1
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Wang C, Chen Z, Copenhaver GP, Wang Y. Heterochromatin in plant meiosis. Nucleus 2024; 15:2328719. [PMID: 38488152 PMCID: PMC10950279 DOI: 10.1080/19491034.2024.2328719] [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: 09/11/2023] [Accepted: 03/05/2024] [Indexed: 03/19/2024] Open
Abstract
Heterochromatin is an organizational property of eukaryotic chromosomes, characterized by extensive DNA and histone modifications, that is associated with the silencing of transposable elements and repetitive sequences. Maintaining heterochromatin is crucial for ensuring genomic integrity and stability during the cell cycle. During meiosis, heterochromatin is important for homologous chromosome synapsis, recombination, and segregation, but our understanding of meiotic heterochromatin formation and condensation is limited. In this review, we focus on the dynamics and features of heterochromatin and how it condenses during meiosis in plants. We also discuss how meiotic heterochromatin influences the interaction and recombination of homologous chromosomes during prophase I.
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Affiliation(s)
- Cong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Zhiyu Chen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Gregory P. Copenhaver
- Department of Biology and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Yingxiang Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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2
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Haider S, Farrona S. Decoding histone 3 lysine methylation: Insights into seed germination and flowering. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102598. [PMID: 38986392 DOI: 10.1016/j.pbi.2024.102598] [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: 04/01/2024] [Revised: 06/01/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
Histone lysine methylation is a highly conserved epigenetic modification across eukaryotes that contributes to creating different dynamic chromatin states, which may result in transcriptional changes. Over the years, an accumulated set of evidence has shown that histone methylation allows plants to align their development with their surroundings, enabling them to respond and memorize past events due to changes in the environment. In this review, we discuss the molecular mechanisms of histone methylation in plants. Writers, readers, and erasers of Arabidopsis histone methylation marks are described with an emphasis on their role in two of the most important developmental transition phases in plants, seed germination and flowering. Further, the crosstalk between different methylation marks is also discussed. An overview of the mechanisms of histone methylation modifications and their biological outcomes will shed light on existing research gaps and may provide novel perspectives to increase crop yield and resistance in the era of global climate change.
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Affiliation(s)
- Saqlain Haider
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland
| | - Sara Farrona
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland.
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3
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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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4
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Song D, Hu F, Huang C, Lan J, She X, Zhao C, Wu H, Liu A, Wu Q, Chen Y, Luo X, Feng Y, Yang X, Xu C, Hu J, Wang G. Tiam1 methylation by NSD2 promotes Rac1 signaling activation and colon cancer metastasis. Proc Natl Acad Sci U S A 2023; 120:e2305684120. [PMID: 38113258 PMCID: PMC10756287 DOI: 10.1073/pnas.2305684120] [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: 04/15/2023] [Accepted: 10/03/2023] [Indexed: 12/21/2023] Open
Abstract
Metastasis is a major cause of cancer therapy failure and mortality. However, targeting metastatic seeding and colonization remains a significant challenge. In this study, we identified NSD2, a histone methyltransferase responsible for dimethylating histone 3 at lysine 36, as being overexpressed in metastatic tumors. Our findings suggest that NSD2 overexpression enhances tumor metastasis both in vitro and in vivo. Further analysis revealed that NSD2 promotes tumor metastasis by activating Rac1 signaling. Mechanistically, NSD2 combines with and activates Tiam1 (T lymphoma invasion and metastasis 1) and promotes Rac1 signaling by methylating Tiam1 at K724. In vivo and in vitro studies revealed that Tiam1 K724 methylation could be a predictive factor for cancer prognosis and a potential target for metastasis inhibition. Furthermore, we have developed inhibitory peptide which was proved to inhibit tumor metastasis through blocking the interaction between NSD2 and Tiam1. Our results demonstrate that NSD2-methylated Tiam1 promotes Rac1 signaling and cancer metastasis. These results provide insights into the inhibition of tumor metastasis.
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Affiliation(s)
- Da Song
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Fuqing Hu
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Changsheng Huang
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Jingqin Lan
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Xiaowei She
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Chongchong Zhao
- Department of Protein Chemistry and Proteinomics Facility at Technology Center for Protein Sciences, Tsinghua University, Beijing100084, China
| | - Hong Wu
- Department of Integrative Cancer Center and Cancer Clinical Research Center, Sichuan Cancer Hospital and Institute Sichuan Cancer Center, School of Medicine University of Electronic Science and Technology, Chengdu610000, China
| | - Anyi Liu
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Qi Wu
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Yaqi Chen
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Xuelai Luo
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Yongdong Feng
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Xiangping Yang
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Chuan Xu
- Department of Integrative Cancer Center and Cancer Clinical Research Center, Sichuan Cancer Hospital and Institute Sichuan Cancer Center, School of Medicine University of Electronic Science and Technology, Chengdu610000, China
| | - Junbo Hu
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
| | - Guihua Wang
- Department of Gastrointestinal Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan430030, China
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5
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Wang Z, Castillo-González CM, Zhao C, Tong CY, Li C, Zhong S, Liu Z, Xie K, Zhu J, Wu Z, Peng X, Jacob Y, Michaels SD, Jacobsen SE, Zhang X. H3.1K27me1 loss confers Arabidopsis resistance to Geminivirus by sequestering DNA repair proteins onto host genome. Nat Commun 2023; 14:7484. [PMID: 37980416 PMCID: PMC10657422 DOI: 10.1038/s41467-023-43311-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/06/2023] [Indexed: 11/20/2023] Open
Abstract
The H3 methyltransferases ATXR5 and ATXR6 deposit H3.1K27me1 to heterochromatin to prevent genomic instability and transposon re-activation. Here, we report that atxr5 atxr6 mutants display robust resistance to Geminivirus. The viral resistance is correlated with activation of DNA repair pathways, but not with transposon re-activation or heterochromatin amplification. We identify RAD51 and RPA1A as partners of virus-encoded Rep protein. The two DNA repair proteins show increased binding to heterochromatic regions and defense-related genes in atxr5 atxr6 vs wild-type plants. Consequently, the proteins have reduced binding to viral DNA in the mutant, thus hampering viral amplification. Additionally, RAD51 recruitment to the host genome arise via BRCA1, HOP2, and CYCB1;1, and this recruitment is essential for viral resistance in atxr5 atxr6. Thus, Geminiviruses adapt to healthy plants by hijacking DNA repair pathways, whereas the unstable genome, triggered by reduced H3.1K27me1, could retain DNA repairing proteins to suppress viral amplification in atxr5 atxr6.
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Affiliation(s)
- Zhen Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX, 77843, USA
| | | | - Changjiang Zhao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Chun-Yip Tong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Changhao Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Songxiao Zhong
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Zhiyang Liu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Kaili Xie
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Jiaying Zhu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Zhongshou Wu
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Xu Peng
- Department of Molecular Physiology, College of Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Yannick Jacob
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Scott D Michaels
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Steven E Jacobsen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
- Molecular and Environmental Plant Sciences, Texas A&M University, College Station, TX, 77843, USA.
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
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6
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Joly V, Jacob Y. Mitotic inheritance of genetic and epigenetic information via the histone H3.1 variant. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102401. [PMID: 37302254 PMCID: PMC11168788 DOI: 10.1016/j.pbi.2023.102401] [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: 04/03/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023]
Abstract
The replication-dependent histone H3.1 variant, ubiquitous in multicellular eukaryotes, has been proposed to play key roles during chromatin replication due to its unique expression pattern restricted to the S phase of the cell cycle. Here, we describe recent discoveries in plants regarding molecular mechanisms and cellular pathways involving H3.1 that contribute to the maintenance of genomic and epigenomic information. First, we highlight new advances concerning the contribution of the histone chaperone CAF-1 and the TSK-H3.1 DNA repair pathway in preventing genomic instability during replication. We then summarize the evidence connecting H3.1 to specific roles required for the mitotic inheritance of epigenetic states. Finally, we discuss the recent identification of a specific interaction between H3.1 and DNA polymerase epsilon and its functional implications.
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Affiliation(s)
- Valentin Joly
- 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; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06511, USA.
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7
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Jiang D, Berger F. Variation is important: Warranting chromatin function and dynamics by histone variants. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102408. [PMID: 37399781 DOI: 10.1016/j.pbi.2023.102408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 07/05/2023]
Abstract
The chromatin of flowering plants exhibits a wide range of sequence variants of the core and linker histones. Recent studies have demonstrated that specific histone variant enrichment, combined with post-translational modifications (PTMs) of histones, defines distinct chromatin states that impact specific chromatin functions. Chromatin remodelers are emerging as key regulators of histone variant dynamics, contributing to shaping chromatin states and regulating gene transcription in response to environment. Recognizing the histone variants by their specific readers, controlled by histone PTMs, is crucial for maintaining genome and chromatin integrity. In addition, various histone variants have been shown to play essential roles in remodeling chromatin domains to facilitate important programmed transitions throughout the plant life cycle. In this review, we discuss recent findings in this exciting field of research, which holds immense promise for many surprising discoveries related to the evolution of complexity in plant organization through a seemingly simple protein family.
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Affiliation(s)
- Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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8
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Seni S, Singh RK, Prasad M. Dynamics of epigenetic control in plants via SET domain containing proteins: Structural and functional insights. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194966. [PMID: 37532097 DOI: 10.1016/j.bbagrm.2023.194966] [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: 05/30/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/04/2023]
Abstract
Plants control expression of their genes in a way that involves manipulating the chromatin structural dynamics in order to adapt to environmental changes and carry out developmental processes. Histone modifications like histone methylation are significant epigenetic marks which profoundly and globally modify chromatin, potentially affecting the expression of several genes. Methylation of histones is catalyzed by histone lysine methyltransferases (HKMTs), that features an evolutionary conserved domain known as SET [Su(var)3-9, E(Z), Trithorax]. This methylation is directed at particular lysine (K) residues on H3 or H4 histone. Plant SET domain group (SDG) proteins are categorized into different classes that have been conserved through evolution, and each class have specificity that influences how the chromatin structure operates. The domains discovered in plant SET domain proteins have typically been linked to protein-protein interactions, suggesting that majority of the SDGs function in complexes. Additionally, SDG-mediated histone mark deposition also affects alternative splicing events. In present review, we discussed the diversity of SDGs in plants including their structural properties. Additionally, we have provided comprehensive summary of the functions of the SDG-domain containing proteins in plant developmental processes and response to environmental stimuli have also been highlighted.
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Affiliation(s)
- Sushmita Seni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India.
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9
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Dickinson L, Yuan W, LeBlanc C, Thomson G, Wang S, Jacob Y. Regulation of gene editing using T-DNA concatenation. NATURE PLANTS 2023; 9:1398-1408. [PMID: 37653336 PMCID: PMC11193869 DOI: 10.1038/s41477-023-01495-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/18/2023] [Indexed: 09/02/2023]
Abstract
Transformation via Agrobacterium tumefaciens is the predominant method used to introduce exogenous DNA into plant genomes1,2. Transfer DNA (T-DNA) originating from Agrobacterium can be integrated as a single copy or in complex concatenated forms3,4, but the mechanisms affecting final T-DNA structure remain unknown. Here we demonstrate that inclusion of retrotransposon (RT)-derived sequences in T-DNA can increase T-DNA copy number by more than 50-fold in Arabidopsis thaliana. These additional T-DNA copies are organized into large concatemers, an effect primarily induced by the long terminal repeats (LTRs) of RTs that can be replicated using non-LTR DNA repeats. We found that T-DNA concatenation is dependent on the activity of the DNA repair proteins MRE11, RAD17 and ATR. Finally, we show that T-DNA concatenation can be used to increase the frequency of targeted mutagenesis and gene targeting. Overall, this work uncovers molecular determinants that modulate T-DNA copy number in Arabidopsis and demonstrates the utility of inducing T-DNA concatenation for plant gene editing.
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Affiliation(s)
- Lauren Dickinson
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, USA
| | - Wenxin Yuan
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, USA
| | - Chantal LeBlanc
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, USA
| | - Geoffrey Thomson
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, USA
| | - Siyuan Wang
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Yannick Jacob
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, USA.
- Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, USA.
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10
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Distinct roles of Arabidopsis ORC1 proteins in DNA replication and heterochromatic H3K27me1 deposition. Nat Commun 2023; 14:1270. [PMID: 36882445 PMCID: PMC9992703 DOI: 10.1038/s41467-023-37024-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/24/2023] [Indexed: 03/09/2023] Open
Abstract
Most cellular proteins involved in genome replication are conserved in all eukaryotic lineages including yeast, plants and animals. However, the mechanisms controlling their availability during the cell cycle are less well defined. Here we show that the Arabidopsis genome encodes for two ORC1 proteins highly similar in amino acid sequence and that have partially overlapping expression domains but with distinct functions. The ancestral ORC1b gene, present before the partial duplication of the Arabidopsis genome, has retained the canonical function in DNA replication. ORC1b is expressed in both proliferating and endoreplicating cells, accumulates during G1 and is rapidly degraded upon S-phase entry through the ubiquitin-proteasome pathway. In contrast, the duplicated ORC1a gene has acquired a specialized function in heterochromatin biology. ORC1a is required for efficient deposition of the heterochromatic H3K27me1 mark by the ATXR5/6 histone methyltransferases. The distinct roles of the two ORC1 proteins may be a feature common to other organisms with duplicated ORC1 genes and a major difference with animal cells.
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11
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Dickinson L, Yuan W, LeBlanc C, Thomson G, Wang S, Jacob Y. Induction of T-DNA amplification by retrotransposon-derived sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.05.531200. [PMID: 36945545 PMCID: PMC10028825 DOI: 10.1101/2023.03.05.531200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Transformation via Agrobacterium tumefaciens (Agrobacterium) is the predominant method used to introduce exogenous DNA into plants. Transfer DNA (T-DNA) originating from Agrobacterium can be integrated as a single copy or in concatenated forms in plant genomes, but the mechanisms affecting final T-DNA structure remain unknown. In this study, we demonstrate that the inclusion of retrotransposon (RT)-derived sequences in T-DNA can increase transgene copy number by more than 50-fold in Arabidopsis thaliana (Arabidopsis). RT-mediated amplification of T-DNA results in large concatemers in the Arabidopsis genome, which are primarily induced by the long terminal repeats (LTRs) of RTs. T-DNA amplification is dependent on the activity of DNA repair proteins associated with theta-mediated end joining (TMEJ). Finally, we show that T-DNA amplification can increase the frequency of targeted mutagenesis and gene targeting. Overall, this work uncovers molecular determinants that modulate T-DNA copy number in Arabidopsis and demonstrates the utility of inducing T-DNA amplification for plant gene editing.
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Affiliation(s)
- Lauren Dickinson
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
| | - Wenxin Yuan
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
| | - Chantal LeBlanc
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
| | - Geoffrey Thomson
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
| | - Siyuan Wang
- Yale University, Department of Genetics, Yale School of Medicine; New Haven, Connecticut 06510, USA
- Yale University, Department of Cell Biology, Yale School of Medicine; New Haven, Connecticut 06510, USA
| | - Yannick Jacob
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; New Haven, Connecticut 06511, USA
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12
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Vaquero-Sedas MI, Vega-Palas MA. Epigenetic nature of Arabidopsis thaliana telomeres. PLANT PHYSIOLOGY 2023; 191:47-55. [PMID: 36218957 PMCID: PMC9806604 DOI: 10.1093/plphys/kiac471] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/22/2022] [Indexed: 05/15/2023]
Abstract
The epigenetic features of defined chromosomal domains condition their biochemical and functional properties. Therefore, there is considerable interest in studying the epigenetic marks present at relevant chromosomal loci. Telomeric regions, which include telomeres and subtelomeres, have been traditionally considered heterochromatic. However, whereas the heterochromatic nature of subtelomeres has been widely accepted, the epigenetic status of telomeres remains controversial. Here, we studied the epigenetic features of Arabidopsis (Arabidopsis thaliana) telomeres by analyzing multiple genome-wide ChIP-seq experiments. Our analyses revealed that Arabidopsis telomeres are not significantly enriched either in euchromatic marks like H3K4me2, H3K9ac, and H3K27me3 or in heterochromatic marks such as H3K27me1 and H3K9me2. Thus, telomeric regions in Arabidopsis have a bimodal chromatin organization with telomeres lacking significant levels of canonical euchromatic and heterochromatic marks followed by heterochromatic subtelomeres. Since heterochromatin is known to influence telomere function, the heterochromatic modifications present at Arabidopsis subtelomeres could play a relevant role in telomere biology.
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Affiliation(s)
- María I Vaquero-Sedas
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Universidad de Sevilla, IBVF (CSIC-US), Seville E41092, Spain
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13
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Zhao X, Wang J, Jin D, Cheng J, Chen H, Li Z, Wang Y, Lou H, Zhu JK, Du X, Gong Z. AtMCM10 promotes DNA replication-coupled nucleosome assembly in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:203-222. [PMID: 36541721 DOI: 10.1111/jipb.13438] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Minichromosome Maintenance protein 10 (MCM10) is essential for DNA replication initiation and DNA elongation in yeasts and animals. Although the functions of MCM10 in DNA replication and repair have been well documented, the detailed mechanisms for MCM10 in these processes are not well known. Here, we identified AtMCM10 gene through a forward genetic screening for releasing a silenced marker gene. Although plant MCM10 possesses a similar crystal structure as animal MCM10, AtMCM10 is not essential for plant growth or development in Arabidopsis. AtMCM10 can directly bind to histone H3-H4 and promotes nucleosome assembly in vitro. The nucleosome density is decreased in Atmcm10, and most of the nucleosome density decreased regions in Atmcm10 are also regulated by newly synthesized histone chaperone Chromatin Assembly Factor-1 (CAF-1). Loss of both AtMCM10 and CAF-1 is embryo lethal, indicating that AtMCM10 and CAF-1 are indispensable for replication-coupled nucleosome assembly. AtMCM10 interacts with both new and parental histones. Atmcm10 mutants have lower H3.1 abundance and reduced H3K27me1/3 levels with releasing some silenced transposons. We propose that AtMCM10 deposits new and parental histones during nucleosome assembly, maintaining proper epigenetic modifications and genome stability during DNA replication.
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Affiliation(s)
- Xinjie Zhao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, The Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dan Jin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jinkui Cheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hui Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhen Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Yu Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Huiqiang Lou
- State Key Laboratory of Agro-Biotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jian-Kang Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Science, Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuan Du
- Department of Biochemistry and Molecular Biology, International Cancer Center, Shenzhen University Medical School, Shenzhen, 518060, China
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, 518060, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
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14
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DNA polymerase epsilon binds histone H3.1-H4 and recruits MORC1 to mediate meiotic heterochromatin condensation. Proc Natl Acad Sci U S A 2022; 119:e2213540119. [PMID: 36260743 PMCID: PMC9618065 DOI: 10.1073/pnas.2213540119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterochromatin is essential for genomic integrity and stability in eukaryotes. The mechanisms that regulate meiotic heterochromatin formation remain largely undefined. Here, we show that the catalytic subunit (POL2A) of Arabidopsis DNA polymerase epsilon (POL ε) is required for proper formation of meiotic heterochromatin. The POL2A N terminus interacts with the GHKL adenosine triphosphatase (ATPase) MORC1 (Microrchidia 1), and POL2A is required for MORC1's localization on meiotic heterochromatin. Mutations affecting the POL2A N terminus cause aberrant morphology of meiotic heterochromatin, which is also observed in morc1. Moreover, the POL2A C-terminal zinc finger domain (ZF1) specifically binds to histone H3.1-H4 dimer or tetramer and is important for meiotic heterochromatin condensation. Interestingly, we also found similar H3.1-binding specificity for the mouse counterpart. Together, our results show that two distinct domains of POL2A, ZF1 and N terminus bind H3.1-H4 and recruit MORC1, respectively, to induce a continuous process of meiotic heterochromatin organization. These activities expand the functional repertoire of POL ε beyond its classic role in DNA replication and appear to be conserved in animals and plants.
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15
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Huang YC, Yuan W, Jacob Y. The Role of the TSK/TONSL-H3.1 Pathway in Maintaining Genome Stability in Multicellular Eukaryotes. Int J Mol Sci 2022; 23:9029. [PMID: 36012288 PMCID: PMC9409234 DOI: 10.3390/ijms23169029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/22/2022] Open
Abstract
Replication-dependent histone H3.1 and replication-independent histone H3.3 are nearly identical proteins in most multicellular eukaryotes. The N-terminal tails of these H3 variants, where the majority of histone post-translational modifications are made, typically differ by only one amino acid. Despite extensive sequence similarity with H3.3, the H3.1 variant has been hypothesized to play unique roles in cells, as it is specifically expressed and inserted into chromatin during DNA replication. However, identifying a function that is unique to H3.1 during replication has remained elusive. In this review, we discuss recent findings regarding the involvement of the H3.1 variant in regulating the TSK/TONSL-mediated resolution of stalled or broken replication forks. Uncovering this new function for the H3.1 variant has been made possible by the identification of the first proteins containing domains that can selectively bind or modify the H3.1 variant. The functional characterization of H3-variant-specific readers and writers reveals another layer of chromatin-based information regulating transcription, DNA replication, and DNA repair.
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Affiliation(s)
| | | | - Yannick Jacob
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, 260 Whitney Avenue, New Haven, CT 06511, USA
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16
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Gutierrez C. A Journey to the Core of the Plant Cell Cycle. Int J Mol Sci 2022; 23:8154. [PMID: 35897730 PMCID: PMC9330084 DOI: 10.3390/ijms23158154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/16/2022] [Accepted: 07/21/2022] [Indexed: 02/04/2023] Open
Abstract
Production of new cells as a result of progression through the cell division cycle is a fundamental biological process for the perpetuation of both unicellular and multicellular organisms. In the case of plants, their developmental strategies and their largely sessile nature has imposed a series of evolutionary trends. Studies of the plant cell division cycle began with cytological and physiological approaches in the 1950s and 1960s. The decade of 1990 marked a turn point with the increasing development of novel cellular and molecular protocols combined with advances in genetics and, later, genomics, leading to an exponential growth of the field. In this article, I review the current status of plant cell cycle studies but also discuss early studies and the relevance of a multidisciplinary background as a source of innovative questions and answers. In addition to advances in a deeper understanding of the plant cell cycle machinery, current studies focus on the intimate interaction of cell cycle components with almost every aspect of plant biology.
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Affiliation(s)
- Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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17
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Zhang Y, Tang M, Huang M, Xie J, Cheng J, Fu Y, Jiang D, Yu X, Li B. Dynamic enhancer transcription associates with reprogramming of immune genes during pattern triggered immunity in Arabidopsis. BMC Biol 2022; 20:165. [PMID: 35864475 PMCID: PMC9301868 DOI: 10.1186/s12915-022-01362-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 06/24/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Enhancers are cis-regulatory elements present in eukaryote genomes, which constitute indispensable determinants of gene regulation by governing the spatiotemporal and quantitative expression dynamics of target genes, and are involved in multiple life processes, for instance during development and disease states. The importance of enhancer activity has additionally been highlighted for immune responses in animals and plants; however, the dynamics of enhancer activities and molecular functions in plant innate immunity are largely unknown. Here, we investigated the involvement of distal enhancers in early innate immunity in Arabidopsis thaliana. RESULTS A group of putative distal enhancers producing low-abundance transcripts either unidirectionally or bidirectionally are identified. We show that enhancer transcripts are dynamically modulated in plant immunity triggered by microbe-associated molecular patterns and are strongly correlated with open chromatin, low levels of methylated DNA, and increases in RNA polymerase II targeting and acetylated histone marks. Dynamic enhancer transcription is correlated with target early immune gene expression patterns. Cis motifs that are bound by immune-related transcription factors, such as WRKYs and SARD1, are highly enriched within upregulated enhancers. Moreover, a subset of core pattern-induced enhancers are upregulated by multiple patterns from diverse pathogens. The expression dynamics of putative immunity-related enhancers and the importance of WRKY binding motifs for enhancer function were also validated. CONCLUSIONS Our study demonstrates the general occurrence of enhancer transcription in plants and provides novel information on the distal regulatory landscape during early plant innate immunity, providing new insights into immune gene regulation and ultimately improving the mechanistic understanding of the plant immune system.
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Affiliation(s)
- Ying Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
| | - Meng Tang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
| | - Mengling Huang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yanping Fu
- Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
- Hubei Hongshan Laboratory, Wuhan, 430070, Hubei, China.
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18
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Dubos T, Poulet A, Thomson G, Péry E, Chausse F, Tatout C, Desset S, van Wolfswinkel JC, Jacob Y. NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects. BMC Bioinformatics 2022; 23:216. [PMID: 35668354 PMCID: PMC9169307 DOI: 10.1186/s12859-022-04743-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The three-dimensional nuclear arrangement of chromatin impacts many cellular processes operating at the DNA level in animal and plant systems. Chromatin organization is a dynamic process that can be affected by biotic and abiotic stresses. Three-dimensional imaging technology allows to follow these dynamic changes, but only a few semi-automated processing methods currently exist for quantitative analysis of the 3D chromatin organization. RESULTS We present an automated method, Nuclear Object DetectionJ (NODeJ), developed as an imageJ plugin. This program segments and analyzes high intensity domains in nuclei from 3D images. NODeJ performs a Laplacian convolution on the mask of a nucleus to enhance the contrast of intra-nuclear objects and allow their detection. We reanalyzed public datasets and determined that NODeJ is able to accurately identify heterochromatin domains from a diverse set of Arabidopsis thaliana nuclei stained with DAPI or Hoechst. NODeJ is also able to detect signals in nuclei from DNA FISH experiments, allowing for the analysis of specific targets of interest. CONCLUSION AND AVAILABILITY NODeJ allows for efficient automated analysis of subnuclear structures by avoiding the semi-automated steps, resulting in reduced processing time and analytical bias. NODeJ is written in Java and provided as an ImageJ plugin with a command line option to perform more high-throughput analyses. NODeJ can be downloaded from https://gitlab.com/axpoulet/image2danalysis/-/releases with source code, documentation and further information avaliable at https://gitlab.com/axpoulet/image2danalysis . The images used in this study are publicly available at https://www.brookes.ac.uk/indepth/images/ and https://doi.org/10.15454/1HSOIE .
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Affiliation(s)
- Tristan Dubos
- GReD, CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
- Institut Pascal, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Axel Poulet
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA
| | - Geoffrey Thomson
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA
| | - Emilie Péry
- Institut Pascal, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Frédéric Chausse
- Institut Pascal, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Christophe Tatout
- GReD, CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sophie Desset
- GReD, CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Josien C. van Wolfswinkel
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA
| | - Yannick Jacob
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, USA
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19
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Hu H, Du J. Structure and mechanism of histone methylation dynamics in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102211. [PMID: 35452951 DOI: 10.1016/j.pbi.2022.102211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Histone methylation plays a central role in regulating chromatin state and gene expression in Arabidopsis and is involved in a variety of physiological and developmental processes. Dynamic regulation of histone methylation relies on both histone methyltransferase "writer" and histone demethylases "eraser" proteins. In this review, we focus on the four major histone methylation modifications in Arabidopsis H3, H3K4, H3K9, H3K27, and H3K36, and summarize current knowledge of the dynamic regulation of these modifications, with an emphasis on the biochemical and structural perspectives of histone methyltransferases and demethylases.
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Affiliation(s)
- Hongmiao Hu
- 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 518055, 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 518055, China.
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20
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Abstract
The histone H3.1 variant deposited at replication forks docks DNA repair machinery.
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Affiliation(s)
- Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
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21
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Davarinejad H, Huang YC, Mermaz B, LeBlanc C, Poulet A, Thomson G, Joly V, Muñoz M, Arvanitis-Vigneault A, Valsakumar D, Villarino G, Ross A, Rotstein BH, Alarcon EI, Brunzelle JS, Voigt P, Dong J, Couture JF, Jacob Y. The histone H3.1 variant regulates TONSOKU-mediated DNA repair during replication. Science 2022; 375:1281-1286. [PMID: 35298257 PMCID: PMC9153895 DOI: 10.1126/science.abm5320] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The tail of replication-dependent histone H3.1 varies from that of replication-independent H3.3 at the amino acid located at position 31 in plants and animals, but no function has been assigned to this residue to demonstrate a unique and conserved role for H3.1 during replication. We found that TONSOKU (TSK/TONSL), which rescues broken replication forks, specifically interacts with H3.1 via recognition of alanine 31 by its tetratricopeptide repeat domain. Our results indicate that genomic instability in the absence of ATXR5/ATXR6-catalyzed histone H3 lysine 27 monomethylation in plants depends on H3.1, TSK, and DNA polymerase theta (Pol θ). This work reveals an H3.1-specific function during replication and a common strategy used in multicellular eukaryotes for regulating post-replicative chromatin maturation and TSK, which relies on histone monomethyltransferases and reading of the H3.1 variant.
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Affiliation(s)
- Hossein Davarinejad
- Ottawa Institute of Systems Biology; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa; Ottawa, Ontario K1H 8M5, Canada
| | - Yi-Chun Huang
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
| | - Benoit Mermaz
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
| | - Chantal LeBlanc
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
| | - Axel Poulet
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
| | - Geoffrey Thomson
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
| | - Valentin Joly
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
| | - Marcelo Muñoz
- Ottawa Institute of Systems Biology; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa; Ottawa, Ontario K1H 8M5, Canada
| | - Alexis Arvanitis-Vigneault
- Ottawa Institute of Systems Biology; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa; Ottawa, Ontario K1H 8M5, Canada
| | - Devisree Valsakumar
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; Edinburgh, EH9 3BF, United Kingdom
- Epigenetics Programme, Babraham Institute; Cambridge, CB22 3AT, United Kingdom
| | - Gonzalo Villarino
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
| | - Alex Ross
- BEaTS Research Laboratory, Division of Cardiac Surgery, University of Ottawa Heart Institute; Ottawa, ON K1Y4W7, Canada
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa; Ottawa, ON K1H 8M5, Canada
| | - Benjamin H. Rotstein
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa; Ottawa, ON K1H 8M5, Canada
- University of Ottawa Heart Institute; Ottawa, ON K1Y4W7, Canada
| | - Emilio I. Alarcon
- BEaTS Research Laboratory, Division of Cardiac Surgery, University of Ottawa Heart Institute; Ottawa, ON K1Y4W7, Canada
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa; Ottawa, ON K1H 8M5, Canada
| | - Joseph S. Brunzelle
- Feinberg School of Medicine, Department of Molecular Pharmacology and Biological Chemistry, Northwestern University; Chicago, Illinois 60611, USA
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; Edinburgh, EH9 3BF, United Kingdom
- Epigenetics Programme, Babraham Institute; Cambridge, CB22 3AT, United Kingdom
| | - Jie Dong
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
- Institute of Crop Science, Zhejiang University; Hangzhou 310058, China
| | - Jean-François Couture
- Ottawa Institute of Systems Biology; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa; Ottawa, Ontario K1H 8M5, Canada
| | - Yannick Jacob
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences; 260 Whitney Avenue, New Haven, Connecticut 06511, USA
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22
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Sablowski R, Gutierrez C. Cycling in a crowd: Coordination of plant cell division, growth, and cell fate. THE PLANT CELL 2022; 34:193-208. [PMID: 34498091 PMCID: PMC8774096 DOI: 10.1093/plcell/koab222] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/31/2021] [Indexed: 05/25/2023]
Abstract
The reiterative organogenesis that drives plant growth relies on the constant production of new cells, which remain encased by interconnected cell walls. For these reasons, plant morphogenesis strictly depends on the rate and orientation of both cell division and cell growth. Important progress has been made in recent years in understanding how cell cycle progression and the orientation of cell divisions are coordinated with cell and organ growth and with the acquisition of specialized cell fates. We review basic concepts and players in plant cell cycle and division, and then focus on their links to growth-related cues, such as metabolic state, cell size, cell geometry, and cell mechanics, and on how cell cycle progression and cell division are linked to specific cell fates. The retinoblastoma pathway has emerged as a major player in the coordination of the cell cycle with both growth and cell identity, while microtubule dynamics are central in the coordination of oriented cell divisions. Future challenges include clarifying feedbacks between growth and cell cycle progression, revealing the molecular basis of cell division orientation in response to mechanical and chemical signals, and probing the links between cell fate changes and chromatin dynamics during the cell cycle.
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Affiliation(s)
| | - Crisanto Gutierrez
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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23
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The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis. Proc Natl Acad Sci U S A 2022; 119:2115570119. [PMID: 35027454 PMCID: PMC8784105 DOI: 10.1073/pnas.2115570119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2021] [Indexed: 01/07/2023] Open
Abstract
The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the tissue-specific defects correlate with residual ATXR6 expression. We also determined that ATXR5/6 function is essential for female germline development. Furthermore, we provide a comprehensive analysis of H3K27me1 changes in relation to other epigenetic marks. We also determined that some previously reported suppressors of atxr5/6 may act by restoring the levels of H3K27me1, such as through up-regulation of the ATXR6 transcript in the atxr6 hypomorphic promoter allele. ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) AND ATXR6 are required for the deposition of H3K27me1 and for maintaining genomic stability in Arabidopsis. Reduction of ATXR5/6 activity results in activation of DNA damage response genes, along with tissue-specific derepression of transposable elements (TEs), chromocenter decompaction, and genomic instability characterized by accumulation of excess DNA from heterochromatin. How loss of ATXR5/6 and H3K27me1 leads to these phenotypes remains unclear. Here we provide extensive characterization of the atxr5/6 hypomorphic mutant by comprehensively examining gene expression and epigenetic changes in the mutant. We found that the tissue-specific phenotypes of TE derepression and excessive DNA in this atxr5/6 mutant correlated with residual ATXR6 expression from the hypomorphic ATXR6 allele. However, up-regulation of DNA damage genes occurred regardless of ATXR6 levels and thus appears to be a separable process. We also isolated an atxr6-null allele which showed that ATXR5 and ATXR6 are required for female germline development. Finally, we characterize three previously reported suppressors of the hypomorphic atxr5/6 mutant and show that these rescue atxr5/6 via distinct mechanisms, two of which involve increasing H3K27me1 levels.
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24
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Erlendson AA, Freitag M. Not all Is SET for Methylation: Evolution of Eukaryotic Protein Methyltransferases. Methods Mol Biol 2022; 2529:3-40. [PMID: 35733008 DOI: 10.1007/978-1-0716-2481-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Dynamic posttranslational modifications to canonical histones that constitute the nucleosome (H2A, H2B, H3, and H4) control all aspects of enzymatic transactions with DNA. Histone methylation has been studied heavily for the past 20 years, and our mechanistic understanding of the control and function of individual methylation events on specific histone arginine and lysine residues has been greatly improved over the past decade, driven by excellent new tools and methods. Here, we will summarize what is known about the distribution and some of the functions of protein methyltransferases from all major eukaryotic supergroups. The main conclusion is that protein, and specifically histone, methylation is an ancient process. Many taxa in all supergroups have lost some subfamilies of both protein arginine methyltransferases (PRMT) and the heavily studied SET domain lysine methyltransferases (KMT). Over time, novel subfamilies, especially of SET domain proteins, arose. We use the interactions between H3K27 and H3K36 methylation as one example for the complex circuitry of histone modifications that make up the "histone code," and we discuss one recent example (Paramecium Ezl1) for how extant enzymes that may resemble more ancient SET domain KMTs are able to modify two lysine residues that have divergent functions in plants, fungi, and animals. Complexity of SET domain KMT function in the well-studied plant and animal lineages arose not only by gene duplication but also acquisition of novel DNA- and histone-binding domains in certain subfamilies.
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Affiliation(s)
- Allyson A Erlendson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.
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Inagaki S. Silencing and anti-silencing mechanisms that shape the epigenome in plants. Genes Genet Syst 2021; 96:217-228. [PMID: 34719532 DOI: 10.1266/ggs.21-00041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Epigenome information mediates genome function and maintenance by regulating gene expression and chromatin organization. Because the epigenome pattern can change in response to internal and external environments, it may underlie an adaptive genome response that modulates phenotypes during development and in changing environments. Here I summarize recent progress in our understanding of how epigenome patterns are shaped and modulated by concerted actions of silencing and anti-silencing factors mainly in Arabidopsis thaliana. I discuss the dynamic nature of epigenome regulation, which is realized by cooperation and counteraction among silencing and anti-silencing factors, and how the dynamic epigenome mediates robust and plastic responses of plants to fluctuating environments.
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Affiliation(s)
- Soichi Inagaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo.,PRESTO, Japan Science and Technology Agency
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Takatsuka H, Shibata A, Umeda M. Genome Maintenance Mechanisms at the Chromatin Level. Int J Mol Sci 2021; 22:ijms221910384. [PMID: 34638727 PMCID: PMC8508675 DOI: 10.3390/ijms221910384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
Genome integrity is constantly threatened by internal and external stressors, in both animals and plants. As plants are sessile, a variety of environment stressors can damage their DNA. In the nucleus, DNA twines around histone proteins to form the higher-order structure “chromatin”. Unraveling how chromatin transforms on sensing genotoxic stress is, thus, key to understanding plant strategies to cope with fluctuating environments. In recent years, accumulating evidence in plant research has suggested that chromatin plays a crucial role in protecting DNA from genotoxic stress in three ways: (1) changes in chromatin modifications around damaged sites enhance DNA repair by providing a scaffold and/or easy access to DNA repair machinery; (2) DNA damage triggers genome-wide alterations in chromatin modifications, globally modulating gene expression required for DNA damage response, such as stem cell death, cell-cycle arrest, and an early onset of endoreplication; and (3) condensed chromatin functions as a physical barrier against genotoxic stressors to protect DNA. In this review, we highlight the chromatin-level control of genome stability and compare the regulatory systems in plants and animals to find out unique mechanisms maintaining genome integrity under genotoxic stress.
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Affiliation(s)
- Hirotomo Takatsuka
- School of Biological Science and Technology, College of Science and Engineering, Kanazawa University, Kakuma-Machi, Kanazawa 920-1192, Japan;
| | - Atsushi Shibata
- Signal Transduction Program, Gunma University Initiative for Advanced Research (GIAR), 3-39-22, Showa-Machi, Maebashi 371-8511, Japan;
| | - Masaaki Umeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
- Correspondence:
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He K, Cao X, Deng X. Histone methylation in epigenetic regulation and temperature responses. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102001. [PMID: 33508540 DOI: 10.1016/j.pbi.2021.102001] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 05/26/2023]
Abstract
Methylation of histones on different lysine residues is dynamically added by distinct writer enzymes, interpreted by reader proteins, and removed by eraser enzymes. This epigenetic mark has widespread, dynamic roles in plant development and environmental responses. For example, histone methylation plays a key role in mediating plant responses to temperature, including alterations of flowering time. In this review, we summarize recent advances in understanding the mechanism by which histone methylation regulates these processes, and discuss the role of histone methylation in temperature responses, based on data from Arabidopsis thaliana.
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Affiliation(s)
- Kaixuan He
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Shahid S. The making and unmaking of the silenced chromatin. THE PLANT CELL 2021; 33:786-787. [PMID: 35234961 PMCID: PMC8226284 DOI: 10.1093/plcell/koab001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 01/01/2021] [Indexed: 06/14/2023]
Affiliation(s)
- Saima Shahid
- Donald Danforth Plant Science Center, St. Louis, MO, USA
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29
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Dong J, LeBlanc C, Poulet A, Mermaz B, Villarino G, Webb KM, Joly V, Mendez J, Voigt P, Jacob Y. H3.1K27me1 maintains transcriptional silencing and genome stability by preventing GCN5-mediated histone acetylation. THE PLANT CELL 2021; 33:961-979. [PMID: 33793815 PMCID: PMC8226292 DOI: 10.1093/plcell/koaa027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/25/2020] [Indexed: 05/17/2023]
Abstract
Epigenetic mechanisms play diverse roles in the regulation of genome stability in eukaryotes. In Arabidopsis thaliana, genome stability is maintained during DNA replication by the H3.1K27 methyltransferases ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 (ATXR5) and ATXR6, which catalyze the deposition of K27me1 on replication-dependent H3.1 variants. The loss of H3.1K27me1 in atxr5 atxr6 double mutants leads to heterochromatin defects, including transcriptional de-repression and genomic instability, but the molecular mechanisms involved remain largely unknown. In this study, we identified the transcriptional co-activator and conserved histone acetyltransferase GCN5 as a mediator of transcriptional de-repression and genomic instability in the absence of H3.1K27me1. GCN5 is part of a SAGA-like complex in plants that requires the GCN5-interacting protein ADA2b and the chromatin remodeler CHR6 to mediate the heterochromatic defects in atxr5 atxr6 mutants. Our results also indicate that Arabidopsis GCN5 acetylates multiple lysine residues on H3.1 variants, but H3.1K27 and H3.1K36 play essential functions in inducing genomic instability in the absence of H3.1K27me1. Finally, we show that H3.1K36 acetylation by GCN5 is negatively regulated by H3.1K27me1 in vitro. Overall, this work reveals a key molecular role for H3.1K27me1 in maintaining transcriptional silencing and genome stability in heterochromatin by restricting GCN5-mediated histone acetylation in plants.
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Affiliation(s)
- Jie Dong
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Chantal LeBlanc
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Axel Poulet
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Benoit Mermaz
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Gonzalo Villarino
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Kimberly M Webb
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF
| | - Valentin Joly
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Josefina Mendez
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF
| | - Yannick Jacob
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CN 06511
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Bourguet P, Picard CL, Yelagandula R, Pélissier T, Lorković ZJ, Feng S, Pouch-Pélissier MN, Schmücker A, Jacobsen SE, Berger F, Mathieu O. The histone variant H2A.W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation. Nat Commun 2021; 12:2683. [PMID: 33976212 PMCID: PMC8113232 DOI: 10.1038/s41467-021-22993-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 04/09/2021] [Indexed: 12/12/2022] Open
Abstract
In flowering plants, heterochromatin is demarcated by the histone variant H2A.W, elevated levels of the linker histone H1, and specific epigenetic modifications, such as high levels of DNA methylation at both CG and non-CG sites. How H2A.W regulates heterochromatin organization and interacts with other heterochromatic features is unclear. Here, we create a h2a.w null mutant via CRISPR-Cas9, h2a.w-2, to analyze the in vivo function of H2A.W. We find that H2A.W antagonizes deposition of H1 at heterochromatin and that non-CG methylation and accessibility are moderately decreased in h2a.w-2 heterochromatin. Compared to H1 loss alone, combined loss of H1 and H2A.W greatly increases accessibility and facilitates non-CG DNA methylation in heterochromatin, suggesting co-regulation of heterochromatic features by H2A.W and H1. Our results suggest that H2A.W helps maintain optimal heterochromatin accessibility and DNA methylation by promoting chromatin compaction together with H1, while also inhibiting excessive H1 incorporation.
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Affiliation(s)
- Pierre Bourguet
- CNRS, Université Clermont Auvergne, Inserm, Institut Génétique Reproduction et Développement (iGReD), Clermont-Ferrand, France
| | - Colette L Picard
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Ramesh Yelagandula
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Thierry Pélissier
- CNRS, Université Clermont Auvergne, Inserm, Institut Génétique Reproduction et Développement (iGReD), Clermont-Ferrand, France
| | - Zdravko J Lorković
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Marie-Noëlle Pouch-Pélissier
- CNRS, Université Clermont Auvergne, Inserm, Institut Génétique Reproduction et Développement (iGReD), Clermont-Ferrand, France
| | - Anna Schmücker
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Olivier Mathieu
- CNRS, Université Clermont Auvergne, Inserm, Institut Génétique Reproduction et Développement (iGReD), Clermont-Ferrand, France.
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Histone lactylation drives oncogenesis by facilitating m 6A reader protein YTHDF2 expression in ocular melanoma. Genome Biol 2021; 22:85. [PMID: 33726814 PMCID: PMC7962360 DOI: 10.1186/s13059-021-02308-z] [Citation(s) in RCA: 298] [Impact Index Per Article: 99.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
Abstract
Background Histone lactylation, a metabolic stress-related histone modification, plays an important role in the regulation of gene expression during M1 macrophage polarization. However, the role of histone lactylation in tumorigenesis remains unclear. Results Here, we show histone lactylation is elevated in tumors and is associated with poor prognosis of ocular melanoma. Target correction of aberrant histone lactylation triggers therapeutic efficacy both in vitro and in vivo. Mechanistically, histone lactylation contributes to tumorigenesis by facilitating YTHDF2 expression. Moreover, YTHDF2 recognizes the m6A modified PER1 and TP53 mRNAs and promotes their degradation, which accelerates tumorigenesis of ocular melanoma. Conclusion We reveal the oncogenic role of histone lactylation, thereby providing novel therapeutic targets for ocular melanoma therapy. We also bridge histone modifications with RNA modifications, which provides novel understanding of epigenetic regulation in tumorigenesis. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02308-z.
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Rougée M, Quadrana L, Zervudacki J, Hure V, Colot V, Navarro L, Deleris A. Polycomb mutant partially suppresses DNA hypomethylation-associated phenotypes in Arabidopsis. Life Sci Alliance 2020; 4:4/2/e202000848. [PMID: 33443101 PMCID: PMC7756957 DOI: 10.26508/lsa.202000848] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 12/16/2022] Open
Abstract
A mutation in Arabidopsis polycomb repressive complex 2 partially suppresses the transposon activity observed in a DNA methylation mutant, challenging expectations. In plants and mammals, DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3), which is deposited by the polycomb repressive complex 2, are considered as two specialized systems for the epigenetic silencing of transposable element (TE) and genes, respectively. Nevertheless, many TE sequences acquire H3K27me3 when DNA methylation is lost. Here, we show in Arabidopsis thaliana that the gain of H3K27me3 observed at hundreds of TEs in the ddm1 mutant defective in the maintenance of DNA methylation, essentially depends on CURLY LEAF (CLF), one of two partially redundant H3K27 methyltransferases active in vegetative tissues. Surprisingly, the complete loss of H3K27me3 in ddm1 clf double mutant plants was not associated with further reactivation of TE expression nor with a burst of transposition. Instead, ddm1 clf plants exhibited less activated TEs, and a chromatin recompaction as well as hypermethylation of linker DNA compared with ddm1. Thus, a mutation in polycomb repressive complex 2 does not aggravate the molecular phenotypes linked to ddm1 but instead partially suppresses them, challenging our assumptions of the relationship between two conserved epigenetic silencing pathways.
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Affiliation(s)
- Martin Rougée
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Jérôme Zervudacki
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Valentin Hure
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Lionel Navarro
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, Sciences and Lettres (PSL) Research University, Paris, France
| | - Angélique Deleris
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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Bourguet P, López-González L, Gómez-Zambrano Á, Pélissier T, Hesketh A, Potok ME, Pouch-Pélissier MN, Perez M, Da Ines O, Latrasse D, White CI, Jacobsen SE, Benhamed M, Mathieu O. DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis. Genome Biol 2020; 21:283. [PMID: 33234150 PMCID: PMC7687843 DOI: 10.1186/s13059-020-02190-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications must be faithfully passed on to daughter strands. There is evidence that DNA polymerases play a role in transcriptional silencing, but the extent of their contribution and how it relates to heterochromatin maintenance is unclear. RESULTS We isolate a strong hypomorphic Arabidopsis thaliana mutant of the POL2A catalytic subunit of DNA polymerase epsilon and show that POL2A is required to stabilize heterochromatin silencing genome-wide, likely by preventing replicative stress. We reveal that POL2A inhibits DNA methylation and histone H3 lysine 9 methylation. Hence, the release of heterochromatin silencing in POL2A-deficient mutants paradoxically occurs in a chromatin context of increased levels of these two repressive epigenetic marks. At the nuclear level, the POL2A defect is associated with fragmentation of heterochromatin. CONCLUSION These results indicate that POL2A is critical to heterochromatin structure and function, and that unhindered replisome progression is required for the faithful propagation of DNA methylation throughout the cell cycle.
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Affiliation(s)
- Pierre Bourguet
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Leticia López-González
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Ángeles Gómez-Zambrano
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
- Present Address: Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Cartuja, Avda, Américo Vespucio, 49., 41092, Sevilla, Spain
| | - Thierry Pélissier
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Amy Hesketh
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Magdalena E Potok
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Marie-Noëlle Pouch-Pélissier
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Magali Perez
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Olivier Da Ines
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Charles I White
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Olivier Mathieu
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France.
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Antunez-Sanchez J, Naish M, Ramirez-Prado JS, Ohno S, Huang Y, Dawson A, Opassathian K, Manza-Mianza D, Ariel F, Raynaud C, Wibowo A, Daron J, Ueda M, Latrasse D, Slotkin RK, Weigel D, Benhamed M, Gutierrez-Marcos J. A new role for histone demethylases in the maintenance of plant genome integrity. eLife 2020. [PMID: 33107825 DOI: 10.7554/elife.58533.sa2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
Histone modifications deposited by the Polycomb repressive complex 2 (PRC2) play a critical role in the control of growth, development, and adaptation to environmental fluctuations of most multicellular eukaryotes. The catalytic activity of PRC2 is counteracted by Jumonji-type (JMJ) histone demethylases, which shapes the genomic distribution of H3K27me3. Here, we show that two JMJ histone demethylases in Arabidopsis, EARLY FLOWERING 6 (ELF6) and RELATIVE OF EARLY FLOWERING 6 (REF6), play distinct roles in H3K27me3 and H3K27me1 homeostasis. We show that failure to reset these chromatin marks during sexual reproduction results in the transgenerational inheritance of histone marks, which cause a loss of DNA methylation at heterochromatic loci and transposon activation. Thus, Jumonji-type histone demethylases play a dual role in plants by helping to maintain transcriptional states through development and safeguard genome integrity during sexual reproduction.
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Affiliation(s)
| | - Matthew Naish
- School of Life Science, University of Warwick, Coventry, United Kingdom
| | | | - Sho Ohno
- School of Life Science, University of Warwick, Coventry, United Kingdom
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Alexander Dawson
- School of Life Science, University of Warwick, Coventry, United Kingdom
| | | | - Deborah Manza-Mianza
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Federico Ariel
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Cecile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - Anjar Wibowo
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Josquin Daron
- Department of Molecular Genetics, The Ohio State University, Columbus, United States
| | - Minako Ueda
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, United States
- Division of Biological Sciences, University of Missouri, Columbia, United States
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), F-75006, Paris, France
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Antunez-Sanchez J, Naish M, Ramirez-Prado JS, Ohno S, Huang Y, Dawson A, Opassathian K, Manza-Mianza D, Ariel F, Raynaud C, Wibowo A, Daron J, Ueda M, Latrasse D, Slotkin RK, Weigel D, Benhamed M, Gutierrez-Marcos J. A new role for histone demethylases in the maintenance of plant genome integrity. eLife 2020; 9:e58533. [PMID: 33107825 PMCID: PMC7671693 DOI: 10.7554/elife.58533] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 10/26/2020] [Indexed: 12/16/2022] Open
Abstract
Histone modifications deposited by the Polycomb repressive complex 2 (PRC2) play a critical role in the control of growth, development, and adaptation to environmental fluctuations of most multicellular eukaryotes. The catalytic activity of PRC2 is counteracted by Jumonji-type (JMJ) histone demethylases, which shapes the genomic distribution of H3K27me3. Here, we show that two JMJ histone demethylases in Arabidopsis, EARLY FLOWERING 6 (ELF6) and RELATIVE OF EARLY FLOWERING 6 (REF6), play distinct roles in H3K27me3 and H3K27me1 homeostasis. We show that failure to reset these chromatin marks during sexual reproduction results in the transgenerational inheritance of histone marks, which cause a loss of DNA methylation at heterochromatic loci and transposon activation. Thus, Jumonji-type histone demethylases play a dual role in plants by helping to maintain transcriptional states through development and safeguard genome integrity during sexual reproduction.
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Affiliation(s)
| | - Matthew Naish
- School of Life Science, University of WarwickCoventryUnited Kingdom
| | | | - Sho Ohno
- School of Life Science, University of WarwickCoventryUnited Kingdom
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-kuKyotoJapan
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - Alexander Dawson
- School of Life Science, University of WarwickCoventryUnited Kingdom
| | | | - Deborah Manza-Mianza
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - Federico Ariel
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - Cecile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - Anjar Wibowo
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Josquin Daron
- Department of Molecular Genetics, The Ohio State UniversityColumbusUnited States
| | - Minako Ueda
- Institute of Transformative Bio-Molecules, Nagoya UniversityNagoyaJapan
- Division of Biological Science, Graduate School of Science, Nagoya UniversityNagoyaJapan
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
| | - R Keith Slotkin
- Donald Danforth Plant Science CenterSt. LouisUnited States
- Division of Biological Sciences, University of MissouriColumbiaUnited States
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental BiologyTübingenGermany
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2)OrsayFrance
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), F-75006ParisFrance
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Wear EE, Song J, Zynda GJ, Mickelson-Young L, LeBlanc C, Lee TJ, Deppong DO, Allen GC, Martienssen RA, Vaughn MW, Hanley-Bowdoin L, Thompson WF. Comparing DNA replication programs reveals large timing shifts at centromeres of endocycling cells in maize roots. PLoS Genet 2020; 16:e1008623. [PMID: 33052904 PMCID: PMC7588055 DOI: 10.1371/journal.pgen.1008623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 10/26/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022] Open
Abstract
Plant cells undergo two types of cell cycles–the mitotic cycle in which DNA replication is coupled to mitosis, and the endocycle in which DNA replication occurs in the absence of cell division. To investigate DNA replication programs in these two types of cell cycles, we pulse labeled intact root tips of maize (Zea mays) with 5-ethynyl-2’-deoxyuridine (EdU) and used flow sorting of nuclei to examine DNA replication timing (RT) during the transition from a mitotic cycle to an endocycle. Comparison of the sequence-based RT profiles showed that most regions of the maize genome replicate at the same time during S phase in mitotic and endocycling cells, despite the need to replicate twice as much DNA in the endocycle and the fact that endocycling is typically associated with cell differentiation. However, regions collectively corresponding to 2% of the genome displayed significant changes in timing between the two types of cell cycles. The majority of these regions are small with a median size of 135 kb, shift to a later RT in the endocycle, and are enriched for genes expressed in the root tip. We found larger regions that shifted RT in centromeres of seven of the ten maize chromosomes. These regions covered the majority of the previously defined functional centromere, which ranged between 1 and 2 Mb in size in the reference genome. They replicate mainly during mid S phase in mitotic cells but primarily in late S phase of the endocycle. In contrast, the immediately adjacent pericentromere sequences are primarily late replicating in both cell cycles. Analysis of CENH3 enrichment levels in 8C vs 2C nuclei suggested that there is only a partial replacement of CENH3 nucleosomes after endocycle replication is complete. The shift to later replication of centromeres and possible reduction in CENH3 enrichment after endocycle replication is consistent with a hypothesis that centromeres are inactivated when their function is no longer needed. In traditional cell division, or mitosis, a cell’s genetic material is duplicated and then split between two daughter cells. In contrast, in some specialized cell types, the DNA is duplicated a second time without an intervening division step, resulting in cells that carry twice as much DNA. This phenomenon, which is called the endocycle, is common during plant development. At each step, DNA replication follows an ordered program in which highly compacted DNA is unraveled and replicated in sections at different times during the synthesis (S) phase. In plants, it is unclear whether traditional and endocycle programs are the same, especially since endocycling cells are typically in the process of differentiation. Using root tips of maize, we found that in comparison to replication in the mitotic cell cycle, there is a small portion of the genome whose replication in the endocycle is shifted in time, usually to later in S phase. Some of these regions are scattered around the genome and mostly coincide with active genes. However, the most prominent shifts occur in centromeres. The shift to later replication in centromeres is noteworthy because they orchestrate the process of separating duplicated chromosomes into daughter cells, a function that is not needed in the endocycle.
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Affiliation(s)
- Emily E. Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
| | - Jawon Song
- Texas Advanced Computing Center, University of Texas, Austin, Texas, United States of America
| | - Gregory J. Zynda
- Texas Advanced Computing Center, University of Texas, Austin, Texas, United States of America
| | - Leigh Mickelson-Young
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Chantal LeBlanc
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Tae-Jin Lee
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - David O. Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - George C. Allen
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Matthew W. Vaughn
- Texas Advanced Computing Center, University of Texas, Austin, Texas, United States of America
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - William F. Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, United States of America
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Wang L, Qiao H. Chromatin regulation in plant hormone and plant stress responses. CURRENT OPINION IN PLANT BIOLOGY 2020; 57:164-170. [PMID: 33142261 PMCID: PMC8237520 DOI: 10.1016/j.pbi.2020.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 05/05/2023]
Abstract
The gene expression is tightly regulated temporally and spatially to ensure the plant and animal proper development, function, growth, and survival under different environmental conditions. Chromatin regulation plays a central role in the gene expression by providing transcription factors and the transcription machinery with dynamic access to an otherwise tightly packaged genome. In this review, we will summarize recent progress in understanding the roles of chromatin regulation in the gene expression, and their contribution to the plant hormone and stress responses. We highlight the most recent publications within this topic and underline the roles of chromatin regulation in gene expression.
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Affiliation(s)
- Likai Wang
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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Ning YQ, Liu N, Lan KK, Su YN, Li L, Chen S, He XJ. DREAM complex suppresses DNA methylation maintenance genes and precludes DNA hypermethylation. NATURE PLANTS 2020; 6:942-956. [PMID: 32661276 DOI: 10.1038/s41477-020-0710-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 05/27/2020] [Indexed: 05/27/2023]
Abstract
The DNA methyltransferases MET1 and CMT3 are known to be responsible for maintenance of DNA methylation at symmetric CG and CHG sites, respectively, in Arabidopsis thaliana. However, it is unknown how the expression of methyltransferase genes is regulated in different cell states and whether change in expression affects DNA methylation at the whole-genome level. Using a reverse genetic screen, we identified TCX5, a tesmin/TSO1-like CXC domain-containing protein, and demonstrated that it is a transcriptional repressor of genes required for maintenance of DNA methylation, which include MET1, CMT3, DDM1, KYP and VIMs. TCX5 functions redundantly with its paralogue TCX6 in repressing the expression of these genes. In the tcx5 tcx6 double mutant, expression of these genes is markedly increased, thereby leading to markedly increased DNA methylation at CHG sites and, to a lesser extent, at CG sites at the whole-genome level. Furthermore, our whole-genome DNA methylation analysis indicated that the CG and CHG methylation level is lower in differentiated quiescent cells than in dividing cells in the wild type but is comparable in the tcx5/6 mutant, suggesting that TCX5/6 are required for maintenance of the difference in DNA methylation between the two cell types. We identified TCX5/6-containing multi-subunit complexes, which are known as DREAM in other eukaryotes, and demonstrated that the Arabidopsis DREAM components function as a whole to preclude DNA hypermethylation. Given that the DREAM complexes are conserved from plants to animals, the preclusion of DNA hypermethylation by DREAM complexes may represent a conserved mechanism in eukaryotes.
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Affiliation(s)
- Yong-Qiang Ning
- National Institute of Biological Sciences, Beijing, China
- The College of Life Sciences, Northwest University, Xi'an, China
| | - Na Liu
- National Institute of Biological Sciences, Beijing, China
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ke-Ke Lan
- National Institute of Biological Sciences, Beijing, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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Zhou H, Liu Y, Liang Y, Zhou D, Li S, Lin S, Dong H, Huang L. The function of histone lysine methylation related SET domain group proteins in plants. Protein Sci 2020; 29:1120-1137. [PMID: 32134523 DOI: 10.1002/pro.3849] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/30/2020] [Accepted: 03/03/2020] [Indexed: 11/08/2022]
Abstract
Histone methylation, which is mediated by the histone lysine (K) methyltransferases (HKMTases), is a mechanism associated with many pathways in eukaryotes. Most HKMTases have a conserved SET (Su(var) 3-9,E(z),Trithorax) domain, while the HKMTases with SET domains are called the SET domain group (SDG) proteins. In plants, only SDG proteins can work as HKMTases. In this review, we introduced the classification of SDG family proteins in plants and the structural characteristics of each subfamily, surmise the functions of SDG family members in plant growth and development processes, including pollen and female gametophyte development, flowering, plant morphology and the responses to stresses. This review will help researchers better understand the SDG proteins and histone methylation in plants and lay a basic foundation for further studies on SDG proteins.
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Affiliation(s)
- Huiyan Zhou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Yanhong Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Yuwei Liang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Dong Zhou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
| | - Shuifeng Li
- Hangzhou Xiaoshan District Agricultural Technology Extension Center, Hangzhou, China
| | - Sue Lin
- Institute of Life Sciences, Wenzhou University, Wenzhou, China
| | - Heng Dong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, Engineering Laboratory of Development and Application of Traditional Chinese Medicine from Zhejiang Province, School of Medicine, Holistic Integrative Pharmacy Institutes (HIPI), Hangzhou Normal University, Hangzhou, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
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Chen DH, Qiu HL, Huang Y, Zhang L, Si JP. Genome-wide identification and expression profiling of SET DOMAIN GROUP family in Dendrobium catenatum. BMC PLANT BIOLOGY 2020; 20:40. [PMID: 31992218 PMCID: PMC6986063 DOI: 10.1186/s12870-020-2244-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 01/13/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND Dendrobium catenatum, as a precious Chinese herbal medicine, is an epiphytic orchid plant, which grows on the trunks and cliffs and often faces up to diverse environmental stresses. SET DOMAIN GROUP (SDG) proteins act as histone lysine methyltransferases, which are involved in pleiotropic developmental events and stress responses through modifying chromatin structure and regulating gene transcription, but their roles in D. catenatum are unknown. RESULTS In this study, we identified 44 SDG proteins from D. catenatum genome. Subsequently, comprehensive analyses related to gene structure, protein domain organization, and phylogenetic relationship were performed to evaluate these D. catenatum SDG (DcSDG) proteins, along with the well-investigated homologs from the model plants Arabidopsis thaliana and Oryza sativa as well as the newly characterized 42 SDG proteins from a closely related orchid plant Phalaenopsis equestris. We showed DcSDG proteins can be grouped into eight distinct classes (I~VII and M), mostly consistent with the previous description. Based on the catalytic substrates of the reported SDG members mainly in Arabidopsis, Class I (E(z)-Like) is predicted to account for the deposition of H3K27me2/3, Class II (Ash-like) for H3K36me, Class III (Trx/ATX-like) for H3K4me2/3, Class M (ATXR3/7) for H3K4me, Class IV (Su (var)-like) for H3K27me1, Class V (Suv-like) for H3K9me, as well as class VI (S-ET) and class VII (RBCMT) for methylation of both histone and non-histone proteins. RNA-seq derived expression profiling showed that DcSDG proteins usually displayed wide but distinguished expressions in different tissues and organs. Finally, environmental stresses examination showed the expressions of DcASHR3, DcSUVR3, DcATXR4, DcATXR5b, and DcSDG49 are closely associated with drought-recovery treatment, the expression of DcSUVH5a, DcATXR5a and DcSUVR14a are significantly influenced by low temperature, and even 61% DcSDG genes are in response to heat shock. CONCLUSIONS This study systematically identifies and classifies SDG genes in orchid plant D. catenatum, indicates their functional divergence during the evolution, and discovers their broad roles in the developmental programs and stress responses. These results provide constructive clues for further functional investigation and epigenetic mechanism dissection of SET-containing proteins in orchids.
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Affiliation(s)
- Dong-Hong Chen
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium catenatum (D. officinale), Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.
| | - Han-Lin Qiu
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium catenatum (D. officinale), Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Yong Huang
- Key Laboratory of Education Department of Hunan Province on Plant Genetics and Molecular Biology, Hunan Agricultural University, Changsha, 410128, China
| | - Lei Zhang
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium catenatum (D. officinale), Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China
| | - Jin-Ping Si
- State Key Laboratory of Subtropical Silviculture, SFGA Engineering Research Center for Dendrobium catenatum (D. officinale), Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.
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Achrem M, Szućko I, Kalinka A. The epigenetic regulation of centromeres and telomeres in plants and animals. COMPARATIVE CYTOGENETICS 2020; 14:265-311. [PMID: 32733650 PMCID: PMC7360632 DOI: 10.3897/compcytogen.v14i2.51895] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/18/2020] [Indexed: 05/10/2023]
Abstract
The centromere is a chromosomal region where the kinetochore is formed, which is the attachment point of spindle fibers. Thus, it is responsible for the correct chromosome segregation during cell division. Telomeres protect chromosome ends against enzymatic degradation and fusions, and localize chromosomes in the cell nucleus. For this reason, centromeres and telomeres are parts of each linear chromosome that are necessary for their proper functioning. More and more research results show that the identity and functions of these chromosomal regions are epigenetically determined. Telomeres and centromeres are both usually described as highly condensed heterochromatin regions. However, the epigenetic nature of centromeres and telomeres is unique, as epigenetic modifications characteristic of both eu- and heterochromatin have been found in these areas. This specificity allows for the proper functioning of both regions, thereby affecting chromosome homeostasis. This review focuses on demonstrating the role of epigenetic mechanisms in the functioning of centromeres and telomeres in plants and animals.
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Affiliation(s)
- Magdalena Achrem
- Institute of Biology, University of Szczecin, Szczecin, PolandUniversity of SzczecinSzczecinPoland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, PolandUniversity of SzczecinSzczecinPoland
| | - Izabela Szućko
- Institute of Biology, University of Szczecin, Szczecin, PolandUniversity of SzczecinSzczecinPoland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, PolandUniversity of SzczecinSzczecinPoland
| | - Anna Kalinka
- Institute of Biology, University of Szczecin, Szczecin, PolandUniversity of SzczecinSzczecinPoland
- Molecular Biology and Biotechnology Center, University of Szczecin, Szczecin, PolandUniversity of SzczecinSzczecinPoland
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Abstract
Maintenance of genome integrity is a key process in all organisms. DNA polymerases (Pols) are central players in this process as they are in charge of the faithful reproduction of the genetic information, as well as of DNA repair. Interestingly, all eukaryotes possess a large repertoire of polymerases. Three protein complexes, DNA Pol α, δ, and ε, are in charge of nuclear DNA replication. These enzymes have the fidelity and processivity required to replicate long DNA sequences, but DNA lesions can block their progression. Consequently, eukaryotic genomes also encode a variable number of specialized polymerases (between five and 16 depending on the organism) that are involved in the replication of damaged DNA, DNA repair, and organellar DNA replication. This diversity of enzymes likely stems from their ability to bypass specific types of lesions. In the past 10–15 years, our knowledge regarding plant DNA polymerases dramatically increased. In this review, we discuss these recent findings and compare acquired knowledge in plants to data obtained in other eukaryotes. We also discuss the emerging links between genome and epigenome replication.
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Heterogeneous transposable elements as silencers, enhancers and targets of meiotic recombination. Chromosoma 2019; 128:279-296. [PMID: 31332531 DOI: 10.1007/s00412-019-00718-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 06/25/2019] [Accepted: 07/01/2019] [Indexed: 02/01/2023]
Abstract
During meiosis, DNA double-strand breaks are initiated by the topoisomerase-like enzyme SPO11 and are repaired by inter-sister chromatid and inter-homologue DNA repair pathways. Genome-wide maps of initiating DNA double-strand breaks and inter-homologue repair events are now available for a number of mammalian, fungal and plant species. In mammals, PRDM9 specifies the location of meiotic recombination initiation via recognition of specific DNA sequence motifs by its C2H2 zinc finger array. In fungi and plants, meiotic recombination appears to be initiated less discriminately in accessible chromatin, including at gene promoters. Generally, meiotic crossover is suppressed in highly repetitive genomic regions that are made up of transposable elements (TEs), to prevent deleterious non-allelic homologous recombination events. However, recent and older studies have revealed intriguing relationships between meiotic recombination initiation and repair, and transposable elements. For instance, gene conversion events have been detected in maize centromeric retroelements, mouse MULE-MuDR DNA transposons undergo substantial meiotic recombination initiation, Arabidopsis Helitron TEs are among the hottest of recombination initiation hotspots, and human TE sequences can modify the crossover rate at adjacent PRDM9 motifs in cis. Here, we summarize the relationship between meiotic recombination and TEs, discuss recent insights from highly divergent eukaryotes and highlight outstanding questions in the field.
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Abstract
DNA replication starts with the opening of DNA at sites called DNA replication origins. From the single sequence-specific DNA replication origin of the small Escherichia coli genome, up to thousands of origins that are necessary to replicate the large human genome, strict sequence specificity has been lost. Nevertheless, genome-wide analyses performed in the recent years, using different mapping methods, demonstrated that there are precise locations along the metazoan genome from which replication initiates. These sites contain relaxed sequence consensus and epigenetic features. There is flexibility in the choice of origins to be used during a given cell cycle, probably imposed by evolution and developmental constraints. Here, we will briefly describe their main features.
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45
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Peroxisomal β-oxidation regulates histone acetylation and DNA methylation in Arabidopsis. Proc Natl Acad Sci U S A 2019; 116:10576-10585. [PMID: 31064880 DOI: 10.1073/pnas.1904143116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Epigenetic markers, such as histone acetylation and DNA methylation, determine chromatin organization. In eukaryotic cells, metabolites from organelles or the cytosol affect epigenetic modifications. However, the relationships between metabolites and epigenetic modifications are not well understood in plants. We found that peroxisomal acyl-CoA oxidase 4 (ACX4), an enzyme in the fatty acid β-oxidation pathway, is required for suppressing the silencing of some endogenous loci, as well as Pro35S:NPTII in the ProRD29A:LUC/C24 transgenic line. The acx4 mutation reduces nuclear histone acetylation and increases DNA methylation at the NOS terminator of Pro35S:NPTII and at some endogenous genomic loci, which are also targeted by the demethylation enzyme REPRESSOR OF SILENCING 1 (ROS1). Furthermore, mutations in multifunctional protein 2 (MFP2) and 3-ketoacyl-CoA thiolase-2 (KAT2/PED1/PKT3), two enzymes in the last two steps of the β-oxidation pathway, lead to similar patterns of DNA hypermethylation as in acx4 Thus, metabolites from fatty acid β-oxidation in peroxisomes are closely linked to nuclear epigenetic modifications, which may affect diverse cellular processes in plants.
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Fernandes JB, Wlodzimierz P, Henderson IR. Meiotic recombination within plant centromeres. CURRENT OPINION IN PLANT BIOLOGY 2019; 48:26-35. [PMID: 30954771 DOI: 10.1016/j.pbi.2019.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/21/2019] [Accepted: 02/28/2019] [Indexed: 05/18/2023]
Abstract
Meiosis is a conserved eukaryotic cell division that increases genetic diversity in sexual populations. During meiosis homologous chromosomes pair and undergo recombination that can result in reciprocal genetic exchange, termed crossover. The frequency of crossover is highly variable along chromosomes, with hot spots and cold spots. For example, the centromeres that contain the kinetochore, which attach chromosomes to the microtubular spindle, are crossover cold spots. Plant centromeres typically consist of large tandemly repeated arrays of satellite sequences and retrotransposons, a subset of which assemble CENH3-variant nucleosomes, which bind to kinetochore proteins. Although crossovers are suppressed in centromeres, there is abundant evidence for gene conversion and homologous recombination between repeats, which plays a role in satellite array change. We review the evidence for recombination within plant centromeres and the implications for satellite sequence evolution. We speculate on the genetic and epigenetic features of centromeres that may influence meiotic recombination in these regions. We also highlight unresolved questions relating to centromere function and sequence change and how the advent of new technologies promises to provide insights.
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Affiliation(s)
- Joiselle B Fernandes
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Piotr Wlodzimierz
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Ian R Henderson
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom.
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ATXR5/6 Forms Alternative Protein Complexes with PCNA and the Nucleosome Core Particle. J Mol Biol 2019; 431:1370-1379. [PMID: 30826376 DOI: 10.1016/j.jmb.2019.02.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/15/2019] [Accepted: 02/15/2019] [Indexed: 12/11/2022]
Abstract
The proliferating cell nuclear antigen (PCNA) is a sliding clamp associated with DNA polymerases and serves as a binding platform for the recruitment of regulatory proteins linked to DNA damage repair, cell cycle regulation, and epigenetic signaling. The histone H3 lysine-27 (H3K27) mono-methyltransferase Arabidopsis trithorax-related protein 5/6 (ATXR5/6) associates with PCNA, and this interaction has been proposed to act as a key determinant controlling the reestablishment of H3K27 mono-methylation following replication. In this study, we provide biochemical evidence showing that PCNA inhibits ATXR6 enzymatic activity. The structure of the ATXR6 PCNA-interacting peptide (PIP) in complex with PCNA indicates that a trio of hydrophobic residues contributes to the binding of the enzyme to the sliding clamp. Finally, despite the presence of three PIP binding clefts, only two molecules of ATXR6 bind to PCNA likely enabling the recruitment of a third protein to the sliding clamp. Collectively, these results rule out the model wherein PCNA-bound ATXR6 actively reestablishes H3K27 mono-methylation following DNA replication and provides insights into the role of ATXR6 PIP motif in its interaction with PCNA.
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SETDB1-mediated methylation of Akt promotes its K63-linked ubiquitination and activation leading to tumorigenesis. Nat Cell Biol 2019; 21:214-225. [PMID: 30692626 PMCID: PMC6414065 DOI: 10.1038/s41556-018-0266-1] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 12/12/2018] [Indexed: 11/12/2022]
Abstract
The serine/threonine kinase Akt plays a central role in cell proliferation, survival and metabolism and its hyperactivation is linked to cancer progression. Here we report that Akt undergoes K64 methylation by SETDB1, which is crucial for cell membrane recruitment, phosphorylation and activation of Akt upon growth factor stimulation. Furthermore, we reveal an adaptor function of histone demethylase JMJD2A, which recognizes Akt K64 methylation and recruits E3 ligase TRAF6 and Skp2-SCF to the Akt complex, independently of its demethylase activity, thereby initiating K63-linked ubiquitination, cell membrane recruitment and activation of Akt. Notably, cancer associated Akt mutant (E17K) displays enhanced K64 methylation, leading to its hyper-phosphorylation and activation. SETDB1-mediated Akt K64 methylation is upregulated and correlated with Akt hyperactivation in non-small-cell lung carcinoma (NSCLC), promotes tumor development and predicts poor outcome. Collectively, these findings reveal complicated layers of Akt activation regulation coordinated by SETDB1-mediated Akt K64 methylation to drive tumorigenesis.
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Rodrigues AS, De Vega JJ, Miguel CM. Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos. BMC PLANT BIOLOGY 2018; 18:379. [PMID: 30594130 PMCID: PMC6310951 DOI: 10.1186/s12870-018-1564-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 11/22/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND There are clear differences in embryo development between angiosperm and gymnosperm species. Most of the current knowledge on gene expression and regulation during plant embryo development has derived from studies on angiosperms species, in particular from the model plant Arabidopsis thaliana. The few published studies on transcript profiling of conifer embryogenesis show the existence of many putative embryo-specific transcripts without an assigned function. In order to extend the knowledge on the transcriptomic expression during conifer embryogenesis, we sequenced the transcriptome of zygotic embryos for several developmental stages that cover most of Pinus pinaster (maritime pine) embryogenesis. RESULTS Total RNA samples collected from five zygotic embryo developmental stages were sequenced with Illumina technology. A de novo transcriptome was assembled as no genome sequence is yet published for Pinus pinaster. The transcriptome of reference for the period of zygotic embryogenesis in maritime pine contains 67,429 transcripts, which likely encode 58,527 proteins. The annotation shows a significant percentage, 31%, of predicted proteins exclusively present in pine embryogenesis. Functional categories and enrichment analysis of the differentially expressed transcripts evidenced carbohydrate transport and metabolism over-representation in early embryo stages, as highlighted by the identification of many putative glycoside hydrolases, possibly associated with cell wall modification, and carbohydrate transport transcripts. Moreover, the predominance of chromatin remodelling events was detected in early to middle embryogenesis, associated with an active synthesis of histones and their post-translational modifiers related to increased transcription, as well as silencing of transposons. CONCLUSIONS Our results extend the understanding of gene expression and regulation during zygotic embryogenesis in conifers and are a valuable resource to support further improvements in somatic embryogenesis for vegetative propagation of conifer species. Specific transcripts associated with carbohydrate metabolism, monosaccharide transport and epigenetic regulation seem to play an important role in pine early embryogenesis and may be a source of reliable molecular markers for early embryogenesis.
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Affiliation(s)
- Andreia S. Rodrigues
- Instituto de Biologia Experimental e Tecnológica (iBET), Apartado 12, 2780-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - José J. De Vega
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK
| | - Célia M. Miguel
- Instituto de Biologia Experimental e Tecnológica (iBET), Apartado 12, 2780-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
- Universidade de Lisboa, Faculdade de Ciências, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, 1749-016 Lisbon, Portugal
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Ma Z, Castillo-González C, Wang Z, Sun D, Hu X, Shen X, Potok ME, Zhang X. Arabidopsis Serrate Coordinates Histone Methyltransferases ATXR5/6 and RNA Processing Factor RDR6 to Regulate Transposon Expression. Dev Cell 2018; 45:769-784.e6. [PMID: 29920280 DOI: 10.1016/j.devcel.2018.05.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 04/04/2018] [Accepted: 05/20/2018] [Indexed: 12/25/2022]
Abstract
Serrate (SE) is a key component in RNA metabolism. Little is known about whether and how it can regulate epigenetic silencing. Here, we report histone methyltransferases ATXR5 and ATXR6 (ATXR5/6) as novel partners of SE. ATXR5/6 deposit histone 3 lysine 27 monomethylation (H3K27me1) to promote heterochromatin formation, repress transposable elements (TEs), and control genome stability in Arabidopsis. SE binds to ATXR5/6-regulated TE loci and promotes H3K27me1 accumulation in these regions. Furthermore, SE directly enhances ATXR5 enzymatic activity in vitro. Unexpectedly, se mutation suppresses the TE reactivation and DNA re-replication phenotypes in the atxr5 atxr6 mutant. The suppression of TE expression results from triggering RNA-dependent RNA polymerase 6 (RDR6)-dependent RNA silencing in the se atxr5 atxr6 mutant. We propose that SE facilitates ATXR5/6-mediated deposition of the H3K27me1 mark while inhibiting RDR6-mediated RNA silencing to protect TE transcripts. Hence, SE coordinates epigenetic silencing and RNA processing machineries to fine-tune the TE expression.
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Affiliation(s)
- Zeyang Ma
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Claudia Castillo-González
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Zhiye Wang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Di Sun
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Xiaomei Hu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA
| | - Xuefeng Shen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA; College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Magdalena E Potok
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Xiuren Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843, USA.
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