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Wang W, Sung S. Chromatin sensing: integration of environmental signals to reprogram plant development through chromatin regulators. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4332-4345. [PMID: 38436409 PMCID: PMC11263488 DOI: 10.1093/jxb/erae086] [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: 12/19/2023] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Chromatin regulation in eukaryotes plays pivotal roles in controlling the developmental regulatory gene network. This review explores the intricate interplay between chromatin regulators and environmental signals, elucidating their roles in shaping plant development. As sessile organisms, plants have evolved sophisticated mechanisms to perceive and respond to environmental cues, orchestrating developmental programs that ensure adaptability and survival. A central aspect of this dynamic response lies in the modulation of versatile gene regulatory networks, mediated in part by various chromatin regulators. Here, we summarized current understanding of the molecular mechanisms through which chromatin regulators integrate environmental signals, influencing key aspects of plant development.
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Affiliation(s)
- Wenli Wang
- Department of Molecular Biosciences, The University of Texas at Austin, TX 78712, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, TX 78712, USA
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2
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Ohm H, Åstrand J, Ceplitis A, Bengtsson D, Hammenhag C, Chawade A, Grimberg Å. Novel SNP markers for flowering and seed quality traits in faba bean ( Vicia faba L.): characterization and GWAS of a diversity panel. FRONTIERS IN PLANT SCIENCE 2024; 15:1348014. [PMID: 38510437 PMCID: PMC10950902 DOI: 10.3389/fpls.2024.1348014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
Faba bean (Vicia faba L.) is a legume crop grown in diverse climates worldwide. It has a high potential for increased cultivation to meet the need for more plant-based proteins in human diets, a prerequisite for a more sustainable food production system. Characterization of diversity panels of crops can identify variation in and genetic markers for target traits of interest for plant breeding. In this work, we collected a diversity panel of 220 accessions of faba bean from around the world consisting of gene bank material and commercially available cultivars. The aims of this study were to quantify the phenotypic diversity in target traits to analyze the impact of breeding on these traits, and to identify genetic markers associated with traits through a genome-wide association study (GWAS). Characterization under field conditions at Nordic latitude across two years revealed a large genotypic variation and high broad-sense heritability for eleven agronomic and seed quality traits. Pairwise correlations showed that seed yield was positively correlated to plant height, number of seeds per plant, and days to maturity. Further, susceptibility to bean weevil damage was significantly higher for early flowering accessions and accessions with larger seeds. In this study, no yield penalty was found for higher seed protein content, but protein content was negatively correlated to starch content. Our results showed that while breeding advances in faba bean germplasm have resulted in increased yields and number of seeds per plant, they have also led to a selection pressure towards delayed onset of flowering and maturity. DArTseq genotyping identified 6,606 single nucleotide polymorphisms (SNPs) by alignment to the faba bean reference genome. These SNPs were used in a GWAS, revealing 51 novel SNP markers significantly associated with ten of the assessed traits. Three markers for days to flowering were found in predicted genes encoding proteins for which homologs in other plant species regulate flowering. Altogether, this work enriches the growing pool of phenotypic and genotypic data on faba bean as a valuable resource for developing efficient breeding strategies to expand crop cultivation.
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Affiliation(s)
- Hannah Ohm
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
| | - Johanna Åstrand
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
- Lantmännen Agriculture, Plant Breeding, Svalöv, Sweden
| | - Alf Ceplitis
- Lantmännen Agriculture, Plant Breeding, Svalöv, Sweden
| | | | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
| | - Åsa Grimberg
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
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3
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Yin C, Sun A, Zhou Y, Liu K, Wang P, Ye W, Fang Y. The dynamics of Arabidopsis H2A.Z on SMALL AUXIN UP RNAs regulates abscisic acid-auxin signaling crosstalk. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad131. [PMID: 37022978 DOI: 10.1093/jxb/erad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Indexed: 06/19/2023]
Abstract
Extreme environmental changes threaten plant survival and worldwide food production. In response to osmotic stresses, plant hormone ABA activates stress responses and restricts plant growth. However, the epigenetic regulation of the ABA signaling and ABA-auxin crosstalk are not well known. Here we report that the histone variant H2A.Z knockdown mutant in Arabidopsis Col-0 ecotype, h2a.z-kd, has altered ABA signaling and stress performances. RNA-sequencing data showed that a majority of stress related genes are activated in h2a.z-kd. In addition, we revealed that ABA directly promotes the deposition of H2A.Z on SMALL AUXIN UP RNAs (SAURs), which is involved in ABA-repressed SAUR expression. Moreover, we found that ABA represses the transcription of H2A.Z genes through suppressing ARF7/19-HB22/25 module. Our results shed light on a dynamic and reciprocal regulation hub through H2A.Z deposition on SAURs and ARF7/19-HB22/25-mediated H2A.Z transcription to integrate ABA/auxin signaling and regulate stress responses in Arabidopsis.
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Affiliation(s)
- Chunmei Yin
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Aiqing Sun
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ying Zhou
- National key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Kunpeng Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Pan Wang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wenjing Ye
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuda Fang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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4
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Huang Y, Cai W, Lu Q, Lv J, Wan M, Guan D, Yang S, He S. PMT6 Is Required for SWC4 in Positively Modulating Pepper Thermotolerance. Int J Mol Sci 2023; 24:ijms24054849. [PMID: 36902276 PMCID: PMC10003703 DOI: 10.3390/ijms24054849] [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: 01/14/2023] [Revised: 01/31/2023] [Accepted: 02/03/2023] [Indexed: 03/06/2023] Open
Abstract
High temperature stress (HTS), with growth and development impairment, is one of the most important abiotic stresses frequently encountered by plants, in particular solanacaes such as pepper, that mainly distribute in tropical and subtropical regions. Plants activate thermotolerance to cope with this stress; however, the underlying mechanism is currently not fully understood. SWC4, a shared component of SWR1- and NuA4 complexes implicated in chromatin remodeling, was previously found to be involved in the regulation of pepper thermotolerance, but the underlying mechanism remains poorly understood. Herein, PMT6, a putative methyltranferase was originally found to interact with SWC4 by co-immunoprecipitation (Co-IP)-combined LC/MS assay. This interaction was further confirmed by bimolecular fluorescent complimentary (BiFC) and Co-IP assay, and PMT6 was further found to confer SWC4 methylation. By virus-induced gene silencing, it was found that PMT6 silencing significantly reduced pepper basal thermotolerance and transcription of CaHSP24 and significantly reduced the enrichment of chromatin-activation-related H3K9ac, H4K5ac, and H3K4me3 in TSS of CaHSP24, which was previously found to be positively regulated by CaSWC4. By contrast, the overexpression of PMT6 significantly enhanced basal thermotolerance of pepper plants. All these data indicate that PMT6 acts as a positive regulator in pepper thermotolerance, likely by methylating SWC4.
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Affiliation(s)
- Yu Huang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiwei Cai
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiaoling Lu
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jingang Lv
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meiyun Wan
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Deyi Guan
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sheng Yang
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (S.Y.); (S.H.)
| | - Shuilin He
- Key Laboratory of Applied Genetics of Universities in Fujian Province, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Agricultural College, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (S.Y.); (S.H.)
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5
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Hayashi K, Alseekh S, Fernie AR. Genetic and epigenetic control of the plant metabolome. Proteomics 2023:e2200104. [PMID: 36781168 DOI: 10.1002/pmic.202200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023]
Abstract
Plant metabolites are mainly produced through chemical reactions catalysed by enzymes encoded in the genome. Mutations in enzyme-encoding or transcription factor-encoding genes can alter the metabolome by changing the enzyme's catalytic activity or abundance, respectively. Insertion of transposable elements into non-coding regions has also been reported to affect transcription and ultimately metabolite content. In addition to genetic mutations, transgenerational epigenetic variations have also been found to affect metabolic content by controlling the transcription of metabolism-related genes. However, the majority of cases reported so far, in which epigenetic mechanisms are associated with metabolism, are non-transgenerational, and are triggered by developmental signals or environmental stress. Although, accumulating research has provided evidence of strong genetic control of the metabolome, epigenetic control has been largely untouched. Here, we provide a review of the genetic and epigenetic control of metabolism with a focus on epigenetics. We discuss both transgenerational and non-transgenerational epigenetic marks regulating metabolism as well as prospects of the field of metabolic control where intricate interactions between genetics and epigenetics are involved.
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Affiliation(s)
- Koki Hayashi
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center for Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center for Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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6
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Parakkunnel R, Naik K B, Vanishree G, C S, Purru S, Bhaskar K U, Bhat KV, Kumar S. Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome. FRONTIERS IN PLANT SCIENCE 2022; 13:1076229. [PMID: 36618639 PMCID: PMC9817154 DOI: 10.3389/fpls.2022.1076229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Evolutionary dynamics of AP2/ERF and WRKY genes, the major components of defense response were studied extensively in the sesame pan-genome. Massive variation was observed for gene copy numbers, genome location, domain structure, exon-intron structure and protein parameters. In the pan-genome, 63% of AP2/ERF members were devoid of introns whereas >99% of WRKY genes contained multiple introns. AP2 subfamily was found to be micro-exon rich with the adjoining intronic sequences sharing sequence similarity to many stress-responsive and fatty acid metabolism genes. WRKY family included extensive multi-domain gene fusions where the additional domains significantly enhanced gene and exonic sizes as well as gene copy numbers. The fusion genes were found to have roles in acquired immunity, stress response, cell and membrane integrity as well as ROS signaling. The individual genomes shared extensive synteny and collinearity although ecological adaptation was evident among the Chinese and Indian accessions. Significant positive selection effects were noticed for both micro-exon and multi-domain genes. Splice variants with changes in acceptor, donor and branch sites were common and 6-7 splice variants were detected per gene. The study ascertained vital roles of lipid metabolism and chlorophyll biosynthesis in the defense response and stress signaling pathways. 60% of the studied genes localized in the nucleus while 20% preferred chloroplast. Unique cis-element distribution was noticed in the upstream promoter region with MYB and STRE in WRKY genes while MYC was present in the AP2/ERF genes. Intron-less genes exhibited great diversity in the promoter sequences wherein the predominance of dosage effect indicated variable gene expression levels. Mimicking the NBS-LRR genes, a chloroplast localized WRKY gene, Swetha_24868, with additional domains of chorismate mutase, cAMP and voltage-dependent potassium channel was found to act as a master regulator of defense signaling, triggering immunity and reducing ROS levels.
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Affiliation(s)
- Ramya Parakkunnel
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Bhojaraja Naik K
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Girimalla Vanishree
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Susmita C
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh, India
| | - Supriya Purru
- ICAR- National Academy of Agricultural Research Management, Hyderabad, Telengana, India
| | - Udaya Bhaskar K
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - KV. Bhat
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kumar
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh, India
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7
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Sun A, Yin C, Ma M, Zhou Y, Zheng X, Tu X, Fang Y. Feedback regulation of auxin signaling through the transcription of H2A.Z and deposition of H2A.Z to SMALL AUXIN UP RNAs in Arabidopsis. THE NEW PHYTOLOGIST 2022; 236:1721-1733. [PMID: 36017638 DOI: 10.1111/nph.18440] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Auxin is a critical phytohormone that is involved in the regulation of most plant growth and developmental responses. In particular, epigenetic mechanisms, like histone modifications and DNA methylation, were reported to affect auxin biosynthesis and transport. However, the involvement of other epigenetic factors, such as histone variant H2A.Z, in the auxin-related developmental regulation remains unclear. We report that the histone variant H2A.Z knockdown mutant in Arabidopsis Col-0 ecotype, h2a.z-kd, has more lateral roots and weak gravitational responses related to auxin-regulated growth performances. Further study revealed that auxin promotes the eviction of H2A.Z from the auxin-responsive genes SMALL AUXIN-UP RNAs (SAURs) to activate their transcriptions. We found that IAA promotes the transcription of H2A.Z genes through HOMEOBOX PROTEIN 22/25 (AtHB22/25) transcription factors which work as downstream targets of ARF7/19 in auxin signaling. Double mutant of hb22 hb25 showed similar lateral root and gravitropism phenotypes to h2a.z-kd. Our results shed light on a reciprocal regulation hub through INOSITOL AUXOTROPHY 80-mediated H2A.Z eviction and ARF7/19-HB22/25-mediated H2A.Z transcription to modulate the activation of SAURs and plant growth in Arabidopsis.
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Affiliation(s)
- Aiqing Sun
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunmei Yin
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Min Ma
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ying Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaoyun Zheng
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoyu Tu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuda Fang
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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8
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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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9
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Liu H, Able AJ, Able JA. Priming crops for the future: rewiring stress memory. TRENDS IN PLANT SCIENCE 2022; 27:699-716. [PMID: 34906381 DOI: 10.1016/j.tplants.2021.11.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 05/12/2023]
Abstract
The agricultural sector must produce resilient and climate-smart crops to meet the increasing needs of global food production. Recent advancements in elucidating the mechanistic basis of plant stress memory have provided new opportunities for crop improvement. Stress memory-coordinated changes at the organismal, cellular, and various omics levels prepare plants to be more responsive to reoccurring stress within or across generation(s). The exposure to a primary stress, or stress priming, can also elicit a beneficial impact when encountering a secondary abiotic or biotic stress through the convergence of synergistic signalling pathways, referred to as cross-stress tolerance. 'Rewired plants' with stress memory provide a new means to stimulate adaptable stress responses, safeguard crop reproduction, and engineer climate-smart crops for the future.
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Affiliation(s)
- Haipei Liu
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA 5064, Australia
| | - Amanda J Able
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA 5064, Australia
| | - Jason A Able
- School of Agriculture, Food & Wine, Waite Research Institute, The University of Adelaide, Urrbrae, SA 5064, Australia.
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10
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Blanco-Touriñán N, Esteve-Bruna D, Serrano-Mislata A, Esquinas-Ariza RM, Resentini F, Forment J, Carrasco-López C, Novella-Rausell C, Palacios-Abella A, Carrasco P, Salinas J, Blázquez MÁ, Alabadí D. A genetic approach reveals different modes of action of prefoldins. PLANT PHYSIOLOGY 2021; 187:1534-1550. [PMID: 34618031 PMCID: PMC8566299 DOI: 10.1093/plphys/kiab348] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/05/2021] [Indexed: 05/25/2023]
Abstract
The prefoldin complex (PFDc) was identified in humans as a co-chaperone of the cytosolic chaperonin T-COMPLEX PROTEIN RING COMPLEX (TRiC)/CHAPERONIN CONTAINING TCP-1 (CCT). PFDc is conserved in eukaryotes and is composed of subunits PFD1-6, and PFDc-TRiC/CCT folds actin and tubulins. PFDs also participate in a wide range of cellular processes, both in the cytoplasm and in the nucleus, and their malfunction causes developmental alterations and disease in animals and altered growth and environmental responses in yeast and plants. Genetic analyses in yeast indicate that not all of their functions require the canonical complex. The lack of systematic genetic analyses in plants and animals, however, makes it difficult to discern whether PFDs participate in a process as the canonical complex or in alternative configurations, which is necessary to understand their mode of action. To tackle this question, and on the premise that the canonical complex cannot be formed if one subunit is missing, we generated an Arabidopsis (Arabidopsis thaliana) mutant deficient in the six PFDs and compared various growth and environmental responses with those of the individual mutants. In this way, we demonstrate that the PFDc is required for seed germination, to delay flowering, or to respond to high salt stress or low temperature, whereas at least two PFDs redundantly attenuate the response to osmotic stress. A coexpression analysis of differentially expressed genes in the sextuple mutant identified several transcription factors, including ABA INSENSITIVE 5 (ABI5) and PHYTOCHROME-INTERACTING FACTOR 4, acting downstream of PFDs. Furthermore, the transcriptomic analysis allowed assigning additional roles for PFDs, for instance, in response to higher temperature.
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Affiliation(s)
- Noel Blanco-Touriñán
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
| | - David Esteve-Bruna
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
| | - Antonio Serrano-Mislata
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
| | - Rosa María Esquinas-Ariza
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
| | - Francesca Resentini
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20133 Milano, Italy
| | - Javier Forment
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
| | - Cristian Carrasco-López
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain
| | - Claudio Novella-Rausell
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
| | - Alberto Palacios-Abella
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
| | - Pedro Carrasco
- Departament de Bioquímica i Biologia Molecular, Universitat de València, 46100 Burjassot, Spain
| | - Julio Salinas
- Departamento de Biotecnología Microbiana y de Plantas, Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain
| | - Miguel Á Blázquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
| | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022 Valencia, Spain
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11
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Shang JY, Lu YJ, Cai XW, Su YN, Feng C, Li L, Chen S, He XJ. COMPASS functions as a module of the INO80 chromatin remodeling complex to mediate histone H3K4 methylation in Arabidopsis. THE PLANT CELL 2021; 33:3250-3271. [PMID: 34270751 PMCID: PMC8505878 DOI: 10.1093/plcell/koab187] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 07/11/2021] [Indexed: 05/26/2023]
Abstract
In the INO80 chromatin remodeling complex, all of the accessory subunits are assembled on the following three domains of INO80: N-terminal domain (NTD), HSA domain, and ATPase domain. Although the ATPase and HSA domains and their interacting accessory subunits are known to be responsible for chromatin remodeling, it is largely unknown how the accessory subunits that interact with the INO80 NTD regulate chromatin status. Here, we identify both conserved and nonconserved accessory subunits that interact with the three domains in the INO80 complex in Arabidopsis thaliana. While the accessory subunits that interact with all the three INO80 domains can mediate transcriptional repression, the INO80 NTD and the accessory subunits interact with it can contribute to transcriptional activation even when the ATPase domain is absent, suggesting that INO80 has an ATPase-independent role. A subclass of the COMPASS histone H3K4 methyltransferase complexes interact with the INO80 NTD in the INO80 complex and function together with the other accessory subunits that interact with the INO80 NTD, thereby facilitating H3K4 trimethylation and transcriptional activation. This study suggests that the opposite effects of the INO80 complex on transcription are required for the balance between vegetative growth and flowering under diverse environmental conditions.
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Affiliation(s)
| | | | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Chao Feng
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
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Banerjee S, Roy S. An insight into understanding the coupling between homologous recombination mediated DNA repair and chromatin remodeling mechanisms in plant genome: an update. Cell Cycle 2021; 20:1760-1784. [PMID: 34437813 DOI: 10.1080/15384101.2021.1966584] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Plants, with their obligatory immobility, are vastly exposed to a wide range of environmental agents and also various endogenous processes, which frequently cause damage to DNA and impose genotoxic stress. These factors subsequently increase genome instability, thus affecting plant growth and productivity. Therefore, to survive under frequent and extreme environmental stress conditions, plants have developed highly efficient and powerful defense mechanisms to repair the damages in the genome for maintaining genome stability. Such multi-dimensional signaling response, activated in presence of damage in the DNA, is collectively known as DNA Damage Response (DDR). DDR plays a crucial role in the remarkably efficient detection, signaling, and repair of damages in the genome for maintaining plant genome stability and normal growth responses. Like other highly advanced eukaryotic systems, chromatin dynamics play a key role in regulating cell cycle progression in plants through remarkable orchestration of environmental and developmental signals. The regulation of chromatin architecture and nucleosomal organization in DDR is mainly modulated by the ATP dependent chromatin remodelers (ACRs), chromatin modifiers, and histone chaperones. ACRs are mainly responsible for transcriptional regulation of several homologous recombination (HR) repair genes in plants under genotoxic stress. The HR-based repair of DNA damage has been considered as the most error-free mechanism of repair and represents one of the essential sources of genetic diversity and new allelic combinations in plants. The initiation of DDR signaling and DNA damage repair pathway requires recruitment of epigenetic modifiers for remodeling of the damaged chromatin while accumulating evidence has shown that chromatin remodeling and DDR share part of the similar signaling pathway through the altered epigenetic status of the associated chromatin region. In this review, we have integrated information to provide an overview on the association between chromatin remodeling mediated regulation of chromatin structure stability and DDR signaling in plants, with emphasis on the scope of the utilization of the available knowledge for the improvement of plant health and productivity.Abbreviation: ADH: Alcohol Dehydrogenase; AGO2: Argonaute 2; ARP: Actin-Related Protein; ASF:1- Anti-Silencing Function-1; ATM: Ataxia Telangiectasia Mutated; ATR: ATM and Rad3- Related; AtSWI3c: Arabidopsis thaliana Switch 3c; ATXR5: Arabidopsis Trithorax-Related5; ATXR6: Arabidopsis Trithorax-Related6; BER: Base Excision Repair; BRCA1: Breast Cancer Associated 1; BRM: BRAHMA; BRU1: BRUSHY1; CAF:1- Chromatin Assembly Factor-1; CHD: Chromodomain Helicase DNA; CHR5: Chromatin Remodeling Protein 5; CHR11/17: Chromatin Remodeling Protein 11/17; CIPK11- CBL- Interacting Protein Kinase 11; CLF: Curly Leaf; CMT3: Chromomethylase 3; COR15A: Cold Regulated 15A; COR47: Cold Regulated 47; CRISPR: Clustered Regulatory Interspaced Short Palindromic Repeats; DDM1: Decreased DNA Methylation1; DRR: DNA Repair and Recombination; DSBs: Double-Strand Breaks; DDR: DNA Damage Response; EXO1: Exonuclease 1; FAS1/2: Fasciata1/2; FACT: Facilitates Chromatin Transcription; FT: Flowering Locus T; GMI1: Gamma-Irradiation And Mitomycin C Induced 1; HAC1: Histone Acetyltransferase of the CBP Family 1; HAM1: Histone Acetyltransferase of the MYST Family 1; HAM2: Histone Acetyltransferase of the MYST Family 2; HAF1: Histone Acetyltransferase of the TAF Family 1; HAT: Histone Acetyl Transferase; HDA1: Histone Deacetylase 1; HDA6: Histone Deacetylase 6; HIRA: Histone Regulatory Homolog A; HR- Homologous recombination; HAS: Helicase SANT Associated; HSS: HAND-SLANT-SLIDE; ICE1: Inducer of CBF Expression 1; INO80: Inositol Requiring Mutant 80; ISW1: Imitation Switch 1; KIN1/2: Kinase 1 /2; MET1: Methyltransferase 1; MET2: Methyltransferase 2; MINU: MINUSCULE; MMS: Methyl Methane Sulfonate; MMS21: Methyl Methane Sulfonate Sensitivity 21; MRN: MRE11, RAD50 and NBS1; MSI1: Multicopy Suppressor Of Ira1; NAP1: Nucleosome Assembly Protein 1; NRP1/NRP2: NAP1-Related Protein; NER: Nucleotide Excision Repair; NHEJ: Non-Homologous End Joining; PARP1: Poly-ADP Ribose Polymerase; PIE1: Photoperiod Independent Early Flowering 1; PIKK: Phosphoinositide 3-Kinase-Like Kinase; PKL: PICKLE; PKR1/2: PICKLE Related 1/2; RAD: Radiation Sensitive Mutant; RD22: Responsive To Desiccation 22; RD29A: Responsive To Desiccation 29A; ROS: Reactive Oxygen Species; ROS1: Repressor of Silencing 1; RPA1E: Replication Protein A 1E; SANT: Swi3, Ada2, N-Cor and TFIIIB; SEP3: SEPALLATA3; SCC3: Sister Chromatid Cohesion Protein 3; SMC1: Structural Maintenance of Chromosomes Protein 1; SMC3: Structural Maintenance of Chromosomes Protein 3; SOG1: Suppressor of Gamma Response 1; SWC6: SWR1 Complex Subunit 6; SWR1: SWI2/SNF2-Related 1; SYD: SPLAYED; SMC5: Structural Maintenance of Chromosome 5; SWI/SNF: Switch/Sucrose Non-Fermentable; TALENs: Transcription Activators Like Effector Nucleases; TRRAP: Transformation/Transactivation Domain-Associated Protein; ZFNs: Zinc Finger Nucleases.
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Affiliation(s)
- Samrat Banerjee
- Department of Botany, UGC Centre for Advanced Studies, the University of Burdwan, Golapbag Campus, Burdwan, West Bengal, India
| | - Sujit Roy
- Department of Botany, UGC Centre for Advanced Studies, the University of Burdwan, Golapbag Campus, Burdwan, West Bengal, India
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Nie WF, Wang J. Actin-Related Protein 4 Interacts with PIE1 and Regulates Gene Expression in Arabidopsis. Genes (Basel) 2021; 12:genes12040520. [PMID: 33918349 PMCID: PMC8066076 DOI: 10.3390/genes12040520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/25/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022] Open
Abstract
As essential structural components of ATP-dependent chromatin-remodeling complex, the nucleolus-localized actin-related proteins (ARPs) play critical roles in many biological processes. Among them, ARP4 is identified as an integral subunit of chromatin remodeling complex SWR1, which is conserved in yeast, humans and plants. It was shown that RNAi mediated knock-down of Arabidopsisthaliana ARP4 (AtARP4) could affect plant development, specifically, leading to early flowering. However, so far, little is known about how ARP4 functions in the SWR1 complex in plant. Here, we identified a loss-of-function mutant of AtARP4 with a single nucleotide change from glycine to arginine, which had significantly smaller leaf size. The results from the split luciferase complementation imaging (LCI) and yeast two hybrid (Y2H) assays confirmed its physical interaction with the scaffold and catalytic subunit of SWR1 complex, photoperiod-independent early flowering 1 (PIE1). Furthermore, mutation of AtARP4 caused altered transcription response of hundreds of genes, in which the number of up-regulated differentially expressed genes (DEGs) was much larger than those down-regulated. Although most DEGs in atarp4 are related to plant defense and response to hormones such as salicylic acid, overall, it has less overlapping with other swr1 mutants and the hta9 hta11 double-mutant. In conclusion, our results reveal that AtARP4 is important for plant growth and such an effect is likely attributed to its repression on gene expression, typically at defense-related loci, thus providing some evidence for the coordination of plant growth and defense, while the regulatory patterns and mechanisms are distinctive from other SWR1 complex components.
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Costantini L, Moreno-Sanz P, Nwafor CC, Lorenzi S, Marrano A, Cristofolini F, Gottardini E, Raimondi S, Ruffa P, Gribaudo I, Schneider A, Grando MS. Somatic variants for seed and fruit set in grapevine. BMC PLANT BIOLOGY 2021; 21:135. [PMID: 33711928 PMCID: PMC7955655 DOI: 10.1186/s12870-021-02865-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Grapevine reproductive development has direct implications on yield. It also impacts on berry and wine quality by affecting traits like seedlessness, berry and bunch size, cluster compactness and berry skin to pulp ratio. Seasonal fluctuations in yield, fruit composition and wine attributes, which are largely driven by climatic factors, are major challenges for worldwide table grape and wine industry. Accordingly, a better understanding of reproductive processes such as gamete development, fertilization, seed and fruit set is of paramount relevance for managing yield and quality. With the aim of providing new insights into this field, we searched for clones with contrasting seed content in two germplasm collections. RESULTS We identified eight variant pairs that seemingly differ only in seed-related characteristics while showing identical genotype when tested with the GrapeReSeq_Illumina_20K_SNP_chip and several microsatellites. We performed multi-year observations on seed and fruit set deriving from different pollination treatments, with special emphasis on the pair composed by Sangiovese and its seedless variant locally named Corinto Nero. The pollen of Corinto Nero failed to germinate in vitro and gave poor berry set when used to pollinate other varieties. Most berries from both open- and cross-pollinated Corinto Nero inflorescences did not contain seeds. The genetic analysis of seedlings derived from occasional Corinto Nero normal seeds revealed that the few Corinto Nero functional gametes are mostly unreduced. Moreover, three genotypes, including Sangiovese and Corinto Nero, were unexpectedly found to develop fruits without pollen contribution and occasionally showed normal-like seeds. Five missense single nucleotide polymorphisms were identified between Corinto Nero and Sangiovese from transcriptomic data. CONCLUSIONS Our observations allowed us to attribute a seedlessness type to some variants for which it was not documented in the literature. Interestingly, the VvAGL11 mutation responsible for Sultanina stenospermocarpy was also discovered in a seedless mutant of Gouais Blanc. We suggest that Corinto Nero parthenocarpy is driven by pollen and/or embryo sac defects, and both events likely arise from meiotic anomalies. The single nucleotide polymorphisms identified between Sangiovese and Corinto Nero are suitable for testing as traceability markers for propagated material and as functional candidates for the seedless phenotype.
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Affiliation(s)
- Laura Costantini
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy.
| | - Paula Moreno-Sanz
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy
- Center Agriculture Food Environment (C3A), University of Trento, Via. E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Chinedu Charles Nwafor
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy
- Center for Plant Science Innovation & Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Silvia Lorenzi
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Annarita Marrano
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Fabiana Cristofolini
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Elena Gottardini
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Stefano Raimondi
- Institute for Sustainable Plant Protection - Research Council of Italy, Largo P. Braccini 2, 10095, Grugliasco, Italy
| | - Paola Ruffa
- Institute for Sustainable Plant Protection - Research Council of Italy, Largo P. Braccini 2, 10095, Grugliasco, Italy
| | - Ivana Gribaudo
- Institute for Sustainable Plant Protection - Research Council of Italy, Largo P. Braccini 2, 10095, Grugliasco, Italy
| | - Anna Schneider
- Institute for Sustainable Plant Protection - Research Council of Italy, Largo P. Braccini 2, 10095, Grugliasco, Italy
| | - Maria Stella Grando
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010, San Michele all'Adige, Italy
- Center Agriculture Food Environment (C3A), University of Trento, Via. E. Mach 1, 38010, San Michele all'Adige, Italy
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Neve B, Jonckheere N, Vincent A, Van Seuningen I. Long non-coding RNAs: the tentacles of chromatin remodeler complexes. Cell Mol Life Sci 2021; 78:1139-1161. [PMID: 33001247 PMCID: PMC11072783 DOI: 10.1007/s00018-020-03646-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/01/2020] [Accepted: 09/12/2020] [Indexed: 02/07/2023]
Abstract
Chromatin remodeler complexes regulate gene transcription, DNA replication and DNA repair by changing both nucleosome position and post-translational modifications. The chromatin remodeler complexes are categorized into four families: the SWI/SNF, INO80/SWR1, ISWI and CHD family. In this review, we describe the subunits of these chromatin remodeler complexes, in particular, the recently identified members of the ISWI family and novelties of the CHD family. Long non-coding (lnc) RNAs regulate gene expression through different epigenetic mechanisms, including interaction with chromatin remodelers. For example, interaction of lncBRM with BRM inhibits the SWI/SNF complex associated with a differentiated phenotype and favors assembly of a stem cell-related SWI/SNF complex. Today, over 50 lncRNAs have been shown to affect chromatin remodeler complexes and we here discuss the mechanisms involved.
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Affiliation(s)
- Bernadette Neve
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France.
| | - Nicolas Jonckheere
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
| | - Audrey Vincent
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
| | - Isabelle Van Seuningen
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
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Du K, Luo Q, Yin L, Wu J, Liu Y, Gan J, Dong A, Shen WH. OsChz1 acts as a histone chaperone in modulating chromatin organization and genome function in rice. Nat Commun 2020; 11:5717. [PMID: 33177521 PMCID: PMC7658359 DOI: 10.1038/s41467-020-19586-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023] Open
Abstract
While the yeast Chz1 acts as a specific histone-chaperone for H2A.Z, functions of CHZ-domain proteins in multicellular eukaryotes remain obscure. Here, we report on the functional characterization of OsChz1, a sole CHZ-domain protein identified in rice. OsChz1 interacts with both the canonical H2A-H2B dimer and the variant H2A.Z-H2B dimer. Within crystal structure the C-terminal region of OsChz1 binds H2A-H2B via an acidic region, pointing to a previously unknown recognition mechanism. Knockout of OsChz1 leads to multiple plant developmental defects. At genome-wide level, loss of OsChz1 causes mis-regulations of thousands of genes and broad alterations of nucleosome occupancy as well as reductions of H2A.Z-enrichment. While OsChz1 associates with chromatin regions enriched of repressive histone marks (H3K27me3 and H3K4me2), its loss does not affect the genome landscape of DNA methylation. Taken together, it is emerging that OsChz1 functions as an important H2A/H2A.Z-H2B chaperone in dynamic regulation of chromatin for higher eukaryote development. Function of CHZ-domain proteins in multicellular eukaryotes remains unclear. Here, the authors characterize the sole CHZ-domain protein identified in rice and show that it functions as an H2A/H2A.Z-H2B chaperone in dynamic regulation of chromatin organization and genome function.
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Affiliation(s)
- Kangxi Du
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qiang Luo
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Liufan Yin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jiabing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yuhao Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jianhua Gan
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Aiwu Dong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Wen-Hui Shen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China. .,Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg, Cédex, France.
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Ha NT, Lee CH. Roles of Farnesyl-Diphosphate Farnesyltransferase 1 in Tumour and Tumour Microenvironments. Cells 2020; 9:cells9112352. [PMID: 33113804 PMCID: PMC7693003 DOI: 10.3390/cells9112352] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 12/14/2022] Open
Abstract
Farnesyl-diphosphate farnesyltransferase 1 (FDFT1, squalene synthase), a membrane-associated enzyme, synthesizes squalene via condensation of two molecules of farnesyl pyrophosphate. Accumulating evidence has noted that FDFT1 plays a critical role in cancer, particularly in metabolic reprogramming, cell proliferation, and invasion. Based on these advances in our knowledge, FDFT1 could be a potential target for cancer treatment. This review focuses on the contribution of FDFT1 to the hallmarks of cancer, and further, we discuss the applicability of FDFT1 as a cancer prognostic marker and target for anticancer therapy.
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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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Chromatin, Epigenetics and Plant Physiology. Int J Mol Sci 2020; 21:ijms21082763. [PMID: 32316114 PMCID: PMC7215297 DOI: 10.3390/ijms21082763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/31/2022] Open
Abstract
The ever-increasing interest in epigenetics comes from the fact that in the diverse life situations of organisms, e [...].
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Kang H, Wu D, Fan T, Zhu Y. Activities of Chromatin Remodeling Factors and Histone Chaperones and Their Effects in Root Apical Meristem Development. Int J Mol Sci 2020; 21:ijms21030771. [PMID: 31991579 PMCID: PMC7038114 DOI: 10.3390/ijms21030771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 01/01/2023] Open
Abstract
Eukaryotic genes are packaged into dynamic but stable chromatin structures to deal with transcriptional reprogramming and inheritance during development. Chromatin remodeling factors and histone chaperones are epigenetic factors that target nucleosomes and/or histones to establish and maintain proper chromatin structures during critical physiological processes such as DNA replication and transcriptional modulation. Root apical meristems are vital for plant root development. Regarding the well-characterized transcription factors involved in stem cell proliferation and differentiation, there is increasing evidence of the functional implications of epigenetic regulation in root apical meristem development. In this review, we focus on the activities of chromatin remodeling factors and histone chaperones in the root apical meristems of the model plant species Arabidopsis and rice.
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Lei B, Berger F. H2A Variants in Arabidopsis: Versatile Regulators of Genome Activity. PLANT COMMUNICATIONS 2020; 1:100015. [PMID: 33404536 PMCID: PMC7747964 DOI: 10.1016/j.xplc.2019.100015] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/13/2019] [Accepted: 12/11/2019] [Indexed: 05/16/2023]
Abstract
The eukaryotic nucleosome prevents access to the genome. Convergently evolving histone isoforms, also called histone variants, form diverse families that are enriched over distinct features of plant genomes. Among the diverse families of plant histone variants, H2A.Z exclusively marks genes. Here we review recent research progress on the genome-wide distribution patterns and deposition of H2A.Z in plants as well as its association with histone modifications and roles in plant chromatin regulation. We also discuss some hypotheses that explain the different findings about the roles of H2A.Z in plants.
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