organisms. For instance, it has been proposed that plant chromatin can be arranged into different conformations such as Rabl, Rosette-like, and Bouquet, and that both short- and long-range chromatin interactions occur in Arabidopsis. In this review, we compile the current knowledge about chromosome architecture characteristics in plants, as well as the molecular events and elements (including long non-coding RNAs, histone and DNA modifications, chromatin remodeling complexes, and transcription factors) shaping the genome three-dimensional conformation. Furthermore, we discuss the developmental outputs of genome topology-mediated gene expression regulation. It is becoming increasingly clear that new tools and techniques with higher resolution need to be developed and implemented in Arabidopsis and other model plants in order to better understand chromosome architecture dynamics, from an integrative perspective with other fields of plant biology such as development, stress biology, and finally agriculture.
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Affiliation(s)
- Natalia Y Rodriguez-Granados
- 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
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Alaguraj Veluchamy
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Federico Ariel
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
| | - Moussa Benhamed
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment 630, 91405 Orsay, France
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75
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Simon L, Voisin M, Tatout C, Probst AV. Structure and Function of Centromeric and Pericentromeric Heterochromatin in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2015; 6:1049. [PMID: 26648952 PMCID: PMC4663263 DOI: 10.3389/fpls.2015.01049] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 11/09/2015] [Indexed: 05/23/2023]
Abstract
The centromere is a specific chromosomal region where the kinetochore assembles to ensure the faithful segregation of sister chromatids during mitosis and meiosis. Centromeres are defined by a local enrichment of the specific histone variant CenH3 mostly at repetitive satellite sequences. A larger pericentromeric region containing repetitive sequences and transposable elements surrounds the centromere that adopts a particular chromatin state characterized by specific histone variants and post-translational modifications and forms a transcriptionally repressive chromosomal environment. In the model organism Arabidopsis thaliana centromeric and pericentromeric domains form conspicuous heterochromatin clusters called chromocenters in interphase. Here we discuss, using Arabidopsis as example, recent insight into mechanisms involved in maintenance and establishment of centromeric and pericentromeric chromatin signatures as well as in chromocenter formation.
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Affiliation(s)
| | - Maxime Voisin
- †These authors have contributed equally to this work.
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