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Yu G, Chen D, Ye M, Wu X, Zhu Z, Shen Y, Mehareb EM, Esh A, Raza G, Wang K, Wang Q, Jin JB. H3K27 demethylase SsJMJ4 negatively regulates drought-stress responses in sugarcane. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:3040-3053. [PMID: 38310636 DOI: 10.1093/jxb/erae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/02/2024] [Indexed: 02/06/2024]
Abstract
Sugarcane (Saccharum spp.), a leading sugar and energy crop, is seriously impacted by drought stress. However, the molecular mechanisms underlying sugarcane drought resistance, especially the functions of epigenetic regulators, remain elusive. Here, we show that a S. spontaneum KDM4/JHDM3 group JmjC protein, SsJMJ4, negatively regulates drought-stress responses through its H3K27me3 demethylase activity. Ectopic overexpression of SsJMJ4 in Arabidopsis reduced drought resistance possibly by promoting expression of AtWRKY54 and AtWRKY70, encoding two negative regulators of drought stress. SsJMJ4 directly bound to AtWRKY54 and AtWRKY70, and reduced H3K27me3 levels at these loci to ensure their proper transcription under normal conditions. Drought stress down-regulated both transcription and protein abundance of SsJMJ4, which was correlated with the reduced occupancy of SsJMJ4 at AtWRKY54 and AtWRKY70 chromatin, increased H3K27me3 levels at these loci, as well as reduced transcription levels of these genes. In S. spontaneum, drought stress-repressed transcription of SsWRKY122, an ortholog of AtWRKY54 and AtWRKY70, was associated with increased H3K27me3 levels at these loci. Transient overexpression of SsJMJ4 in S. spontaneum protoplasts raised transcription of SsWRKY122, paralleled with reduced H3K27me3 levels at its loci. These results suggest that the SsJMJ4-mediated dynamic deposition of H3K27me3 is required for an appropriate response to drought stress.
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Affiliation(s)
- Guangrun Yu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Daoqian Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Meiling Ye
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Xiaoge Wu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Zhiying Zhu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Yan Shen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Eid M Mehareb
- Sugar Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Ayman Esh
- Sugar Crops Research Institute, Agricultural Research Center, Giza 12619, Egypt
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, 38000, Pakistan
| | - Kai Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- School of Life Sciences, Nantong University, Nantong 226019, China
| | - Qiongli Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jing Bo Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
- Academician Workstation of Agricultural High-tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying, Shandong, China
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2
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Wang S, Zhang C, Chen R, Cheng K, Ma L, Wang W, Yang N. H 2S is involved in drought-mediated stomatal closure through PLDα1 in Arabidopsis. PLANTA 2024; 259:142. [PMID: 38702456 DOI: 10.1007/s00425-024-04421-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
MAIN CONCLUSION PLDα1 promoted H2S production by positively regulating the expression of LCD. Stomatal closure promoted by PLDα1 required the accumulation of H2S under drought stress. Phospholipase Dα1 (PLDα1) acting as one of the signal enzymes can respond to drought stress. It is well known that hydrogen sulfide (H2S) plays an important role in plant responding to biotic or abiotic stress. In this study, the functions and relationship between PLDα1 and H2S in drought stress resistance in Arabidopsis were explored. Our results indicated that drought stress promotes PLDα1 and H2S production by inducing the expression of PLDα1 and LCD genes. PLDα1 and LCD enhanced plant tolerance to drought by regulating membrane lipid peroxidation, proline accumulation, H2O2 content and stomatal closure. Under drought stress, the H2O2 content of PLDα1-deficient mutant (pldα1), L-cysteine desulfhydrase (LCD)-deficient mutant (lcd) was higher than that of ecotype (WT), the stomatal aperture of pldα1 and lcd was larger than that of WT. The transcriptional and translational levels of LCD were lower in pldα1 than that in WT. Exogenous application of the H2S donor NaHS or GYY reduced the stomatal aperture of WT, pldα1, PLDα1-CO, and PLDα1-OE lines, while exogenous application of the H2S scavenger hypotaurine (HT) increased the stomatal aperture. qRT-PCR analysis of stomatal movement-related genes showed that the expression of CAX1, ABCG5, SCAB1, and SLAC1 genes in pldα1 and lcd were down-regulated, while ACA1 and OST1 gene expression was significantly up-regulated. Thus, PLDα1 and LCD are required for stomatal closure to improve drought stress tolerance.
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Affiliation(s)
- Simin Wang
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Cuixia Zhang
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Rongshan Chen
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Kailin Cheng
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Liai Ma
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Wei Wang
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Ning Yang
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China.
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3
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Jia J, Luo Y, Wu Z, Ji Y, Liu S, Shu J, Chen B, Liu J. OsJMJ718, a histone demethylase gene, positively regulates seed germination in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:191-202. [PMID: 38116956 DOI: 10.1111/tpj.16600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/27/2023] [Accepted: 12/09/2023] [Indexed: 12/21/2023]
Abstract
Seed vigor has major impact on the rate and uniformity of seedling growth, crop yield, and quality. However, the epigenetic regulatory mechanism of crop seed vigor remains unclear. In this study, a (jumonji C) JmjC gene of the histone lysine demethylase OsJMJ718 was cloned in rice, and its roles in seed germination and its epigenetic regulation mechanism were investigated. OsJMJ718 was located in the nucleus and was engaged in H3K9 methylation. Histochemical GUS staining analysis revealed OsJMJ718 was highly expressed in seed embryos. Abiotic stress strongly induced the OsJMJ718 transcriptional accumulation level. Germination percentage and seedling vigor index of OsJMJ718 knockout lines (OsJMJ718-CR) were lower than those of the wild type (WT). Chromatin immunoprecipitation followed by sequencing (ChIP-seq) of seeds imbibed for 24 h showed an increase in H3K9me3 deposition of thousands of genes in OsJMJ718-CR. ChIP-seq results and transcriptome analysis showed that differentially expressed genes were enriched in ABA and ethylene signal transduction pathways. The content of ABA in OsJMJ718-CR was higher than that in WT seeds. OsJMJ718 overexpression enhanced sensitivity to ABA during germination and early seedling growth. In the seed imbibition stage, ABA and ethylene content diminished and augmented, separately, suggesting that OsJMJ718 may adjust rice seed germination through the ABA and ethylene signal transduction pathways. This study displayed the important function of OsJMJ718 in adjusting rice seed germination and vigor, which will provide an essential reference for practical issues, such as improving rice vigor and promoting direct rice sowing production.
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Affiliation(s)
- Junting Jia
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yongjian Luo
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Zhiyuan Wu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yufang Ji
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Shuangxing Liu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jie Shu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Bingxian Chen
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jun Liu
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
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4
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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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5
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Nishio H, Kawakatsu T, Yamaguchi N. Beyond heat waves: Unlocking epigenetic heat stress memory in Arabidopsis. PLANT PHYSIOLOGY 2024; 194:1934-1951. [PMID: 37878744 DOI: 10.1093/plphys/kiad558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/27/2023]
Abstract
Plants remember their exposure to environmental changes and respond more effectively the next time they encounter a similar change by flexibly altering gene expression. Epigenetic mechanisms play a crucial role in establishing such memory of environmental changes and fine-tuning gene expression. With the recent advancements in biochemistry and sequencing technologies, it has become possible to characterize the dynamics of epigenetic changes on scales ranging from short term (minutes) to long term (generations). Here, our main focus is on describing the current understanding of the temporal regulation of histone modifications and chromatin changes during exposure to short-term recurring high temperatures and reevaluating them in the context of natural environments. Investigations of the dynamics of histone modifications and chromatin structural changes in Arabidopsis after repeated exposure to heat at short intervals have revealed the detailed molecular mechanisms of short-term heat stress memory, which include histone modification enzymes, chromatin remodelers, and key transcription factors. In addition, we summarize the spatial regulation of heat responses. Based on the natural temperature patterns during summer, we discuss how plants cope with recurring heat stress occurring at various time intervals by utilizing 2 distinct types of heat stress memory mechanisms. We also explore future research directions to provide a more precise understanding of the epigenetic regulation of heat stress memory.
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Affiliation(s)
- Haruki Nishio
- Data Science and AI Innovation Research Promotion Center, Shiga University, Shiga 522-8522, Japan
- Center for Ecological Research, Kyoto University, Shiga 520-2113, Japan
| | - Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
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6
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Yang L, Xu L, Guo J, Li A, Qi H, Wang J, Song S. SNAC1-OsERF103-OsSDG705 module mediates drought response in rice. THE NEW PHYTOLOGIST 2024; 241:2480-2494. [PMID: 38296835 DOI: 10.1111/nph.19552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Drought stress profoundly hampers both plant growth and crop yield. To combat this, plants have evolved intricate transcriptional regulation mechanisms as a pivotal strategy. Through a genetic screening with rice genome-scale mutagenesis pool under drought stress, we identified an APETALA2/Ethylene Responsive Factor, namely OsERF103, positively responds to drought tolerance in rice. Combining chromatin immunoprecipitation sequencing and RNA sequencing analyses, we pinpointed c. 1000 genes directly influenced by OsERF103. Further results revealed that OsERF103 interacts with Stress-responsive NAC1 (SNAC1), a positive regulator of drought tolerance in rice, to synergistically regulate the expression of key drought-related genes, such as OsbZIP23. Moreover, we found that OsERF103 recruits a Su(var)3-9,enhancer of zeste and trithorax-domain group protein 705, which encodes a histone 3 lysine 4 (H3K4)-specific methyltransferase to specifically affect the deposition of H3K4me3 at loci like OsbZIP23 and other genes linked to dehydration responses. Additionally, the natural alleles of OsERF103 are selected during the domestication of both indica and japonica rice varieties and exhibit significant geographic distribution. Collectively, our findings have unfurled a comprehensive mechanistic framework underlying the OsERF103-mediated cascade regulation of drought response. This discovery not only enhances our understanding of drought signaling but also presents a promising avenue for the genetic improvement of drought-tolerant rice cultivars.
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Affiliation(s)
- Lijia Yang
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Liang Xu
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jiazhuo Guo
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Aipeng Li
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Haoyue Qi
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jiaxuan Wang
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shiyong Song
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
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7
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Zhang H, Jin Z, Cui F, Zhao L, Zhang X, Chen J, Zhang J, Li Y, Li Y, Niu Y, Zhang W, Gao C, Fu X, Tong Y, Wang L, Ling HQ, Li J, Xiao J. Epigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat. Nat Commun 2023; 14:8238. [PMID: 38086830 PMCID: PMC10716289 DOI: 10.1038/s41467-023-44003-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
The breeding of crops with improved nitrogen use efficiency (NUE) is crucial for sustainable agriculture, but the involvement of epigenetic modifications remains unexplored. Here, we analyze the chromatin landscapes of two wheat cultivars (KN9204 and J411) that differ in NUE under varied nitrogen conditions. The expression of nitrogen metabolism genes is closely linked to variation in histone modification instead of differences in DNA sequence. Epigenetic modifications exhibit clear cultivar-specificity, which likely contributes to distinct agronomic traits. Additionally, low nitrogen (LN) induces H3K27ac and H3K27me3 to significantly enhance root growth in KN9204, while remarkably inducing NRT2 in J411. Evidence from histone deacetylase inhibitor treatment and transgenic plants with loss function of H3K27me3 methyltransferase shows that changes in epigenetic modifications could alter the strategy preference for root development or nitrogen uptake in response to LN. Here, we show the importance of epigenetic regulation in mediating cultivar-specific adaptation to LN in wheat.
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Affiliation(s)
- Hao Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiyuan Jin
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050024, China
| | - Fa Cui
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China
| | - Long Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyu Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinchao Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanyan Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, Hebei, China
| | - Yongpeng Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, Hebei, China
| | - Yanxiao Niu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, Hebei Normal University, Shijiazhuang, 050024, China
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050024, China
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, CICMCP, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, Hebei, China
| | - Hong-Qing Ling
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China.
| | - Junming Li
- Hebei Collaboration Innovation Center for Cell Signaling, Shijiazhuang, 050024, China.
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, China.
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, Hebei, China.
| | - Jun Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Centre of Excellence for Plant and Microbial Science (CEPAMS), JIC-CAS, Beijing, China.
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8
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Julian R, Patrick RM, Li Y. Organ-specific characteristics govern the relationship between histone code dynamics and transcriptional reprogramming during nitrogen response in tomato. Commun Biol 2023; 6:1225. [PMID: 38044380 PMCID: PMC10694154 DOI: 10.1038/s42003-023-05601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/17/2023] [Indexed: 12/05/2023] Open
Abstract
Environmental stimuli trigger rapid transcriptional reprogramming of gene networks. These responses occur in the context of the local chromatin landscape, but the contribution of organ-specific dynamic chromatin modifications in responses to external signals remains largely unexplored. We treated tomato seedlings with a supply of nitrate and measured the genome-wide changes of four histone marks, the permissive marks H3K27ac, H3K4me3, and H3K36me3 and repressive mark H3K27me3, in shoots and roots separately, as well as H3K9me2 in shoots. Dynamic and organ-specific histone acetylation and methylation were observed at functionally relevant gene loci. Integration of transcriptomic and epigenomic datasets generated from the same organ revealed largely syngenetic relations between changes in transcript levels and histone modifications, with the exception of H3K27me3 in shoots, where an increased level of this repressive mark is observed at genes activated by nitrate. Application of a machine learning approach revealed organ-specific rules regarding the importance of individual histone marks, as H3K36me3 is the most successful mark in predicting gene regulation events in shoots, while H3K4me3 is the strongest individual predictor in roots. Our integrated study substantiates a view that during plant environmental responses, the relationships between histone code dynamics and gene regulation are highly dependent on organ-specific contexts.
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Affiliation(s)
- Russell Julian
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Ryan M Patrick
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Ying Li
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA.
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9
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Sharma M, Sidhu AK, Samota MK, Gupta M, Koli P, Choudhary M. Post-Translational Modifications in Histones and Their Role in Abiotic Stress Tolerance in Plants. Proteomes 2023; 11:38. [PMID: 38133152 PMCID: PMC10747722 DOI: 10.3390/proteomes11040038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Abiotic stresses profoundly alter plant growth and development, resulting in yield losses. Plants have evolved adaptive mechanisms to combat these challenges, triggering intricate molecular responses to maintain tissue hydration and temperature stability during stress. A pivotal player in this defense is histone modification, governing gene expression in response to diverse environmental cues. Post-translational modifications (PTMs) of histone tails, including acetylation, phosphorylation, methylation, ubiquitination, and sumoylation, regulate transcription, DNA processes, and stress-related traits. This review comprehensively explores the world of PTMs of histones in plants and their vital role in imparting various abiotic stress tolerance in plants. Techniques, like chromatin immune precipitation (ChIP), ChIP-qPCR, mass spectrometry, and Cleavage Under Targets and Tag mentation, have unveiled the dynamic histone modification landscape within plant cells. The significance of PTMs in enhancing the plants' ability to cope with abiotic stresses has also been discussed. Recent advances in PTM research shed light on the molecular basis of stress tolerance in plants. Understanding the intricate proteome complexity due to various proteoforms/protein variants is a challenging task, but emerging single-cell resolution techniques may help to address such challenges. The review provides the future prospects aimed at harnessing the full potential of PTMs for improved plant responses under changing climate change.
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Affiliation(s)
- Madhvi Sharma
- Post Graduate Department of Biotechnology, Khalsa College, Amritsar 143009, India; (M.S.); (A.K.S.)
| | - Amanpreet K. Sidhu
- Post Graduate Department of Biotechnology, Khalsa College, Amritsar 143009, India; (M.S.); (A.K.S.)
| | - Mahesh Kumar Samota
- ICAR-Central Institute of Post-Harvest Engineering and Technology, Regional Station, Abohar 152116, India
| | - Mamta Gupta
- ICAR-Indian Institute of Maize Research, Ludhiana 141001, India;
| | - Pushpendra Koli
- Plant Animal Relationship Division, ICAR-Indian Grassland and Fodder Research Institute, Jhansi 284003, India;
- Post-Harvest Biosecurity, Murdoch University, Perth, WA 6150, Australia
| | - Mukesh Choudhary
- ICAR-Indian Institute of Maize Research, Ludhiana 141001, India;
- School of Agriculture and Environment, The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
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10
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Wang Z, Zhang Y, Kang Z, Mao H. Improvement of wheat drought tolerance through editing of TaATX4 by CRISPR/Cas9. J Genet Genomics 2023; 50:913-916. [PMID: 37820936 DOI: 10.1016/j.jgg.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/13/2023]
Affiliation(s)
- Zhongxue Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yifang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Yangling Seed Industry Innovation Center, Yangling, Shaanxi 712100, China
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
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11
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Kovalchuk I. Role of Epigenetic Factors in Response to Stress and Establishment of Somatic Memory of Stress Exposure in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3667. [PMID: 37960024 PMCID: PMC10648063 DOI: 10.3390/plants12213667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023]
Abstract
All species are well adapted to their environment. Stress causes a magnitude of biochemical and molecular responses in plants, leading to physiological or pathological changes. The response to various stresses is genetically predetermined, but is also controlled on the epigenetic level. Most plants are adapted to their environments through generations of exposure to all elements. Many plant species have the capacity to acclimate or adapt to certain stresses using the mechanism of priming. In most cases, priming is a somatic response allowing plants to deal with the same or similar stress more efficiently, with fewer resources diverted from growth and development. Priming likely relies on multiple mechanisms, but the differential expression of non-coding RNAs, changes in DNA methylation, histone modifications, and nucleosome repositioning play a crucial role. Specifically, we emphasize the role of BRM/CHR17, BRU1, FGT1, HFSA2, and H2A.Z proteins as positive regulators, and CAF-1, MOM1, DDM1, and SGS3 as potential negative regulators of somatic stress memory. In this review, we will discuss the role of epigenetic factors in response to stress, priming, and the somatic memory of stress exposures.
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Affiliation(s)
- Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
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12
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Kumar M, Rani K. Epigenomics in stress tolerance of plants under the climate change. Mol Biol Rep 2023:10.1007/s11033-023-08539-6. [PMID: 37294468 DOI: 10.1007/s11033-023-08539-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND Climate change has had a tremendous impact on the environment in general as well as agricultural crops grown in these situations as time passed. Agricultural production of crops is less suited and of lower quality due to disturbances in plant metabolism brought on by sensitivity to environmental stresses, which are brought on by climate change. Abiotic stressors that are specific to climate change, including as drought, extremes in temperature, increasing CO2, waterlogging from heavy rain, metal toxicity, and pH changes, are known to negatively affect an array of species. Plants adapt to these challenges by undergoing genome-wide epigenetic changes, which are frequently accompanied by differences in transcriptional gene expression. The sum of a cell's biochemical modifications to its nuclear DNA, post-translational modifications to histones, and variations in the synthesis of non-coding RNAs is called an epigenome. These modifications frequently lead to variations in gene expression that occur without any alteration in the underlying base sequence. EPIGENETIC MECHANISMS AND MARKS The methylation of homologous loci by three different modifications-genomic (DNA methylation), chromatin (histone modifications), and RNA-directed DNA methylation (RdDM)-could be regarded as epigenetic mechanisms that control the regulation of differential gene expression. Stresses from the environment cause chromatin remodelling, which enables plant cells to adjust their expression patterns temporarily or permanently. EPIGENOMICS' CONSEQUENCES FOR GENOME STABILITY AND GENE EXPRESSION: DNA methylation affects gene expression in response to abiotic stressors by blocking or suppressing transcription. Environmental stimuli cause changes in DNA methylation levels, either upward in the case of hypermethylation or downward in the case of hypomethylation. The type of stress response that occurs as a result also affects the degree of DNA methylation alterations. Stress is also influenced by DRM2 and CMT3 methylating CNN, CNG, and CG. Both plant development and stress reactions depend on histone changes. Gene up-regulation is associated with histone tail phosphorylation, ubiquitination, and acetylation, while gene down-regulation is associated with de-acetylation and biotinylation. Plants undergo a variety of dynamic changes to histone tails in response to abiotic stressors. The relevance of these transcripts against stress is highlighted by the accumulation of numerous additional antisense transcripts, a source of siRNAs, caused by abiotic stresses. The study highlights the finding that plants can be protected from a range of abiotic stresses by epigenetic mechanisms such DNA methylation, histone modification, and RNA-directed DNA methylation. TRANSGENERATIONAL INHERITANCE AND SOURCES OF EPIGENETIC VARIATION: Stress results in the formation of epialleles, which are either transient or enduring epigenetic stress memory in plants. After the stress is gone, the stable memory is kept for the duration of the plant's remaining developmental cycles or passed on to the next generations, leading to plant evolution and adaptability. The bulk of epigenetic changes brought on by stress are temporary and return to normal after the stress has passed. Some of the modifications, however, might be long-lasting and transmitted across mitotic or even meiotic cell divisions. Epialleles often have genetic or non-genetic causes. Epialleles can arise spontaneously due to improper methylation state maintenance, short RNA off-target effects, or other non-genetic causes. Developmental or environmental variables that influence the stability of epigenetic states or direct chromatin modifications may also be non-genetic drivers of epigenetic variation. Transposon insertions that change local chromatin and structural rearrangements, such copy number changes that are genetically related or unrelated, are two genetic sources of epialleles. EPIGENOMICS IN CROP IMPROVEMENT To include epigenetics into crop breeding, it is necessary to create epigenetic variation as well as to identify and evaluate epialleles. Epigenome editing or epi-genomic selection may be required for epiallele creation and identification. In order to combat the challenges given by changing environments, these epigenetic mechanisms have generated novel epialleles that can be exploited to develop new crop types that are more climate-resilient. Numerous techniques can be used to alter the epigenome generally or at specific target loci in order to induce the epigenetic alterations necessary for crop development. Technologies like CRISPR/Cas9 and dCas, which have recently advanced, have opened up new avenues for the study of epigenetics. Epialleles could be employed in epigenomics-assisted breeding in addition to sequence-based markers for crop breeding. CONCLUSIONS AND FUTURE PROSPECTUS A few of the exciting questions that still need to be resolved in the area of heritable epigenetic variation include a better understanding of the epigenetic foundation of characteristics, the stability and heritability of epialleles, and the sources of epigenetic variation in crops. Investigating long intergenic non-coding RNAs (lincRNAs) as an epigenetic process might open up a new path to understanding crop plant's ability to withstand abiotic stress. For many of these technologies and approaches to be more applicable and deployable at a lower cost, technological breakthroughs will also be necessary. Breeders will probably need to pay closer attention to crop epialleles and how they can affect future responses to climate changes. The development of epialleles suitable for particular environmental circumstances may be made possible by creating targeted epigenetic changes in pertinent genes and by comprehending the molecular underpinnings of trans generational epigenetic inheritance. More research on a wider variety of plant species is required in order to fully comprehend the mechanisms that produce and stabilise epigenetic variation in crops. In addition to a collaborative and multidisciplinary effort by researchers in many fields of plant science, this will require a greater integration of the epigenomic data gathered in many crops. Before it may be applied generally, more study is required.
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Affiliation(s)
- Mithlesh Kumar
- AICRN On Potential Crops, ARS Mandor, Agriculture University, Jodhpur, 342 304, Rajasthan, India.
| | - Kirti Rani
- ICAR-National Bureau of Plant Genetic Resources (NBPGR), Regional Station, Jodhpur, 342 003, Rajasthan, India
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13
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Wang M, Zhong Z, Gallego-Bartolomé J, Feng S, Shih YH, Liu M, Zhou J, Richey JC, Ng C, Jami-Alahmadi Y, Wohlschlegel J, Wu K, Jacobsen SE. Arabidopsis TRB proteins function in H3K4me3 demethylation by recruiting JMJ14. Nat Commun 2023; 14:1736. [PMID: 36977663 PMCID: PMC10049986 DOI: 10.1038/s41467-023-37263-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Arabidopsis telomeric repeat binding factors (TRBs) can bind telomeric DNA sequences to protect telomeres from degradation. TRBs can also recruit Polycomb Repressive Complex 2 (PRC2) to deposit tri-methylation of H3 lysine 27 (H3K27me3) over certain target loci. Here, we demonstrate that TRBs also associate and colocalize with JUMONJI14 (JMJ14) and trigger H3K4me3 demethylation at some loci. The trb1/2/3 triple mutant and the jmj14-1 mutant show an increased level of H3K4me3 over TRB and JMJ14 binding sites, resulting in up-regulation of their target genes. Furthermore, tethering TRBs to the promoter region of genes with an artificial zinc finger (TRB-ZF) successfully triggers target gene silencing, as well as H3K27me3 deposition, and H3K4me3 removal. Interestingly, JMJ14 is predominantly recruited to ZF off-target sites with low levels of H3K4me3, which is accompanied with TRB-ZFs triggered H3K4me3 removal at these loci. These results suggest that TRB proteins coordinate PRC2 and JMJ14 activities to repress target genes via H3K27me3 deposition and H3K4me3 removal.
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Affiliation(s)
- Ming Wang
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Zhenhui Zhong
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Javier Gallego-Bartolomé
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, 46022, Valencia, Spain
| | - Suhua Feng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Yuan-Hsin Shih
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Mukun Liu
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Jessica Zhou
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - John Curtis Richey
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Charmaine Ng
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Yasaman Jami-Alahmadi
- Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA, 90095, USA.
- Howard Hughes Medical Institute (HHMI), University of California at Los Angeles, Los Angeles, CA, 90095, USA.
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14
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Jiang K, Guo H, Zhai J. Interplay of phytohormones and epigenetic regulation: A recipe for plant development and plasticity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:381-398. [PMID: 36223083 DOI: 10.1111/jipb.13384] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Both phytohormone signaling and epigenetic mechanisms have long been known to play crucial roles in plant development and plasticity in response to ambient stimuli. Indeed, diverse signaling pathways mediated by phytohormones and epigenetic processes integrate multiple upstream signals to regulate various plant traits. Emerging evidence indicates that phytohormones and epigenetic processes interact at multiple levels. In this review, we summarize the current knowledge of the interplay between phytohormones and epigenetic processes from the perspective of phytohormone biology. We also review chemical regulators used in epigenetic studies and propose strategies for developing novel regulators using multidisciplinary approaches.
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Affiliation(s)
- Kai Jiang
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Hongwei Guo
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Jixian Zhai
- Institute of Plant and Food Science, Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
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15
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Nunez-Vazquez R, Desvoyes B, Gutierrez C. Histone variants and modifications during abiotic stress response. FRONTIERS IN PLANT SCIENCE 2022; 13:984702. [PMID: 36589114 PMCID: PMC9797984 DOI: 10.3389/fpls.2022.984702] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 09/28/2022] [Indexed: 06/17/2023]
Abstract
Plants have developed multiple mechanisms as an adaptive response to abiotic stresses, such as salinity, drought, heat, cold, and oxidative stress. Understanding these regulatory networks is critical for coping with the negative impact of abiotic stress on crop productivity worldwide and, eventually, for the rational design of strategies to improve plant performance. Plant alterations upon stress are driven by changes in transcriptional regulation, which rely on locus-specific changes in chromatin accessibility. This process encompasses post-translational modifications of histone proteins that alter the DNA-histones binding, the exchange of canonical histones by variants that modify chromatin conformation, and DNA methylation, which has an implication in the silencing and activation of hypervariable genes. Here, we review the current understanding of the role of the major epigenetic modifications during the abiotic stress response and discuss the intricate relationship among them.
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16
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Liu Y, Wang J, Liu B, Xu ZY. Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2252-2274. [PMID: 36149776 DOI: 10.1111/jipb.13368] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.
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Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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17
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Yang L, Zhang P, Wang Y, Hu G, Guo W, Gu X, Pu L. Plant synthetic epigenomic engineering for crop improvement. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2191-2204. [PMID: 35851940 DOI: 10.1007/s11427-021-2131-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
Efforts have been directed to redesign crops with increased yield, stress adaptability, and nutritional value through synthetic biology-the application of engineering principles to biology. A recent expansion in our understanding of how epigenetic mechanisms regulate plant development and stress responses has unveiled a new set of resources that can be harnessed to develop improved crops, thus heralding the promise of "synthetic epigenetics." In this review, we summarize the latest advances in epigenetic regulation and highlight how innovative sequencing techniques, epigenetic editing, and deep learning-driven predictive tools can rapidly extend these insights. We also proposed the future directions of synthetic epigenetics for the development of engineered smart crops that can actively monitor and respond to internal and external cues throughout their life cycles.
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Affiliation(s)
- Liwen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yifan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guihua Hu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weijun Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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18
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Shen Y, Chi Y, Lu S, Lu H, Shi L. Involvement of JMJ15 in the dynamic change of genome-wide H3K4me3 in response to salt stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1009723. [PMID: 36226276 PMCID: PMC9549339 DOI: 10.3389/fpls.2022.1009723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Post-translational histone modifications play important roles in regulating chromatin structure and transcriptional regulation. Histone 3 lysine 4 trimethylation (H3K4me3) is a prominent histone modification mainly associated with gene activation. Here we showed that a histone demethylase, JMJ15, belonging to KDM5/JARID group, is involved in salt stress response in Arabidopsis thaliana. Jmj15 loss-of-function mutants displayed increased sensitivity to salt stress. Moreover, knockout of JMJ15 impaired the salt responsive gene expression program and affected H3K4me3 levels of many stress-related genes under salt-stressed condition. Importantly, we demonstrated that JMJ15 regulated the expression level of two WRKY transcription factors, WRKY46 and WRKY70, which were negatively involved in abiotic stress tolerance. Furthermore, JMJ15 directly bound to and demethylated H3K4me3 mark in the promoter and coding regions of WRKY46 and WRKY70, thereby repressing these two WRKY gene expression under salt stress. Overall, our study revealed a novel molecular function of the histone demethylase JMJ15 under salt stress in plants.
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Affiliation(s)
- Yuan Shen
- School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Yuhao Chi
- School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Shun Lu
- School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Huijuan Lu
- School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Lei Shi
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
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19
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Wang X, Pan C, Long J, Bai S, Yao M, Chen J, Sun G, Fan Y, Wang Z, Liu F, Liu C, Li Q. Genome-wide identification of the jumonji C domain- containing histone demethylase gene family in wheat and their expression analysis under drought stress. FRONTIERS IN PLANT SCIENCE 2022; 13:987257. [PMID: 36092409 PMCID: PMC9453444 DOI: 10.3389/fpls.2022.987257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
Methylation and demethylation of histone play a crucial role in regulating chromatin formation and gene expression. The jumonji C (JmjC) domain-containing proteins are demethylases that are involved in regulating epigenetic modification in plants. In our study, the JmjC genes in Triticum aestivum L., Triticum turgidum L., Triticum dicoccoides L., Triticum urartu L., and Aegilops tauschii L. were identified. Phylogenetic relationship and colinearity analysis revealed that the wheat JmjC genes were conserved in A, B, and D subgenomes during evolution. Cis-acting elements analysis showed that elements related to stress response, hormone response, and light response were found in wheat JmjC genes. The expression of JmjC genes was affected by tissue types and developmental stages, and members of the same subfamily tended to have similar expression patterns in wheat. They also showed a unique expression pattern in root during PEG (Polyethylene glycol) treatment. In conclusion, comprehensive analysis indicated that three members (Tr-1A-JMJ2, Tr-1B-JMJ2, and Tr-1D-JMJ2) might be regulated by several hormones and function in the early stages of drought stress, while eight members (Tr-1B-JMJ3, Tr-4B-JMJ1, Tr-7A-JMJ1, etc.) displayed a significantly high expression after 24 h of PEG treatment, indicating a role in the later stages of drought stress. This research presents the first genome-wide study of the JmjC family in wheat, and lays the foundation for promoting the study of their functional characterization in wheat drought resistance.
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Affiliation(s)
- Xinhua Wang
- School of Agriculture, Ningxia University, Yinchuan, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Cuili Pan
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Jiaohui Long
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Shuangyu Bai
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Mingming Yao
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Jiajing Chen
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Gang Sun
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yalei Fan
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Zhangjun Wang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Fenglou Liu
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Caixia Liu
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Qingfeng Li
- School of Agriculture, Ningxia University, Yinchuan, China
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20
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Xiao M, Wang J, Xu F. Methylation hallmarks on the histone tail as a linker of osmotic stress and gene transcription. FRONTIERS IN PLANT SCIENCE 2022; 13:967607. [PMID: 36035677 PMCID: PMC9399788 DOI: 10.3389/fpls.2022.967607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/25/2022] [Indexed: 06/12/2023]
Abstract
Plants dynamically manipulate their gene expression in acclimation to the challenging environment. Hereinto, the histone methylation tunes the gene transcription via modulation of the chromatin accessibility to transcription machinery. Osmotic stress, which is caused by water deprivation or high concentration of ions, can trigger remarkable changes in histone methylation landscape and genome-wide reprogramming of transcription. However, the dynamic regulation of genes, especially how stress-inducible genes are timely epi-regulated by histone methylation remains largely unclear. In this review, recent findings on the interaction between histone (de)methylation and osmotic stress were summarized, with emphasis on the effects on histone methylation profiles imposed by stress and how histone methylation works to optimize the performance of plants under stress.
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21
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Li Y, Zhuang F, Zeng J, Yang C, Li Y, Luo M, Wang Y. Identification of the histone demethylases gene family in
Glycyrrhiza inflata
reveals genes responding to abiotic stresses. J Cell Biochem 2022; 123:1780-1792. [DOI: 10.1002/jcb.30315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Yuping Li
- 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 China
| | - Feng Zhuang
- 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 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
| | - Jiangyi Zeng
- 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 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
| | - Chao 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 China
| | - Yongqing Li
- 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 China
| | - Ming Luo
- 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 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing China
| | - Ying Wang
- 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 China
- College of Life Sciences Gannan Normal University Ganzhou Jiangxi China
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22
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Hu H, Du J. Structure and mechanism of histone methylation dynamics in Arabidopsis. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102211. [PMID: 35452951 DOI: 10.1016/j.pbi.2022.102211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
Histone methylation plays a central role in regulating chromatin state and gene expression in Arabidopsis and is involved in a variety of physiological and developmental processes. Dynamic regulation of histone methylation relies on both histone methyltransferase "writer" and histone demethylases "eraser" proteins. In this review, we focus on the four major histone methylation modifications in Arabidopsis H3, H3K4, H3K9, H3K27, and H3K36, and summarize current knowledge of the dynamic regulation of these modifications, with an emphasis on the biochemical and structural perspectives of histone methyltransferases and demethylases.
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Affiliation(s)
- Hongmiao Hu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiamu Du
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
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23
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Zhao W, Wang X, Zhang Q, Zheng Q, Yao H, Gu X, Liu D, Tian X, Wang X, Li Y, Zhu Z. H3K36 demethylase JMJ710 negatively regulates drought tolerance by suppressing MYB48-1 expression in rice. PLANT PHYSIOLOGY 2022; 189:1050-1064. [PMID: 35253881 PMCID: PMC9157158 DOI: 10.1093/plphys/kiac095] [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: 11/19/2021] [Accepted: 01/31/2022] [Indexed: 05/14/2023]
Abstract
The homeostasis of histone methylation is maintained by histone methyltransferases and demethylases, which are important for the regulation of gene expression. Here, we report a histone demethylase from rice (Oryza sativa), Jumonji C domain-containing protein (JMJ710), which belongs to the JMJD6 group and plays an important role in the response to drought stress. Overexpression of JMJ710 causes a drought-sensitive phenotype, while RNAi and clustered regularly interspaced short palindromic repeats (CRISPR)-knockout mutant lines show drought tolerance. In vitro and in vivo assays showed that JMJ710 is a histone demethylase. It targets to MYB TRANSCRIPTION FACTOR 48 (MYB48-1) chromatin, demethylates H3K36me2, and negatively regulates the expression of MYB48-1, a positive regulator of drought tolerance. Under drought stress, JMJ710 is downregulated and the expression of MYB48-1 increases, and the subsequent activation of its downstream drought-responsive genes leads to drought tolerance. This research reports a negative regulator of drought stress-responsive genes, JMJ710, that ensures that the drought tolerance mechanism is not mis-activated under normal conditions but allows quick activation upon drought stress.
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Affiliation(s)
- Weijie Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xiaoyan Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qian Zhang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qian Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Haitao Yao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xiangyang Gu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Dongliang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xuemin Tian
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Xiaoji Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Yongqing Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengge Zhu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
- Author for correspondence:
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24
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Oberkofler V, Bäurle I. Inducible epigenome editing probes for the role of histone H3K4 methylation in Arabidopsis heat stress memory. PLANT PHYSIOLOGY 2022; 189:703-714. [PMID: 35285498 PMCID: PMC9157090 DOI: 10.1093/plphys/kiac113] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/15/2022] [Indexed: 05/26/2023]
Abstract
Histone modifications play a crucial role in the integration of environmental signals to mediate gene expression outcomes. However, genetic and pharmacological interference often causes pleiotropic effects, creating the urgent need for methods that allow locus-specific manipulation of histone modifications, preferably in an inducible manner. Here, we report an inducible system for epigenome editing in Arabidopsis (Arabidopsis thaliana) using a heat-inducible dCas9 to target a JUMONJI (JMJ) histone H3 lysine 4 (H3K4) demethylase domain to a locus of interest. As a model locus, we target the ASCORBATE PEROXIDASE2 (APX2) gene that shows transcriptional memory after heat stress (HS), correlating with H3K4 hyper-methylation. We show that dCas9-JMJ is targeted in a HS-dependent manner to APX2 and that the HS-induced overaccumulation of H3K4 trimethylation (H3K4me3) decreases when dCas9-JMJ binds to the locus. This results in reduced HS-mediated transcriptional memory at the APX2 locus. Targeting an enzymatically inactive JMJ protein in an analogous manner affected transcriptional memory less than the active JMJ protein; however, we still observed a decrease in H3K4 methylation levels. Thus, the inducible targeting of dCas9-JMJ to APX2 was effective in reducing H3K4 methylation levels. As the effect was not fully dependent on enzyme activity of the eraser domain, the dCas9-JMJ fusion protein may act in part independently of its demethylase activity. This underlines the need for caution in the design and interpretation of epigenome editing studies. We expect our versatile inducible epigenome editing system to be especially useful for studying temporal dynamics of chromatin modifications.
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Affiliation(s)
- Vicky Oberkofler
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
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25
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Halder K, Chaudhuri A, Abdin MZ, Majee M, Datta A. Chromatin-Based Transcriptional Reprogramming in Plants under Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022; 11:1449. [PMID: 35684223 PMCID: PMC9182740 DOI: 10.3390/plants11111449] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
Plants' stress response machinery is characterized by an intricate network of signaling cascades that receive and transmit environmental cues and ultimately trigger transcriptional reprogramming. The family of epigenetic regulators that are the key players in the stress-induced signaling cascade comprise of chromatin remodelers, histone modifiers, DNA modifiers and regulatory non-coding RNAs. Changes in the histone modification and DNA methylation lead to major alterations in the expression level and pattern of stress-responsive genes to adjust with abiotic stress conditions namely heat, cold, drought and salinity. The spotlight of this review falls primarily on the chromatin restructuring under severe abiotic stresses, crosstalk between epigenetic regulators along with a brief discussion on stress priming in plants.
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Affiliation(s)
- Koushik Halder
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India;
| | - Abira Chaudhuri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
| | - Malik Z. Abdin
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India;
| | - Manoj Majee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
| | - Asis Datta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
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26
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Li Y, Zhu S, Yao J, Fang S, Li T, Li B, Wang X, Wang M, Wu L, Pan J, Feng X, Chen W, Zhang Y. Genome-wide Characterization of the JmjC Domain-Containing Histone Demethylase Gene Family Reveals GhJMJ24 and GhJMJ49 Involving in Somatic Embryogenesis Process in Cotton. Front Mol Biosci 2022; 9:888983. [PMID: 35573733 PMCID: PMC9091307 DOI: 10.3389/fmolb.2022.888983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/08/2022] [Indexed: 11/16/2022] Open
Abstract
The Jumonji C (JmjC) domain-containing protein family, an important family of histone demethylase in plants, can directly reverse histone methylation and play important roles in various growth and development processes. In the present study, 51 JmjC genes (GhJMJs) were identified by genome-wide analysis in upland cotton (Gossypium hirsutum), which can be categorized into six distinct groups by phylogenetic analysis. Extensive syntenic relationship events were found between G. hirsutum and Theobroma cacao. We have further explored the putative molecular regulatory mechanisms of the JmjC gene family in cotton. GhJMJ24 and GhJMJ49 were both preferentially expressed in embryogenic callus compared to nonembryogenic callus in cotton tissue culture, which might be regulated by transcription factors and microRNAs to some extent. Further experiments indicated that GhJMJ24 and GhJMJ49 might interact with SUVH4, SUVH6, DDM1, CMT3, and CMT1 in the nucleus, potentially in association with demethylation of H3K9me2. Taken together, our results provide a foundation for future research on the biological functions of GhJMJ genes in cotton, especially in somatic embryogenesis in cotton tissue culture, which is crucial for the regeneration of transgenic plants.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shouhong Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jinbo Yao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shengtao Fang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Tengyu Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xinyu Wang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Mingyang Wang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Lanxin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jingwen Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xuemei Feng
- Shandong Denghai Shengfeng Seed Industry Co., Ltd., Jining, china
| | - Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Wei Chen, ; Yongshan Zhang,
| | - Yongshan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
- *Correspondence: Wei Chen, ; Yongshan Zhang,
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27
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Liu Q, Liu R, Zhou Y, Wang W, Wu G, Yang N. Phospholipase Dδ and H 2S increase the production of NADPH oxidase-dependent H 2O 2 to respond to osmotic stress-induced stomatal closure in Arabidopsis thaliana. JOURNAL OF PLANT PHYSIOLOGY 2022; 270:153617. [PMID: 35042010 DOI: 10.1016/j.jplph.2022.153617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
Osmotic stress is one of the main stresses that seriously affects the survival of plants, destroying normal cell activities, and potentially leading to plant death. Phospholipase D (PLD), a major lipid hydrolase, hydrolyzes membrane phospholipids to produce phosphatidic acid (PA) and responds to many abiotic stresses. Hydrogen sulfide (H2S) emerges as the third gaseous signaling molecule involved in the complex network of signaling events. Hydrogen peroxide (H2O2) plays a crucial role as a signaling molecule in plant development and growth, and responds to various abiotic and biotic stresses. In this study, the functions and the relationship of PLDδ, H2S, and H2O2 in osmotic stress-induced stomatal closure were explored. By using the seedlings of ecotype (WT), PLDδ-deficient mutant (pldδ), l-cysteine desulfhydrase (LCD)-deficient mutant (lcd), and pldδlcd double mutant, atrbohD, and atrbohF mutant as materials, and the stomatal aperture were analyzed. The relative water loss of pldδ, lcd, and pldδlcd was higher than that of WT. Exogenous PA and NaHS could partially alleviate the leaf wilting and yellowing phenotypes of pldδ, lcd, and pldδlcd under osmotic stress, but the mutants could not be restored to the same phenotype as WT. The fluorescence intensity of H2O2 in guard cells of pldδ, lcd, and pldδlcd was lower than that of WT, indicating that PLDδ and LCD were involved in the production of H2O2 in guard cells. Exogenous application of H2O2 to WT, pldδ, lcd, and pldδlcd significantly induced stomatal closure under osmotic stress. Exogenous NaHS induced stomatal closure of WT, but could not induce stomatal closure of atrbohD and atrbohF under osmotic stress. These results suggest that the accumulation of H2O2 was essential to induce stomatal closure under osmotic stress, and PLDδ and LCD acted upstream of H2O2.
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Affiliation(s)
- Qin Liu
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Ruirui Liu
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Yaping Zhou
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Wei Wang
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Guofan Wu
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China
| | - Ning Yang
- College of Life Science, Northwest Normal University, Lanzhou, 730070, China.
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28
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Guarino F, Cicatelli A, Castiglione S, Agius DR, Orhun GE, Fragkostefanakis S, Leclercq J, Dobránszki J, Kaiserli E, Lieberman-Lazarovich M, Sõmera M, Sarmiento C, Vettori C, Paffetti D, Poma AMG, Moschou PN, Gašparović M, Yousefi S, Vergata C, Berger MMJ, Gallusci P, Miladinović D, Martinelli F. An Epigenetic Alphabet of Crop Adaptation to Climate Change. Front Genet 2022; 13:818727. [PMID: 35251130 PMCID: PMC8888914 DOI: 10.3389/fgene.2022.818727] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/28/2022] [Indexed: 01/10/2023] Open
Abstract
Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In addition, we discuss a speculative point of view, in which we try to decipher the “epigenetic alphabet” that underlies crop adaptation mechanisms to climate change. The understanding of these mechanisms will pave the way to new strategies to design and implement the next generation of cultivars with a broad range of tolerance/resistance to stresses as well as balanced agronomic traits, with a limited loss of (epi)genetic variability.
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Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Dolores R. Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Gul Ebru Orhun
- Bayramic Vocational College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | | | - Julie Leclercq
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Institut Agro, Montpellier, France
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, FAFSEM, University of Debrecen, Debrecen, Hungary
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Anna M. G. Poma
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, Aquila, Italy
| | - Panagiotis N. Moschou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, Zagreb, Croatia
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Chiara Vergata
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Margot M. J. Berger
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
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29
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Ding X, Liu X, Jiang G, Li Z, Song Y, Zhang D, Jiang Y, Duan X. SlJMJ7 orchestrates tomato fruit ripening via crosstalk between H3K4me3 and DML2-mediated DNA demethylation. THE NEW PHYTOLOGIST 2022; 233:1202-1219. [PMID: 34729792 DOI: 10.1111/nph.17838] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
The ripening of fleshy fruits is a unique developmental process that Arabidopsis and rice lack. This process is driven by hormones and transcription factors. However, the critical and early regulators of fruit ripening are still poorly understood. Here, we revealed that SlJMJ7, an H3K4 demethylase, is a critical negative regulator of fruit ripening in tomato. Combined genome-wide transcription, binding sites, histone H3K4me3 and DNA methylation analyses demonstrated that SlJMJ7 regulates a key group of ripening-related genes, including ethylene biosynthesis (ACS2, ACS4 and ACO6), transcriptional regulation (RIN and NOR) and DNA demethylation (DML2) genes, by H3K4me3 demethylation. Moreover, loss of SlJMJ7 function leads to increased H3K4me3 levels, which directly activates ripening-related genes, and to global DML2-mediated DNA hypomethylation in fruit, which indirectly prompts expression of ripening-related genes. Together, these effects lead to accelerated fruit ripening in sljmj7 mutant. Our findings demonstrate that SlJMJ7 acts as a master negative regulator of fruit ripening not only through direct removal of H3K4me3 from multiple key ripening-related factors, but also through crosstalk between histone and DNA demethylation. These findings reveal a novel crosstalk between histone methylation and DNA methylation to regulate gene expression in plant developmental processes.
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Affiliation(s)
- Xiaochun Ding
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xuncheng Liu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Guoxiang Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Zhiwei Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yunbo Song
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Dandan Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Xuewu Duan
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
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30
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Lohani N, Singh MB, Bhalla PL. Biological Parts for Engineering Abiotic Stress Tolerance in Plants. BIODESIGN RESEARCH 2022; 2022:9819314. [PMID: 37850130 PMCID: PMC10521667 DOI: 10.34133/2022/9819314] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/17/2021] [Indexed: 10/19/2023] Open
Abstract
It is vital to ramp up crop production dramatically by 2050 due to the increasing global population and demand for food. However, with the climate change projections showing that droughts and heatwaves becoming common in much of the globe, there is a severe threat of a sharp decline in crop yields. Thus, developing crop varieties with inbuilt genetic tolerance to environmental stresses is urgently needed. Selective breeding based on genetic diversity is not keeping up with the growing demand for food and feed. However, the emergence of contemporary plant genetic engineering, genome-editing, and synthetic biology offer precise tools for developing crops that can sustain productivity under stress conditions. Here, we summarize the systems biology-level understanding of regulatory pathways involved in perception, signalling, and protective processes activated in response to unfavourable environmental conditions. The potential role of noncoding RNAs in the regulation of abiotic stress responses has also been highlighted. Further, examples of imparting abiotic stress tolerance by genetic engineering are discussed. Additionally, we provide perspectives on the rational design of abiotic stress tolerance through synthetic biology and list various bioparts that can be used to design synthetic gene circuits whose stress-protective functions can be switched on/off in response to environmental cues.
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Affiliation(s)
- Neeta Lohani
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
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31
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Ding X, Zhang D, Gu D, Li Z, Liang H, Zhu H, Jiang Y, Duan X. Histone H3K27 demethylase SlJMJ4 promotes dark- and ABA- induced leaf senescence in tomato. HORTICULTURE RESEARCH 2022; 9:uhab077. [PMID: 35043207 PMCID: PMC8973004 DOI: 10.1093/hr/uhab077] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/28/2021] [Accepted: 10/31/2021] [Indexed: 06/12/2023]
Abstract
Leaf senescence is a highly-programmed developmental process during the plant life cycle. ABA plays an important role in leaf senescence. However, the mechanism underlying ABA-mediated leaf senescence, particularly the upstream epigenetic regulatory network, remains largely unclear. Here, we identified that SlJMJ4, a Jumonji C (jmjC) domain-containing protein in tomato, specifically demethylates di- and tri-methylations of lysine 27 of histone H3 (H3K27) in vitro and in vivo. Overexpression of SlJMJ4 results in premature senescence phenotype and promotes dark- and ABA-induced leaf senescence in tomato. Under dark condition, SlJMJ4-promoted leaf senescence is associated with upregulated expression of transcription factors (SlORE1 and SlNAP2) and senescence-associated genes (SlSAG113, SlSAG12) via removal of H3K27me3. In responses to ABA, overexpression of SlJMJ4 increases its binding at the loci of SlORE1, SlNAP2, SlSAG113, SlSAG12, SlABI5 and SlNCED3 and decreases their H3K27me3 levels, and therefore activates their expression and mediates ABA-induced leaf senescence in tomato. Taken together, these results demonstrate that SlJMJ4 plays a positive role in leaf senescence in tomato and is implicated in ABA-induced leaf senescence by binding to many key genes related to ABA synthesis and signaling, transcription regulation and senescence and hence promoting their H3K27me3 demethylation.
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Affiliation(s)
- Xiaochun Ding
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Dandan Zhang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Dachuan Gu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zhiwei Li
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanzhi Liang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hong Zhu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xuewu Duan
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
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Wu LY, Shang GD, Wang FX, Gao J, Wan MC, Xu ZG, Wang JW. Dynamic chromatin state profiling reveals regulatory roles of auxin and cytokinin in shoot regeneration. Dev Cell 2022; 57:526-542.e7. [DOI: 10.1016/j.devcel.2021.12.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/31/2021] [Accepted: 12/19/2021] [Indexed: 02/06/2023]
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Chen B, Ali S, Zhang X, Zhang Y, Wang M, Zhang Q, Xie L. Genome-wide identification, classification, and expression analysis of the JmjC domain-containing histone demethylase gene family in birch. BMC Genomics 2021; 22:772. [PMID: 34711171 PMCID: PMC8555302 DOI: 10.1186/s12864-021-08063-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 10/06/2021] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Histone methylation occurs primarily on lysine residues and requires a set of enzymes capable of reading, writing, and erasing to control its establishment and deletion, which is essential for maintaining chromatin structure and gene expression. Histone methylation and demethylation are contributed to plant growth and development, and are involved in adapting to environmental stresses. The JmjC domain-containing proteins are extensively studied for their function in histone lysine demethylation in plants, and play a critical role in sustaining histone methylation homeostasis. RESULTS In this study, a total of 21 JmjC domain-containing histone demethylase proteins (JHDMs) in birch were identified and classified into five subfamilies based on structural characteristics and phylogenetic relationships among Arabidopsis, rice, maize, and birch. Although the BpJMJ genes displayed significant schematic variation, their distribution on the chromosomes is relatively uniform. Additionally, the BpJMJ genes in birch have never experienced a tandem-duplication event proved by WGD analysis and were remaining underwent purifying selection (Ka/Ks < < 1). A typical JmjC domain was found in all BpJMJ genes, some of which have other essential domains for their functions. In the promoter regions of BpJMJ genes, cis-acting elements associated with hormone and abiotic stress responses were overrepresented. Under abiotic stresses, the transcriptome profile reveals two contrasting expression patterns within 21 BpJMJ genes. Furthermore, it was established that most BpJMJ genes had higher expression in young tissues under normal conditions, with BpJMJ06/16 having the highest expression in germinating seeds and participating in the regulation of BpGA3ox1/2 gene expression. Eventually, BpJMJ genes were found to directly interact with genes involved in the "intracellular membrane" in respond to cold stress. CONCLUSIONS The present study will provide a foundation for future experiments on histone demethylases in birch and a theoretical basis for epigenetic research on growth and development in response to abiotic stresses.
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Affiliation(s)
- Bowei Chen
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Shahid Ali
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Xu Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yonglan Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Min Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Qingzhu Zhang
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Linan Xie
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China.
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
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Huang S, Ma Z, Hu L, Huang K, Zhang M, Zhang S, Jiang W, Wu T, Du X. Involvement of rice transcription factor OsERF19 in response to ABA and salt stress responses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 167:22-30. [PMID: 34329842 DOI: 10.1016/j.plaphy.2021.07.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/14/2021] [Accepted: 07/23/2021] [Indexed: 05/24/2023]
Abstract
Soil salinity is a major environmental stressor that restricts the growth and yield of crops. Plants have evolved more complicated and precise mechanisms to cope with salt stress, as they cannot escape from harmful environments. In the current study we identified and characterized an AP2/ERF transcription factor in rice, OsERF19. The expression of OsERF19 was slightly repressed by salt stress or abscisic acid (ABA) treatment. OsERF19-overexpression (OsERF19-OX) plants displayed enhanced tolerance to salt stress and ABA hypersensitivity compared to wild type and control plants. Furthermore, OsLEA3, OsNHX1, OsHKT6, and OsOTS1 were upregulated in OsERF19-OX plants when the plants were subjected to salt stress. OsRAB21, OsNCED5, and OsP5CS1 were also upregulated in OsERF19-OX plants treated with ABA. Yeast one-hybrid and dual luciferase reporter assays demonstrated that OsERF19 directly targets the promoters of OsOTS1 and OsNCED5 and further increases their transcription. These results suggest that the transcription factor OsERF19 plays a positive role in salt stress and ABA responses in rice.
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Affiliation(s)
- Shuangzhan Huang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Ziming Ma
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Lanjuan Hu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Kai Huang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Mingxing Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Shihan Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Wenzhu Jiang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Tao Wu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China.
| | - Xinglin Du
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China.
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Wang Q, Liu P, Jing H, Zhou XF, Zhao B, Li Y, Jin JB. JMJ27-mediated histone H3K9 demethylation positively regulates drought-stress responses in Arabidopsis. THE NEW PHYTOLOGIST 2021; 232:221-236. [PMID: 34197643 DOI: 10.1111/nph.17593] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Dimethylation of histone H3 at lysine 9 (H3K9me2) is associated with heterochromatinization and transcriptional gene silencing in plants. The activation of sets of genes by drought stress is correlated with reduced H3K9me2 levels, but the role of H3K9 methylation in the regulation of drought-stress responses remains elusive. Here, we show that the Jumonji domain-containing H3K9 demethylase JMJ27 positively regulates drought-stress responses through its histone demethylase activity. RNA-seq analysis identified JMJ27-regulated genes, including positive regulators of drought stress GALACTINOL SYNTHASE 2 (GOLS2) and RESPONSE TO DESICCATION 20 (RD20). Genetic analysis demonstrated that JMJ27 positively regulates drought-stress responses at least partly through GOLS2 and RD20. JMJ27 directly associated with GOLS2 and RD20, and protected these loci from silencing by reducing H3K9me2 levels under normal conditions. REGULATORY PARTICLE NON-ATPASE 1a (RPN1a), a subunit of the 26S proteasome, interacted with JMJ27 and negatively regulated JMJ27 accumulation. Drought stress diminished RPN1a abundance, resulting in increased JMJ27 abundance. The drought stress-promoted occupancy of JMJ27 at GOLS2 and RD20 chromatin may reinforce their transcriptional induction by locally reducing the H3K9me2 levels. These results indicate that the RPN1a-JMJ27 module precisely regulates dynamic H3K9me2 deposition plasticity, ensuring proper adaptation to drought stress in Arabidopsis.
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Affiliation(s)
- Qiongli Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Peng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hua Jing
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Feng Zhou
- Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China
| | - Bo Zhao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuan Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing Bo Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
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36
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Epigenetic control of abiotic stress signaling in plants. Genes Genomics 2021; 44:267-278. [PMID: 34515950 DOI: 10.1007/s13258-021-01163-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Although plants may be regularly exposed to various abiotic stresses, including drought, salt, cold, heat, heavy metals, and UV-B throughout their lives, it is not possible to actively escape from such stresses due to the immobile nature of plants. To overcome adverse environmental stresses, plants have developed adaptive systems that allow appropriate responses to diverse environmental cues; such responses can be achieved by fine-tuning or controlling genetic and epigenetic regulatory systems. Epigenetic mechanisms such as DNA or histone modifications and modulation of chromatin accessibility have been shown to regulate the expression of stress-responsive genes in struggles against abiotic stresses. OBJECTIVE Herein, the current progress in elucidating the epigenetic regulation of abiotic stress signaling in plants has been summarized in order to further understand the systems plants utilize to effectively respond to abiotic stresses. METHODS This review focuses on the action mechanisms of various components that epigenetically regulate plant abiotic stress responses, mainly in terms of DNA methylation, histone methylation/acetylation, and chromatin remodeling. CONCLUSIONS This review can be considered a basis for further research into understanding the epigenetic control system for abiotic stress responses in plants. Moreover, the knowledge of such systems can be effectively applied in developing novel methods to generate abiotic stress resistant crops.
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Huang S, Hu L, Zhang S, Zhang M, Jiang W, Wu T, Du X. Rice OsWRKY50 Mediates ABA-Dependent Seed Germination and Seedling Growth, and ABA-Independent Salt Stress Tolerance. Int J Mol Sci 2021; 22:ijms22168625. [PMID: 34445331 PMCID: PMC8395310 DOI: 10.3390/ijms22168625] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/08/2021] [Accepted: 08/09/2021] [Indexed: 11/16/2022] Open
Abstract
Plant WRKY transcription factors play crucial roles in plant growth and development, as well as plant responses to biotic and abiotic stresses. In this study, we identified and characterized a WRKY transcription factor in rice, OsWRKY50. OsWRKY50 functions as a transcriptional repressor in the nucleus. The transcription of OsWRKY50 was repressed under salt stress conditions, but activated after abscisic acid (ABA) treatment. OsWRKY50-overexpression (OsWRKY50-OX) plants displayed increased tolerance to salt stress compared to wild type and control plants. The expression of OsLEA3, OsRAB21, OsHKT1;5, and OsP5CS1 in OsWRKY50-OX were much higher than wild type and control plants under salt stress. Furthermore, OsWRKY50-OX displayed hyposensitivity to ABA-regulated seed germination and seedling establishment. The protoplast-based transient expression system and yeast hybrid assay demonstrated that OsWRKY50 directly binds to the promoter of OsNCED5, and thus further inhibits its transcription. Taken together, our results demonstrate that rice transcription repressor OsWRKY50 mediates ABA-dependent seed germination and seedling growth and enhances salt stress tolerance via an ABA-independent pathway.
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Affiliation(s)
| | | | | | | | | | - Tao Wu
- Correspondence: (T.W.); (X.D.)
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Woodson JD. All in the timing: epigenetic control of greening. THE NEW PHYTOLOGIST 2021; 231:907-909. [PMID: 34125971 DOI: 10.1111/nph.17454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Jesse D Woodson
- The School of Plant Sciences, University of Arizona, Tucson, AZ, 85721-0036, USA
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Islam MT, Wang LC, Chen IJ, Lo KL, Lo WS. Arabidopsis JMJ17 promotes cotyledon greening during de-etiolation by repressing genes involved in tetrapyrrole biosynthesis in etiolated seedlings. THE NEW PHYTOLOGIST 2021; 231:1023-1039. [PMID: 33666236 DOI: 10.1111/nph.17327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Arabidopsis histone H3 lysine 4 (H3K4) demethylases play crucial roles in several developmental processes, but their involvement in seedling establishment remain unexplored. Here, we show that Arabidopsis JUMONJI DOMAIN-CONTAINING PROTEIN17 (JMJ17), an H3K4me3 demethylase, is involved in cotyledon greening during seedling establishment. Dark-grown seedlings of jmj17 accumulated a high concentration of protochlorophyllide, an intermediate metabolite in the tetrapyrrole biosynthesis (TPB) pathway that generates chlorophyll (Chl) during photomorphogenesis. Upon light irradiation, jmj17 mutants displayed decreased cotyledon greening and reduced Chl level compared with the wild-type; overexpression of JMJ17 completely rescued the jmj17-5 phenotype. Transcriptomics analysis uncovered that several genes encoding key enzymes involved in TPB were upregulated in etiolated jmj17 seedlings. Consistently, chromatin immunoprecipitation-quantitative PCR revealed elevated H3K4me3 level at the promoters of target genes. Chromatin association of JMJ17 was diminished upon light exposure. Furthermore, JMJ17 interacted with PHYTOCHROME INTERACTING FACTOR1 in the yeast two-hybrid assay. JMJ17 binds directly to gene promoters to demethylate H3K4me3 to suppress PROTOCHLOROPHYLLIDE OXIDOREDUCTASE C expression and TPB in the dark. Light results in de-repression of gene expression to modulate seedling greening during de-etiolation. Our study reveals a new role for histone demethylase JMJ17 in controlling cotyledon greening in etiolated seedlings during the dark-to-light transition.
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Affiliation(s)
- Md Torikul Islam
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Long-Chi Wang
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - I-Ju Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuan-Lin Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Wan-Sheng Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
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Mladenov V, Fotopoulos V, Kaiserli E, Karalija E, Maury S, Baranek M, Segal N, Testillano PS, Vassileva V, Pinto G, Nagel M, Hoenicka H, Miladinović D, Gallusci P, Vergata C, Kapazoglou A, Abraham E, Tani E, Gerakari M, Sarri E, Avramidou E, Gašparović M, Martinelli F. Deciphering the Epigenetic Alphabet Involved in Transgenerational Stress Memory in Crops. Int J Mol Sci 2021; 22:7118. [PMID: 34281171 PMCID: PMC8268041 DOI: 10.3390/ijms22137118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/16/2021] [Accepted: 06/27/2021] [Indexed: 12/11/2022] Open
Abstract
Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics.
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Affiliation(s)
- Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology & Food Science, Cyprus University of Technology, Lemesos 3036, Cyprus;
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Erna Karalija
- Laboratory for Plant Physiology, Department for Biology, Faculty of Science, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Stephane Maury
- INRAe, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, 45067 Orléans, France;
| | - Miroslav Baranek
- Mendeleum—Insitute of Genetics, Faculty of Horticulture, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Naama Segal
- Israel Oceanographic and Limnological Research, The National Center for Mariculture (NCM), P.O.B. 1212, Eilat 88112, Israel;
| | - Pilar S. Testillano
- Center of Biological Research Margarita Salas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain;
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bldg. 21, 1113 Sofia, Bulgaria;
| | - Glória Pinto
- Centre for Environmental and Marine Studies (CESAM), Biology Department, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal;
| | - Manuela Nagel
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany;
| | - Hans Hoenicka
- Genomic Research Department, Thünen Institute of Forest Genetics, 22927 Grosshansdorf, Germany;
| | - Dragana Miladinović
- Laboratory for Biotechnology, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia;
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—CS5000833882 Villenave d’Ornon, 33076 Bordeaux, France;
| | - Chiara Vergata
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-Dimitra (HAO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece;
| | - Eleni Abraham
- Laboratory of Range Science, School of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Evaggelia Avramidou
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.T.); (M.G.); (E.S.); (E.A.)
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, 10000 Zagreb, Croatia;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
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He K, Cao X, Deng X. Histone methylation in epigenetic regulation and temperature responses. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102001. [PMID: 33508540 DOI: 10.1016/j.pbi.2021.102001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/21/2020] [Accepted: 01/04/2021] [Indexed: 05/26/2023]
Abstract
Methylation of histones on different lysine residues is dynamically added by distinct writer enzymes, interpreted by reader proteins, and removed by eraser enzymes. This epigenetic mark has widespread, dynamic roles in plant development and environmental responses. For example, histone methylation plays a key role in mediating plant responses to temperature, including alterations of flowering time. In this review, we summarize recent advances in understanding the mechanism by which histone methylation regulates these processes, and discuss the role of histone methylation in temperature responses, based on data from Arabidopsis thaliana.
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Affiliation(s)
- Kaixuan He
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Srivastava AK, Suresh Kumar J, Suprasanna P. Seed 'primeomics': plants memorize their germination under stress. Biol Rev Camb Philos Soc 2021; 96:1723-1743. [PMID: 33961327 DOI: 10.1111/brv.12722] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/28/2022]
Abstract
Seed priming is a pre-germination treatment administered through various chemical, physical and biological agents, which induce mild stress during the early phases of germination. Priming facilitates synchronized seed germination, better seedling establishment, improved plant growth and enhanced yield, especially in stressful environments. In parallel, the phenomenon of 'stress memory' in which exposure to a sub-lethal stress leads to better responses to future or recurring lethal stresses has gained widespread attention in recent years. The versatility and realistic yield gains associated with seed priming and its connection with stress memory make a critical examination useful for the design of robust approaches for maximizing future yield gains. Herein, a literature review identified selenium, salicylic acid, poly-ethylene glycol, CaCl2 and thiourea as the seed priming agents (SPRs) for which the most studies have been carried out. The average priming duration for SPRs generally ranged from 2 to 48 h, i.e. during phase I/II of germination. The major signalling events for regulating early seed germination, including the DOG1 (delay of germination 1)-abscisic acid (ABA)-heme regulatory module, ABA-gibberellic acid antagonism and nucleus-organelle communication are detailed. We propose that both seed priming and stress memory invoke a 'bet-hedging' strategy in plants, wherein their growth under optimal conditions is compromised in exchange for better growth under stressful conditions. The molecular basis of stress memory is explained at the level of chromatin reorganization, alternative transcript splicing, metabolite accumulation and autophagy. This provides a useful framework to study similar mechanisms operating during seed priming. In addition, we highlight the potential for merging findings on seed priming with those of stress memory, with the dual benefit of advancing fundamental research and boosting crop productivity. Finally, a roadmap for future work, entailing identification of SPR-responsive varieties and the development of dual/multiple-benefit SPRs, is proposed for enhancing SPR-mediated agricultural productivity worldwide.
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Affiliation(s)
- Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.,Homi Bhabha National Institute, Mumbai, 400094, India
| | - Jisha Suresh Kumar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
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Morán-Diez ME, Martínez de Alba ÁE, Rubio MB, Hermosa R, Monte E. Trichoderma and the Plant Heritable Priming Responses. J Fungi (Basel) 2021; 7:jof7040318. [PMID: 33921806 PMCID: PMC8072925 DOI: 10.3390/jof7040318] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 01/08/2023] Open
Abstract
There is no doubt that Trichoderma is an inhabitant of the rhizosphere that plays an important role in how plants interact with the environment. Beyond the production of cell wall degrading enzymes and metabolites, Trichoderma spp. can protect plants by inducing faster and stronger immune responses, a mechanism known as priming, which involves enhanced accumulation of dormant cellular proteins that function in intracellular signal amplification. One example of these proteins is the mitogen-activated protein kinases (MAPK) that are triggered by the rise of cytosolic calcium levels and cellular redox changes following a stressful challenge. Transcription factors such as WRKYs, MYBs, and MYCs, play important roles in priming as they act as regulatory nodes in the transcriptional network of systemic defence after stress recognition. In terms of long-lasting priming, Trichoderma spp. may be involved in plants epigenetic regulation through histone modifications and replacements, DNA (hypo)methylation, and RNA-directed DNA methylation (RdDM). Inheritance of these epigenetic marks for enhanced resistance and growth promotion, without compromising the level of resistance of the plant’s offspring to abiotic or biotic stresses, seems to be an interesting path to be fully explored.
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Wang TJ, Huang S, Zhang A, Guo P, Liu Y, Xu C, Cong W, Liu B, Xu ZY. JMJ17-WRKY40 and HY5-ABI5 modules regulate the expression of ABA-responsive genes in Arabidopsis. THE NEW PHYTOLOGIST 2021; 230:567-584. [PMID: 33423315 DOI: 10.1111/nph.17177] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 12/25/2020] [Indexed: 05/09/2023]
Abstract
Abscisic acid (ABA) plays a crucial role in the adaptation of young seedlings to environmental stresses. However, the role of epigenetic components and core transcriptional machineries in the effect of ABA on seed germination and seedling growth remain unclear. Here, we show that a histone 3 lysine 4 (H3K4) demethylase, JMJ17, regulates the expression of ABA-responsive genes during seed germination and seedling growth. Using comparative interactomics, WRKY40, a central transcriptional repressor in ABA signaling, was shown to interact with JMJ17. WRKY40 facilitates the recruitment of JMJ17 to the ABI5 chromatin, which removes gene activation marks (H3K4me3) from the ABI5 chromatin, thereby repressing its expression. Additionally, WRKY40 represses the transcriptional activation activity of HY5, which can activate ABI5 expression by directly binding to its promoter. An increase in ABA concentrations decreases the affinity of WRKY40 for the ABI5 promoter. Thus, WRKY40 and JMJ17 are released from the ABI5 chromatin, activating HY5. The accumulated ABI5 protein further shows heteromeric interaction with HY5, and thus synergistically activates its own expression. Our findings reveal a novel transcriptional switch, composed of JMJ17-WRKY40 and HY5-ABI5 modules, which regulates the ABA response during seed germination and seedling development in Arabidopsis.
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Affiliation(s)
- Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Shuangzhan Huang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Peng Guo
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Chunming Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Weixuan Cong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Multifaceted Chromatin Structure and Transcription Changes in Plant Stress Response. Int J Mol Sci 2021; 22:ijms22042013. [PMID: 33670556 PMCID: PMC7922328 DOI: 10.3390/ijms22042013] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/06/2023] Open
Abstract
Sessile plants are exposed throughout their existence to environmental abiotic and biotic stress factors, such as cold, heat, salinity, drought, dehydration, submergence, waterlogging, and pathogen infection. Chromatin organization affects genome stability, and its dynamics are crucial in plant stress responses. Chromatin dynamics are epigenetically regulated and are required for stress-induced transcriptional regulation or reprogramming. Epigenetic regulators facilitate the phenotypic plasticity of development and the survival and reproduction of plants in unfavorable environments, and they are highly diversified, including histone and DNA modifiers, histone variants, chromatin remodelers, and regulatory non-coding RNAs. They contribute to chromatin modifications, remodeling and dynamics, and constitute a multilayered and multifaceted circuitry for sophisticated and robust epigenetic regulation of plant stress responses. However, this complicated epigenetic regulatory circuitry creates challenges for elucidating the common or differential roles of chromatin modifications for transcriptional regulation or reprogramming in different plant stress responses. Particularly, interacting chromatin modifications and heritable stress memories are difficult to identify in the aspect of chromatin-based epigenetic regulation of transcriptional reprogramming and memory. Therefore, this review discusses the recent updates from the three perspectives—stress specificity or dependence of transcriptional reprogramming, the interplay of chromatin modifications, and transcriptional stress memory in plants. This helps solidify our knowledge on chromatin-based transcriptional reprogramming for plant stress response and memory.
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Yao T, Zhang J, Xie M, Yuan G, Tschaplinski TJ, Muchero W, Chen JG. Transcriptional Regulation of Drought Response in Arabidopsis and Woody Plants. FRONTIERS IN PLANT SCIENCE 2021; 11:572137. [PMID: 33488639 PMCID: PMC7820124 DOI: 10.3389/fpls.2020.572137] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 11/25/2020] [Indexed: 05/24/2023]
Abstract
Within the context of global warming, long-living plants such as perennial woody species endure adverse conditions. Among all of the abiotic stresses, drought stress is one of the most detrimental stresses that inhibit plant growth and productivity. Plants have evolved multiple mechanisms to respond to drought stress, among which transcriptional regulation is one of the key mechanisms. In this review, we summarize recent progress on the regulation of drought response by transcription factor (TF) families, which include abscisic acid (ABA)-dependent ABA-responsive element/ABRE-binding factors (ABRE/ABF), WRKY, and Nuclear Factor Y families, as well as ABA-independent AP2/ERF and NAC families, in the model plant Arabidopsis. We also review what is known in woody species, particularly Populus, due to its importance and relevance in economic and ecological processes. We discuss opportunities for a deeper understanding of drought response in woody plants with the development of high-throughput omics analyses and advanced genome editing techniques.
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Affiliation(s)
- Tao Yao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Meng Xie
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Biology Department, Brookhaven National Laboratory, Upton, NY, United States
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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Foroozani M, Vandal MP, Smith AP. H3K4 trimethylation dynamics impact diverse developmental and environmental responses in plants. PLANTA 2021; 253:4. [PMID: 33387051 DOI: 10.1007/s00425-020-03520-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
The H3K4me3 histone mark in plants functions in the regulation of gene expression and transcriptional memory, and influences numerous developmental processes and stress responses. Plants execute developmental programs and respond to changing environmental conditions via adjustments in gene expression, which are modulated in part by chromatin structure dynamics. Histone modifications alter chromatin in precise ways on a global scale, having the potential to influence the expression of numerous genes. Trimethylation of lysine 4 on histone H3 (H3K4me3) is a prominent histone modification that is dogmatically associated with gene activity, but more recently has also been linked to gene repression. As in other eukaryotes, the distribution of H3K4me3 in plant genomes suggests it plays a central role in gene expression regulation, however the underlying mechanisms are not fully understood. Transcript levels of many genes related to flowering, root, and shoot development are affected by dynamic H3K4me3 levels, as are those for a number of stress-responsive and stress memory-related genes. This review examines the current understanding of how H3K4me3 functions in modulating plant responses to developmental and environmental cues.
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Affiliation(s)
- Maryam Foroozani
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Matthew P Vandal
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Aaron P Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.
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Wang J, Nan N, Shi L, Li N, Huang S, Zhang A, Liu Y, Guo P, Liu B, Xu ZY. Arabidopsis BRCA1 represses RRTF1-mediated ROS production and ROS-responsive gene expression under dehydration stress. THE NEW PHYTOLOGIST 2020; 228:1591-1610. [PMID: 32621388 DOI: 10.1111/nph.16786] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Reactive oxygen species (ROS) act as important secondary messengers in abscisic acid (ABA) signaling and induce stomatal closure under dehydration stress. The breast cancer susceptibility gene 1 (BRCA1), an important tumor suppressor in animals, functions primarily in the maintenance of genome integrity in animals and plants. However, whether and how the plant BRCA1 regulates intracellular ROS homeostasis in guard cells under dehydration stress remains unknown. Here, we found that Arabidopsis atbrca1 loss-of-function mutants showed dehydration stress tolerance. This stress tolerant phenotype of atbrca1 was a result of ABA- and ROS-induced stomatal closure, which was enhanced in atbrca1 mutants compared with the wild-type. AtBRCA1 downregulated the expression of ROS-responsive and marker genes. Notably, these genes were also the targets of the AP2/ERF transcriptional activator RRTF1/ERF109. Under normal conditions, AtBRCA1 physically interacted with RRTF1 and inhibited its binding to the GCC-box-like sequence in target gene promoters. Under dehydration stress, the expression of AtBRCA1 was dramatically reduced and that of RRTF1 was activated, thus inducing the expression of ROS-responsive genes. Overall, our study reveals a novel molecular function of AtBRCA1 in the transcriptional regulation of intracellular ROS homeostasis under dehydration stress.
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Affiliation(s)
- Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Nan Nan
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Lulu Shi
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Shuangzhan Huang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Peng Guo
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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Characterization and Stress Response of the JmjC Domain-Containing Histone Demethylase Gene Family in the Allotetraploid Cotton Species Gossypium hirsutum. PLANTS 2020; 9:plants9111617. [PMID: 33233854 PMCID: PMC7709011 DOI: 10.3390/plants9111617] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 12/22/2022]
Abstract
Histone modification is an important epigenetic modification that controls gene transcriptional regulation in eukaryotes. Histone methylation is accomplished by histone methyltransferase and can occur on two amino acid residues, arginine and lysine. JumonjiC (JmjC) domain-containing histone demethylase regulates gene transcription and chromatin structure by changing the methylation state of the lysine residue site and plays an important role in plant growth and development. In this study, we carried out genome-wide identification and comprehensive analysis of JmjC genes in the allotetraploid cotton species Gossypium hirsutum. In total, 50 JmjC genes were identified and in G. hirsutum, and 25 JmjC genes were identified in its two diploid progenitors, G. arboreum and G. raimondii, respectively. Phylogenetic analysis divided these JmjC genes into five subfamilies. A collinearity analysis of the two subgenomes of G. hirsutum and the genomes of G. arboreum and G. raimondii uncovered a one-to-one relationship between homologous genes of the JmjC gene family. Most homologs in the JmjC gene family between A and D subgenomes of G. hirsutum have similar exon-intron structures, which indicated that JmjC family genes were conserved after the polyploidization. All G. hirsutumJmjC genes were found to have a typical JmjC domain, and some genes also possess other special domains important for their function. Analysis of promoter regions revealed that cis-acting elements, such as those related to hormone and abiotic stress response, were enriched in G. hirsutum JmjC genes. According to a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis, most G. hirsutumJmjC genes had high abundance expression at developmental stages of fibers, suggesting that they might participate in cotton fiber development. In addition, some G. hirsutumJmjC genes were found to have different degrees of response to cold or osmotic stress, thus indicating their potential role in these types of abiotic stress response. Our results provide useful information for understanding the evolutionary history and biological function of JmjC genes in cotton.
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Wang J, Nan N, Li N, Liu Y, Wang TJ, Hwang I, Liu B, Xu ZY. A DNA Methylation Reader-Chaperone Regulator-Transcription Factor Complex Activates OsHKT1;5 Expression during Salinity Stress. THE PLANT CELL 2020; 32:3535-3558. [PMID: 32938753 PMCID: PMC7610284 DOI: 10.1105/tpc.20.00301] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/31/2020] [Accepted: 09/13/2020] [Indexed: 05/20/2023]
Abstract
Irrigated lands are increasingly salinized, which adversely affects agricultural productivity. To respond to high sodium (Na+) concentrations, plants harbor multiple Na+ transport systems. Rice (Oryza sativa) HIGH-AFFINITY POTASSIUM (K+) TRANSPORTER1;5 (OsHKT1;5), a Na+-selective transporter, maintains K+/Na+ homeostasis under salt stress. However, the mechanism regulating OsHKT1;5 expression remains unknown. Here, we present evidence that a protein complex consisting of rice BCL-2-ASSOCIATED ATHANOGENE4 (OsBAG4), OsMYB106, and OsSUVH7 regulates OsHKT1;5 expression in response to salt stress. We isolated a salt stress-sensitive mutant, osbag4-1, that showed significantly reduced OsHKT1;5 expression and reduced K+ and elevated Na+ levels in shoots. Using comparative interactomics, we isolated two OsBAG4-interacting proteins, OsMYB106 (a MYB transcription factor) and OsSUVH7 (a DNA methylation reader), that were crucial for OsHKT1;5 expression. OsMYB106 and OsSUVH7 bound to the MYB binding cis-element (MYBE) and the miniature inverted-repeat transposable element (MITE) upstream of the MYBE, respectively, in the OsHKT1;5 promoter. OsBAG4 functioned as a bridge between OsSUVH7 and OsMYB106 to facilitate OsMYB106 binding to the consensus MYBE in the OsHKT1;5 promoter, thereby activating the OsHKT1;5 expression. Elimination of the MITE or knockout of OsMYB106 or OsSUVH7 decreased OsHKT1;5 expression and increased salt sensitivity. Our findings reveal a transcriptional complex, consisting of a DNA methylation reader, a chaperone regulator, and a transcription factor, that collaboratively regulate OsHKT1;5 expression during salinity stress.
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Affiliation(s)
- Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, People's Republic of China
| | - Nan Nan
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, People's Republic of China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, People's Republic of China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, People's Republic of China
| | - Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, People's Republic of China
| | - Inhwan Hwang
- Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, People's Republic of China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, People's Republic of China
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