1
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Wu J, Liu B, Dong A. Interplay between histone variants and chaperones in plants. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102551. [PMID: 38776573 DOI: 10.1016/j.pbi.2024.102551] [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: 03/18/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024]
Abstract
Histone chaperones and histone variants play crucial roles in DNA replication, gene transcription, and DNA repair in eukaryotes. Histone chaperones reversibly promote nucleosome assembly and disassembly by incorporating or evicting histones and histone variants to modulate chromatin accessibility, thereby altering the chromatin states and modulating DNA-related biological processes. Cofactors assist histone chaperones to target specific chromatin regions to regulate the exchange of histones and histone variants. In this review, we summarize recent progress in the interplay between histone variants and chaperones in plants. We discuss the structural basis of chaperone-histone complexes and the mechanisms of their cooperation in regulating gene transcription and plant development.
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Affiliation(s)
- Jiabing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, PR China; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, 200438, PR China
| | - Bing Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, PR China.
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2
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Baile F, Calonje M. Dynamics of polycomb group marks in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2024; 80:102553. [PMID: 38776572 DOI: 10.1016/j.pbi.2024.102553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/08/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
Polycomb Group (PcG) histone-modifying system is key in maintaining gene repression, providing a mitotically heritable cellular memory. Nevertheless, to allow plants to transition through distinct transcriptional programs during development or to respond to external cues, PcG-mediated repression requires reversibility. Several data suggest that the dynamics of PcG marks may vary considerably in different cell contexts; however, how PcG marks are established, maintained, or removed in each case is far from clear. In this review, we survey the knowns and unknowns of the molecular mechanisms underlying the maintenance or turnover of PcG marks in different cell stages.
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Affiliation(s)
- Fernando Baile
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092, Seville, Spain.
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3
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Mateo-Bonmatí E, Montez M, Maple R, Fiedler M, Fang X, Saalbach G, Passmore LA, Dean C. A CPF-like phosphatase module links transcription termination to chromatin silencing. Mol Cell 2024; 84:2272-2286.e7. [PMID: 38851185 DOI: 10.1016/j.molcel.2024.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 02/28/2024] [Accepted: 05/15/2024] [Indexed: 06/10/2024]
Abstract
The interconnections between co-transcriptional regulation, chromatin environment, and transcriptional output remain poorly understood. Here, we investigate the mechanism underlying RNA 3' processing-mediated Polycomb silencing of Arabidopsis FLOWERING LOCUS C (FLC). We show a requirement for ANTHESIS PROMOTING FACTOR 1 (APRF1), a homolog of yeast Swd2 and human WDR82, known to regulate RNA polymerase II (RNA Pol II) during transcription termination. APRF1 interacts with TYPE ONE SERINE/THREONINE PROTEIN PHOSPHATASE 4 (TOPP4) (yeast Glc7/human PP1) and LUMINIDEPENDENS (LD), the latter showing structural features found in Ref2/PNUTS, all components of the yeast and human phosphatase module of the CPF 3' end-processing machinery. LD has been shown to co-associate in vivo with the histone H3 K4 demethylase FLOWERING LOCUS D (FLD). This work shows how the APRF1/LD-mediated polyadenylation/termination process influences subsequent rounds of transcription by changing the local chromatin environment at FLC.
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Affiliation(s)
- Eduardo Mateo-Bonmatí
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)/CSIC, Pozuelo de Alarcón, Madrid 28223, Spain.
| | - Miguel Montez
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Robert Maple
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Marc Fiedler
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Xiaofeng Fang
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Gerhard Saalbach
- Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | | | - Caroline Dean
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
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4
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Franek M, Dadejová MN, Pírek P, Kryštofová K, Dobisová T, Zdráhal Z, Dvořáčková M, Lochmanová G. Histone chaperone deficiency in Arabidopsis plants triggers adaptive epigenetic changes in histone variants and modifications. Mol Cell Proteomics 2024:100795. [PMID: 38848995 DOI: 10.1016/j.mcpro.2024.100795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/14/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024] Open
Abstract
At the molecular scale, adaptive advantages during plant growth and development rely on modulation of gene expression, primarily provided by epigenetic machinery. One crucial part of this machinery is histone post-translational modifications (PTMs), which form a flexible system, driving transient changes in chromatin and defining particular epigenetic states. PTMs work in concert with replication-independent histone variants further adapted for transcriptional regulation and chromatin repair. However, little is known about how such complex regulatory pathways are orchestrated and interconnected in cells. In this work, we demonstrate the utility of mass spectrometry-based approaches to explore how different epigenetic layers interact in Arabidopsis mutants lacking certain histone chaperones. We show that defects in histone chaperone function (e.g., CAF-1 or NAP1 mutations) translate into an altered epigenetic landscape, which aids the plant in mitigating internal instability. We observe changes in both the levels and distribution of H2A.W.7, altogether with partial repurposing of H3.3 and changes in the key repressive (H3K27me1/2) or euchromatic marks (H3K36me1/2). These shifts in the epigenetic profile serve as a compensatory mechanism in response to impaired integration of the H3.1 histone in the fas1 mutants. Altogether, our findings suggest that maintaining genome stability involves a two-tiered approach. The first relies on flexible adjustments in histone marks, while the second level requires the assistance of chaperones for histone variant replacement.
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Affiliation(s)
- Michal Franek
- Mendel Center for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czech Republic
| | - Martina Nešpor Dadejová
- Mendel Center for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czech Republic
| | - Pavlína Pírek
- Mendel Center for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czech Republic
| | - Karolína Kryštofová
- Mendel Center for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Zbyněk Zdráhal
- Mendel Center for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martina Dvořáčková
- Mendel Center for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
| | - Gabriela Lochmanová
- Mendel Center for Plant Genomics and Proteomics, Central European Institute of Technology, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
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5
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Bergis-Ser C, Reji M, Latrasse D, Bergounioux C, Benhamed M, Raynaud C. Chromatin dynamics and RNA metabolism are double-edged swords for the maintenance of plant genome integrity. NATURE PLANTS 2024; 10:857-873. [PMID: 38658791 DOI: 10.1038/s41477-024-01678-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024]
Abstract
Maintenance of genome integrity is an essential process in all organisms. Mechanisms avoiding the formation of DNA lesions or mutations are well described in animals because of their relevance to human health and cancer. In plants, they are of growing interest because DNA damage accumulation is increasingly recognized as one of the consequences of stress. Although the cellular response to DNA damage is mostly studied in response to genotoxic treatments, the main source of DNA lesions is cellular activity itself. This can occur through the production of reactive oxygen species as well as DNA processing mechanisms such as DNA replication or transcription and chromatin dynamics. In addition, how lesions are formed and repaired is greatly influenced by chromatin features and dynamics and by DNA and RNA metabolism. Notably, actively transcribed regions or replicating DNA, because they are less condensed and are sites of DNA processing, are more exposed to DNA damage. However, at the same time, a wealth of cellular mechanisms cooperate to favour DNA repair at these genomic loci. These intricate relationships that shape the distribution of mutations along the genome have been studied extensively in animals but much less in plants. In this Review, we summarize how chromatin dynamics influence lesion formation and DNA repair in plants, providing a comprehensive view of current knowledge and highlighting open questions with regard to what is known in other organisms.
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Affiliation(s)
- Clara Bergis-Ser
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Meega Reji
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
- Indian Institute of Science Education and Research Thiruvananthapuram, Vithura, India
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Catherine Bergounioux
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France
- Université Paris Cité, Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette, France
- Institut Universitaire de France, Orsay, France
| | - Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Université d'Evry, Institute of Plant Sciences Paris-Saclay, Orsay, France.
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6
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Florez-Rueda AM, Miguel CM, Figueiredo DD. Comparative transcriptomics of seed nourishing tissues: uncovering conserved and divergent pathways in seed plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38709819 DOI: 10.1111/tpj.16786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/04/2024] [Accepted: 04/12/2024] [Indexed: 05/08/2024]
Abstract
The evolutionary and ecological success of spermatophytes is intrinsically linked to the seed habit, which provides a protective environment for the initial development of the new generation. This environment includes an ephemeral nourishing tissue that supports embryo growth. In gymnosperms this tissue originates from the asexual proliferation of the maternal megagametophyte, while in angiosperms it is a product of fertilization, and is called the endosperm. The emergence of these nourishing tissues is of profound evolutionary value, and they are also food staples for most of the world's population. Here, using Orthofinder to infer orthologue genes among newly generated and previously published datasets, we provide a comparative transcriptomic analysis of seed nourishing tissues from species of several angiosperm clades, including those of early diverging lineages, as well as of one gymnosperm. Our results show that, although the structure and composition of seed nourishing tissues has seen significant divergence along evolution, there are signatures that are conserved throughout the phylogeny. Conversely, we identified processes that are specific to species within the clades studied, and thus illustrate their functional divergence. With this, we aimed to provide a foundation for future studies on the evolutionary history of seed nourishing structures, as well as a resource for gene discovery in future functional studies.
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Affiliation(s)
- Ana Marcela Florez-Rueda
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
- University of Potsdam, Karl-Liebknechts-Str. 24-25, Haus 26, 14476, Potsdam, Germany
| | - Célia M Miguel
- Faculty of Sciences, Biosystems and Integrative Sciences Institute (BioISI), University of Lisbon, Lisboa, Portugal
| | - Duarte D Figueiredo
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Mühlenberg 1, 14476, Potsdam, Germany
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7
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Blanco-Touriñán N, Pérez-Alemany J, Bourbousse C, Latrasse D, Ait-Mohamed O, Benhamed M, Barneche F, Blázquez MA, Gallego-Bartolomé J, Alabadí D. The plant POLYMERASE-ASSOCIATED FACTOR1 complex links transcription and H2B monoubiquitination genome wide. PLANT PHYSIOLOGY 2024; 195:640-651. [PMID: 38285074 PMCID: PMC11060679 DOI: 10.1093/plphys/kiae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/30/2024]
Abstract
The evolutionarily conserved POLYMERASE-ASSOCIATED FACTOR1 complex (Paf1C) participates in transcription, and research in animals and fungi suggests that it facilitates RNA POLYMERASE II (RNAPII) progression through chromatin. We examined the genomic distribution of the EARLY FLOWERING7 (ELF7) and VERNALIZATION INDEPENDENCE3 subunits of Paf1C in Arabidopsis (Arabidopsis thaliana). The occupancy of both subunits was confined to thousands of gene bodies and positively associated with RNAPII occupancy and the level of gene expression, supporting a role as a transcription elongation factor. We found that monoubiquitinated histone H2B, which marks most transcribed genes, was strongly reduced genome wide in elf7 seedlings. Genome-wide profiling of RNAPII revealed that in elf7 mutants, RNAPII occupancy was reduced throughout the gene body and at the transcription end site of Paf1C-targeted genes, suggesting a direct role for the complex in transcription elongation. Overall, our observations suggest a direct functional link between Paf1C activity, monoubiquitination of histone H2B, and the transition of RNAPII to productive elongation. However, for several genes, Paf1C may also act independently of H2Bub deposition or occupy these genes more stable than H2Bub marking, possibly reflecting the dynamic nature of Paf1C association and H2Bub turnover during transcription.
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Affiliation(s)
- Noel Blanco-Touriñán
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain
| | - Jaime Pérez-Alemany
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain
| | - Clara Bourbousse
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (CNRS), CNRS, INSERM, Université PSL, 75230 Paris, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (Université Paris-Saclay-CNRS), 91190 Gif-sur-Yvette, France
| | - Ouardia Ait-Mohamed
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (CNRS), CNRS, INSERM, Université PSL, 75230 Paris, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (Université Paris-Saclay-CNRS), 91190 Gif-sur-Yvette, France
| | - Fredy Barneche
- Ecole Normale Supérieure, Institut de Biologie de l'Ecole Normale Supérieure (CNRS), CNRS, INSERM, Université PSL, 75230 Paris, France
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain
| | | | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), 46022 Valencia, Spain
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8
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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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9
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Liu Y, Zhang Z, Hu H, Chen W, Zhang F, Wang Q, Wang C, Yan K, Du J. Molecular basis of chromatin remodelling by DDM1 involved in plant DNA methylation. NATURE PLANTS 2024; 10:374-380. [PMID: 38413824 DOI: 10.1038/s41477-024-01640-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/31/2024] [Indexed: 02/29/2024]
Abstract
Eukaryotic gene regulation occurs at the chromatin level, which requires changing the chromatin structure by a group of ATP-dependent DNA translocases-namely, the chromatin remodellers1. In plants, chromatin remodellers function in various biological processes and possess both conserved and plant-specific components2-5. DECREASE IN DNA METHYLATION 1 (DDM1) is a plant chromatin remodeller that plays a key role in the maintenance DNA methylation6-11. Here we determined the structures of Arabidopsis DDM1 in complex with nucleosome in ADP-BeFx-bound, ADP-bound and nucleotide-free conformations. We show that DDM1 specifically recognizes the H4 tail and nucleosomal DNA. The conformational differences between ADP-BeFx-bound, ADP-bound and nucleotide-free DDM1 suggest a chromatin remodelling cycle coupled to ATP binding, hydrolysis and ADP release. This, in turn, triggers conformational changes in the DDM1-bound nucleosomal DNA, which alters the nucleosome structure and promotes DNA sliding. Together, our data reveal the molecular basis of chromatin remodelling by DDM1.
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Affiliation(s)
- Yue Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Zhihui Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Hongmiao Hu
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Wei Chen
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fan Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Qian Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Changshi Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Kaige Yan
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China.
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China.
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10
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Roces V, Guerrero S, Álvarez A, Pascual J, Meijón M. PlantFUNCO: Integrative Functional Genomics Database Reveals Clues into Duplicates Divergence Evolution. Mol Biol Evol 2024; 41:msae042. [PMID: 38411627 PMCID: PMC10917205 DOI: 10.1093/molbev/msae042] [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: 09/06/2023] [Revised: 02/08/2024] [Accepted: 02/16/2024] [Indexed: 02/28/2024] Open
Abstract
Evolutionary epigenomics and, more generally, evolutionary functional genomics, are emerging fields that study how non-DNA-encoded alterations in gene expression regulation are an important form of plasticity and adaptation. Previous evidence analyzing plants' comparative functional genomics has mostly focused on comparing same assay-matched experiments, missing the power of heterogeneous datasets for conservation inference. To fill this gap, we developed PlantFUN(ctional)CO(nservation) database, which is constituted by several tools and two main resources: interspecies chromatin states and functional genomics conservation scores, presented and analyzed in this work for three well-established plant models (Arabidopsis thaliana, Oryza sativa, and Zea mays). Overall, PlantFUNCO elucidated evolutionary information in terms of cross-species functional agreement. Therefore, providing a new complementary comparative-genomics source for assessing evolutionary studies. To illustrate the potential applications of this database, we replicated two previously published models predicting genetic redundancy in A. thaliana and found that chromatin states are a determinant of paralogs degree of functional divergence. These predictions were validated based on the phenotypes of mitochondrial alternative oxidase knockout mutants under two different stressors. Taking all the above into account, PlantFUNCO aim to leverage data diversity and extrapolate molecular mechanisms findings from different model organisms to determine the extent of functional conservation, thus, deepening our understanding of how plants epigenome and functional noncoding genome have evolved. PlantFUNCO is available at https://rocesv.github.io/PlantFUNCO.
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Affiliation(s)
- Víctor Roces
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of Asturias, University of Oviedo, Asturias, Spain
| | - Sara Guerrero
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of Asturias, University of Oviedo, Asturias, Spain
| | - Ana Álvarez
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of Asturias, University of Oviedo, Asturias, Spain
| | - Jesús Pascual
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of Asturias, University of Oviedo, Asturias, Spain
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of Asturias, University of Oviedo, Asturias, Spain
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11
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Chowdary KVSKA, Saini R, Singh AK. Epigenetic regulation during meiosis and crossover. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1945-1958. [PMID: 38222277 PMCID: PMC10784443 DOI: 10.1007/s12298-023-01390-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/01/2023] [Accepted: 11/10/2023] [Indexed: 01/16/2024]
Abstract
Meiosis is a distinctive type of cell division that reorganizes genetic material between generations. The initial stages of meiosis consist of several crucial steps which include double strand break, homologous chromosome pairing, break repair and crossover. Crossover frequency varies depending on the position on the chromosome, higher at euchromatin region and rare at heterochromatin, centromeres, telomeres and ribosomal DNA. Crossover positioning is dependent on various factors, especially epigenetic modifications. DNA methylation, histone post-translational modifications, histone variants and non-coding RNAs are most probably playing an important role in positioning of crossovers on a chromosomal level as well as hotspot level. DNA methylation negatively regulates crossover frequency and its effect is visible in centromeres, pericentromeres and heterochromatin regions. Pericentromeric chromatin and heterochromatin mark studies have been a centre of attraction in meiosis. Crossover hotspots are associated with euchromatin regions having specific chromatin modifications such as H3K4me3, H2A.Z. and H3 acetylation. This review will provide the current understanding of the epigenetic role in plants during meiotic recombination, chromosome synapsis, double strand break and hotspots with special attention to euchromatin and heterochromatin marks. Further, the role of epigenetic modifications in regulating meiosis and crossover in other organisms is also discussed.
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Affiliation(s)
- K. V. S. K. Arjun Chowdary
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Ramswaroop Saini
- Department of Biotechnology, Joy University, Vadakangulam, Tirunelveli, Tamil Nadu 627116 India
| | - Amit Kumar Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
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12
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Murphy PJ, Berger F. The chromatin source-sink hypothesis: a shared mode of chromatin-mediated regulations. Development 2023; 150:dev201989. [PMID: 38771301 PMCID: PMC10629678 DOI: 10.1242/dev.201989] [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: 05/13/2023] [Accepted: 09/12/2023] [Indexed: 11/05/2023]
Abstract
We propose that several chromatin-mediated regulatory processes are dominated by source-sink relationships in which factors operate as 'sources' to produce or provide a resource and compete with each other to occupy separate 'sinks'. In this model, large portions of genomic DNA operate as 'sinks', which are filled by 'sources', such as available histone variants, covalent modifications to histones, the readers of these modifications and non-coding RNAs. Competing occupation for the sinks by different sources leads to distinct states of genomic equilibrium in differentiated cells. During dynamic developmental events, such as sexual reproduction, we propose that dramatic and rapid reconfiguration of source-sink relationships modifies chromatin states. We envision that re-routing of sources could occur by altering the dimensions of the sink, by reconfiguration of existing sink occupation or by varying the size of the source, providing a central mechanism to explain a plethora of epigenetic phenomena, which contribute to phenotypic variegation, zygotic genome activation and nucleolar dominance.
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Affiliation(s)
- Patrick J. Murphy
- University of Rochester, Department of Biomedical Genetics and Department of Biology, 601 Elmwood Ave., Rochester NY 14620, USA
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter; Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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Meng FW, Murphy KE, Makowski CE, Delatte B, Murphy PJ. Competition for H2A.Z underlies the developmental impacts of repetitive element de-repression. Development 2023; 150:dev202338. [PMID: 37938830 PMCID: PMC10651094 DOI: 10.1242/dev.202338] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/10/2023] [Indexed: 11/10/2023]
Abstract
The histone variant H2A.Z is central to early embryonic development, determining transcriptional competency through chromatin regulation of gene promoters and enhancers. In addition to genic loci, we find that H2A.Z resides at a subset of evolutionarily young repetitive elements, including DNA transposons, long interspersed nuclear elements and long terminal repeats, during early zebrafish development. Moreover, increases in H2A.Z occur when repetitive elements become transcriptionally active. Acquisition of H2A.Z corresponds with a reduction in the levels of the repressive histone modification H3K9me3 and a moderate increase in chromatin accessibility. Notably, however, de-repression of repetitive elements also leads to a significant reduction in H2A.Z over non-repetitive genic loci. Genic loss of H2A.Z is accompanied by transcriptional silencing at adjacent coding sequences, but remarkably, these impacts are mitigated by augmentation of total H2A.Z protein via transgenic overexpression. Our study reveals that levels of H2A.Z protein determine embryonic sensitivity to de-repression of repetitive elements, that repetitive elements can function as a nuclear sink for epigenetic factors and that competition for H2A.Z greatly influences overall transcriptional output during development. These findings uncover general mechanisms in which counteractive biological processes underlie phenotypic outcomes.
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Affiliation(s)
- Fanju W. Meng
- University of Rochester Medical Center, Rochester, NY 14642, USA
| | | | | | - Benjamin Delatte
- Advanced Research Laboratory, Active Motif, 1914 Palomar Oaks Way STE 150, Carlsbad, CA 92008, USA
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Melters DP, Neuman KC, Bentahar RS, Rakshit T, Dalal Y. Single molecule analysis of CENP-A chromatin by high-speed atomic force microscopy. eLife 2023; 12:e86709. [PMID: 37728600 PMCID: PMC10511241 DOI: 10.7554/elife.86709] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/01/2023] [Indexed: 09/21/2023] Open
Abstract
Chromatin accessibility is modulated in a variety of ways to create open and closed chromatin states, both of which are critical for eukaryotic gene regulation. At the single molecule level, how accessibility is regulated of the chromatin fiber composed of canonical or variant nucleosomes is a fundamental question in the field. Here, we developed a single-molecule tracking method where we could analyze thousands of canonical H3 and centromeric variant nucleosomes imaged by high-speed atomic force microscopy. This approach allowed us to investigate how changes in nucleosome dynamics in vitro inform us about transcriptional potential in vivo. By high-speed atomic force microscopy, we tracked chromatin dynamics in real time and determined the mean square displacement and diffusion constant for the variant centromeric CENP-A nucleosome. Furthermore, we found that an essential kinetochore protein CENP-C reduces the diffusion constant and mobility of centromeric nucleosomes along the chromatin fiber. We subsequently interrogated how CENP-C modulates CENP-A chromatin dynamics in vivo. Overexpressing CENP-C resulted in reduced centromeric transcription and impaired loading of new CENP-A molecules. From these data, we speculate that factors altering nucleosome mobility in vitro, also correspondingly alter transcription in vivo. Subsequently, we propose a model in which variant nucleosomes encode their own diffusion kinetics and mobility, and where binding partners can suppress or enhance nucleosome mobility.
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Affiliation(s)
- Daniël P Melters
- National Cancer Institute, Center for Cancer Research, Laboratory Receptor Biology and Gene ExpressionBethesdaUnited States
| | - Keir C Neuman
- National Heart, Lung, and Blood Institute, Laboratory of Single Molecule BiophysicsBethesdaUnited States
| | - Reda S Bentahar
- National Cancer Institute, Center for Cancer Research, Laboratory Receptor Biology and Gene ExpressionBethesdaUnited States
| | - Tatini Rakshit
- National Cancer Institute, Center for Cancer Research, Laboratory Receptor Biology and Gene ExpressionBethesdaUnited States
- Department of Chemistry, Shiv Nadar UniversityDadriIndia
| | - Yamini Dalal
- National Cancer Institute, Center for Cancer Research, Laboratory Receptor Biology and Gene ExpressionBethesdaUnited States
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