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Zheng S, Zhao W, Liu Z, Geng Z, Li Q, Liu B, Li B, Bai J. Establishment and Maintenance of Heat-Stress Memory in Plants. Int J Mol Sci 2024; 25:8976. [PMID: 39201662 PMCID: PMC11354667 DOI: 10.3390/ijms25168976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/15/2024] [Accepted: 08/15/2024] [Indexed: 09/02/2024] Open
Abstract
Among the rich repertoire of strategies that allow plants to adapt to high-temperature stress is heat-stress memory. The mechanisms underlying the establishment and maintenance of heat-stress memory are poorly understood, although the chromatin opening state appears to be an important structural basis for maintaining heat-stress memory. The chromatin opening state is influenced by epigenetic modifications, making DNA and histone modifications important entry points for understanding heat-shock memory. Current research suggests that traditional heat-stress signaling pathway components might be involved in chromatin opening, thereby promoting the establishment of heat-stress memory in plants. In this review, we discuss the relationship between chromatin structure-based maintenance and the establishment of heat-stress memory. We also discuss the association between traditional heat-stress signals and epigenetic modifications. Finally, we discuss potential research ideas for exploring plant adaptation to high-temperature stress in the future.
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Affiliation(s)
- Shuzhi Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Weishuang Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Zimeng Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Ziyue Geng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qiang Li
- Dryland Farming Institute of Hebei Academy of Agricultural and Forestry Science, Key Laboratory of Crop Drought Tolerance Research of Hebei Province, Hengshui 053000, China
| | - Binhui Liu
- Dryland Farming Institute of Hebei Academy of Agricultural and Forestry Science, Key Laboratory of Crop Drought Tolerance Research of Hebei Province, Hengshui 053000, China
| | - Bing Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Jiaoteng Bai
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
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Gómez-Martínez D, Barrero-Gil J, Tranque E, Ruiz MF, Catalá R, Salinas J. SVALKA-POLYCOMB REPRESSIVE COMPLEX2 module controls C-REPEAT BINDING FACTOR3 induction during cold acclimation. PLANT PHYSIOLOGY 2024; 195:1152-1160. [PMID: 38124468 PMCID: PMC11142377 DOI: 10.1093/plphys/kiad671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/23/2023]
Abstract
C-REPEAT BINDING FACTORS (CBFs) are highly conserved plant transcription factors that promote cold tolerance. In Arabidopsis (Arabidopsis thaliana), three CBFs (CBF1 to CBF3) play a critical role in cold acclimation, and the expression of their corresponding genes is rapidly and transiently induced during this adaptive response. Cold induction of CBFs has been extensively studied and shown to be tightly controlled, yet the molecular mechanisms that restrict the expression of each CBF after their induction during cold acclimation are poorly understood. Here, we present genetic and molecular evidence that the decline in the induction of CBF3 during cold acclimation is epigenetically regulated through the Polycomb Repressive Complex (PRC) 2. We show that this complex promotes the deposition of the repressive mark H3K27me3 at the coding region of CBF3, silencing its expression. Our results indicate that the cold-inducible long noncoding RNA SVALKA is essential for this regulation by recruiting PRC2 to CBF3. These findings unveil a SVALKA-PRC2 regulatory module that ensures the precise timing of CBF3 induction during cold acclimation and the correct development of this adaptive response.
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Affiliation(s)
- Diego Gómez-Martínez
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Javier Barrero-Gil
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Eduardo Tranque
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - María Fernanda Ruiz
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Rafael Catalá
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Julio Salinas
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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Rodríguez-Bolaños M, Martínez T, Juárez S, Quiroz S, Domínguez A, Garay-Arroyo A, Sanchez MDLP, Álvarez-Buylla ER, García-Ponce B. XAANTAL1 Reveals an Additional Level of Flowering Regulation in the Shoot Apical Meristem in Response to Light and Increased Temperature in Arabidopsis. Int J Mol Sci 2023; 24:12773. [PMID: 37628953 PMCID: PMC10454237 DOI: 10.3390/ijms241612773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Light and photoperiod are environmental signals that regulate flowering transition. In plants like Arabidopsis thaliana, this regulation relies on CONSTANS, a transcription factor that is negatively posttranslational regulated by phytochrome B during the morning, while it is stabilized by PHYA and cryptochromes 1/2 at the end of daylight hours. CO induces the expression of FT, whose protein travels from the leaves to the apical meristem, where it binds to FD to regulate some flowering genes. Although PHYB delays flowering, we show that light and PHYB positively regulate XAANTAL1 and other flowering genes in the shoot apices. Also, the genetic data indicate that XAL1 and FD participate in the same signaling pathway in flowering promotion when plants are grown under a long-day photoperiod at 22 °C. By contrast, XAL1 functions independently of FD or PIF4 to induce flowering at higher temperatures (27 °C), even under long days. Furthermore, XAL1 directly binds to FD, SOC1, LFY, and AP1 promoters. Our findings lead us to propose that light and temperature influence the floral network at the meristem level in a partially independent way of the signaling generated from the leaves.
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Affiliation(s)
- Mónica Rodríguez-Bolaños
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Tania Martínez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Saray Juárez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Stella Quiroz
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
- Laboratory of Pathogens and Host Immunity, University of Montpellier, 34 090 Montpellier, France
| | - Andrea Domínguez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Adriana Garay-Arroyo
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - María de la Paz Sanchez
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Elena R. Álvarez-Buylla
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
| | - Berenice García-Ponce
- Instituto de Ecologίa, Departamento de Ecologίa Funcional, Universidad Nacional Autónoma de México, Circuito ext. s/no. Ciudad Universitaria, Coyoacán 04510, CDMX, Mexico
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Kramer MC, Kim HJ, Palos KR, Garcia BA, Lyons E, Beilstein MA, Nelson ADL, Gregory BD. A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences, lncCOBRA1, Affects Arabidopsis Germination and Development. FRONTIERS IN PLANT SCIENCE 2022; 13:906603. [PMID: 35693169 PMCID: PMC9175010 DOI: 10.3389/fpls.2022.906603] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/04/2022] [Indexed: 05/04/2023]
Abstract
Long non-coding RNAs (lncRNAs) are an increasingly studied group of non-protein coding transcripts with a wide variety of molecular functions gaining attention for their roles in numerous biological processes. Nearly 6,000 lncRNAs have been identified in Arabidopsis thaliana but many have yet to be studied. Here, we examine a class of previously uncharacterized lncRNAs termed CONSERVED IN BRASSICA RAPA (lncCOBRA) transcripts that were previously identified for their high level of sequence conservation in the related crop species Brassica rapa, their nuclear-localization and protein-bound nature. In particular, we focus on lncCOBRA1 and demonstrate that its abundance is highly tissue and developmental specific, with particularly high levels early in germination. lncCOBRA1 contains two snoRNAs domains within it, making it the first sno-lincRNA example in a non-mammalian system. However, we find that it is processed differently than its mammalian counterparts. We further show that plants lacking lncCOBRA1 display patterns of delayed germination and are overall smaller than wild-type plants. Lastly, we identify the proteins that interact with lncCOBRA1 and propose a novel mechanism of lincRNA action in which it may act as a scaffold with the RACK1A protein to regulate germination and development, possibly through a role in ribosome biogenesis.
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Affiliation(s)
- Marianne C. Kramer
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, United States
| | - Kyle R. Palos
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
- CyVerse Inc., Tucson, AZ, United States
| | - Mark A. Beilstein
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
| | | | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- *Correspondence: Brian D. Gregory,
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Li G, Kuijer HNJ, Yang X, Liu H, Shen C, Shi J, Betts N, Tucker MR, Liang W, Waugh R, Burton RA, Zhang D. MADS1 maintains barley spike morphology at high ambient temperatures. NATURE PLANTS 2021; 7:1093-1107. [PMID: 34183784 DOI: 10.1038/s41477-021-00957-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 06/02/2021] [Indexed: 05/05/2023]
Abstract
Temperature stresses affect plant phenotypic diversity. The developmental stability of the inflorescence, required for reproductive success, is tightly regulated by the interplay of genetic and environmental factors. However, the mechanisms underpinning how plant inflorescence architecture responds to temperature are largely unknown. We demonstrate that the barley SEPALLATA MADS-box protein HvMADS1 is responsible for maintaining an unbranched spike architecture at high temperatures, while the loss-of-function mutant forms a branched inflorescence-like structure. HvMADS1 exhibits increased binding to target promoters via A-tract CArG-box motifs, which change conformation with temperature. Target genes for high-temperature-dependent HvMADS1 activation are predominantly associated with inflorescence differentiation and phytohormone signalling. HvMADS1 directly regulates the cytokinin-degrading enzyme HvCKX3 to integrate temperature response and cytokinin homeostasis, which is required to repress meristem cell cycle/division. Our findings reveal a mechanism by which genetic factors direct plant thermomorphogenesis, extending the recognized role of plant MADS-box proteins in floral development.
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Affiliation(s)
- Gang Li
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia.
- School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, China.
| | - Hendrik N J Kuijer
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
| | - Xiujuan Yang
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
| | - Huiran Liu
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chaoqun Shen
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Natalie Betts
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
| | - Matthew R Tucker
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Robbie Waugh
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
- James Hutton Institute, Dundee, UK
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, UK
| | - Rachel A Burton
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia
| | - Dabing Zhang
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Waite Campus, Glen Osmond, South Australia, Australia.
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
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Yang L, Chen X, Wang Z, Sun Q, Hong A, Zhang A, Zhong X, Hua J. HOS15 and HDA9 negatively regulate immunity through histone deacetylation of intracellular immune receptor NLR genes in Arabidopsis. THE NEW PHYTOLOGIST 2020; 226:507-522. [PMID: 31854111 PMCID: PMC7080574 DOI: 10.1111/nph.16380] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/08/2019] [Indexed: 05/08/2023]
Abstract
Plant immune responses need to be tightly controlled for growth-defense balance. The mechanism underlying this tight control is not fully understood. Here we identify epigenetic regulation of nucleotide-binding leucine rich repeat or Nod-Like Receptor (NLR) genes as an important mechanism for immune responses. Through a sensitized genetic screen and molecular studies, we identified and characterized HOS15 and its associated protein HDA9 as negative regulators of immunity and NLR gene expression. The loss-of-function of HOS15 or HDA9 confers enhanced resistance to pathogen infection accompanied with increased expression of one-third of the 207 NLR genes in Arabidopsis thaliana. HOS15 and HDA9 are physically associated with some of these NLR genes and repress their expression likely through reducing the acetylation of H3K9 at these loci. In addition, these NLR genes are repressed by HOS15 under both pathogenic and nonpathogenic conditions but by HDA9 only under infection condition. Together, this study uncovers a previously uncharacterized histone deacetylase complex in plant immunity and highlights the importance of epigenetic regulation of NLR genes in modulating growth-defense balance.
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Affiliation(s)
- Leiyun Yang
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Xiangsong Chen
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, 53706, USA
| | - Zhixue Wang
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Qi Sun
- Cornell Computational Biology Service Unit, Cornell University, Ithaca, 14853, USA
| | - Anna Hong
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Aiqin Zhang
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
| | - Xuehua Zhong
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, 53706, USA
- For correspondence: Jian Hua: Tel (+1) 607-255-5554;; Xuehua Zhong: Tel (+1) 608-316-4421;
| | - Jian Hua
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, 14853, USA
- For correspondence: Jian Hua: Tel (+1) 607-255-5554;; Xuehua Zhong: Tel (+1) 608-316-4421;
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Abstract
The long linear chromosomes of eukaryotic organisms are tightly packed into the nucleus of the cell. Beyond a first organization into nucleosomes and higher-order chromatin fibers, the positioning of nuclear DNA within the three-dimensional space of the nucleus plays a critical role in genome function and gene expression. Different techniques have been developed to assess nanoscale chromatin organization, nuclear position of genomic regions or specific chromatin features and binding proteins as well as higher-order chromatin organization. Here, I present an overview of imaging and molecular techniques applied to study nuclear architecture in plants, with special attention to the related protocols published in the "Plant Chromatin Dynamics" edition from Methods in Molecular Biology.
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Affiliation(s)
- Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001, Clermont-Ferrand, France.
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9
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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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Abstract
Identification of chromatin modifications, e.g., histone acetylation and methylation, among others, is widely carried out by using a chromatin immunoprecipitation (ChIP) strategy. The information obtained with these procedures is useful to gain an overall picture of modifications present in all cells of the population under study. It also serves as a basis to figure out the mechanisms of chromatin organization and gene regulation at the population level. However, the ultimate goal is to understand gene regulation at the level of single chromatin fibers. This requires the identification of chromatin modifications that occur at a given genomic location and within the same chromatin fiber. This is achieved by following a sequential ChIP strategy using two antibodies to distinguish different chromatin modifications. Here, we describe a sequential ChIP protocol (Re-ChIP), paying special attention to the controls needed and the required steps to obtain meaningful and reproducible results. The protocol is developed for young Arabidopsis seedlings but could be adapted to other plant materials.
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Abstract
Identifying and characterizing highly accessible chromatin regions assists in determining the location of genomic regulatory elements and understanding transcriptional regulation. In this chapter, we describe an approach to map accessible chromatin features in plants using the Assay for Transposase-Accessible Chromatin, combined with high-throughput sequencing (ATAC-seq), which was originally developed for cultured animal cells. This technique utilizes a hyperactive Tn5 transposase to cause DNA cleavage and simultaneous insertion of sequencing adapters into open chromatin regions of the input nuclei. The application of ATAC-seq to plant tissue has been challenging due to the difficulty of isolating nuclei sufficiently free of interfering organellar DNA. Here we present two different approaches to purify plant nuclei for ATAC-seq: the INTACT method (Isolation of Nuclei TAgged in specific Cell Types) to isolate nuclei from individual cell types of the plant, and tissue lysis followed by sucrose sedimentation to isolate sufficiently pure total nuclei. We provide detailed instructions for transposase treatment of nuclei isolated using either approach, as well as subsequent preparation of ATAC-seq libraries. Sequencing-ready ATAC-seq libraries can be prepared from plant tissue in as little as one day. The procedures described here are optimized for Arabidopsis thaliana but can also be applied to other plant species.
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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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