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Franek M, Nešpor Dadejová M, 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; 23:100795. [PMID: 38848995 PMCID: PMC11263794 DOI: 10.1016/j.mcpro.2024.100795] [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: 01/11/2024] [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 posttranslational modifications, which form a flexible system, driving transient changes in chromatin, and defining particular epigenetic states. Posttranslational modifications 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., chromatin assembly factor-1 or nucleosome assembly protein 1 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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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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Corcoran ET, Jacob Y. Direct assessment of histone function using histone replacement. Trends Biochem Sci 2023; 48:53-70. [PMID: 35853806 PMCID: PMC9789166 DOI: 10.1016/j.tibs.2022.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 02/09/2023]
Abstract
Histones serve many purposes in eukaryotic cells in the regulation of diverse genomic processes, including transcription, replication, DNA repair, and chromatin organization. As such, experimental systems to assess histone function are fundamental resources toward elucidating the regulation of activities occurring on chromatin. One set of important tools for investigating histone function are histone replacement systems, in which endogenous histone expression can be partially or completely replaced with a mutant histone. Histone replacement systems allow systematic screens of histone regulatory functions and the direct assessment of functions for histone residues. In this review, we describe existing histone replacement systems in model organisms, the benefits and limitations of these systems, and opportunities for future research with histone replacement strategies.
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Affiliation(s)
- Emma Tung Corcoran
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CT 06511, USA
| | - Yannick Jacob
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CT 06511, USA.
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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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Affiliation(s)
| | - Bénédicte Desvoyes
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Programa de Dinámica y Función del Genoma, Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Programa de Dinámica y Función del Genoma, Madrid, Spain
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Osakabe A, Molaro A. Histone renegades: Unusual H2A histone variants in plants and animals. Semin Cell Dev Biol 2022; 135:35-42. [PMID: 35570098 DOI: 10.1016/j.semcdb.2022.05.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/19/2022] [Accepted: 05/04/2022] [Indexed: 12/27/2022]
Abstract
H2A variants are histones that carry out specialized nucleosome function during the eukaryote genome packaging. Most genes encoding H2A histone variants arose in the distant past, and have highly conserved domains and structures. Yet, novel H2A variants have continued to arise throughout the radiation of eukaryotes and disturbed the apparent tranquility of nucleosomes. These species-specific H2A variants contributed to the functional diversification of nucleosomes through changes in both their structure and expression patterns. In this short review, we discuss the evolutionary trajectories of these histone renegades in plants and animal genomes.
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Affiliation(s)
- Akihisa Osakabe
- Laboratory of Genetics, Department of Biological Sciences, The University of Tokyo, Tokyo, Japan; Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan.
| | - Antoine Molaro
- Genetics, Reproduction & Development Institute (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France.
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Jiménez-Castilla L, Marín-Royo G, Orejudo M, Opazo-Ríos L, Caro-Ordieres T, Artaiz I, Suárez-Cortés T, Zazpe A, Hernández G, Gómez-Guerrero C, Egido J. Nephroprotective Effects of Synthetic Flavonoid Hidrosmin in Experimental Diabetic Nephropathy. Antioxidants (Basel) 2021; 10:1920. [PMID: 34943023 PMCID: PMC8750193 DOI: 10.3390/antiox10121920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/22/2021] [Accepted: 11/26/2021] [Indexed: 12/29/2022] Open
Abstract
Diabetes mellitus (DM) is a high-impact disease commonly characterized by hyperglycemia, inflammation, and oxidative stress. Diabetic nephropathy (DN) is a common diabetic microvascular complication and the leading cause of chronic kidney disease worldwide. This study investigates the protective effects of the synthetic flavonoid hidrosmin (5-O-(beta-hydroxyethyl) diosmin) in experimental DN induced by streptozotocin injection in apolipoprotein E deficient mice. Oral administration of hidrosmin (300 mg/kg/day, n = 11) to diabetic mice for 7 weeks markedly reduced albuminuria (albumin-to-creatinine ratio: 47 ± 11% vs. control) and ameliorated renal pathological damage and expression of kidney injury markers. Kidneys of hidrosmin-treated mice exhibited lower content of macrophages and T cells, reduced expression of cytokines and chemokines, and attenuated inflammatory signaling pathways. Hidrosmin treatment improved the redox balance by reducing prooxidant enzymes and enhancing antioxidant genes, and also decreased senescence markers in diabetic kidneys. In vitro, hidrosmin dose-dependently reduced the expression of inflammatory and oxidative genes in tubuloepithelial cells exposed to either high-glucose or cytokines, with no evidence of cytotoxicity at effective concentrations. In conclusion, the synthetic flavonoid hidrosmin exerts a beneficial effect against DN by reducing inflammation, oxidative stress, and senescence pathways. Hidrosmin could have a potential role as a coadjutant therapy for the chronic complications of DM.
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Affiliation(s)
- Luna Jiménez-Castilla
- Renal, Vascular and Diabetes Research Laboratory, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (L.J.-C.); (G.M.-R.); (M.O.); (J.E.)
- Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain
| | - Gema Marín-Royo
- Renal, Vascular and Diabetes Research Laboratory, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (L.J.-C.); (G.M.-R.); (M.O.); (J.E.)
| | - Macarena Orejudo
- Renal, Vascular and Diabetes Research Laboratory, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (L.J.-C.); (G.M.-R.); (M.O.); (J.E.)
| | - Lucas Opazo-Ríos
- Renal, Vascular and Diabetes Research Laboratory, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (L.J.-C.); (G.M.-R.); (M.O.); (J.E.)
| | - Teresa Caro-Ordieres
- Department of Research, Development, and Innovation, FAES Farma, 48940 Leioa, Spain; (T.C.-O.); (I.A.); (T.S.-C.); (A.Z.); (G.H.)
| | - Inés Artaiz
- Department of Research, Development, and Innovation, FAES Farma, 48940 Leioa, Spain; (T.C.-O.); (I.A.); (T.S.-C.); (A.Z.); (G.H.)
| | - Tatiana Suárez-Cortés
- Department of Research, Development, and Innovation, FAES Farma, 48940 Leioa, Spain; (T.C.-O.); (I.A.); (T.S.-C.); (A.Z.); (G.H.)
| | - Arturo Zazpe
- Department of Research, Development, and Innovation, FAES Farma, 48940 Leioa, Spain; (T.C.-O.); (I.A.); (T.S.-C.); (A.Z.); (G.H.)
| | - Gonzalo Hernández
- Department of Research, Development, and Innovation, FAES Farma, 48940 Leioa, Spain; (T.C.-O.); (I.A.); (T.S.-C.); (A.Z.); (G.H.)
| | - Carmen Gómez-Guerrero
- Renal, Vascular and Diabetes Research Laboratory, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (L.J.-C.); (G.M.-R.); (M.O.); (J.E.)
- Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain
| | - Jesús Egido
- Renal, Vascular and Diabetes Research Laboratory, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (L.J.-C.); (G.M.-R.); (M.O.); (J.E.)
- Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), 28029 Madrid, Spain
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