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Li J, Zhang Q, Wang Z, Liu Q. The roles of epigenetic regulators in plant regeneration: Exploring patterns amidst complex conditions. PLANT PHYSIOLOGY 2024; 194:2022-2038. [PMID: 38290051 PMCID: PMC10980418 DOI: 10.1093/plphys/kiae042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/06/2023] [Accepted: 12/17/2023] [Indexed: 02/01/2024]
Abstract
Plants possess remarkable capability to regenerate upon tissue damage or optimal environmental stimuli. This ability not only serves as a crucial strategy for immobile plants to survive through harsh environments, but also made numerous modern plant improvements techniques possible. At the cellular level, this biological process involves dynamic changes in gene expression that redirect cell fate transitions. It is increasingly recognized that chromatin epigenetic modifications, both activating and repressive, intricately interact to regulate this process. Moreover, the outcomes of epigenetic regulation on regeneration are influenced by factors such as the differences in regenerative plant species and donor tissue types, as well as the concentration and timing of hormone treatments. In this review, we focus on several well-characterized epigenetic modifications and their regulatory roles in the expression of widely studied morphogenic regulators, aiming to enhance our understanding of the mechanisms by which epigenetic modifications govern plant regeneration.
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Affiliation(s)
- Jiawen Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qiyan Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Zejia Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qikun Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
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2
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Jinteng L, Peitao X, Wenhui Y, Guiwen Y, Feng Y, Xiaojun X, Zepeng S, Jiajie L, Yunshu C, Zhaoqiang Z, Yipeng Z, Zhikun L, Pei F, Qian C, Dateng L, Zhongyu X, Yanfeng W, Huiyong S. BMAL1-TTK-H2Bub1 loop deficiency contributes to impaired BM-MSC-mediated bone formation in senile osteoporosis. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 31:568-585. [PMID: 36910712 PMCID: PMC9996134 DOI: 10.1016/j.omtn.2023.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
During the aging process, the reduced osteogenic differentiation of bone marrow mesenchymal stem cells (BM-MSCs) results in decreased bone formation, which contributes to senile osteoporosis. Previous studies have confirmed that interrupted circadian rhythm plays an indispensable role in age-related disease. However, the mechanism underlying the impaired osteogenic differentiation of BM-MSCs during aging and its relationship with interrupted circadian rhythm remains unclear. In this study, we confirmed that the circadian rhythm was interrupted in aging mouse skeletal systems. The level of the core rhythm component BMAL1 but not that of CLOCK in the osteoblast lineage was decreased in senile osteoporotic specimens from both human and mouse. BMAL1 targeted TTK as a circadian-controlled gene to phosphorylate MDM2 and regulate H2Bub1 level, while H2Bub1 in turn regulated the expression of BMAL1. The osteogenic capacity of BM-MSCs was maintained by a positive loop formed by BMAL1-TTK-MDM2-H2Bub1. Furthermore, we demonstrated that using bone-targeting recombinant adeno-associated virus 9 (rAAV9) to enhance Bmal1 or Ttk might have a therapeutic effect on senile osteoporosis and delays bone repair in aging mice. In summary, our study indicated that targeting the BMAL1-TTK-MDM2-H2Bub1 axis via bone-targeting rAAV9 might be a promising strategy for the treatment of senile osteoporosis.
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Affiliation(s)
- Li Jinteng
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Xu Peitao
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Yu Wenhui
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Ye Guiwen
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Ye Feng
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Xu Xiaojun
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Su Zepeng
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Lin Jiajie
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Che Yunshu
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Zhang Zhaoqiang
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Zeng Yipeng
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Li Zhikun
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Feng Pei
- Center for Biotherapy, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Cao Qian
- Center for Biotherapy, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Li Dateng
- Department of Statistical Science, Southern Methodist University, Dallas, TX, USA
| | - Xie Zhongyu
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Wu Yanfeng
- Center for Biotherapy, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
| | - Shen Huiyong
- Department of Orthopedics, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen 518003, P.R. China
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Temman H, Sakamoto T, Ueda M, Sugimoto K, Migihashi M, Yamamoto K, Tsujimoto-Inui Y, Sato H, Shibuta MK, Nishino N, Nakamura T, Shimada H, Taniguchi YY, Takeda S, Aida M, Suzuki T, Seki M, Matsunaga S. Histone deacetylation regulates de novo shoot regeneration. PNAS NEXUS 2023; 2:pgad002. [PMID: 36845349 PMCID: PMC9944245 DOI: 10.1093/pnasnexus/pgad002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
During de novo plant organ regeneration, auxin induction mediates the formation of a pluripotent cell mass called callus, which regenerates shoots upon cytokinin induction. However, molecular mechanisms underlying transdifferentiation remain unknown. Here, we showed that the loss of HDA19, a histone deacetylase (HDAC) family gene, suppresses shoot regeneration. Treatment with an HDAC inhibitor revealed that the activity of this gene is essential for shoot regeneration. Further, we identified target genes whose expression was regulated through HDA19-mediated histone deacetylation during shoot induction and found that ENHANCER OF SHOOT REGENERATION 1 and CUP-SHAPED COTYLEDON 2 play important roles in shoot apical meristem formation. Histones at the loci of these genes were hyperacetylated and markedly upregulated in hda19. Transient ESR1 or CUC2 overexpression impaired shoot regeneration, as observed in hda19. Therefore, HDA19 mediates direct histone deacetylation of CUC2 and ESR1 loci to prevent their overexpression at the early stages of shoot regeneration.
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Affiliation(s)
| | | | - Minoru Ueda
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan,Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kaoru Sugimoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Masako Migihashi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Kazunari Yamamoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Yayoi Tsujimoto-Inui
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Hikaru Sato
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Mio K Shibuta
- Academic Assembly (Faculty of Science), Yamagata University, Kojirakawa, Yamagata 990-8560, Japan
| | - Norikazu Nishino
- Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, 2-4 Hibikino, Wakamatsu-ku, Kitakyushu-shi, Fukuoka 808-0196, Japan
| | - Tomoe Nakamura
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan,Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Hiroaki Shimada
- Department of Biological Science and Technology, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo 125-8585, Japan
| | - Yukimi Y Taniguchi
- School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, Hyogo 669–1337, Japan
| | - Seiji Takeda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo Hangi-cho, Sakyo-ku, Kyoto 60-8522, Japan,Biotechnology Research Department, Kyoto Prefectural Agriculture Forestry and Fisheries Technology Centre, 74 Kitaina Yazuma Oji, Seika, Kyoto 619-0244, Japan
| | - Mitsuhiro Aida
- International Research Organization for Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan,International Research Center for Agricultural and Environmental Biology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-855, Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan,Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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Hung FY, Shih YH, Lin PY, Feng YR, Li C, Wu K. WRKY63 transcriptional activation of COOLAIR and COLDAIR regulates vernalization-induced flowering. PLANT PHYSIOLOGY 2022; 190:532-547. [PMID: 35708655 PMCID: PMC9434252 DOI: 10.1093/plphys/kiac295] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/21/2022] [Indexed: 05/10/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) FLOWERING LOCUS C (FLC) acts as a key flowering regulator by repressing the expression of the floral integrator FLOWERING LOCUS T (FT). Prolonged exposure to cold (vernalization) induces flowering by reducing FLC expression. The long noncoding RNAs (lncRNAs) COOLAIR and COLDAIR, which are transcribed from the 3' end and the first intron of FLC, respectively, are important for FLC repression under vernalization. However, the molecular mechanism of how COOLAIR and COLDAIR are transcriptionally activated remains elusive. In this study, we found that the group-III WRKY transcription factor WRKY63 can directly activate FLC. wrky63 mutant plants display an early flowering phenotype and are insensitive to vernalization. Interestingly, we found that WRKY63 can activate the expression of COOLAIR and COLDAIR by binding to their promoters.WRKY63 therefore acts as a dual regulator that activates FLC directly under non-vernalization conditions but represses FLC indirectly during vernalization through inducing COOLAIR and COLDAIR. Furthermore, genome-wide occupancy profile analyses indicated that the binding of WRKY63 to vernalization-induced genes increases after vernalization. In addition, WRKY63 binding is associated with decreased levels of the repressive marker Histone H3 Lysine 27 trimethylation (H3K27me3). Collectively, our results indicate that WRKY63 is an important flowering regulator involved in vernalization-induced transcriptional regulation.
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Affiliation(s)
| | | | - Pei-Yu Lin
- Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Yun-Ru Feng
- Institute of Plant Biology, National Taiwan University, Taipei 10617, Taiwan
| | - Chenlong Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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5
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Sun C, Liu S, He C, Zhong C, Liu H, Luo X, Li K, Zhang K, Wang Q, Chen C, Tang Y, Yang B, Chen X, Xu P, Zou T, Li S, Qin P, Wang P, Chu C, Deng X. Crosstalk between the Circadian Clock and Histone Methylation. Int J Mol Sci 2022; 23:ijms23126465. [PMID: 35742907 PMCID: PMC9224359 DOI: 10.3390/ijms23126465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 02/05/2023] Open
Abstract
The circadian clock and histone modifications could form a feedback loop in Arabidopsis; whether a similar regulatory mechanism exists in rice is still unknown. Previously, we reported that SDG724 and OsLHY are two rice heading date regulators in rice. SDG724 encodes a histone H3K36 methyltransferase, and OsLHY is a vital circadian rhythm transcription factor. Both could be involved in transcription regulatory mechanisms and could affect gene expression in various pathways. To explore the crosstalk between the circadian clock and histone methylation in rice, we studied the relationship between OsLHY and SDG724 via the transcriptome analysis of their single and double mutants, oslhy, sdg724, and oslhysdg724. Screening of overlapped DEGs and KEGG pathways between OsLHY and SDG724 revealed that they could control many overlapped pathways indirectly. Furthermore, we identified three candidate targets (OsGI, OsCCT38, and OsPRR95) of OsLHY and one candidate target (OsCRY1a) of SDG724 in the clock pathway. Our results showed a regulatory relationship between OsLHY and SDG724, which paved the way for revealing the interaction between the circadian clock and histone H3K36 methylation.
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Affiliation(s)
- Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
- Correspondence: (C.S.); (X.D.)
| | - Shihang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Changcai He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Chao Zhong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Hongying Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Xu Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Ke Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Kuan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Qian Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Congping Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Yulin Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Bin Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Xiaoqiong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Peizhou Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Ting Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Shuangcheng Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Peng Qin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Pingrong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
| | - Chengcai Chu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
| | - Xiaojian Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (S.L.); (C.H.); (C.Z.); (H.L.); (X.L.); (K.L.); (K.Z.); (Q.W.); (C.C.); (Y.T.); (B.Y.); (X.C.); (P.X.); (T.Z.); (S.L.); (P.Q.); (P.W.)
- Correspondence: (C.S.); (X.D.)
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6
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Liu M, Jiang J, Han Y, Shi M, Li X, Wang Y, Dong Z, Yang C. Functional Characterization of the Lysine-Specific Histone Demethylases Family in Soybean. PLANTS 2022; 11:plants11111398. [PMID: 35684171 PMCID: PMC9182794 DOI: 10.3390/plants11111398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022]
Abstract
Histone modifications, such as methylation and demethylation, have crucial roles in regulating chromatin structure and gene expression. Lysine-specific histone demethylases (LSDs) belong to the amine oxidase family, which is an important family of histone lysine demethylases (KDMs), and functions in maintaining homeostasis of histone methylation. Here, we identified six LSD-like (LDL) genes from the important leguminous soybean. Phylogenetic analyses divided the six GmLDLs into four clusters with two highly conserved SWRIM and amine oxidase domains. Indeed, demethylase activity assay using recombinant GmLDL proteins in vitro demonstrated that GmLDLs have demethylase activity toward mono- and dimethylated Lys4 but not trimethylated histone 3, similar to their orthologs previously reported in animals. Using real-time PCR experiments in combination with public transcriptome data, we found that these six GmLDL genes exhibit comparable expressions in multiple tissues or in response to different abiotic stresses. Moreover, our genetic variation investigation of GmLDL genes among 761 resequenced soybean accessions indicates that GmLDLs are well conserved during soybean domestication and improvement. Taken together, these findings demonstrate that GmFLD, GmLDL1a, and GmLDL1b are bona fide H3K4 demethylases towards H4K4me1/2 and GmLDLs exist in various members with likely conserved and divergent roles in soybeans.
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Affiliation(s)
- Mengshi Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Subcenter of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (M.L.); (J.J.); (M.S.); (X.L.)
| | - Jiacan Jiang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Subcenter of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (M.L.); (J.J.); (M.S.); (X.L.)
| | - Yapeng Han
- State Key Laboratory of Genetic Engineering and Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200240, China; (Y.H.); (Y.W.)
| | - Mengying Shi
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Subcenter of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (M.L.); (J.J.); (M.S.); (X.L.)
| | - Xianli Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Subcenter of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (M.L.); (J.J.); (M.S.); (X.L.)
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Institute of Genetics, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200240, China; (Y.H.); (Y.W.)
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China
- College of Life Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhicheng Dong
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
- Correspondence: (Z.D.); (C.Y.)
| | - Cunyi Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, Guangdong Subcenter of National Center for Soybean Improvement, College of Agriculture, South China Agricultural University, Guangzhou 510642, China; (M.L.); (J.J.); (M.S.); (X.L.)
- Correspondence: (Z.D.); (C.Y.)
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7
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Uehara TN, Nonoyama T, Taki K, Kuwata K, Sato A, Fujimoto KJ, Hirota T, Matsuo H, Maeda AE, Ono A, Takahara TT, Tsutsui H, Suzuki T, Yanai T, Kay SA, Itami K, Kinoshita T, Yamaguchi J, Nakamichi N. Phosphorylation of RNA Polymerase II by CDKC;2 Maintains the Arabidopsis Circadian Clock Period. PLANT & CELL PHYSIOLOGY 2022; 63:450-462. [PMID: 35086143 PMCID: PMC9016870 DOI: 10.1093/pcp/pcac011] [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] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/19/2022] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The circadian clock is an internal timekeeping system that governs about 24 h biological rhythms of a broad range of developmental and metabolic activities. The clocks in eukaryotes are thought to rely on lineage-specific transcriptional-translational feedback loops. However, the mechanisms underlying the basic transcriptional regulation events for clock function have not yet been fully explored. Here, through a combination of chemical biology and genetic approaches, we demonstrate that phosphorylation of RNA polymerase II by CYCLIN DEPENDENT KINASE C; 2 (CDKC;2) is required for maintaining the circadian period in Arabidopsis. Chemical screening identified BML-259, the inhibitor of mammalian CDK2/CDK5, as a compound lengthening the circadian period of Arabidopsis. Short-term BML-259 treatment resulted in decreased expression of most clock-associated genes. Development of a chemical probe followed by affinity proteomics revealed that BML-259 binds to CDKC;2. Loss-of-function mutations of cdkc;2 caused a long period phenotype. In vitro experiments demonstrated that the CDKC;2 immunocomplex phosphorylates the C-terminal domain of RNA polymerase II, and BML-259 inhibits this phosphorylation. Collectively, this study suggests that transcriptional activity maintained by CDKC;2 is required for proper period length, which is an essential feature of the circadian clock in Arabidopsis.
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Affiliation(s)
| | | | | | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Kazuhiro J Fujimoto
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Hiromi Matsuo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Akari E Maeda
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Azusa Ono
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Tomoaki T Takahara
- Department of Applied Chemistry, Waseda University, 513 Wasedatsurumakicho, Shinjuku, Tokyo, 162-0041 Japan
| | - Hiroki Tsutsui
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Takamasa Suzuki
- College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, 487-8501 Japan
| | - Takeshi Yanai
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Steve A Kay
- Keck School of Medicine, University of Southern California, 1975 Zonal Avenue, Los Angeles, CA 90033, USA
| | - Kenichiro Itami
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
- JST ERATO, Itami Molecular Nanocarbon Project, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
| | - Toshinori Kinoshita
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8601 Japan
| | - Junichiro Yamaguchi
- *Corresponding authors: Norihito Nakamichi, E-mail, ; Junichiro Yamaguchi, E-mail,
| | - Norihito Nakamichi
- *Corresponding authors: Norihito Nakamichi, E-mail, ; Junichiro Yamaguchi, E-mail,
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8
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Regulatory Role of Circadian Clocks on ABA Production and Signaling, Stomatal Responses, and Water-Use Efficiency under Water-Deficit Conditions. Cells 2022; 11:cells11071154. [PMID: 35406719 PMCID: PMC8997731 DOI: 10.3390/cells11071154] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/15/2022] [Accepted: 03/25/2022] [Indexed: 02/04/2023] Open
Abstract
Plants deploy molecular, physiological, and anatomical adaptations to cope with long-term water-deficit exposure, and some of these processes are controlled by circadian clocks. Circadian clocks are endogenous timekeepers that autonomously modulate biological systems over the course of the day–night cycle. Plants’ responses to water deficiency vary with the time of the day. Opening and closing of stomata, which control water loss from plants, have diurnal responses based on the humidity level in the rhizosphere and the air surrounding the leaves. Abscisic acid (ABA), the main phytohormone modulating the stomatal response to water availability, is regulated by circadian clocks. The molecular mechanism of the plant’s circadian clock for regulating stress responses is composed not only of transcriptional but also posttranscriptional regulatory networks. Despite the importance of regulatory impact of circadian clock systems on ABA production and signaling, which is reflected in stomatal responses and as a consequence influences the drought tolerance response of the plants, the interrelationship between circadian clock, ABA homeostasis, and signaling and water-deficit responses has to date not been clearly described. In this review, we hypothesized that the circadian clock through ABA directs plants to modulate their responses and feedback mechanisms to ensure survival and to enhance their fitness under drought conditions. Different regulatory pathways and challenges in circadian-based rhythms and the possible adaptive advantage through them are also discussed.
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9
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Wang X, Ke L, Wang S, Fu J, Xu J, Hao Y, Kang C, Guo W, Deng X, Xu Q. Variation burst during dedifferentiation and increased CHH-type DNA methylation after 30 years of in vitro culture of sweet orange. HORTICULTURE RESEARCH 2022; 9:uhab036. [PMID: 35039837 PMCID: PMC8824543 DOI: 10.1093/hr/uhab036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 01/18/2022] [Accepted: 10/15/2021] [Indexed: 06/14/2023]
Abstract
Somaclonal variation arising from tissue culture may provide a valuable resource for the selection of new germplasm, but may not preserve true-to-type characteristics, which is a major concern for germplasm conservation or genome editing. The genomic changes associated with dedifferentiation and somaclonal variation during long-term in vitro culture are largely unknown. Sweet orange was one of the earliest plant species to be cultured in vitro and induced via somatic embryogenesis. We compared four sweet orange callus lines after 30 years of constant tissue culture with newly induced calli by comprehensively determining the single-nucleotide polymorphisms, copy number variations, transposable element insertions, methylomic and transcriptomic changes. We identified a burst of variation during early dedifferentiation, including a retrotransposon outbreak, followed by a variation purge during long-term in vitro culture. Notably, CHH methylation showed a dynamic pattern, initially disappearing during dedifferentiation and then more than recovering after 30 years of in vitro culture. We also analyzed the effects of somaclonal variation on transcriptional reprogramming, and indicated subgenome dominance was evident in the tetraploid callus. We identified a retrotransposon insertion and DNA modification alternations in the potential regeneration-related gene CLAVATA3/EMBRYO SURROUNDING REGION-RELATED 16. This study provides the foundation to harness in vitro variation and offers a deeper understanding of the variation introduced by tissue culture during germplasm conservation, somatic embryogenesis, gene editing, and breeding programs.
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Affiliation(s)
- Xia Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Lili Ke
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Shuting Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Jialing Fu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Jidi Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Yujin Hao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Chunying Kang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Wenwu Guo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University,
No. 1, Shizishan Street, Wuhan 430070, China
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10
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Gao S, Zeng X, Wang J, Xu Y, Yu C, Huang Y, Wang F, Wu K, Yang S. Arabidopsis SUMO E3 Ligase SIZ1 Interacts with HDA6 and Negatively Regulates HDA6 Function during Flowering. Cells 2021; 10:cells10113001. [PMID: 34831226 PMCID: PMC8616286 DOI: 10.3390/cells10113001] [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: 07/26/2021] [Revised: 10/13/2021] [Accepted: 10/31/2021] [Indexed: 01/12/2023] Open
Abstract
The changes in histone acetylation mediated by histone deacetylases (HDAC) play a crucial role in plant development and response to environmental changes. Mammalian HDACs are regulated by post-translational modifications (PTM), such as phosphorylation, acetylation, ubiquitination and small ubiquitin-like modifier (SUMO) modification (SUMOylation), which affect enzymatic activity and transcriptional repression. Whether PTMs of plant HDACs alter their functions are largely unknown. In this study, we demonstrated that the Arabidopsis SUMO E3 ligase SAP AND MIZ1 DOMAIN-CONTAINING LIGASE1 (SIZ1) interacts with HISTONE DEACETYLASE 6 (HDA6) both in vitro and in vivo. Biochemical analyses indicated that HDA6 is not modified by SUMO1. Overexpression of HDA6 in siz1-3 background results in a decreased level of histone H3 acetylation, indicating that the activity of HDA6 is increased in siz1-3 plants. Chromatin immunoprecipitation (ChIP) assays showed that SIZ1 represses HDA6 binding to its target genes FLOWERING LOCUS C (FLC) and MADS AFFECTING FLOWERING 4 (MAF4), resulting in the upregulation of FLC and MAF4 by increasing the level of histone H3 acetylation. Together, these findings indicate that the Arabidopsis SUMO E3 ligase SIZ1 interacts with HDA6 and negatively regulates HDA6 function.
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Affiliation(s)
- Sujuan Gao
- Key Laboratory of Green Processing and Intelligent Manufacturing of Lingnan Specialty Food, College of Light Industry and Food Science, Zhongkai University of Agriculture and Engineering, Ministry of Agriculture, Guangzhou 510225, China;
| | - Xueqin Zeng
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (X.Z.); (F.W.)
| | - Jianhao Wang
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510000, China;
| | - Yingchao Xu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (Y.X.); (Y.H.)
| | - Chunwei Yu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan;
| | - Yishui Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (Y.X.); (Y.H.)
| | - Feng Wang
- Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (X.Z.); (F.W.)
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan;
- Correspondence: (K.W.); (S.Y.)
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; (Y.X.); (Y.H.)
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Correspondence: (K.W.); (S.Y.)
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11
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Tian W, Wang R, Bo C, Yu Y, Zhang Y, Shin GI, Kim WY, Wang L. SDC mediates DNA methylation-controlled clock pace by interacting with ZTL in Arabidopsis. Nucleic Acids Res 2021; 49:3764-3780. [PMID: 33675668 PMCID: PMC8053106 DOI: 10.1093/nar/gkab128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/13/2021] [Accepted: 02/16/2021] [Indexed: 12/29/2022] Open
Abstract
Molecular bases of eukaryotic circadian clocks mainly rely on transcriptional-translational feedback loops (TTFLs), while epigenetic codes also play critical roles in fine-tuning circadian rhythms. However, unlike histone modification codes that play extensive and well-known roles in the regulation of circadian clocks, whether DNA methylation (5mC) can affect the circadian clock, and the associated underlying molecular mechanisms, remains largely unexplored in many organisms. Here we demonstrate that global genome DNA hypomethylation can significantly lengthen the circadian period of Arabidopsis. Transcriptomic and genetic evidence demonstrate that SUPPRESSOR OF drm1 drm2 cmt3 (SDC), encoding an F-box containing protein, is required for the DNA hypomethylation-tuned circadian clock. Moreover, SDC can physically interact with another F-box containing protein ZEITLUPE (ZTL) to diminish its accumulation. Genetic analysis further revealed that ZTL and its substrate TIMING OF CAB EXPRESSION 1 (TOC1) likely act downstream of DNA methyltransferases to control circadian rhythm. Together, our findings support the notion that DNA methylation is important to maintain proper circadian pace in Arabidopsis, and further established that SDC links DNA hypomethylation with a proteolytic cascade to assist in tuning the circadian clock.
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Affiliation(s)
- Wenwen Tian
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Ruyi Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Cunpei Bo
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yingjun Yu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Yuanyuan Zhang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21Plus), Research Institute of Life Sciences (RILS) and Institute of Agricultural and Life Science(IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21Plus), Research Institute of Life Sciences (RILS) and Institute of Agricultural and Life Science(IALS), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People's Republic of China.,University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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12
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Kumar V, Thakur JK, Prasad M. Histone acetylation dynamics regulating plant development and stress responses. Cell Mol Life Sci 2021; 78:4467-4486. [PMID: 33638653 PMCID: PMC11072255 DOI: 10.1007/s00018-021-03794-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/21/2021] [Accepted: 02/18/2021] [Indexed: 12/17/2022]
Abstract
Crop productivity is directly dependent on the growth and development of plants and their adaptation during different environmental stresses. Histone acetylation is an epigenetic modification that regulates numerous genes essential for various biological processes, including development and stress responses. Here, we have mainly discussed the impact of histone acetylation dynamics on vegetative growth, flower development, fruit ripening, biotic and abiotic stress responses. Besides, we have also emphasized the information gaps which are obligatory to be examined for understanding the complete role of histone acetylation dynamics in plants. A comprehensive knowledge about the histone acetylation dynamics will ultimately help to improve stress resistance and reduce yield losses in different crops due to climate changes.
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Affiliation(s)
- Verandra Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Thakur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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13
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Noh SW, Seo RR, Park HJ, Jung HW. Two Arabidopsis Homologs of Human Lysine-Specific Demethylase Function in Epigenetic Regulation of Plant Defense Responses. FRONTIERS IN PLANT SCIENCE 2021; 12:688003. [PMID: 34194459 PMCID: PMC8236864 DOI: 10.3389/fpls.2021.688003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/18/2021] [Indexed: 05/02/2023]
Abstract
Epigenetic marks such as covalent histone modification and DNA methylation are crucial for mitotically and meiotically inherited cellular memory-based plant immunity. However, the roles of individual players in the epigenetic regulation of plant immunity are not fully understood. Here we reveal the functions of two Arabidopsis thaliana homologs of human lysine-specific demethylase1-like1, LDL1 and LDL2, in the maintenance of methyl groups at lysine 4 of histone H3 and in plant immunity to Pseudomonas syringae infection. The growth of virulent P. syringae strains was reduced in ldl1 and ldl2 single mutants compared to wild-type plants. Local and systemic disease resistance responses, which coincided with the rapid, robust transcription of defense-related genes, were more stably expressed in ldl1 ldl2 double mutants than in the single mutants. At the nucleosome level, mono-methylated histone H3K4 accumulated in ldl1 ldl2 plants genome-wide and in the mainly promoter regions of the defense-related genes examined in this study. Furthermore, in silico comparative analysis of RNA-sequencing and chromatin immunoprecipitation data suggested that several WRKY transcription factors, e.g., WRKY22/40/70, might be partly responsible for the enhanced immunity of ldl1 ldl2. These findings suggest that LDL1 and LDL2 control the transcriptional sensitivity of a group of defense-related genes to establish a primed defense response in Arabidopsis.
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Affiliation(s)
- Seong Woo Noh
- Department of Applied Bioscience, Dong-A University, Busan, South Korea
| | - Ri-Ra Seo
- Department of Applied Bioscience, Dong-A University, Busan, South Korea
| | - Hee Jin Park
- Institute of Agricultural Life Science, Dong-A University, Busan, South Korea
- *Correspondence: Hee Jin Park,
| | - Ho Won Jung
- Institute of Agricultural Life Science, Dong-A University, Busan, South Korea
- Department of Molecular Genetics, Dong-A University, Busan, South Korea
- Ho Won Jung,
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14
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Plant Volatile Organic Compounds Evolution: Transcriptional Regulation, Epigenetics and Polyploidy. Int J Mol Sci 2020; 21:ijms21238956. [PMID: 33255749 PMCID: PMC7728353 DOI: 10.3390/ijms21238956] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/18/2020] [Accepted: 11/23/2020] [Indexed: 12/15/2022] Open
Abstract
Volatile organic compounds (VOCs) are emitted by plants as a consequence of their interaction with biotic and abiotic factors, and have a very important role in plant evolution. Floral VOCs are often involved in defense and pollinator attraction. These interactions often change rapidly over time, so a quick response to those changes is required. Epigenetic factors, such as DNA methylation and histone modification, which regulate both genes and transcription factors, might trigger adaptive responses to these evolutionary pressures as well as regulating the rhythmic emission of VOCs through circadian clock regulation. In addition, transgenerational epigenetic effects and whole genome polyploidy could modify the generation of VOCs’ profiles of offspring, contributing to long-term evolutionary shifts. In this article, we review the available knowledge about the mechanisms that may act as epigenetic regulators of the main VOC biosynthetic pathways, and their importance in plant evolution.
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15
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de Rooij PGH, Perrella G, Kaiserli E, van Zanten M. The diverse and unanticipated roles of histone deacetylase 9 in coordinating plant development and environmental acclimation. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6211-6225. [PMID: 32687569 PMCID: PMC7586748 DOI: 10.1093/jxb/eraa335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/15/2020] [Indexed: 05/04/2023]
Abstract
Plants tightly control gene transcription to adapt to environmental conditions and steer growth and development. Different types of epigenetic modifications are instrumental in these processes. In recent years, an important role for the chromatin-modifying RPD3/HDA1 class I HDAC HISTONE DEACETYLASE 9 (HDA9) emerged in the regulation of a multitude of plant traits and responses. HDACs are widely considered transcriptional repressors and are typically part of multiprotein complexes containing co-repressors, DNA, and histone-binding proteins. By catalyzing the removal of acetyl groups from lysine residues of histone protein tails, HDA9 negatively controls gene expression in many cases, in concert with interacting proteins such as POWERDRESS (PWR), HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 15 (HOS15), WRKY53, ELONGATED HYPOCOTYL 5 (HY5), ABA INSENSITIVE 4 (ABI4), and EARLY FLOWERING 3 (ELF3). However, HDA9 activity has also been directly linked to transcriptional activation. In addition, following the recent breakthrough discovery of mutual negative feedback regulation between HDA9 and its interacting WRKY-domain transcription factor WRKY53, swift progress in gaining understanding of the biology of HDA9 is expected. In this review, we summarize knowledge on this intriguing versatile-and long under-rated-protein and propose novel leads to further unravel HDA9-governed molecular networks underlying plant development and environmental biology.
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Affiliation(s)
- Peter G H de Rooij
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan, CH Utrecht, The Netherlands
| | - Giorgio Perrella
- Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- ENEA - Trisaia Research Centre 75026, Rotondella (Matera), Italy
| | - Eirini Kaiserli
- Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan, CH Utrecht, The Netherlands
- Correspondence:
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16
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Maric A, Mas P. Chromatin Dynamics and Transcriptional Control of Circadian Rhythms in Arabidopsis. Genes (Basel) 2020; 11:E1170. [PMID: 33036236 PMCID: PMC7601625 DOI: 10.3390/genes11101170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/01/2020] [Accepted: 10/04/2020] [Indexed: 02/06/2023] Open
Abstract
Circadian rhythms pervade nearly all aspects of plant growth, physiology, and development. Generation of the rhythms relies on an endogenous timing system or circadian clock that generates 24-hour oscillations in multiple rhythmic outputs. At its bases, the plant circadian function relies on dynamic interactive networks of clock components that regulate each other to generate rhythms at specific phases during the day and night. From the initial discovery more than 13 years ago of a parallelism between the oscillations in chromatin status and the transcriptional rhythms of an Arabidopsis clock gene, a number of studies have later expanded considerably our view on the circadian epigenome and transcriptome landscapes. Here, we describe the most recent identification of chromatin-related factors that are able to directly interact with Arabidopsis clock proteins to shape the transcriptional waveforms of circadian gene expression and clock outputs. We discuss how changes in chromatin marks associate with transcript initiation, elongation, and the rhythms of nascent RNAs, and speculate on future interesting research directions in the field.
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Affiliation(s)
- Aida Maric
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain;
| | - Paloma Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193 Barcelona, Spain;
- Consejo Superior de Investigaciones Científicas (CSIC), 08028 Barcelona, Spain
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17
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Hung FY, Chen C, Yen MR, Hsieh JWA, Li C, Shih YH, Chen FF, Chen PY, Cui Y, Wu K. The expression of long non-coding RNAs is associated with H3Ac and H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex in Arabidopsis. NAR Genom Bioinform 2020; 2:lqaa066. [PMID: 33575615 PMCID: PMC7671367 DOI: 10.1093/nargab/lqaa066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 07/21/2020] [Accepted: 08/25/2020] [Indexed: 01/03/2023] Open
Abstract
In recent years, eukaryotic long non-coding RNAs (lncRNAs) have been identified as important factors involved in a wide variety of biological processes, including histone modification, alternative splicing and transcription enhancement. The expression of lncRNAs is highly tissue-specific and is regulated by environmental stresses. Recently, a large number of plant lncRNAs have been identified, but very few of them have been studied in detail. Furthermore, the mechanism of lncRNA expression regulation remains largely unknown. Arabidopsis HISTONE DEACETYLASE 6 (HDA6) and LSD1-LIKE 1/2 (LDL1/2) can repress gene expression synergistically by regulating H3Ac/H3K4me. In this research, we performed RNA-seq and ChIP-seq analyses to further clarify the function of HDA6-LDL1/2. Our results indicated that the global expression of lncRNAs is increased in hda6/ldl1/2 and that this increased lncRNA expression is particularly associated with H3Ac/H3K4me2 changes. In addition, we found that HDA6-LDL1/2 is important for repressing lncRNAs that are non-expressed or show low-expression, which may be strongly associated with plant development. GO-enrichment analysis also revealed that the neighboring genes of the lncRNAs that are upregulated in hda6/ldl1/2 are associated with various developmental processes. Collectively, our results revealed that the expression of lncRNAs is associated with H3Ac/H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex.
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Affiliation(s)
- Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei 10617 Taiwan
| | - Chen Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON N5V 4T3 Canada
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | | | - Chenlong Li
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON N5V 4T3 Canada
| | - Yuan-Hsin Shih
- Institute of Plant Biology, National Taiwan University, Taipei 10617 Taiwan
| | - Fang-Fang Chen
- Institute of Plant Biology, National Taiwan University, Taipei 10617 Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON N5V 4T3 Canada
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 10617 Taiwan
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18
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Jiang J, Ding AB, Liu F, Zhong X. Linking signaling pathways to histone acetylation dynamics in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5179-5190. [PMID: 32333777 PMCID: PMC7475247 DOI: 10.1093/jxb/eraa202] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/22/2020] [Indexed: 05/04/2023]
Abstract
As sessile organisms, plants face versatile environmental challenges and require proper responses at multiple levels for survival. Epigenetic modification of DNA and histones is a conserved gene-regulatory mechanism and plays critical roles in diverse aspects of biological processes, ranging from genome defense and imprinting to development and physiology. In recent years, emerging studies have revealed the interplay between signaling transduction pathways, epigenetic modifications, and chromatin cascades. Specifically, histone acetylation and deacetylation dictate plant responses to environmental cues by modulating chromatin dynamics to regulate downstream gene expression as signaling outputs. In this review, we summarize current understandings of the link between plant signaling pathways and epigenetic modifications with a focus on histone acetylation and deacetylation.
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Affiliation(s)
- Jianjun Jiang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu, China
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Adeline B Ding
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
| | - Fengquan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of Ministry of Science and Technology, Nanjing, Jiangsu, China
- Correspondence: or
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, USA
- Correspondence: or
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19
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Lin J, Hung FY, Ye C, Hong L, Shih YH, Wu K, Li QQ. HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis. Genome Res 2020; 30:1407-1417. [PMID: 32759225 PMCID: PMC7605263 DOI: 10.1101/gr.255232.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 07/28/2020] [Indexed: 12/21/2022]
Abstract
Eukaryotic histone deacetylation, critical for maintaining nucleosome structure and regulating gene expression, is mediated by histone deacetylases (HDACs). Although nucleosomes have been reported to regulate mRNA polyadenylation in humans, the role of HDACs in regulating polyadenylation has not been uncovered. Taking advantage of phenotypic studies on Arabidopsis, HDA6 (one of HDACs) was found to be a critical part of many biological processes. Here, we report that HDA6 affects mRNA polyadenylation in Arabidopsis. Poly(A) sites of up-regulated transcripts are closer to the histone acetylation peaks in hda6 compared to the wild-type Col-0. HDA6 is required for the deacetylation of histones around DNA on nucleosomes, which solely coincides with up-regulated or uniquely presented poly(A) sites in hda6. Furthermore, defective HDA6 results in an overrepresentation of the canonical poly(A) signal (AAUAAA) usage. Chromatin loci for generating AAUAAA-type transcripts have a comparatively low H3K9K14ac around poly(A) sites when compared to other noncanonical poly(A) signal–containing transcripts. These results indicate that HDA6 regulates polyadenylation in a histone deacetylation–dependent manner in Arabidopsis.
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Affiliation(s)
- Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan 10617
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Liwei Hong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Yuan-Hsin Shih
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan 10617
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan 10617
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.,Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California 91766, USA
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20
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Ibáñez S, Carneros E, Testillano PS, Pérez-Pérez JM. Advances in Plant Regeneration: Shake, Rattle and Roll. PLANTS (BASEL, SWITZERLAND) 2020; 9:E897. [PMID: 32708602 PMCID: PMC7412315 DOI: 10.3390/plants9070897] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 01/23/2023]
Abstract
Some plant cells are able to rebuild new organs after tissue damage or in response to definite stress treatments and/or exogenous hormone applications. Whole plants can develop through de novo organogenesis or somatic embryogenesis. Recent findings have enlarged our understanding of the molecular and cellular mechanisms required for tissue reprogramming during plant regeneration. Genetic analyses also suggest the key role of epigenetic regulation during de novo plant organogenesis. A deeper understanding of plant regeneration might help us to enhance tissue culture optimization, with multiple applications in plant micropropagation and green biotechnology. In this review, we will provide additional insights into the physiological and molecular framework of plant regeneration, including both direct and indirect de novo organ formation and somatic embryogenesis, and we will discuss the key role of intrinsic and extrinsic constraints for cell reprogramming during plant regeneration.
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Grants
- BIO2015-64255-R Ministerio de Economía, Industria y Competitividad, Gobierno de España
- RTI2018-096505-B-I00 Ministerio de Economía, Industria y Competitividad, Gobierno de España
- AGL2017-82447-R Ministerio de Economía, Industria y Competitividad, Gobierno de España
- IDIFEDER 2018/016 Conselleria de Cultura, Educación y Ciencia, Generalitat Valenciana
- PROMETEO/2019/117 Conselleria de Cultura, Educación y Ciencia, Generalitat Valenciana
- ACIF/2018/220 Conselleria de Cultura, Educación y Ciencia, Generalitat Valenciana
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Affiliation(s)
- Sergio Ibáñez
- Instituto de Bioingeniería, Universidad Miguel Hernández, 03202 Elche, Spain;
| | - Elena Carneros
- Pollen Biotechnology of Crop Plants Group, Margarita Salas Center of Biological Research, CIB Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (E.C.); (P.S.T.)
| | - Pilar S. Testillano
- Pollen Biotechnology of Crop Plants Group, Margarita Salas Center of Biological Research, CIB Margarita Salas-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain; (E.C.); (P.S.T.)
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21
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Segregation of an MSH1 RNAi transgene produces heritable non-genetic memory in association with methylome reprogramming. Nat Commun 2020; 11:2214. [PMID: 32371941 PMCID: PMC7200659 DOI: 10.1038/s41467-020-16036-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 04/09/2020] [Indexed: 12/23/2022] Open
Abstract
MSH1 is a plant-specific protein. RNAi suppression of MSH1 results in phenotype variability for developmental and stress response pathways. Segregation of the RNAi transgene produces non-genetic msh1 ‘memory’ with multi-generational inheritance. First-generation memory versus non-memory comparison, and six-generation inheritance studies, identifies gene-associated, heritable methylation repatterning. Genome-wide methylome analysis integrated with RNAseq and network-based enrichment studies identifies altered circadian clock networks, and phytohormone and stress response pathways that intersect with circadian control. A total of 373 differentially methylated loci comprising these networks are sufficient to discriminate memory from nonmemory full sibs. Methylation inhibitor 5-azacytidine diminishes the differences between memory and wild type for growth, gene expression and methylation patterning. The msh1 reprogramming is dependent on functional HISTONE DEACETYLASE 6 and methyltransferase MET1, and transition to memory requires the RNA-directed DNA methylation pathway. This system of phenotypic plasticity may serve as a potent model for defining accelerated plant adaptation during environmental change. Segregation of an MSH1 RNAi transgene produces non-genetic memory that displays transgenerational inheritance in Arabidopsis. Here, the authors compare memory and non-memory full-sib progenies to show the involvement of DNA methylation reprogramming, involving the RdDM pathway, in transition to a heritable memory state.
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22
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Lindermayr C, Rudolf EE, Durner J, Groth M. Interactions between metabolism and chromatin in plant models. Mol Metab 2020; 38:100951. [PMID: 32199818 PMCID: PMC7300381 DOI: 10.1016/j.molmet.2020.01.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 01/10/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND One of the fascinating aspects of epigenetic regulation is that it provides means to rapidly adapt to environmental change. This is particularly relevant in the plant kingdom, where most species are sessile and exposed to increasing habitat fluctuations due to global warming. Although the inheritance of epigenetically controlled traits acquired through environmental impact is a matter of debate, it is well documented that environmental cues lead to epigenetic changes, including chromatin modifications, that affect cell differentiation or are associated with plant acclimation and defense priming. Still, in most cases, the mechanisms involved are poorly understood. An emerging topic that promises to reveal new insights is the interaction between epigenetics and metabolism. SCOPE OF REVIEW This study reviews the links between metabolism and chromatin modification, in particular histone acetylation, histone methylation, and DNA methylation, in plants and compares them to examples from the mammalian field, where the relationship to human diseases has already generated a larger body of literature. This study particularly focuses on the role of reactive oxygen species (ROS) and nitric oxide (NO) in modulating metabolic pathways and gene activities that are involved in these chromatin modifications. As ROS and NO are hallmarks of stress responses, we predict that they are also pivotal in mediating chromatin dynamics during environmental responses. MAJOR CONCLUSIONS Due to conservation of chromatin-modifying mechanisms, mammals and plants share a common dependence on metabolic intermediates that serve as cofactors for chromatin modifications. In addition, plant-specific non-CG methylation pathways are particularly sensitive to changes in folate-mediated one-carbon metabolism. Finally, reactive oxygen and nitrogen species may fine-tune epigenetic processes and include similar signaling mechanisms involved in environmental stress responses in plants as well as animals.
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Affiliation(s)
- Christian Lindermayr
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 München/Neuherberg, Germany.
| | - Eva Esther Rudolf
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 München/Neuherberg, Germany
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 München/Neuherberg, Germany
| | - Martin Groth
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 München/Neuherberg, Germany.
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23
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Toyoda Y, Matsunaga S. Lysine-Specific Demethylase Epigenetically Regulates Human and Plant Phenomena. CYTOLOGIA 2019. [DOI: 10.1508/cytologia.84.295] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yuma Toyoda
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science
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24
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Chen X, Ding AB, Zhong X. Functions and mechanisms of plant histone deacetylases. SCIENCE CHINA-LIFE SCIENCES 2019; 63:206-216. [PMID: 31879846 DOI: 10.1007/s11427-019-1587-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
Abstract
Lysine acetylation, one of the major types of post-translational modifications, plays critical roles in regulating gene expression and protein function. Histone deacetylases (HDACs) are responsible for removing acetyl groups from lysines of both histone and non-histone proteins. While tremendous progress has been made in understanding the function and mechanism of HDACs in animals in the past two decades, nearly half of the HDAC studies in plants were reported within the past five years. In this review, we summarize the major findings on plant HDACs, with a focus on the model plant Arabidopsis thaliana, and highlight the components, regulatory mechanisms, and biological functions of HDAC complexes.
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Affiliation(s)
- Xiangsong Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Adeline B Ding
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Xuehua Zhong
- Laboratory of Genetics & Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
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25
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Mackenzie SA, Kundariya H. Organellar protein multi-functionality and phenotypic plasticity in plants. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190182. [PMID: 31787051 PMCID: PMC6939364 DOI: 10.1098/rstb.2019.0182] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
With the increasing impact of climate instability on agricultural and ecological systems has come a heightened sense of urgency to understand plant adaptation mechanisms in more detail. Plant species have a remarkable ability to disperse their progeny to a wide range of environments, demonstrating extraordinary resiliency mechanisms that incorporate epigenetics and transgenerational stability. Surprisingly, some of the underlying versatility of plants to adapt to abiotic and biotic stress emerges from the neofunctionalization of organelles and organellar proteins. We describe evidence of possible plastid specialization and multi-functional organellar protein features that serve to enhance plant phenotypic plasticity. These features appear to rely on, for example, spatio-temporal regulation of plastid composition, and unusual interorganellar protein targeting and retrograde signalling features that facilitate multi-functionalization. Although we report in detail on three such specializations, involving MSH1, WHIRLY1 and CUE1 proteins in Arabidopsis, there is ample reason to believe that these represent only a fraction of what is yet to be discovered as we begin to elaborate cross-species diversity. Recent observations suggest that plant proteins previously defined in one context may soon be rediscovered in new roles and that much more detailed investigation of proteins that show subcellular multi-targeting may be warranted. This article is part of the theme issue ‘Linking the mitochondrial genotype to phenotype: a complex endeavour’.
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Affiliation(s)
- Sally A Mackenzie
- Departments of Biology and Plant Science, The Pennsylvania State University, 362 Frear North Building, University Park, PA 16802, USA
| | - Hardik Kundariya
- Departments of Biology and Plant Science, The Pennsylvania State University, 362 Frear North Building, University Park, PA 16802, USA
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26
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Hirakawa T, Kuwata K, Gallego ME, White CI, Nomoto M, Tada Y, Matsunaga S. LSD1-LIKE1-Mediated H3K4me2 Demethylation Is Required for Homologous Recombination Repair. PLANT PHYSIOLOGY 2019; 181:499-509. [PMID: 31366719 PMCID: PMC6776857 DOI: 10.1104/pp.19.00530] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/22/2019] [Indexed: 05/18/2023]
Abstract
Homologous recombination is a key process for maintaining genome integrity and diversity. In eukaryotes, the nucleosome structure of chromatin inhibits the progression of homologous recombination. The DNA repair and recombination protein RAD54 alters the chromatin structure via nucleosome sliding to enable homology searches. For homologous recombination to progress, appropriate recruitment and dissociation of RAD54 is required at the site of homologous recombination; however, little is known about the mechanism regulating RAD54 dynamics in chromatin. Here, we reveal that the histone demethylase LYSINE-SPECIFIC DEMETHYLASE1-LIKE 1 (LDL1) regulates the dissociation of RAD54 at damaged sites during homologous recombination repair in the somatic cells of Arabidopsis (Arabidopsis thaliana). Depletion of LDL1 leads to an overaccumulation of RAD54 at damaged sites with DNA double-strand breaks. Moreover, RAD54 accumulates at damaged sites by recognizing histone H3 Lys 4 di-methylation (H3K4me2); the frequency of the interaction between RAD54 and H3K4me2 increased in the ldl1 mutant with DNA double-strand breaks. We propose that LDL1 removes RAD54 at damaged sites by demethylating H3K4me2 during homologous recombination repair and thereby maintains genome stability in Arabidopsis.
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Affiliation(s)
- Takeshi Hirakawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Maria E Gallego
- Génétique, Reproduction et Développement, Unité de Mixte de Recherche, Centre National de la Recherche Scientifique 6293, Clermont Université, Institut National de la Santé et de la Recherche Médicale U1103, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Charles I White
- Génétique, Reproduction et Développement, Unité de Mixte de Recherche, Centre National de la Recherche Scientifique 6293, Clermont Université, Institut National de la Santé et de la Recherche Médicale U1103, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Mika Nomoto
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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27
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Song Q, Huang TY, Yu HH, Ando A, Mas P, Ha M, Chen ZJ. Diurnal regulation of SDG2 and JMJ14 by circadian clock oscillators orchestrates histone modification rhythms in Arabidopsis. Genome Biol 2019; 20:170. [PMID: 31429787 PMCID: PMC6892391 DOI: 10.1186/s13059-019-1777-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 07/29/2019] [Indexed: 11/23/2022] Open
Abstract
Background Circadian rhythms modulate growth and development in all organisms through interlocking transcriptional-translational feedback loops. The transcriptional loop involves chromatin modifications of central circadian oscillators in mammals and plants. However, the molecular basis for rhythmic epigenetic modifications and circadian regulation is poorly understood. Results Here we report a feedback relationship between diurnal regulation of circadian clock genes and histone modifications in Arabidopsis. On one hand, the circadian oscillators CCA1 and LHY regulate diurnal expression of genes coding for the eraser (JMJ14) directly and writer (SDG2) indirectly for H3K4me3 modification, leading to rhythmic H3K4me3 changes in target genes. On the other hand, expression of circadian oscillator genes including CCA1 and LHY is associated with H3K4me3 levels and decreased in the sdg2 mutant but increased in the jmj14 mutant. At the genome-wide level, diurnal rhythms of H3K4me3 and another histone mark H3K9ac are associated with diurnal regulation of 20–30% of the expressed genes. While the majority (86%) of H3K4me3 and H3K9ac target genes overlap, only 13% of morning-phased and 22% of evening-phased genes had both H3K4me3 and H3K9ac peaks, suggesting specific roles of different histone modifications in diurnal gene expression. Conclusions Circadian clock genes promote diurnal regulation of SDG2 and JMJ14 expression, which in turn regulate rhythmic histone modification dynamics for the clock and its output genes. This reciprocal regulatory module between chromatin modifiers and circadian clock oscillators orchestrates diurnal gene expression that governs plant growth and development. Electronic supplementary material The online version of this article (10.1186/s13059-019-1777-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qingxin Song
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tien-Yu Huang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Helen H Yu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Atsumi Ando
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Paloma Mas
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Misook Ha
- Samsung Advanced Institute of Technology, Samsung Electronics Corporation, Suwon, 443-803, South Korea.
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA. .,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA. .,State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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28
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Lee K, Mas P, Seo PJ. The EC-HDA9 complex rhythmically regulates histone acetylation at the TOC1 promoter in Arabidopsis. Commun Biol 2019; 2:143. [PMID: 31044168 PMCID: PMC6478914 DOI: 10.1038/s42003-019-0377-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 03/06/2019] [Indexed: 12/13/2022] Open
Abstract
Circadian clocks are conserved time-keeper mechanisms in some prokaryotes and higher eukaryotes. Chromatin modification is emerging as key regulatory mechanism for refining core clock gene expression. Rhythmic changes in histone marks are closely associated to the TIMING OF CAB EXPRESSION 1 (TOC1) Arabidopsis clock gene. However, the chromatin-related modifiers responsible for these marks remain largely unknown. Here, we uncover that the chromatin modifier HISTONE DEACETYLASE 9 (HDA9) and the Evening complex (EC) component EARLY FLOWERING 3 (ELF3) directly interact to regulate the declining phase of TOC1 after its peak expression. We found that HDA9 specifically binds to the TOC1 promoter through the interaction with ELF3. The EC-HDA9 complex promotes H3 deacetylation at the TOC1 locus, contributing to suppressing TOC1 expression during the night, the time of EC function. Therefore, we have identified the mechanism by which the circadian clock intertwines with chromatin-related components to shape the circadian waveforms of gene expression in Arabidopsis.
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Affiliation(s)
- Kyounghee Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419 Republic of Korea
| | - Paloma Mas
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Parc de Recerca Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419 Republic of Korea
- Department of Chemistry, Seoul National University, Seoul, 08826 Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
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29
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Abstract
Circadian rhythms in transcription ultimately result in oscillations of key biological processes. Understanding how transcriptional rhythms are generated in plants provides an opportunity for fine-tuning growth, development, and responses to the environment. Here, we present a succinct description of the plant circadian clock, briefly reviewing a number of recent studies but mostly emphasizing the components and mechanisms connecting chromatin remodeling with transcriptional regulation by the clock. The possibility that intergenomic interactions govern hybrid vigor through epigenetic changes at clock loci and the function of epialleles controlling clock output traits during crop domestication are also discussed.
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Affiliation(s)
- Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.,Department of Integrative Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Paloma Mas
- Center for Research in Agricultural Genomics (CRAG), Consortium CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, 08193, Barcelona, Spain. .,Consejo Superior de Investigaciones Científicas, 08028, Barcelona, Spain.
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McClung CR. The Plant Circadian Oscillator. BIOLOGY 2019; 8:E14. [PMID: 30870980 PMCID: PMC6466001 DOI: 10.3390/biology8010014] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/17/2019] [Accepted: 03/09/2019] [Indexed: 12/20/2022]
Abstract
It has been nearly 300 years since the first scientific demonstration of a self-sustaining circadian clock in plants. It has become clear that plants are richly rhythmic, and many aspects of plant biology, including photosynthetic light harvesting and carbon assimilation, resistance to abiotic stresses, pathogens, and pests, photoperiodic flower induction, petal movement, and floral fragrance emission, exhibit circadian rhythmicity in one or more plant species. Much experimental effort, primarily, but not exclusively in Arabidopsis thaliana, has been expended to characterize and understand the plant circadian oscillator, which has been revealed to be a highly complex network of interlocked transcriptional feedback loops. In addition, the plant circadian oscillator has employed a panoply of post-transcriptional regulatory mechanisms, including alternative splicing, adjustable rates of translation, and regulated protein activity and stability. This review focuses on our present understanding of the regulatory network that comprises the plant circadian oscillator. The complexity of this oscillatory network facilitates the maintenance of robust rhythmicity in response to environmental extremes and permits nuanced control of multiple clock outputs. Consistent with this view, the clock is emerging as a target of domestication and presents multiple targets for targeted breeding to improve crop performance.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA.
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Lee HG, Hong C, Seo PJ. The Arabidopsis Sin3-HDAC Complex Facilitates Temporal Histone Deacetylation at the CCA1 and PRR9 Loci for Robust Circadian Oscillation. FRONTIERS IN PLANT SCIENCE 2019; 10:171. [PMID: 30833956 PMCID: PMC6387943 DOI: 10.3389/fpls.2019.00171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/01/2019] [Indexed: 06/09/2023]
Abstract
The circadian clock synchronizes endogenous rhythmic processes with environmental cycles and maximizes plant fitness. Multiple regulatory layers shape circadian oscillation, and chromatin modification is emerging as an important scheme for precise circadian waveforms. Here, we report the role of an evolutionarily conserved Sin3-histone deacetylase complex (HDAC) in circadian oscillation in Arabidopsis. SAP30 FUNCTION-RELATED 1 (AFR1) and AFR2, which are key components of Sin3-HDAC complex, are circadianly-regulated and possibly facilitate the temporal formation of the Arabidopsis Sin3-HDAC complex at dusk. The evening-expressed AFR proteins bind directly to the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and PSEUDO-RESPONSE REGULATOR 9 (PRR9) promoters and catalyze histone 3 (H3) deacetylation at the cognate regions to repress expression, allowing the declining phase of their expression at dusk. In support, the CCA1 and PRR9 genes were de-repressed around dusk in the afr1-1afr2-1 double mutant. These findings indicate that periodic histone deacetylation at the morning genes by the Sin3-HDAC complex contributes to robust circadian maintenance in higher plants.
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Affiliation(s)
- Hong Gil Lee
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Cheljong Hong
- Department of Chemistry, Seoul National University, Seoul, South Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, South Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
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Du S, Chen L, Ge L, Huang W. A Novel Loop: Mutual Regulation Between Epigenetic Modification and the Circadian Clock. FRONTIERS IN PLANT SCIENCE 2019; 10:22. [PMID: 30761168 PMCID: PMC6362098 DOI: 10.3389/fpls.2019.00022] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/08/2019] [Indexed: 05/26/2023]
Abstract
In response to periodic environmental fluctuations generated by the rotation of the earth, nearly all organisms have evolved an intrinsic timekeeper, the circadian clock, which can maintain approximate 24-h rhythmic oscillations in biological processes, ultimately conferring fitness benefits. In the model plant Arabidopsis, the core mechanics of the circadian clock can be described as a complex regulatory network of three feedback loops composed of core oscillator genes. Transcriptional regulation of each oscillator gene is necessary to maintain the structure of the circadian clock. As a gene transcription regulatory mechanism, the epigenetic modification of chromatin affects the spatiotemporal expression of multiple genes. Accumulating evidence indicates that epigenetic modification is associated with circadian clock function in animals and plants. In addition, the rhythms of epigenetic modification have a significant influence on the timing of molecular processes, including gene transcription. In this review, we summarize recent progress in research on the roles of histone acetylation, methylation, and phosphorylation in the regulation of clock gene expression in Arabidopsis.
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Affiliation(s)
- Shenxiu Du
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Liang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Liangfa Ge
- Department of Grassland Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Wei Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
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Hung FY, Chen FF, Li C, Chen C, Chen JH, Cui Y, Wu K. The LDL1/2-HDA6 Histone Modification Complex Interacts With TOC1 and Regulates the Core Circadian Clock Components in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2019; 10:233. [PMID: 30863422 PMCID: PMC6399392 DOI: 10.3389/fpls.2019.00233] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 02/12/2019] [Indexed: 05/18/2023]
Abstract
In Arabidopsis, the circadian rhythm is associated with multiple important biological processes and maintained by multiple interconnected loops that generate robust rhythms. The circadian clock central loop is a negative feedback loop composed of the core circadian clock components. TOC1 (TIMING OF CAB EXPRESSION 1) is highly expressed in the evening and negatively regulates the expression of CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)/LHY (LATE ELONGATED HYPOCOTYL). CCA1/LHY also binds to the promoter of TOC1 and represses the TOC1 expression. Our recent research revealed that the histone modification complex comprising of LYSINE-SPECIFIC DEMETHYLASE 1 (LSD1)-LIKE 1/2 (LDL1/2) and HISTONE DEACETYLASE 6 (HDA6) can be recruited by CCA1/LHY to repress TOC1 expression. In this study, we found that HDA6, LDL1, and LDL2 can interact with TOC1, and the LDL1/2-HDA6 complex is associate with TOC1 to repress the CCA1/LHY expression. Furthermore, LDL1/2-HDA6 and TOC1 co-target a subset of genes involved in the circadian rhythm. Collectively, our results indicate that the LDL1/2-HDA6 histone modification complex is important for the regulation of the core circadian clock components.
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Affiliation(s)
- Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
| | - Fang-Fang Chen
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Chenlong Li
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
- Department of Biology, Western University, London, ON, Canada
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resource, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chen Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
- Department of Biology, Western University, London, ON, Canada
| | - Jian-Hao Chen
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON, Canada
- Department of Biology, Western University, London, ON, Canada
- *Correspondence: Yuhai Cui, Keqiang Wu,
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, Taiwan
- *Correspondence: Yuhai Cui, Keqiang Wu,
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Yang P, Wang J, Huang FY, Yang S, Wu K. The Plant Circadian Clock and Chromatin Modifications. Genes (Basel) 2018; 9:genes9110561. [PMID: 30463332 PMCID: PMC6266252 DOI: 10.3390/genes9110561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 10/27/2018] [Accepted: 11/05/2018] [Indexed: 12/20/2022] Open
Abstract
The circadian clock is an endogenous timekeeping network that integrates environmental signals with internal cues to coordinate diverse physiological processes. The circadian function depends on the precise regulation of rhythmic gene expression at the core of the oscillators. In addition to the well-characterized transcriptional feedback regulation of several clock components, additional regulatory mechanisms, such as alternative splicing, regulation of protein stability, and chromatin modifications are beginning to emerge. In this review, we discuss recent findings in the regulation of the circadian clock function in Arabidopsis thaliana. The involvement of chromatin modifications in the regulation of the core circadian clock genes is also discussed.
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Affiliation(s)
- Ping Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China.
| | - Jianhao Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China.
| | - Fu-Yu Huang
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan.
| | - Songguang Yang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan.
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