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Na J, Tai C, Wang Z, Yang Z, Chen X, Zhang J, Zheng L, Fan Y. Stiff extracellular matrix drives the differentiation of mesenchymal stem cells toward osteogenesis by the multiscale 3D genome reorganization. Biomaterials 2025; 312:122715. [PMID: 39094522 DOI: 10.1016/j.biomaterials.2024.122715] [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: 03/22/2024] [Revised: 07/17/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024]
Abstract
Extracellular matrix (ECM) stiffness is a major driver of stem cell fate. However, the involvement of the three-dimensional (3D) genomic reorganization in response to ECM stiffness remains unclear. Here, we generated comprehensive 3D chromatin landscapes of mesenchymal stem cells (MSCs) exposed to various ECM stiffness. We found that there were more long-range chromatin interactions, but less compartment A in MSCs cultured on stiff ECM than those cultured on soft ECM. However, the switch from compartment B in MSCs cultured on soft ECM to compartment A in MSCs cultured on stiff ECM included genes encoding proteins primarily enriched in cytoskeleton organization. At the topologically associating domains (TADs) level, stiff ECM tends to have merged TADs on soft ECM. These merged TADs on stiff ECM include upregulated genes encoding proteins enriched in osteogenesis, such as SP1, ETS1, and DCHS1, which were validated by quantitative real-time polymerase chain reaction and found to be consistent with the increase of alkaline phosphatase staining. Knockdown of SP1 or ETS1 led to the downregulation of osteogenic marker genes, including COL1A1, RUNX2, ALP, and OCN in MSCs cultured on stiff ECM. Our study provides an important insight into the stiff ECM-mediated promotion of MSC differentiation towards osteogenesis, emphasizing the influence of mechanical cues on the reorganization of 3D genome architecture and stem cell fate.
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Affiliation(s)
- Jing Na
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Chengzheng Tai
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Ziyi Wang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Zhijie Yang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Xinyuan Chen
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China
| | - Jing Zhang
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China; Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Engineering Medicine, Beihang University, Beijing, 100083, China.
| | - Lisha Zheng
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.
| | - Yubo Fan
- Key Laboratory of Biomechanics and Mechanobiology (Beihang University), Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100083, China.
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2
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Rutowicz K, Lüthi J, de Groot R, Holtackers R, Yakimovich Y, Pazmiño DM, Gandrillon O, Pelkmans L, Baroux C. Multiscale chromatin dynamics and high entropy in plant iPSC ancestors. J Cell Sci 2024; 137:jcs261703. [PMID: 38738286 PMCID: PMC11234377 DOI: 10.1242/jcs.261703] [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: 10/10/2023] [Accepted: 04/29/2024] [Indexed: 05/14/2024] Open
Abstract
Plant protoplasts provide starting material for of inducing pluripotent cell masses that are competent for tissue regeneration in vitro, analogous to animal induced pluripotent stem cells (iPSCs). Dedifferentiation is associated with large-scale chromatin reorganisation and massive transcriptome reprogramming, characterised by stochastic gene expression. How this cellular variability reflects on chromatin organisation in individual cells and what factors influence chromatin transitions during culturing are largely unknown. Here, we used high-throughput imaging and a custom supervised image analysis protocol extracting over 100 chromatin features of cultured protoplasts. The analysis revealed rapid, multiscale dynamics of chromatin patterns with a trajectory that strongly depended on nutrient availability. Decreased abundance in H1 (linker histones) is hallmark of chromatin transitions. We measured a high heterogeneity of chromatin patterns indicating intrinsic entropy as a hallmark of the initial cultures. We further measured an entropy decline over time, and an antagonistic influence by external and intrinsic factors, such as phytohormones and epigenetic modifiers, respectively. Collectively, our study benchmarks an approach to understand the variability and evolution of chromatin patterns underlying plant cell reprogramming in vitro.
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Affiliation(s)
- Kinga Rutowicz
- Plant Developmental Genetics, Institute of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Joel Lüthi
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - Reinoud de Groot
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - René Holtackers
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - Yauhen Yakimovich
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - Diana M. Pazmiño
- Plant Developmental Genetics, Institute of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Olivier Gandrillon
- Laboratory of Biology and Modeling of the Cell, University of Lyon, ENS de Lyon,69342 Lyon, France
| | - Lucas Pelkmans
- Department of Molecular Life Sciences, University of Zurich, 8050 Zurich, Switzerland
| | - Célia Baroux
- Plant Developmental Genetics, Institute of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
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3
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Alonso-Serra J, Cheddadi I, Kiss A, Cerutti G, Lang M, Dieudonné S, Lionnet C, Godin C, Hamant O. Water fluxes pattern growth and identity in shoot meristems. Nat Commun 2024; 15:6944. [PMID: 39138210 PMCID: PMC11322635 DOI: 10.1038/s41467-024-51099-x] [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: 10/27/2023] [Accepted: 07/28/2024] [Indexed: 08/15/2024] Open
Abstract
In multicellular organisms, tissue outgrowth creates a new water sink, modifying local hydraulic patterns. Although water fluxes are often considered passive by-products of development, their contribution to morphogenesis remains largely unexplored. Here, we mapped cell volumetric growth across the shoot apex in Arabidopsis thaliana. We found that, as organs grow, a subpopulation of cells at the organ-meristem boundary shrinks. Growth simulations using a model that integrates hydraulics and mechanics revealed water fluxes and predicted a water deficit for boundary cells. In planta, a water-soluble dye preferentially allocated to fast-growing tissues and failed to enter the boundary domain. Cell shrinkage next to fast-growing domains was also robust to different growth conditions and different topographies. Finally, a molecular signature of water deficit at the boundary confirmed our conclusion. Taken together, we propose that the differential sink strength of emerging organs prescribes the hydraulic patterns that define boundary domains at the shoot apex.
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Affiliation(s)
- Juan Alonso-Serra
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, INRIA 46 Allée d'Italie, 69364, Lyon, France.
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
| | - Ibrahim Cheddadi
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, INRIA 46 Allée d'Italie, 69364, Lyon, France
- Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, Grenoble, France
| | - Annamaria Kiss
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, INRIA 46 Allée d'Italie, 69364, Lyon, France
| | - Guillaume Cerutti
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, INRIA 46 Allée d'Italie, 69364, Lyon, France
| | - Marianne Lang
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, INRIA 46 Allée d'Italie, 69364, Lyon, France
| | - Sana Dieudonné
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, INRIA 46 Allée d'Italie, 69364, Lyon, France
| | - Claire Lionnet
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, INRIA 46 Allée d'Italie, 69364, Lyon, France
| | - Christophe Godin
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, INRIA 46 Allée d'Italie, 69364, Lyon, France
| | - Olivier Hamant
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, INRIA 46 Allée d'Italie, 69364, Lyon, France.
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4
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Harris CJ, Zhong Z, Ichino L, Feng S, Jacobsen SE. H1 restricts euchromatin-associated methylation pathways from heterochromatic encroachment. eLife 2024; 12:RP89353. [PMID: 38814684 PMCID: PMC11139477 DOI: 10.7554/elife.89353] [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] [Indexed: 05/31/2024] Open
Abstract
Silencing pathways prevent transposable element (TE) proliferation and help to maintain genome integrity through cell division. Silenced genomic regions can be classified as either euchromatic or heterochromatic, and are targeted by genetically separable epigenetic pathways. In plants, the RNA-directed DNA methylation (RdDM) pathway targets mostly euchromatic regions, while CMT DNA methyltransferases are mainly associated with heterochromatin. However, many epigenetic features - including DNA methylation patterning - are largely indistinguishable between these regions, so how the functional separation is maintained is unclear. The linker histone H1 is preferentially localized to heterochromatin and has been proposed to restrict RdDM from encroachment. To test this hypothesis, we followed RdDM genomic localization in an h1 mutant by performing ChIP-seq on the largest subunit, NRPE1, of the central RdDM polymerase, Pol V. Loss of H1 resulted in NRPE1 enrichment predominantly in heterochromatic TEs. Increased NRPE1 binding was associated with increased chromatin accessibility in h1, suggesting that H1 restricts NRPE1 occupancy by compacting chromatin. However, RdDM occupancy did not impact H1 localization, demonstrating that H1 hierarchically restricts RdDM positioning. H1 mutants experience major symmetric (CG and CHG) DNA methylation gains, and by generating an h1/nrpe1 double mutant, we demonstrate these gains are largely independent of RdDM. However, loss of NRPE1 occupancy from a subset of euchromatic regions in h1 corresponded to the loss of methylation in all sequence contexts, while at ectopically bound heterochromatic loci, NRPE1 deposition correlated with increased methylation specifically in the CHH context. Additionally, we found that H1 similarly restricts the occupancy of the methylation reader, SUVH1, and polycomb-mediated H3K27me3. Together, the results support a model whereby H1 helps maintain the exclusivity of heterochromatin by preventing encroachment from other competing pathways.
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Affiliation(s)
- C Jake Harris
- Department of Molecular, Cell and Developmental Biology, University of California, Los AngelesLos AngelesUnited States
| | - Zhenhui Zhong
- Department of Molecular, Cell and Developmental Biology, University of California, Los AngelesLos AngelesUnited States
| | - Lucia Ichino
- Department of Molecular, Cell and Developmental Biology, University of California, Los AngelesLos AngelesUnited States
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California, Los AngelesLos AngelesUnited States
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los AngelesLos AngelesUnited States
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los AngelesLos AngelesUnited States
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los AngelesLos AngelesUnited States
- Howard Hughes Medical Institute, University of California, Los AngelesLos AngelesUnited States
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5
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Simon L, Probst AV. Maintenance and dynamic reprogramming of chromatin organization during development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:657-670. [PMID: 36700345 DOI: 10.1111/tpj.16119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 06/17/2023]
Abstract
Controlled transcription of genes is critical for cell differentiation and development. Gene expression regulation therefore involves a multilayered control from nucleosome composition in histone variants and their post-translational modifications to higher-order folding of chromatin fibers and chromatin interactions in nuclear space. Recent technological advances have allowed gaining insight into these mechanisms, the interplay between local and higher-order chromatin organization, and the dynamic changes that occur during stress response and developmental transitions. In this review, we will discuss chromatin organization from the nucleosome to its three-dimensional structure in the nucleus, and consider how these different layers of organization are maintained during the cell cycle or rapidly reprogrammed during development.
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Affiliation(s)
- Lauriane Simon
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
| | - Aline V Probst
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000, Clermont-Ferrand, France
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6
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He S, Yu Y, Wang L, Zhang J, Bai Z, Li G, Li P, Feng X. Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis. THE PLANT CELL 2024; 36:1829-1843. [PMID: 38309957 PMCID: PMC11062459 DOI: 10.1093/plcell/koae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/01/2023] [Accepted: 11/25/2023] [Indexed: 02/05/2024]
Abstract
In the eukaryotic nucleus, heterochromatin forms highly condensed, visible foci known as heterochromatin foci (HF). These HF are enriched with linker histone H1, a key player in heterochromatin condensation and silencing. However, it is unknown how H1 aggregates HF and condenses heterochromatin. In this study, we established that H1 facilitates heterochromatin condensation by enhancing inter- and intrachromosomal interactions between and within heterochromatic regions of the Arabidopsis (Arabidopsis thaliana) genome. We demonstrated that H1 drives HF formation via phase separation, which requires its C-terminal intrinsically disordered region (C-IDR). A truncated H1 lacking the C-IDR fails to form foci or recover HF in the h1 mutant background, whereas C-IDR with a short stretch of the globular domain (18 out of 71 amino acids) is sufficient to rescue both defects. In addition, C-IDR is essential for H1's roles in regulating nucleosome repeat length and DNA methylation in Arabidopsis, indicating that phase separation capability is required for chromatin functions of H1. Our data suggest that bacterial H1-like proteins, which have been shown to condense DNA, are intrinsically disordered and capable of mediating phase separation. Therefore, we propose that phase separation mediated by H1 or H1-like proteins may represent an ancient mechanism for condensing chromatin and DNA.
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Affiliation(s)
- Shengbo He
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Yiming Yu
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg 3400, Austria
| | - Liang Wang
- Institute of Biophysics, Chinese Academy of Science, 15 Datun Road, Chaoyang District, Beijing 100101, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jingyi Zhang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Zhengyong Bai
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Guohong Li
- Institute of Biophysics, Chinese Academy of Science, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Pilong Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaoqi Feng
- Institute of Science and Technology Austria (ISTA), Am Campus 1, Klosterneuburg 3400, Austria
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7
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Candela-Ferre J, Diego-Martin B, Pérez-Alemany J, Gallego-Bartolomé J. Mind the gap: Epigenetic regulation of chromatin accessibility in plants. PLANT PHYSIOLOGY 2024; 194:1998-2016. [PMID: 38236303 PMCID: PMC10980423 DOI: 10.1093/plphys/kiae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/07/2023] [Accepted: 11/23/2023] [Indexed: 01/19/2024]
Abstract
Chromatin plays a crucial role in genome compaction and is fundamental for regulating multiple nuclear processes. Nucleosomes, the basic building blocks of chromatin, are central in regulating these processes, determining chromatin accessibility by limiting access to DNA for various proteins and acting as important signaling hubs. The association of histones with DNA in nucleosomes and the folding of chromatin into higher-order structures are strongly influenced by a variety of epigenetic marks, including DNA methylation, histone variants, and histone post-translational modifications. Additionally, a wide array of chaperones and ATP-dependent remodelers regulate various aspects of nucleosome biology, including assembly, deposition, and positioning. This review provides an overview of recent advances in our mechanistic understanding of how nucleosomes and chromatin organization are regulated by epigenetic marks and remodelers in plants. Furthermore, we present current technologies for profiling chromatin accessibility and organization.
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Affiliation(s)
- Joan Candela-Ferre
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Borja Diego-Martin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Jaime Pérez-Alemany
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Javier Gallego-Bartolomé
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
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8
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Vivek Hari Sundar G, Madhu A, Archana A, Shivaprasad PV. Plant histone variants at the nexus of chromatin readouts, stress and development. Biochim Biophys Acta Gen Subj 2024; 1868:130539. [PMID: 38072208 DOI: 10.1016/j.bbagen.2023.130539] [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: 06/02/2023] [Revised: 11/21/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
Histones are crucial proteins that are involved in packaging the DNA as condensed chromatin inside the eukaryotic cell nucleus. Rather than being static packaging units, these molecules undergo drastic variations spatially and temporally to facilitate accessibility of DNA to replication, transcription as well as wide range of gene regulatory machineries. In addition, incorporation of paralogous variants of canonical histones in the chromatin is ascribed to specific functions. Given the peculiar requirement of plants to rapidly modulate gene expression levels on account of their sessile nature, histones and their variants serve as additional layers of gene regulation. This review summarizes the mechanisms and implications of distribution, modifications and differential incorporation of histones and their variants across plant genomes, and outlines emerging themes.
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Affiliation(s)
- G Vivek Hari Sundar
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India
| | - Aravind Madhu
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India; SASTRA University, Thirumalaisamudram, Thanjavur 613 401, India
| | - A Archana
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India; SASTRA University, Thirumalaisamudram, Thanjavur 613 401, India
| | - P V Shivaprasad
- National Centre for Biological Sciences, TIFR, GKVK Campus, Bangalore, India.
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9
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Xu G, Law JA. Loops, crosstalk, and compartmentalization: it takes many layers to regulate DNA methylation. Curr Opin Genet Dev 2024; 84:102147. [PMID: 38176333 PMCID: PMC10922829 DOI: 10.1016/j.gde.2023.102147] [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: 10/08/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 01/06/2024]
Abstract
DNA methylation is a conserved epigenetic modification associated with transposon silencing and gene regulation. The stability of this modification relies on intimate connections between DNA and histone modifications that generate self-reinforcing loops wherein the presence of one mark promotes the other. However, it is becoming increasingly clear that the efficiency of these loops is affected by cross-talk between pathways and by chromatin accessibility, which is heavily influenced by histone variants. Focusing primarily on plants, this review provides an update on the aforementioned self-reinforcing loops, highlights recent advances in understanding how DNA methylation pathways are restricted to prevent encroachment on genes, and discusses the roles of histone variants in compartmentalizing epigenetic pathways within the genome. This multilayered approach facilitates two essential, yet opposing functions, the ability to maintain heritable DNA methylation patterns while retaining the flexibility to modify these patterns during development.
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Affiliation(s)
- Guanghui Xu
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA. https://twitter.com/@GuanghuiXu1
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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10
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Perrella G, Fasano C, Donald NA, Daddiego L, Fang W, Martignago D, Carr C, Conti L, Herzyk P, Amtmann A. Histone Deacetylase Complex 1 and histone 1 epigenetically moderate stress responsiveness of Arabidopsis thaliana seedlings. THE NEW PHYTOLOGIST 2024; 241:166-179. [PMID: 37565540 PMCID: PMC10953426 DOI: 10.1111/nph.19165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023]
Abstract
Early responses of plants to environmental stress factors prevent damage but can delay growth and development in fluctuating conditions. Optimising these trade-offs requires tunability of plant responsiveness to environmental signals. We have previously reported that Histone Deacetylase Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the stress responsiveness of Arabidopsis seedlings, but the underlying mechanism remained elusive. Here, we show that HDC1 attenuates transcriptome re-programming in salt-treated seedlings, and we identify two genes (LEA and MAF5) that inhibit seedling establishment under salt stress downstream of HDC1. HDC1 attenuates their transcriptional induction by salt via a dual mechanism involving H3K9/14 deacetylation and H3K27 trimethylation. The latter, but not the former, was also abolished in a triple knockout mutant of the linker histone H1, which partially mimics the hypersensitivity of the hdc1-1 mutant to salt stress. Although stress-induced H3K27me3 accumulation required both H1 and HDC1, it was not fully recovered by complementing hdc1-1 with a truncated, H1-binding competent HDC1 suggesting other players or independent inputs. The combined findings reveal a dual brake function of HDC1 via regulating both active and repressive epigenetic marks on stress-inducible genes. This natural 'anti-panic' device offers a molecular leaver to tune stress responsiveness in plants.
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Affiliation(s)
- Giorgio Perrella
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
| | - Carlo Fasano
- Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentTrisaia Research CentreRotondella (Matera)75026Italy
| | - Naomi A. Donald
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
| | - Loretta Daddiego
- Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentTrisaia Research CentreRotondella (Matera)75026Italy
| | - Weiwei Fang
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
| | - Damiano Martignago
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
| | - Craig Carr
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
| | - Lucio Conti
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
| | - Pawel Herzyk
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
- Glasgow Polyomics, Wolfson Wohl Cancer Research CentreUniversity of GlasgowGlasgowG61 1QHUK
| | - Anna Amtmann
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
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11
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Archacki R. Finding a good balance: two distinct chromatin factors fine-tune stress response in Arabidopsis seedlings. THE NEW PHYTOLOGIST 2024; 241:7-9. [PMID: 37919230 DOI: 10.1111/nph.19357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Affiliation(s)
- Rafal Archacki
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
- Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106, Warsaw, Poland
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12
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Voichek Y, Hurieva B, Michaud C, Schmücker A, Vergara Z, Desvoyes B, Gutierrez C, Nizhynska V, Jaegle B, Borg M, Berger F, Nordborg M, Ingouff M. Cell cycle status of male and female gametes during Arabidopsis reproduction. PLANT PHYSIOLOGY 2023; 194:412-421. [PMID: 37757882 PMCID: PMC10756760 DOI: 10.1093/plphys/kiad512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/04/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023]
Abstract
Fertilization in Arabidopsis (Arabidopsis thaliana) is a highly coordinated process that begins with a pollen tube delivering the 2 sperm cells into the embryo sac. Each sperm cell can then fertilize either the egg or the central cell to initiate embryo or endosperm development, respectively. The success of this double fertilization process requires a tight cell cycle synchrony between the male and female gametes to allow karyogamy (nuclei fusion). However, the cell cycle status of the male and female gametes during fertilization remains elusive as DNA quantification and DNA replication assays have given conflicting results. Here, to reconcile these results, we quantified the DNA replication state by DNA sequencing and performed microscopic analyses of fluorescent markers covering all phases of the cell cycle. We show that male and female Arabidopsis gametes are both arrested prior to DNA replication at maturity and initiate their DNA replication only during fertilization.
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Affiliation(s)
- Yoav Voichek
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Bohdana Hurieva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | | | - Anna Schmücker
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Zaida Vergara
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | | | | | - Viktoria Nizhynska
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Benjamin Jaegle
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Mathieu Ingouff
- DIADE, IRD, CIRAD, University Montpellier, Montpellier, France
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13
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Wang Y, He S, Fang X. Emerging roles of phase separation in plant transcription and chromatin organization. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102387. [PMID: 37311366 DOI: 10.1016/j.pbi.2023.102387] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 06/15/2023]
Abstract
Transcription is a core step in gene expression. Regulation of transcription is achieved at the level of transcription machinery, local chromatin environment as well as higher-order chromatin organization. Our understanding of transcriptional regulation was advanced by recent introduction of transcription and chromatin-associated condensates, which typically arise via phase separation of proteins and nucleic acids. While studies from mammalian cells are unveiling the mechanisms of phase separation in transcription regulation, those in plants further broaden and deepen our understanding of this process. In this review, we discuss recent progress in plants how phase separation operates in RNA-mediated chromatin silencing, transcription activity, and chromatin compartmentalization.
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Affiliation(s)
- Yunhe Wang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Shengbo He
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.
| | - Xiaofeng Fang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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14
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Jiang D, Berger F. Variation is important: Warranting chromatin function and dynamics by histone variants. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102408. [PMID: 37399781 DOI: 10.1016/j.pbi.2023.102408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 07/05/2023]
Abstract
The chromatin of flowering plants exhibits a wide range of sequence variants of the core and linker histones. Recent studies have demonstrated that specific histone variant enrichment, combined with post-translational modifications (PTMs) of histones, defines distinct chromatin states that impact specific chromatin functions. Chromatin remodelers are emerging as key regulators of histone variant dynamics, contributing to shaping chromatin states and regulating gene transcription in response to environment. Recognizing the histone variants by their specific readers, controlled by histone PTMs, is crucial for maintaining genome and chromatin integrity. In addition, various histone variants have been shown to play essential roles in remodeling chromatin domains to facilitate important programmed transitions throughout the plant life cycle. In this review, we discuss recent findings in this exciting field of research, which holds immense promise for many surprising discoveries related to the evolution of complexity in plant organization through a seemingly simple protein family.
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Affiliation(s)
- Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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15
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Badmi R, Prestwich BD. Linker H1 is an 'epi'centre of plant defence. Trends Genet 2023; 39:644-645. [PMID: 37419697 DOI: 10.1016/j.tig.2023.06.007] [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: 06/02/2023] [Accepted: 06/19/2023] [Indexed: 07/09/2023]
Abstract
The role of linker H1 histones in plant defence has recently been investigated. Sheikh et al. found that Arabidopsis thaliana plants that were lacking all three H1 proteins showed increased disease resistance, but when primed, failed to induce enhanced resistance. Differences in epigenetic patterns could be the cause of defective priming.
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Affiliation(s)
- Raghuram Badmi
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland.
| | - Barbara Doyle Prestwich
- School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
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16
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Teano G, Concia L, Wolff L, Carron L, Biocanin I, Adamusová K, Fojtová M, Bourge M, Kramdi A, Colot V, Grossniklaus U, Bowler C, Baroux C, Carbone A, Probst AV, Schrumpfová PP, Fajkus J, Amiard S, Grob S, Bourbousse C, Barneche F. Histone H1 protects telomeric repeats from H3K27me3 invasion in Arabidopsis. Cell Rep 2023; 42:112894. [PMID: 37515769 DOI: 10.1016/j.celrep.2023.112894] [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: 01/21/2021] [Revised: 12/02/2022] [Accepted: 07/13/2023] [Indexed: 07/31/2023] Open
Abstract
While the pivotal role of linker histone H1 in shaping nucleosome organization is well established, its functional interplays with chromatin factors along the epigenome are just starting to emerge. Here we show that, in Arabidopsis, as in mammals, H1 occupies Polycomb Repressive Complex 2 (PRC2) target genes where it favors chromatin condensation and H3K27me3 deposition. We further show that, contrasting with its conserved function in PRC2 activation at genes, H1 selectively prevents H3K27me3 accumulation at telomeres and large pericentromeric interstitial telomeric repeat (ITR) domains by restricting DNA accessibility to Telomere Repeat Binding (TRB) proteins, a group of H1-related Myb factors mediating PRC2 cis recruitment. This study provides a mechanistic framework by which H1 avoids the formation of gigantic H3K27me3-rich domains at telomeric sequences and contributes to safeguard nucleus architecture.
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Affiliation(s)
- Gianluca Teano
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Université Paris-Saclay, 91190 Orsay, France
| | - Lorenzo Concia
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léa Wolff
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Léopold Carron
- Sorbonne Université, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
| | - Ivona Biocanin
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France; Université Paris-Saclay, 91190 Orsay, France
| | - Kateřina Adamusová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michael Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Amira Kramdi
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Vincent Colot
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Chris Bowler
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Célia Baroux
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Alessandra Carbone
- Sorbonne Université, CNRS, IBPS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France
| | - Aline V Probst
- CNRS UMR6293, Université Clermont Auvergne, INSERM U1103, GReD, CRBC, Clermont-Ferrand, France
| | - Petra Procházková Schrumpfová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Fajkus
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Laboratory of Functional Genomics and Proteomics, NCBR, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Simon Amiard
- CNRS UMR6293, Université Clermont Auvergne, INSERM U1103, GReD, CRBC, Clermont-Ferrand, France
| | - Stefan Grob
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Clara Bourbousse
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Fredy Barneche
- Institut de biologie de l'École normale supérieure (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France.
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17
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Sheikh AH, Nawaz K, Tabassum N, Almeida-Trapp M, Mariappan KG, Alhoraibi H, Rayapuram N, Aranda M, Groth M, Hirt H. Linker histone H1 modulates defense priming and immunity in plants. Nucleic Acids Res 2023; 51:4252-4265. [PMID: 36840717 PMCID: PMC10201415 DOI: 10.1093/nar/gkad106] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 01/17/2023] [Accepted: 02/07/2023] [Indexed: 02/26/2023] Open
Abstract
Linker H1 histones play an important role in animal and human pathogenesis, but their function in plant immunity is poorly understood. Here, we analyzed mutants of the three canonical variants of Arabidopsis H1 histones, namely H1.1, H1.2 and H1.3. We observed that double h1.1h1.2 and triple h1.1h1.2h1.3 (3h1) mutants were resistant to Pseudomonas syringae and Botrytis cinerea infections. Transcriptome analysis of 3h1 mutant plants showed H1s play a key role in regulating the expression of early and late defense genes upon pathogen challenge. Moreover, 3h1 mutant plants showed enhanced production of reactive oxygen species and activation of mitogen activated protein kinases upon pathogen-associated molecular pattern (PAMP) treatment. However, 3h1 mutant plants were insensitive to priming with flg22, a well-known bacterial PAMP which induces enhanced resistance in WT plants. The defective defense response in 3h1 upon priming was correlated with altered DNA methylation and reduced global H3K56ac levels. Our data place H1 as a molecular gatekeeper in governing dynamic changes in the chromatin landscape of defense genes during plant pathogen interaction.
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Affiliation(s)
- Arsheed H Sheikh
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
| | - Kashif Nawaz
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
| | - Naheed Tabassum
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
| | - Marilia Almeida-Trapp
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
| | - Kiruthiga G Mariappan
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
| | - Hanna Alhoraibi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21551Jeddah, Saudi Arabia
| | - Naganand Rayapuram
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
| | - Manuel Aranda
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
| | - Martin Groth
- Institute of Functional Epigenetics, Helmholtz Munich, 85764Neuherberg, Germany
| | - Heribert Hirt
- King Abdullah University of Science and Technology, KAUST, 23955 Thuwal, Saudi Arabia
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18
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Han Q, Hung YH, Zhang C, Bartels A, Rea M, Yang H, Park C, Zhang XQ, Fischer RL, Xiao W, Hsieh TF. Loss of linker histone H1 in the maternal genome influences DEMETER-mediated demethylation and affects the endosperm DNA methylation landscape. FRONTIERS IN PLANT SCIENCE 2022; 13:1070397. [PMID: 36618671 PMCID: PMC9813442 DOI: 10.3389/fpls.2022.1070397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
The Arabidopsis DEMETER (DME) DNA glycosylase demethylates the central cell genome prior to fertilization. This epigenetic reconfiguration of the female gamete companion cell establishes gene imprinting in the endosperm and is essential for seed viability. DME demethylates small and genic-flanking transposons as well as intergenic and heterochromatin sequences, but how DME is recruited to these loci remains unknown. H1.2 was identified as a DME-interacting protein in a yeast two-hybrid screen, and maternal genome H1 loss affects DNA methylation and expression of selected imprinted genes in the endosperm. Yet, the extent to which H1 influences DME demethylation and gene imprinting in the Arabidopsis endosperm has not been investigated. Here, we showed that without the maternal linker histones, DME-mediated demethylation is facilitated, particularly in the heterochromatin regions, indicating that H1-bound heterochromatins are barriers for DME demethylation. Loss of H1 in the maternal genome has a very limited effect on gene transcription or gene imprinting regulation in the endosperm; however, it variably influences euchromatin TE methylation and causes a slight hypermethylation and a reduced expression in selected imprinted genes. We conclude that loss of maternal H1 indirectly influences DME-mediated demethylation and endosperm DNA methylation landscape but does not appear to affect endosperm gene transcription and overall imprinting regulation.
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Affiliation(s)
- Qiang Han
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Yu-Hung Hung
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Changqing Zhang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Arthur Bartels
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Matthew Rea
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Hanwen Yang
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Christine Park
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Xiang-Qian Zhang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
- College of Food Science and Engineering, Foshan University, Foshan, China
| | - Robert L. Fischer
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Wenyan Xiao
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
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19
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Nunez-Vazquez R, Desvoyes B, Gutierrez C. Histone variants and modifications during abiotic stress response. FRONTIERS IN PLANT SCIENCE 2022; 13:984702. [PMID: 36589114 PMCID: PMC9797984 DOI: 10.3389/fpls.2022.984702] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/28/2022] [Indexed: 06/17/2023]
Abstract
Plants have developed multiple mechanisms as an adaptive response to abiotic stresses, such as salinity, drought, heat, cold, and oxidative stress. Understanding these regulatory networks is critical for coping with the negative impact of abiotic stress on crop productivity worldwide and, eventually, for the rational design of strategies to improve plant performance. Plant alterations upon stress are driven by changes in transcriptional regulation, which rely on locus-specific changes in chromatin accessibility. This process encompasses post-translational modifications of histone proteins that alter the DNA-histones binding, the exchange of canonical histones by variants that modify chromatin conformation, and DNA methylation, which has an implication in the silencing and activation of hypervariable genes. Here, we review the current understanding of the role of the major epigenetic modifications during the abiotic stress response and discuss the intricate relationship among them.
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20
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Torres-García E, Pinto-Cámara R, Linares A, Martínez D, Abonza V, Brito-Alarcón E, Calcines-Cruz C, Valdés-Galindo G, Torres D, Jabloñski M, Torres-Martínez HH, Martínez JL, Hernández HO, Ocelotl-Oviedo JP, Garcés Y, Barchi M, D’Antuono R, Bošković A, Dubrovsky JG, Darszon A, Buffone MG, Morales RR, Rendon-Mancha JM, Wood CD, Hernández-García A, Krapf D, Crevenna ÁH, Guerrero A. Extending resolution within a single imaging frame. Nat Commun 2022; 13:7452. [PMID: 36460648 PMCID: PMC9718789 DOI: 10.1038/s41467-022-34693-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 10/27/2022] [Indexed: 12/05/2022] Open
Abstract
The resolution of fluorescence microscopy images is limited by the physical properties of light. In the last decade, numerous super-resolution microscopy (SRM) approaches have been proposed to deal with such hindrance. Here we present Mean-Shift Super Resolution (MSSR), a new SRM algorithm based on the Mean Shift theory, which extends spatial resolution of single fluorescence images beyond the diffraction limit of light. MSSR works on low and high fluorophore densities, is not limited by the architecture of the optical setup and is applicable to single images as well as temporal series. The theoretical limit of spatial resolution, based on optimized real-world imaging conditions and analysis of temporal image stacks, has been measured to be 40 nm. Furthermore, MSSR has denoising capabilities that outperform other SRM approaches. Along with its wide accessibility, MSSR is a powerful, flexible, and generic tool for multidimensional and live cell imaging applications.
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Affiliation(s)
- Esley Torres-García
- grid.412873.b0000 0004 0484 1712Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos Mexico ,grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Raúl Pinto-Cámara
- grid.412873.b0000 0004 0484 1712Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos Mexico ,grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Alejandro Linares
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico ,grid.144532.5000000012169920XAnalytical and Quantitative Light Microscopy, Marine Biological Laboratory, Woods Hole, MA USA
| | - Damián Martínez
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Víctor Abonza
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Eduardo Brito-Alarcón
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Carlos Calcines-Cruz
- grid.9486.30000 0001 2159 0001Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Gustavo Valdés-Galindo
- grid.9486.30000 0001 2159 0001Departamento de Química de Biomacromoléculas, Instituto de Química. Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - David Torres
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Martina Jabloñski
- grid.464644.00000 0004 0637 7271Instituto de Biología y Medicina Experimental (IBYME‐CONICET), Buenos Aires, Argentina
| | - Héctor H. Torres-Martínez
- grid.9486.30000 0001 2159 0001Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - José L. Martínez
- grid.9486.30000 0001 2159 0001Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Haydee O. Hernández
- grid.9486.30000 0001 2159 0001Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - José P. Ocelotl-Oviedo
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Yasel Garcés
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico ,grid.9486.30000 0001 2159 0001Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Marco Barchi
- grid.6530.00000 0001 2300 0941Department of Biomedicine and Prevention, Faculty of Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | - Ana Bošković
- grid.418924.20000 0004 0627 3632Neurobiology and Epigenetics Unit, European Molecular Biology Laboratory, Monterotondo, Rome Italy
| | - Joseph G. Dubrovsky
- grid.9486.30000 0001 2159 0001Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Alberto Darszon
- grid.9486.30000 0001 2159 0001Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Mariano G. Buffone
- grid.464644.00000 0004 0637 7271Instituto de Biología y Medicina Experimental (IBYME‐CONICET), Buenos Aires, Argentina
| | - Roberto Rodríguez Morales
- grid.472559.80000 0004 0498 8706Instituto de Cibernética, Matemática y Física, Ciudad de la Habana, Cuba
| | - Juan Manuel Rendon-Mancha
- grid.412873.b0000 0004 0484 1712Centro de Investigación en Ciencias, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos Mexico
| | - Christopher D. Wood
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Armando Hernández-García
- grid.9486.30000 0001 2159 0001Departamento de Química de Biomacromoléculas, Instituto de Química. Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Diego Krapf
- grid.47894.360000 0004 1936 8083Electrical and Computer Engineering and School of Biomedical Engineering, Colorado State University, Fort Collins, CO USA
| | - Álvaro H. Crevenna
- grid.418924.20000 0004 0627 3632Neurobiology and Epigenetics Unit, European Molecular Biology Laboratory, Monterotondo, Rome Italy
| | - Adán Guerrero
- grid.9486.30000 0001 2159 0001Laboratorio Nacional de Microscopía Avanzada, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
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21
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Ichino L, Picard CL, Yun J, Chotai M, Wang S, Lin EK, Papareddy RK, Xue Y, Jacobsen SE. Single-nucleus RNA-seq reveals that MBD5, MBD6, and SILENZIO maintain silencing in the vegetative cell of developing pollen. Cell Rep 2022; 41:111699. [DOI: 10.1016/j.celrep.2022.111699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/28/2022] [Accepted: 10/28/2022] [Indexed: 11/23/2022] Open
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22
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Kang H, Fan T, Wu J, Zhu Y, Shen WH. Histone modification and chromatin remodeling in plant response to pathogens. FRONTIERS IN PLANT SCIENCE 2022; 13:986940. [PMID: 36262654 PMCID: PMC9574397 DOI: 10.3389/fpls.2022.986940] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
As sessile organisms, plants are constantly exposed to changing environments frequently under diverse stresses. Invasion by pathogens, including virus, bacterial and fungal infections, can severely impede plant growth and development, causing important yield loss and thus challenging food/feed security worldwide. During evolution, plants have adapted complex systems, including coordinated global gene expression networks, to defend against pathogen attacks. In recent years, growing evidences indicate that pathogen infections can trigger local and global epigenetic changes that reprogram the transcription of plant defense genes, which in turn helps plants to fight against pathogens. Here, we summarize up plant defense pathways and epigenetic mechanisms and we review in depth current knowledge's about histone modifications and chromatin-remodeling factors found in the epigenetic regulation of plant response to biotic stresses. It is anticipated that epigenetic mechanisms may be explorable in the design of tools to generate stress-resistant plant varieties.
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Affiliation(s)
- Huijia Kang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
| | - Tianyi Fan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jiabing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yan Zhu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes (IBMP), CNRS, Université de Strasbourg, Strasbourg, France
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23
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Probst AV. Deposition and eviction of histone variants define functional chromatin states in plants. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102266. [PMID: 35981458 DOI: 10.1016/j.pbi.2022.102266] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/30/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
The organization of DNA with histone proteins into chromatin is fundamental for the regulation of gene expression. Incorporation of different histone variants into the nucleosome together with post-translational modifications of these histone variants allows modulating chromatin accessibility and contributes to the establishment of functional chromatin states either permissive or repressive for transcription. This review highlights emerging mechanisms required to deposit or evict histone variants in a timely and locus-specific manner. This review further discusses how assembly of specific histone variants permits to reinforce transmission of chromatin states during replication, to maintain heterochromatin organization and stability and to reprogram existing epigenetic information.
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Affiliation(s)
- Aline V Probst
- iGReD, CNRS, Inserm, Université Clermont Auvergne, 63000 Clermont-Ferrand, France.
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24
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Liu ZW, Simmons CH, Zhong X. Linking transcriptional silencing with chromatin remodeling, folding, and positioning in the nucleus. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102261. [PMID: 35841650 PMCID: PMC10014033 DOI: 10.1016/j.pbi.2022.102261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Chromatin organization is important for many DNA-templated processes in eukaryotic cells such as replication and transcription. Recent studies have uncovered the capacity of epigenetic modifications, phase separation, and nuclear architecture and spatial positioning to regulate chromatin organization in both plants and animals. Here, we provide an overview of the recent progress made in understanding how chromatin is organized within the nucleus at both the local and global levels with respect to the regulation of transcriptional silencing in plants. To be concise while covering important mechanisms across a range of scales, we focus on how epigenetic modifications and chromatin remodelers alter local chromatin structure, how liquid-liquid phase separation physically separates broader chromatin domains into distinct droplets, and how nuclear positioning affects global chromatin organization.
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Affiliation(s)
- Zhang-Wei Liu
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Carl H Simmons
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53706, USA.
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25
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Lan W, Ma W, Zheng S, Qiu Y, Zhang H, Lu H, Zhang Y, Miao Y. Ubiquitome profiling reveals a regulatory pattern of UPL3 with UBP12 on metabolic-leaf senescence. Life Sci Alliance 2022; 5:e202201492. [PMID: 35926874 PMCID: PMC9354775 DOI: 10.26508/lsa.202201492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 12/03/2022] Open
Abstract
The HECT-type UPL3 ligase plays critical roles in plant development and stress protection, but understanding of its regulation remains limited. Here, the multi-omics analyses of ubiquitinated proteins in <i>upl3</i> mutants were performed. A landscape of UPL3-dependent ubiquitinated proteins is constructed: Preferential ubiquitination of proteins related to carbon fixation represented the largest set of proteins with increased ubiquitination in the <i>upl3</i> plant, including most of carbohydrate metabolic enzymes, BRM, and variant histone, whereas a small set of proteins with reduced ubiquitination caused by the <i>upl3</i> mutation were linked to cysteine/methionine synthesis, as well as hexokinase 1 (HXK1) and phosphoenolpyruvate carboxylase 2 (PPC2). Notably, ubiquitin hydrolase 12 (UBP12), BRM, HXK1, and PPC2 were identified as the UPL3-interacting partners in vivo and in vitro. Characterization of <i>brm</i>, <i>upl3</i>, <i>ppc2</i>, <i>gin2</i>, and <i>ubp12</i> mutant plants and proteomic and transcriptomic analysis suggested that UPL3 fine-tunes carbohydrate metabolism, mediating cellular senescence by interacting with UBP12, BRM, HXK1, and PPC2. Our results highlight a regulatory pattern of UPL3 with UBP12 as a hub of regulator on proteolysis-independent regulation and proteolysis-dependent degradation.
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Affiliation(s)
- Wei Lan
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weibo Ma
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuai Zheng
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhao Qiu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Han Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haisen Lu
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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26
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Foroozani M, Holder DH, Deal RB. Histone Variants in the Specialization of Plant Chromatin. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:149-172. [PMID: 35167758 PMCID: PMC9133179 DOI: 10.1146/annurev-arplant-070221-050044] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The basic unit of chromatin, the nucleosome, is an octamer of four core histone proteins (H2A, H2B, H3, and H4) and serves as a fundamental regulatory unit in all DNA-templated processes. The majority of nucleosome assembly occurs during DNA replication when these core histones are produced en masse to accommodate the nascent genome. In addition, there are a number of nonallelic sequence variants of H2A and H3 in particular, known as histone variants, that can be incorporated into nucleosomes in a targeted and replication-independent manner. By virtue of their sequence divergence from the replication-coupled histones, these histone variants can impart unique properties onto the nucleosomes they occupy and thereby influence transcription and epigenetic states, DNA repair, chromosome segregation, and other nuclear processes in ways that profoundly affect plant biology. In this review, we discuss the evolutionary origins of these variants in plants, their known roles in chromatin, and their impacts on plant development and stress responses. We focus on the individual and combined roles of histone variants in transcriptional regulation within euchromatic and heterochromatic genome regions. Finally, we highlight gaps in our understanding of plant variants at the molecular, cellular, and organismal levels, and we propose new directions for study in the field of plant histone variants.
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Affiliation(s)
| | - Dylan H Holder
- Department of Biology, Emory University, Atlanta, Georgia, USA;
- Graduate Program in Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, Georgia, USA;
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27
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Hannan Parker A, Wilkinson SW, Ton J. Epigenetics: a catalyst of plant immunity against pathogens. THE NEW PHYTOLOGIST 2022; 233:66-83. [PMID: 34455592 DOI: 10.1111/nph.17699] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/20/2021] [Indexed: 05/11/2023]
Abstract
The plant immune system protects against pests and diseases. The recognition of stress-related molecular patterns triggers localised immune responses, which are often followed by longer-lasting systemic priming and/or up-regulation of defences. In some cases, this induced resistance (IR) can be transmitted to following generations. Such transgenerational IR is gradually reversed in the absence of stress at a rate that is proportional to the severity of disease experienced in previous generations. This review outlines the mechanisms by which epigenetic responses to pathogen infection shape the plant immune system across expanding time scales. We review the cis- and trans-acting mechanisms by which stress-inducible epigenetic changes at transposable elements (TEs) regulate genome-wide defence gene expression and draw particular attention to one regulatory model that is supported by recent evidence about the function of AGO1 and H2A.Z in transcriptional control of defence genes. Additionally, we explore how stress-induced mobilisation of epigenetically controlled TEs acts as a catalyst of Darwinian evolution by generating (epi)genetic diversity at environmentally responsive genes. This raises questions about the long-term evolutionary consequences of stress-induced diversification of the plant immune system in relation to the long-held dichotomy between Darwinian and Lamarckian evolution.
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Affiliation(s)
- Adam Hannan Parker
- Department of Animal and Plant Sciences, Institute for Sustainable Food, Western Bank, University of Sheffield, Sheffield, S10 2TN, UK
| | - Samuel W Wilkinson
- Department of Animal and Plant Sciences, Institute for Sustainable Food, Western Bank, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jurriaan Ton
- Department of Animal and Plant Sciences, Institute for Sustainable Food, Western Bank, University of Sheffield, Sheffield, S10 2TN, UK
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28
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Kumar S, Kaur S, Seem K, Kumar S, Mohapatra T. Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective. Front Cell Dev Biol 2021; 9:774719. [PMID: 34957106 PMCID: PMC8692796 DOI: 10.3389/fcell.2021.774719] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/23/2021] [Indexed: 01/17/2023] Open
Abstract
The genome of a eukaryotic organism is comprised of a supra-molecular complex of chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal interactions and topological changes in response to the developmental and/or environmental stimuli affect gene expression. Chromatin architecture plays important roles in DNA replication, gene expression, and genome integrity. Higher-order chromatin organizations like chromosome territories (CTs), A/B compartments, topologically associating domains (TADs), and chromatin loops vary among cells, tissues, and species depending on the developmental stage and/or environmental conditions (4D genomics). Every chromosome occupies a separate territory in the interphase nucleus and forms the top layer of hierarchical structure (CTs) in most of the eukaryotes. While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. Chromatin architecture like TADs as well as the local interactions between promoter and regulatory elements correlates with the chromatin activity, which alters during environmental stresses due to relocalization of the architectural proteins. Moreover, chromatin looping brings the gene and regulatory elements in close proximity for interactions. The intricate relationship between nucleotide sequence and chromatin architecture requires a more comprehensive understanding to unravel the genome organization and genetic plasticity. During the last decade, advances in chromatin conformation capture techniques for unravelling 3D genome organizations have improved our understanding of genome biology. However, the recent advances, such as Hi-C and ChIA-PET, have substantially increased the resolution, throughput as well our interest in analysing genome organizations. The present review provides an overview of the historical and contemporary perspectives of chromosome conformation capture technologies, their applications in functional genomics, and the constraints in predicting 3D genome organization. We also discuss the future perspectives of understanding high-order chromatin organizations in deciphering transcriptional regulation of gene expression under environmental stress (4D genomics). These might help design the climate-smart crop to meet the ever-growing demands of food, feed, and fodder.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
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29
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Soshnev AA, Allis CD, Cesarman E, Melnick AM. Histone H1 Mutations in Lymphoma: A Link(er) between Chromatin Organization, Developmental Reprogramming, and Cancer. Cancer Res 2021; 81:6061-6070. [PMID: 34580064 PMCID: PMC8678342 DOI: 10.1158/0008-5472.can-21-2619] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022]
Abstract
Aberrant cell fate decisions due to transcriptional misregulation are central to malignant transformation. Histones are the major constituents of chromatin, and mutations in histone-encoding genes are increasingly recognized as drivers of oncogenic transformation. Mutations in linker histone H1 genes were recently identified as drivers of peripheral lymphoid malignancy. Loss of H1 in germinal center B cells results in widespread chromatin decompaction, redistribution of core histone modifications, and reactivation of stem cell-specific transcriptional programs. This review explores how linker histones and mutations therein regulate chromatin structure, highlighting reciprocal relationships between epigenetic circuits, and discusses the emerging role of aberrant three-dimensional chromatin architecture in malignancy.
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Affiliation(s)
- Alexey A Soshnev
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York.
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Ari M Melnick
- Division of Hematology & Medical Oncology, Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York.
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30
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Di Stefano M, Nützmann HW. Modeling the 3D genome of plants. Nucleus 2021; 12:65-81. [PMID: 34057011 PMCID: PMC8168717 DOI: 10.1080/19491034.2021.1927503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 12/11/2022] Open
Abstract
Chromosomes are the carriers of inheritable traits and define cell function and development. This is not only based on the linear DNA sequence of chromosomes but also on the additional molecular information they are associated with, including the transcription machinery, histone modifications, and their three-dimensional folding. The synergistic application of experimental approaches and computer simulations has helped to unveil how these organizational layers of the genome interplay in various organisms. However, such multidisciplinary approaches are still rarely explored in the plant kingdom. Here, we provide an overview of our current knowledge on plant 3D genome organization and review recent efforts to integrate cutting-edge experiments from microscopy and next-generation sequencing approaches with theoretical models. Building on these recent approaches, we propose possible avenues to extend the application of theoretical modeling in the characterization of the 3D genome organization in plants.
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Affiliation(s)
- Marco Di Stefano
- Institute of Human Genetics, Centre National de la Recherche Scientifique, University of Montpellier, Montpellier, France
| | - Hans-Wilhelm Nützmann
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
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31
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Saintilnord WN, Fondufe-Mittendorf Y. Arsenic-induced epigenetic changes in cancer development. Semin Cancer Biol 2021; 76:195-205. [PMID: 33798722 PMCID: PMC8481342 DOI: 10.1016/j.semcancer.2021.03.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/29/2022]
Abstract
Arsenic is a ubiquitous metalloid whose high levels of toxicity pose major health concerns to millions of people worldwide by increasing susceptibility to various cancers and non-cancer illnesses. Since arsenic is not a mutagen, the mechanism by which it causes changes in gene expression and disease pathogenesis is not clear. One possible mechanism is through generation of reactive oxygen species. Another equally important mechanism still very much in its infancy is epigenetic dysregulation. In this review, we discuss recent discoveries underlying arsenic-induced epigenetic changes in cancer development. Importantly, we highlight the proposed mechanisms targeted by arsenic to drive oncogenic gene expression.
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Affiliation(s)
- Wesley N Saintilnord
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.
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32
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Huang J, Dong J, Qu LJ. From birth to function: Male gametophyte development in flowering plants. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102118. [PMID: 34625367 PMCID: PMC9039994 DOI: 10.1016/j.pbi.2021.102118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/13/2021] [Accepted: 08/25/2021] [Indexed: 05/08/2023]
Abstract
Male germline development in flowering plants involves two distinct and successive phases, microsporogenesis and microgametogenesis, which involve one meiosis followed by two rounds of mitosis. Many aspects of distinctions after mitosis between the vegetative cell and the male germ cells are seen, from morphology to structure, and the differential functions of the two cell types in the male gametophyte are differentially needed and required for double fertilization. The two sperm cells, carriers of the hereditary substances, depend on the vegetative cell/pollen tube to be delivered to the female gametophyte for double fertilization. Thus, the intercellular communication and coordinated activity within the male gametophyte probably represent the most subtle regulation in flowering plants to guarantee the success of reproduction. This review will focus on what we have known about the differentiation process and the functional diversification of the vegetative cell and the male germ cell, the most crucial cell types for plant fertility and crop production.
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Affiliation(s)
- Jiaying Huang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China; Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA; Department of Plant Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08901, USA
| | - Juan Dong
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA; Department of Plant Biology, Rutgers, the State University of New Jersey, Piscataway, NJ 08901, USA.
| | - Li-Jia Qu
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at the College of Life Sciences, Peking University, Beijing 100871, People's Republic of China; The National Plant Gene Research Center (Beijing), Beijing 100101, People's Republic of China.
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33
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Tissue folding at the organ-meristem boundary results in nuclear compression and chromatin compaction. Proc Natl Acad Sci U S A 2021; 118:2017859118. [PMID: 33608459 PMCID: PMC7923354 DOI: 10.1073/pnas.2017859118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Artificial mechanical perturbations affect chromatin in animal cells in culture. Whether this is also relevant to growing tissues in living organisms remains debated. In plants, aerial organ emergence occurs through localized outgrowth at the periphery of the shoot apical meristem, which also contains a stem cell niche. Interestingly, organ outgrowth has been proposed to generate compression in the saddle-shaped organ-meristem boundary domain. Yet whether such growth-induced mechanical stress affects chromatin in plant tissues is unknown. Here, by imaging the nuclear envelope in vivo over time and quantifying nucleus deformation, we demonstrate the presence of active nuclear compression in that domain. We developed a quantitative pipeline amenable to identifying a subset of very deformed nuclei deep in the boundary and in which nuclei become gradually narrower and more elongated as the cell contracts transversely. In this domain, we find that the number of chromocenters is reduced, as shown by chromatin staining and labeling, and that the expression of linker histone H1.3 is induced. As further evidence of the role of forces on chromatin changes, artificial compression with a MicroVice could induce the ectopic expression of H1.3 in the rest of the meristem. Furthermore, while the methylation status of chromatin was correlated with nucleus deformation at the meristem boundary, such correlation was lost in the h1.3 mutant. Altogether, we reveal that organogenesis in plants generates compression that is able to have global effects on chromatin in individual cells.
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34
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Papareddy RK, Páldi K, Smolka AD, Hüther P, Becker C, Nodine MD. Repression of CHROMOMETHYLASE 3 prevents epigenetic collateral damage in Arabidopsis. eLife 2021; 10:e69396. [PMID: 34296996 PMCID: PMC8352596 DOI: 10.7554/elife.69396] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/21/2021] [Indexed: 01/14/2023] Open
Abstract
DNA methylation has evolved to silence mutagenic transposable elements (TEs) while typically avoiding the targeting of endogenous genes. Mechanisms that prevent DNA methyltransferases from ectopically methylating genes are expected to be of prime importance during periods of dynamic cell cycle activities including plant embryogenesis. However, virtually nothing is known regarding how DNA methyltransferase activities are precisely regulated during embryogenesis to prevent the induction of potentially deleterious and mitotically stable genic epimutations. Here, we report that microRNA-mediated repression of CHROMOMETHYLASE 3 (CMT3) and the chromatin features that CMT3 prefers help prevent ectopic methylation of thousands of genes during embryogenesis that can persist for weeks afterwards. Our results are also consistent with CMT3-induced ectopic methylation of promoters or bodies of genes undergoing transcriptional activation reducing their expression. Therefore, the repression of CMT3 prevents epigenetic collateral damage on endogenous genes. We also provide a model that may help reconcile conflicting viewpoints regarding the functions of gene-body methylation that occurs in nearly all flowering plants.
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Affiliation(s)
- Ranjith K Papareddy
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3ViennaAustria
| | - Katalin Páldi
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3ViennaAustria
| | - Anna D Smolka
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3ViennaAustria
| | - Patrick Hüther
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3ViennaAustria
- Genetics, LMU Biocenter, Ludwig-Maximilians UniversityMartinsriedGermany
| | - Claude Becker
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3ViennaAustria
- Genetics, LMU Biocenter, Ludwig-Maximilians UniversityMartinsriedGermany
| | - Michael D Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3ViennaAustria
- Laboratory of Molecular Biology, Wageningen UniversityWageningenNetherlands
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35
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Yamaguchi N. LEAFY, a Pioneer Transcription Factor in Plants: A Mini-Review. FRONTIERS IN PLANT SCIENCE 2021; 12:701406. [PMID: 34290727 PMCID: PMC8287900 DOI: 10.3389/fpls.2021.701406] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/01/2021] [Indexed: 05/25/2023]
Abstract
A subset of eukaryotic transcription factors (TFs) possess the ability to reprogram one cell type into another. Genes important for cellular reprograming are typically located in closed chromatin, which is covered by nucleosomes. Pioneer factors are a special class of TFs that can initially engage their target sites in closed chromatin prior to the engagement with, opening of, or modification of the sites by other factors. Although many pioneer factors are known in animals, a few have been characterized in plants. The TF LEAFY (LFY) acts as a pioneer factor specifying floral fate in Arabidopsis. In response to endogenous and environmental cues, plants produce appropriate floral inducers (florigens). During the vegetative phase, LFY is repressed by the TERMINAL FLOWER 1 (TFL1)-FD complex, which functions as a floral inhibitor, or anti-florigen. The florigen FLOWERING LOCUS T (FT) competes with TFL1 to prevent the binding of the FD TF to the LFY locus. The resulting FT-FD complex functions as a transient stimulus to activate its targets. Once LFY has been transcribed in the appropriate spatiotemporal manner, LFY binds to nucleosomes in closed chromatin regions. Subsequently, LFY opens the chromatin by displacing H1 linker histones and recruiting the SWI/SNF chromatin-remodeling complex. Such local changes permit the binding of other TFs, leading to the expression of the floral meristem identity gene APETALA1. This mini-review describes the latest advances in our understanding of the pioneer TF LFY, providing insight into the establishment of gene expression competence through the shaping of the plant epigenetic landscape.
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Pei L, Li G, Lindsey K, Zhang X, Wang M. Plant 3D genomics: the exploration and application of chromatin organization. THE NEW PHYTOLOGIST 2021; 230:1772-1786. [PMID: 33560539 PMCID: PMC8252774 DOI: 10.1111/nph.17262] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/01/2021] [Indexed: 05/29/2023]
Abstract
Eukaryotic genomes are highly folded for packing into higher-order chromatin structures in the nucleus. With the emergence of state-of-the-art chromosome conformation capture methods and microscopic imaging techniques, the spatial organization of chromatin and its functional implications have been interrogated. Our knowledge of 3D chromatin organization in plants has improved dramatically in the past few years, building on the early advances in animal systems. Here, we review recent advances in 3D genome mapping approaches, our understanding of the sophisticated organization of spatial structures, and the application of 3D genomic principles in plants. We also discuss directions for future developments in 3D genomics in plants.
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Affiliation(s)
- Liuling Pei
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Guoliang Li
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanHubei430070China
| | - Keith Lindsey
- Department of BiosciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
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Borg M, Jiang D, Berger F. Histone variants take center stage in shaping the epigenome. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:101991. [PMID: 33434757 DOI: 10.1016/j.pbi.2020.101991] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/09/2020] [Accepted: 12/17/2020] [Indexed: 05/28/2023]
Abstract
The dynamic properties of the nucleosome are central to genomic activity. Variants of the core histones that form the nucleosome play a pivotal role in modulating nucleosome structure and function. Despite often small differences in sequence, histone variants display remarkable diversity in genomic deposition and post-translational modification. Here, we summarize the roles played by histone variants in the establishment, maintenance and reprogramming of plant chromatin landscapes, with a focus on histone H3 variants. Deposition of replicative H3.1 during DNA replication controls epigenetic inheritance, while local replacement of H3.1 with H3.3 marks cells undergoing terminal differentiation. Deposition of specialized H3 variants in specific cell types is emerging as a novel mechanism of selective epigenetic reprogramming during the plant life cycle.
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Affiliation(s)
- Michael Borg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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Baroux C. Three-dimensional genome organization in epigenetic regulations: cause or consequence? CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102031. [PMID: 33819713 DOI: 10.1016/j.pbi.2021.102031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/09/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
The evolution of the nucleus is an evolutionary milestone. By enabling genome compartmentalization, it contributes to the fine-tuning of genome functions. The genome is partitioned into functional domains differing in spatial positioning and topological folding at different scales. The rise of '3D Genomics' embracing experimental, theoretical, and modeling approaches allowed the proposal of a multiscale model of the eukaryotic genome, capturing its organizing principles and functionalities. In these efforts, resolving causality remains an important objective. Are positioning and folding the cause or consequence of functional states? This minireview presents emerging answers to this question, borrowing examples from recent studies of the three-dimensional genome in both plants and animals.
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Affiliation(s)
- Célia Baroux
- Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Switzerland.
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Bourguet P, Picard CL, Yelagandula R, Pélissier T, Lorković ZJ, Feng S, Pouch-Pélissier MN, Schmücker A, Jacobsen SE, Berger F, Mathieu O. The histone variant H2A.W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation. Nat Commun 2021; 12:2683. [PMID: 33976212 PMCID: PMC8113232 DOI: 10.1038/s41467-021-22993-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/09/2021] [Indexed: 12/12/2022] Open
Abstract
In flowering plants, heterochromatin is demarcated by the histone variant H2A.W, elevated levels of the linker histone H1, and specific epigenetic modifications, such as high levels of DNA methylation at both CG and non-CG sites. How H2A.W regulates heterochromatin organization and interacts with other heterochromatic features is unclear. Here, we create a h2a.w null mutant via CRISPR-Cas9, h2a.w-2, to analyze the in vivo function of H2A.W. We find that H2A.W antagonizes deposition of H1 at heterochromatin and that non-CG methylation and accessibility are moderately decreased in h2a.w-2 heterochromatin. Compared to H1 loss alone, combined loss of H1 and H2A.W greatly increases accessibility and facilitates non-CG DNA methylation in heterochromatin, suggesting co-regulation of heterochromatic features by H2A.W and H1. Our results suggest that H2A.W helps maintain optimal heterochromatin accessibility and DNA methylation by promoting chromatin compaction together with H1, while also inhibiting excessive H1 incorporation.
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Affiliation(s)
- Pierre Bourguet
- CNRS, Université Clermont Auvergne, Inserm, Institut Génétique Reproduction et Développement (iGReD), Clermont-Ferrand, France
| | - Colette L Picard
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Ramesh Yelagandula
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Thierry Pélissier
- CNRS, Université Clermont Auvergne, Inserm, Institut Génétique Reproduction et Développement (iGReD), Clermont-Ferrand, France
| | - Zdravko J Lorković
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Marie-Noëlle Pouch-Pélissier
- CNRS, Université Clermont Auvergne, Inserm, Institut Génétique Reproduction et Développement (iGReD), Clermont-Ferrand, France
| | - Anna Schmücker
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Olivier Mathieu
- CNRS, Université Clermont Auvergne, Inserm, Institut Génétique Reproduction et Développement (iGReD), Clermont-Ferrand, France.
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Liu L, Wang T. Male gametophyte development in flowering plants: A story of quarantine and sacrifice. JOURNAL OF PLANT PHYSIOLOGY 2021; 258-259:153365. [PMID: 33548696 DOI: 10.1016/j.jplph.2021.153365] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/06/2021] [Accepted: 01/06/2021] [Indexed: 05/19/2023]
Abstract
Over 160 years ago, scientists made the first microscopic observations of angiosperm pollen. Unlike in animals, male meiosis in angiosperms produces a haploid microspore that undergoes one asymmetric division to form a vegetative cell and a generative cell. These two cells have distinct fates: the vegetative cell exits the cell cycle and elongates to form a tip-growing pollen tube; the generative cell divides once more in the pollen grain or within the growing pollen tube to form a pair of sperm cells. The concept that male germ cells are less active than the vegetative cell came from biochemical analyses and pollen structure anatomy early in the last century and is supported by the pollen transcriptome data of the last decade. However, the mechanism of how and when the transcriptional repression in male germ cells occurs is still not fully understood. In this review, we provide a brief account of the cytological and metabolic differentiation between the vegetative cell and male germ cells, with emphasis on the role of temporary callose walls, dynamic nuclear pore density, transcription repression, and histone variants. We further discuss the intercellular movement of small interfering RNA (siRNA) derived from transposable elements (TEs) and reexamine the function of TE expression in male germ cells.
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Affiliation(s)
- Lingtong Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Tai Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100093, China.
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Multifaceted Chromatin Structure and Transcription Changes in Plant Stress Response. Int J Mol Sci 2021; 22:ijms22042013. [PMID: 33670556 PMCID: PMC7922328 DOI: 10.3390/ijms22042013] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/06/2023] Open
Abstract
Sessile plants are exposed throughout their existence to environmental abiotic and biotic stress factors, such as cold, heat, salinity, drought, dehydration, submergence, waterlogging, and pathogen infection. Chromatin organization affects genome stability, and its dynamics are crucial in plant stress responses. Chromatin dynamics are epigenetically regulated and are required for stress-induced transcriptional regulation or reprogramming. Epigenetic regulators facilitate the phenotypic plasticity of development and the survival and reproduction of plants in unfavorable environments, and they are highly diversified, including histone and DNA modifiers, histone variants, chromatin remodelers, and regulatory non-coding RNAs. They contribute to chromatin modifications, remodeling and dynamics, and constitute a multilayered and multifaceted circuitry for sophisticated and robust epigenetic regulation of plant stress responses. However, this complicated epigenetic regulatory circuitry creates challenges for elucidating the common or differential roles of chromatin modifications for transcriptional regulation or reprogramming in different plant stress responses. Particularly, interacting chromatin modifications and heritable stress memories are difficult to identify in the aspect of chromatin-based epigenetic regulation of transcriptional reprogramming and memory. Therefore, this review discusses the recent updates from the three perspectives—stress specificity or dependence of transcriptional reprogramming, the interplay of chromatin modifications, and transcriptional stress memory in plants. This helps solidify our knowledge on chromatin-based transcriptional reprogramming for plant stress response and memory.
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Liu S, de Jonge J, Trejo‐Arellano MS, Santos‐González J, Köhler C, Hennig L. Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress. THE NEW PHYTOLOGIST 2021; 229:2238-2250. [PMID: 33091182 PMCID: PMC7894476 DOI: 10.1111/nph.17018] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/09/2020] [Indexed: 05/03/2023]
Abstract
Heat-stressed Arabidopsis plants release heterochromatin-associated transposable element (TE) silencing, yet it is not accompanied by major reductions of epigenetic repressive modifications. In this study, we explored the functional role of histone H1 in repressing heterochromatic TEs in response to heat stress. We generated and analyzed RNA and bisulfite-sequencing data of wild-type and h1 mutant seedlings before and after heat stress. Loss of H1 caused activation of pericentromeric Gypsy elements upon heat treatment, despite these elements remaining highly methylated. By contrast, nonpericentromeric Copia elements became activated concomitantly with loss of DNA methylation. The same Copia elements became activated in heat-treated chromomethylase 2 (cmt2) mutants, indicating that H1 represses Copia elements through maintaining DNA methylation under heat. We discovered that H1 is required for TE repression in response to heat stress, but its functional role differs depending on TE location. Strikingly, H1-deficient plants treated with the DNA methyltransferase inhibitor zebularine were highly tolerant to heat stress, suggesting that both H1 and DNA methylation redundantly suppress the plant response to heat stress.
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Affiliation(s)
- Shujing Liu
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Jennifer de Jonge
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Minerva S. Trejo‐Arellano
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Juan Santos‐González
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Claudia Köhler
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
| | - Lars Hennig
- Department of Plant BiologySwedish University of Agricultural Sciences and Linnean Center for Plant BiologyUppsala75007Sweden
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LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate. Nat Commun 2021; 12:626. [PMID: 33504790 PMCID: PMC7840934 DOI: 10.1038/s41467-020-20883-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 12/22/2020] [Indexed: 01/31/2023] Open
Abstract
Master transcription factors reprogram cell fate in multicellular eukaryotes. Pioneer transcription factors have prominent roles in this process because of their ability to contact their cognate binding motifs in closed chromatin. Reprogramming is pervasive in plants, whose development is plastic and tuned by the environment, yet little is known about pioneer transcription factors in this kingdom. Here, we show that the master transcription factor LEAFY (LFY), which promotes floral fate through upregulation of the floral commitment factor APETALA1 (AP1), is a pioneer transcription factor. In vitro, LFY binds to the endogenous AP1 target locus DNA assembled into a nucleosome. In vivo, LFY associates with nucleosome occupied binding sites at the majority of its target loci, including AP1. Upon binding, LFY 'unlocks' chromatin locally by displacing the H1 linker histone and by recruiting SWI/SNF chromatin remodelers, but broad changes in chromatin accessibility occur later. Our study provides a mechanistic framework for patterning of inflorescence architecture and uncovers striking similarities between LFY and animal pioneer transcription factor.
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Bhadouriya SL, Mehrotra S, Basantani MK, Loake GJ, Mehrotra R. Role of Chromatin Architecture in Plant Stress Responses: An Update. FRONTIERS IN PLANT SCIENCE 2021; 11:603380. [PMID: 33510748 PMCID: PMC7835326 DOI: 10.3389/fpls.2020.603380] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/07/2020] [Indexed: 05/08/2023]
Abstract
Sessile plants possess an assembly of signaling pathways that perceive and transmit environmental signals, ultimately resulting in transcriptional reprogramming. Histone is a key feature of chromatin structure. Numerous histone-modifying proteins act under different environmental stress conditions to help modulate gene expression. DNA methylation and histone modification are crucial for genome reprogramming for tissue-specific gene expression and global gene silencing. Different classes of chromatin remodelers including SWI/SNF, ISWI, INO80, and CHD are reported to act upon chromatin in different organisms, under diverse stresses, to convert chromatin from a transcriptionally inactive to a transcriptionally active state. The architecture of chromatin at a given promoter is crucial for determining the transcriptional readout. Further, the connection between somatic memory and chromatin modifications may suggest a mechanistic basis for a stress memory. Studies have suggested that there is a functional connection between changes in nuclear organization and stress conditions. In this review, we discuss the role of chromatin architecture in different stress responses and the current evidence on somatic, intergenerational, and transgenerational stress memory.
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Affiliation(s)
- Sneha Lata Bhadouriya
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
| | - Sandhya Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
| | - Mahesh K. Basantani
- Institute of Bioscience and Technology, Shri Ramswaroop Memorial University, Lucknow, India
| | - Gary J. Loake
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburg, Edinburg, United Kingdom
| | - Rajesh Mehrotra
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Sancoale, India
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45
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Papareddy RK, Páldi K, Paulraj S, Kao P, Lutzmayer S, Nodine MD. Chromatin regulates expression of small RNAs to help maintain transposon methylome homeostasis in Arabidopsis. Genome Biol 2020; 21:251. [PMID: 32943088 PMCID: PMC7499886 DOI: 10.1186/s13059-020-02163-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Eukaryotic genomes are partitioned into euchromatic and heterochromatic domains to regulate gene expression and other fundamental cellular processes. However, chromatin is dynamic during growth and development and must be properly re-established after its decondensation. Small interfering RNAs (siRNAs) promote heterochromatin formation, but little is known about how chromatin regulates siRNA expression. RESULTS We demonstrate that thousands of transposable elements (TEs) produce exceptionally high levels of siRNAs in Arabidopsis thaliana embryos. TEs generate siRNAs throughout embryogenesis according to two distinct patterns depending on whether they are located in euchromatic or heterochromatic regions of the genome. siRNA precursors are transcribed in embryos, and siRNAs are required to direct the re-establishment of DNA methylation on TEs from which they are derived in the new generation. Decondensed chromatin also permits the production of 24-nt siRNAs from heterochromatic TEs during post-embryogenesis, and siRNA production from bipartite-classified TEs is controlled by their chromatin states. CONCLUSIONS Decondensation of heterochromatin in response to developmental, and perhaps environmental, cues promotes the transcription and function of siRNAs in plants. Our results indicate that chromatin-mediated siRNA transcription provides a cell-autonomous homeostatic control mechanism to help reconstitute pre-existing chromatin states during growth and development including those that ensure silencing of TEs in the future germ line.
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Affiliation(s)
- Ranjith K. Papareddy
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Katalin Páldi
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Subramanian Paulraj
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Ping Kao
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Stefan Lutzmayer
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael D. Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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46
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Perrella G, Zioutopoulou A, Headland LR, Kaiserli E. The impact of light and temperature on chromatin organization and plant adaptation. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5247-5255. [PMID: 32215554 DOI: 10.1093/jxb/eraa154] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/24/2020] [Indexed: 05/23/2023]
Abstract
Light and temperature shape the developmental trajectory and morphology of plants. Changes in chromatin organization and nuclear architecture can modulate gene expression and lead to short- and long-term plant adaptation to the environment. Here, we review recent reports investigating how changes in chromatin composition, structure, and topology modulate gene expression in response to fluctuating light and temperature conditions resulting in developmental and physiological responses. Furthermore, the potential application of novel revolutionary techniques, such Hi-C, RNA fluorescence in situ hybridization (FISH) and padlock-FISH, to study the impact of environmental stimuli such as light and temperature on nuclear compartmentalization in plants is discussed.
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Affiliation(s)
- Giorgio Perrella
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- ENEA-Trisaia Research Centre 75026, Rotondella (Matera), Italy
| | - Anna Zioutopoulou
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Lauren R Headland
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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47
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Probst AV, Desvoyes B, Gutierrez C. Similar yet critically different: the distribution, dynamics and function of histone variants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5191-5204. [PMID: 32392582 DOI: 10.1093/jxb/eraa230] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/06/2020] [Indexed: 05/23/2023]
Abstract
Organization of the genetic information into chromatin plays an important role in the regulation of all DNA template-based reactions. The incorporation of different variant versions of the core histones H3, H2A, and H2B, or the linker histone H1 results in nucleosomes with unique properties. Histone variants can differ by only a few amino acids or larger protein domains and their incorporation may directly affect nucleosome stability and higher order chromatin organization or indirectly influence chromatin function through histone variant-specific binding partners. Histone variants employ dedicated histone deposition machinery for their timely and locus-specific incorporation into chromatin. Plants have evolved specific histone variants with unique expression patterns and features. In this review, we discuss our current knowledge on histone variants in Arabidopsis, their mode of deposition, variant-specific post-translational modifications, and genome-wide distribution, as well as their role in defining different chromatin states.
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Affiliation(s)
- Aline V Probst
- Université Clermont Auvergne, CNRS, Inserm, GReD, Clermont-Ferrand, France
| | - Bénédicte Desvoyes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Cantoblanco, Madrid, Spain
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48
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Bäurle I, Trindade I. Chromatin regulation of somatic abiotic stress memory. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5269-5279. [PMID: 32076719 DOI: 10.1093/jxb/eraa098] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/19/2020] [Indexed: 05/20/2023]
Abstract
In nature, plants are often subjected to periods of recurrent environmental stress that can strongly affect their development and productivity. To cope with these conditions, plants can remember a previous stress, which allows them to respond more efficiently to a subsequent stress, a phenomenon known as priming. This ability can be maintained at the somatic level for a few days or weeks after the stress is perceived, suggesting that plants can store information of a past stress during this recovery phase. While the immediate responses to a single stress event have been extensively studied, knowledge on priming effects and how stress memory is stored is still scarce. At the molecular level, memory of a past condition often involves changes in chromatin structure and organization, which may be maintained independently from transcription. In this review, we will summarize the most recent developments in the field and discuss how different levels of chromatin regulation contribute to priming and plant abiotic stress memory.
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Affiliation(s)
- Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Inês Trindade
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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49
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Martínez-García JF, Moreno-Romero J. Shedding light on the chromatin changes that modulate shade responses. PHYSIOLOGIA PLANTARUM 2020; 169:407-417. [PMID: 32222987 DOI: 10.1111/ppl.13101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/12/2020] [Accepted: 03/24/2020] [Indexed: 05/25/2023]
Abstract
Perception of vegetation proximity or plant shade informs of potential competition for resources by the neighboring vegetation. As vegetation proximity impacts on both light quantity and quality, perception of this cue by plant photoreceptors reprograms development to result in responses that allow plants to compete with the neighboring vegetation. Developmental reprogramming involves massive and rapid changes in gene expression, with the concerted action of photoreceptors and downstream transcription factors. Changes in gene expression can be modulated by epigenetic processes that alter chromatin compaction, influencing the accessibility and binding of transcription factors to regulatory elements in the DNA. However, little is known about the epigenetic regulation of plant responses to the proximity of other plants. In this manuscript, we review what is known about plant shade effects on chromatin changes at the cytological level, that is, changes in nuclear morphology and high order chromatin density. We address which are the specific histone post-transcriptional modifications that have been associated with changes in shade-regulated gene expression, such as histone acetylation and histone methylation. Furthermore, we explore the possible mechanisms that integrate shade signaling components and chromatin remodelers to settle epigenetic marks at specific loci. This review aims to be a starting point to understand how a specific environmental cue, plant shade, integrates with chromatin dynamics to implement the proper acclimation responses.
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Affiliation(s)
- Jaime F Martínez-García
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, Barcelona, 08193, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain
| | - Jordi Moreno-Romero
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Cerdanyola del Vallès, Barcelona, 08193, Spain
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Teif VB, Gould TJ, Clarkson CT, Boyd L, Antwi EB, Ishaque N, Olins AL, Olins DE. Linker histone epitopes are hidden by in situ higher-order chromatin structure. Epigenetics Chromatin 2020; 13:26. [PMID: 32505195 PMCID: PMC7276084 DOI: 10.1186/s13072-020-00345-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 05/13/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone H1 is the most mobile histone in the cell nucleus. Defining the positions of H1 on chromatin in situ, therefore, represents a challenge. Immunoprecipitation of formaldehyde-fixed and sonicated chromatin, followed by DNA sequencing (xChIP-seq), is traditionally the method for mapping histones onto DNA elements. But since sonication fragmentation precedes ChIP, there is a consequent loss of information about chromatin higher-order structure. Here, we present a new method, xxChIP-seq, employing antibody binding to fixed intact in situ chromatin, followed by extensive washing, a second fixation, sonication and immunoprecipitation. The second fixation is intended to prevent the loss of specifically bound antibody during washing and subsequent sonication and to prevent antibody shifting to epitopes revealed by the sonication process. In many respects, xxChIP-seq is comparable to immunostaining microscopy, which also involves interaction of the primary antibody with fixed and permeabilized intact cells. The only epitopes displayed after immunostaining are the "exposed" epitopes, not "hidden" by the fixation of chromatin higher-order structure. Comparison of immunoprecipitated fragments between xChIP-seq versus xxChIP-seq should indicate which epitopes become inaccessible with fixation and identify their associated DNA elements. RESULTS We determined the genomic distribution of histone variants H1.2 and H1.5 in human myeloid leukemia cells HL-60/S4 and compared their epitope exposure by both xChIP-seq and xxChIP-seq, as well as high-resolution microscopy, illustrating the influences of preserved chromatin higher-order structure in situ. We found that xChIP and xxChIP H1 signals are in general negatively correlated, with differences being more pronounced near active regulatory regions. Among the intriguing observations, we find that transcription-related regions and histone PTMs (i.e., enhancers, promoters, CpG islands, H3K4me1, H3K4me3, H3K9ac, H3K27ac and H3K36me3) exhibit significant deficiencies (depletions) in H1.2 and H1.5 xxChIP-seq reads, compared to xChIP-seq. These observations suggest the existence of in situ transcription-related chromatin higher-order structures stabilized by formaldehyde. CONCLUSION Comparison of H1 xxChIP-seq to H1 xChIP-seq allows the development of hypotheses on the chromosomal localization of (stabilized) higher-order structure, indicated by the generation of "hidden" H1 epitopes following formaldehyde crosslinking. Changes in H1 epitope exposure surrounding averaged chromosomal binding sites or epigenetic modifications can also indicate whether these sites have chromatin higher-order structure. For example, comparison between averaged active or inactive promoter regions suggests that both regions can acquire stabilized higher-order structure with hidden H1 epitopes. However, the H1 xChIP-seq comparison cannot define their differences. Application of the xxChIP-seq versus H1 xChIP-seq method is particularly relevant to chromatin-associated proteins, such as linker histones, that play dynamic roles in establishing chromatin higher-order structure.
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Affiliation(s)
- Vladimir B Teif
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester, CO4 3SQ, UK.
| | - Travis J Gould
- Department of Physics & Astronomy, Bates College, Lewiston, ME, USA
| | | | - Logan Boyd
- Department of Physics & Astronomy, Bates College, Lewiston, ME, USA.,StarBird Technologies, LLC, Brunswick, ME, USA
| | - Enoch B Antwi
- Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.,Molecular and Cellular Engineering, Centre for Biological Signalling Studies, University of Freiburg, Schänzlestraße 18, Freiburg im Breisgau, 79104 , Germany
| | - Naveed Ishaque
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Digital Health Centre, Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Str. 2, Berlin, 10178 , Germany
| | - Ada L Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME, 04103, USA
| | - Donald E Olins
- Department of Pharmaceutical Sciences, College of Pharmacy, University of New England, 716 Stevens Avenue, Portland, ME, 04103, USA.
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