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Shi Z, Zhao W, Li C, Tan W, Zhu Y, Han Y, Ai P, Li Z, Wang Z. Overexpression of the Chrysanthemum lavandulifolium ROS1 gene promotes flowering in Arabidopsis thaliana by reducing the methylation level of CONSTANS. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112019. [PMID: 38346563 DOI: 10.1016/j.plantsci.2024.112019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/27/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
DNA demethylation is involved in the regulation of flowering in plants, yet the underlying molecular mechanisms remain largely unexplored. The RELEASE OF SILENCING 1 (ROS1) gene, encoding a DNA demethyltransferase, plays key roles in many developmental processes. In this study, the ROS1 gene was isolated from Chrysanthemum lavandulifolium, where it was strongly expressed in the leaves, buds and flowers. Overexpression of the ClROS1 gene caused an early flowering phenotype in Arabidopsis thaliana. RNA-seq analysis of the transgenic plants revealed that differentially expressed genes (DEGs) were significantly enriched in the circadian rhythm pathway and that the positive regulator of flowering, CONSTANS (CO), was up-regulated. Additionally, whole-genome bisulphite sequencing (WGBS), PCR following methylation-dependent digestion with the enzyme McrBC, and bisulfite sequencing PCR (BSP) confirmed that the methylation level of the AtCO promoter was reduced, specifically in CG context. Overall, our results demonstrated that ClROS1 accelerates flowering by reducing the methylation level of the AtCO promoter. These findings clarify the epigenetic mechanism by which ClROS1-mediated DNA demethylation regulates flowering.
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Affiliation(s)
- Zhongya Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Wenqian Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Chenran Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Wenchao Tan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Yifei Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Yanchao Han
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Penghui Ai
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Zhongai Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Zicheng Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China.
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Sajeev N, Koornneef M, Bentsink L. A commitment for life: Decades of unraveling the molecular mechanisms behind seed dormancy and germination. THE PLANT CELL 2024; 36:1358-1376. [PMID: 38215009 PMCID: PMC11062444 DOI: 10.1093/plcell/koad328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/19/2023] [Indexed: 01/14/2024]
Abstract
Seeds are unique time capsules that can switch between 2 complex and highly interlinked stages: seed dormancy and germination. Dormancy contributes to the survival of plants because it allows to delay germination to optimal conditions. The switch between dormancy and germination occurs in response to developmental and environmental cues. In this review we provide a comprehensive overview of studies that have helped to unravel the molecular mechanisms underlying dormancy and germination over the last decades. Genetic and physiological studies provided a strong foundation for this field of research and revealed the critical role of the plant hormones abscisic acid and gibberellins in the regulation of dormancy and germination, and later natural variation studies together with quantitative genetics identified previously unknown genetic components that control these processes. Omics technologies like transcriptome, proteome, and translatomics analysis allowed us to mechanistically dissect these processes and identify new components in the regulation of seed dormancy and germination.
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Affiliation(s)
- Nikita Sajeev
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, 6708PB Wageningen, the Netherlands
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University, 6708PB Wageningen, the Netherlands
- Max Planck Institute for Plant Breeding Research, Former Department of Plant Breeding and Genetics, Koeln 50829, Germany
| | - Leónie Bentsink
- Wageningen Seed Science Centre, Laboratory of Plant Physiology, Wageningen University, 6708PB Wageningen, the Netherlands
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Ou X, Hua Q, Dong J, Guo K, Wu M, Deng Y, Wu Z. Functional identification of DNA demethylase gene CaROS1 in pepper ( Capsicum annuum L.) involved in salt stress. FRONTIERS IN PLANT SCIENCE 2024; 15:1396902. [PMID: 38756961 PMCID: PMC11097670 DOI: 10.3389/fpls.2024.1396902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Pepper, which is a widely cultivated important vegetable, is sensitive to salt stress, and the continuous intensification of soil salinization has affected pepper production worldwide. However, genes confer to salt tolerance are rarely been cloned in pepper. Since the REPRESSOR OF SILENCING 1 (ROS1) is a DNA demethylase that plays a crucial regulatory role in plants in response to various abiotic stresses, including salt stress. We cloned a ROS1 gene in pepper, named CaROS1 (LOC107843637). Bioinformatic analysis showed that the CaROS1 protein contains the HhH-GPD glycosylase and RRM_DME domains. qRT-PCR analyses showed that the CaROS1 was highly expressed in young and mature fruits of pepper and rapidly induced by salt stress. Functional characterization of the CaROS1 was performed by gene silencing in pepper and overexpressing in tobacco, revealed that the CaROS1 positively regulates salt tolerance ability. More detailly, CaROS1-silenced pepper were more sensitive to salt stress, and their ROS levels, relative conductivity, and malondialdehyde content were significantly higher in leaves than those of the control plants. Besides, CaROS1-overexpressing tobacco plants were more tolerant to salt stress, with a higher relative water content, total chlorophyll content, and antioxidant enzyme activity in leaves compared to those of WT plants during salt stress. These results revealed the CaROS1 dose play a role in salt stress response, providing the theoretical basis for salt tolerance genetic engineering breeding in pepper.
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Affiliation(s)
| | | | | | | | | | | | - Zhiming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
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Junaid MD, Chaudhry UK, Şanlı BA, Gökçe AF, Öztürk ZN. A review of the potential involvement of small RNAs in transgenerational abiotic stress memory in plants. Funct Integr Genomics 2024; 24:74. [PMID: 38600306 DOI: 10.1007/s10142-024-01354-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024]
Abstract
Crop production is increasingly threatened by the escalating weather events and rising temperatures associated with global climate change. Plants have evolved adaptive mechanisms, including stress memory, to cope with abiotic stresses such as heat, drought, and salinity. Stress memory involves priming, where plants remember prior stress exposures, providing enhanced responses to subsequent stress events. Stress memory can manifest as somatic, intergenerational, or transgenerational memory, persisting for different durations. The chromatin, a central regulator of gene expression, undergoes modifications like DNA acetylation, methylation, and histone variations in response to abiotic stress. Histone modifications, such as H3K4me3 and acetylation, play crucial roles in regulating gene expression. Abiotic stresses like drought and salinity are significant challenges to crop production, leading to yield reductions. Plant responses to stress involve strategies like escape, avoidance, and tolerance, each influencing growth stages differently. Soil salinity affects plant growth by disrupting water potential, causing ion toxicity, and inhibiting nutrient uptake. Understanding plant responses to these stresses requires insights into histone-mediated modifications, chromatin remodeling, and the role of small RNAs in stress memory. Histone-mediated modifications, including acetylation and methylation, contribute to epigenetic stress memory, influencing plant adaptation to environmental stressors. Chromatin remodeling play a crucial role in abiotic stress responses, affecting the expression of stress-related genes. Small RNAs; miRNAs and siRNAs, participate in stress memory pathways by guiding DNA methylation and histone modifications. The interplay of these epigenetic mechanisms helps plants adapt to recurring stress events and enhance their resilience. In conclusion, unraveling the epigenetic mechanisms in plant responses to abiotic stresses provides valuable insights for developing resilient agricultural techniques. Understanding how plants utilize stress memory, histone modifications, chromatin remodeling, and small RNAs is crucial for designing strategies to mitigate the impact of climate change on crop production and global food security.
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Affiliation(s)
- Muhammad Daniyal Junaid
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey.
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan.
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
- Pakistan Environmental Protection Agency, Ministry of Climate Change & Environmental Coordination, Islamabad, Pakistan
| | - Beyazıt Abdurrahman Şanlı
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
| | - Ali Fuat Gökçe
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
| | - Zahide Neslihan Öztürk
- Department of Agricultural Genetic Engineering, Ayhan Şahenk Faculty of Agricultural Sciences and Technologies, Niğde Ömer Halisdemir University, Niğde, Türkiye, Turkey
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Zhong S, Zhu H, Li W, Wu D, Miao Y, Dong B, Wang Y, Xiao Z, Fang Q, Deng J, Zhao H. DNA methylome analysis reveals novel insights into active hypomethylated regulatory mechanisms of temperature-dependent flower opening in Osmanthus fragrans. HORTICULTURE RESEARCH 2024; 11:uhae010. [PMID: 38464472 PMCID: PMC10923647 DOI: 10.1093/hr/uhae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/01/2024] [Indexed: 03/12/2024]
Abstract
Short-term ambient low temperature (ALT) stimulation is necessary for Osmanthus fragrans to facilitate continued flower opening after floral bud development reaches maturity. DNA methylation, a vital epigenetic modification, regulates various biological processes in response to temperature fluctuations. However, its role in temperature-driven flower opening remains elusive. In this study, we identified the pivotal timeframe during which O. fragrans promptly detected temperature cues. Using whole-genome bisulfite sequencing, we explored global DNA hypomethylation during this phase, with the most significant changes occurring in CHH sequence contexts. Auxin transport inhibitor (TIBA) application revealed that ALT-induced endogenous auxin accumulation promoted peduncle elongation. In our mRNA-seq analysis, we discovered that the differentially expressed genes (DEGs) with hypo-differentially methylated regions (hypo-DMRs) were mainly enriched in auxin and temperature response, RNA processing, and carbohydrate and lipid metabolism. Transcripts of three DNA demethylase genes (OfROS1a, OfDML3, OfDME) showed upregulation. Furthermore, all DNA methylase genes, except OfCMT2b, also displayed increased expression, specifically with two of them, OfCMT3a and OfCMT1, being associated with hypo-DMRs. Promoter assays showed that OfROS1a, with promoters containing low-temperature- and auxin-responsive elements, were activated by ALT and exogenous IAA at low concentrations but inhibited at high concentrations. Overexpression of OfROS1 reduced endogenous auxin levels but enhanced the expression of genes related to auxin response and spliceosome in petunia. Furthermore, OfROS1 promoted sucrose synthesis in petunia corollas. Our data characterized the rapid response of active DNA hypomethylation to ALT and suggested a possible epiregulation of temperature-dependent flower opening in O. fragrans. This study revealed the pivotal role of DNA hypomethylation in O. fragrans during the ALT-responsive phase before flower opening, involving dynamic DNA demethylation, auxin signaling modulation, and a potential feedback loop between hypomethylation and methylation.
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Affiliation(s)
- Shiwei Zhong
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Huijun Zhu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
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Dong X, Luo H, Yao J, Guo Q, Yu S, Ruan Y, Li F, Jin W, Meng D. The conservation of allelic DNA methylation and its relationship with imprinting in maize. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1376-1389. [PMID: 37935439 PMCID: PMC10901201 DOI: 10.1093/jxb/erad440] [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: 08/08/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
Genomic imprinting refers to allele-specific expression of genes depending on parental origin, and it is regulated by epigenetic modifications. Intraspecific allelic variation for imprinting has been detected; however, the intraspecific genome-wide allelic epigenetic variation in maize and its correlation with imprinting variants remain unclear. Here, three reciprocal hybrids were generated by crossing Zea mays inbred lines CAU5, B73, and Mo17 in order to examine the intraspecific conservation of the imprinted genes in the kernel. The majority of imprinted genes exhibited intraspecific conservation, and these genes also exhibited interspecific conservation (rice, sorghum, and Arabidopsis) and were enriched in some specific pathways. By comparing intraspecific allelic DNA methylation in the endosperm, we found that nearly 15% of DNA methylation existed as allelic variants. The intraspecific whole-genome correlation between DNA methylation and imprinted genes indicated that DNA methylation variants play an important role in imprinting variants. Disruption of two conserved imprinted genes using CRISPR/Cas9 editing resulted in a smaller kernel phenotype. Our results shed light on the intraspecific correlation of DNA methylation variants and variation for imprinting in maize, and show that imprinted genes play an important role in kernel development.
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Affiliation(s)
- Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang 110866, Liaoning, China
| | - Haishan Luo
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Jiabin Yao
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Qingfeng Guo
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Shuai Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang 110866, Liaoning, China
| | - Yanye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang 110866, Liaoning, China
| | - Fenghai Li
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
| | - Weiwei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
- Department of Agronomy, College of Agriculture & Resources and Environmental Sciences, Tianjin Agricultural University, Tianjin 300392, China
| | - Dexuan Meng
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, Liaoning, China
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Bizouerne E, Ly Vu J, Ly Vu B, Diouf I, Bitton F, Causse M, Verdier J, Buitink J, Leprince O. Genetic Variability in Seed Longevity and Germination Traits in a Tomato MAGIC Population in Contrasting Environments. PLANTS (BASEL, SWITZERLAND) 2023; 12:3632. [PMID: 37896095 PMCID: PMC10610530 DOI: 10.3390/plants12203632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023]
Abstract
The stable production of high vigorous seeds is pivotal to crop yield. Also, a high longevity is essential to avoid progressive loss of seed vigour during storage. Both seed traits are strongly influenced by the environment during seed development. Here, we investigated the impact of heat stress (HS) during fruit ripening on tomato seed lifespan during storage at moderate relative humidity, speed (t50) and homogeneity of germination, using a MAGIC population that was produced under optimal and HS conditions. A plasticity index was used to assess the extent of the impact of HS for each trait. HS reduced the average longevity and germination homogeneity by 50% within the parents and MAGIC population. However, there was a high genetic variability in the seed response to heat stress. A total of 39 QTLs were identified, including six longevity QTLs for seeds from control (3) and HS (3) conditions, and six plasticity QTLs for longevity, with only one overlapping with a longevity QTL under HS. Four out of the six longevity QTL co-located with t50 QTL, revealing hotspots for seed quality traits. Twenty-one QTLs with intervals below 3 cM were analyzed using previous transcriptome and gene network data to propose candidate genes for seed vigour and longevity traits.
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Affiliation(s)
- Elise Bizouerne
- Institut Agro, INRAE, University Angers, IRHS, SFR QUASAV, 49000 Angers, France; (E.B.); (J.L.V.); (B.L.V.); (J.V.); (J.B.)
| | - Joseph Ly Vu
- Institut Agro, INRAE, University Angers, IRHS, SFR QUASAV, 49000 Angers, France; (E.B.); (J.L.V.); (B.L.V.); (J.V.); (J.B.)
| | - Benoît Ly Vu
- Institut Agro, INRAE, University Angers, IRHS, SFR QUASAV, 49000 Angers, France; (E.B.); (J.L.V.); (B.L.V.); (J.V.); (J.B.)
| | - Isidore Diouf
- Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, INRAE, UR1052, CS60094, 84143 Avignon, France (F.B.); (M.C.)
| | - Frédérique Bitton
- Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, INRAE, UR1052, CS60094, 84143 Avignon, France (F.B.); (M.C.)
| | - Mathilde Causse
- Génétique et Amélioration des Fruits et Légumes, Centre de Recherche PACA, INRAE, UR1052, CS60094, 84143 Avignon, France (F.B.); (M.C.)
| | - Jérôme Verdier
- Institut Agro, INRAE, University Angers, IRHS, SFR QUASAV, 49000 Angers, France; (E.B.); (J.L.V.); (B.L.V.); (J.V.); (J.B.)
| | - Julia Buitink
- Institut Agro, INRAE, University Angers, IRHS, SFR QUASAV, 49000 Angers, France; (E.B.); (J.L.V.); (B.L.V.); (J.V.); (J.B.)
| | - Olivier Leprince
- Institut Agro, INRAE, University Angers, IRHS, SFR QUASAV, 49000 Angers, France; (E.B.); (J.L.V.); (B.L.V.); (J.V.); (J.B.)
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Dong X, Luo H, Bi W, Chen H, Yu S, Zhang X, Dai Y, Cheng X, Xing Y, Fan X, Zhu Y, Guo Y, Meng D. Transcriptome-wide identification and characterization of genes exhibit allele-specific imprinting in maize embryo and endosperm. BMC PLANT BIOLOGY 2023; 23:470. [PMID: 37803280 PMCID: PMC10557216 DOI: 10.1186/s12870-023-04473-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND Genomic imprinting refers to a subset of genes that are expressed from only one parental allele during seed development in plants. Studies on genomic imprinting have revealed that intraspecific variations in genomic imprinting expression exist in naturally genetic varieties. However, there have been few studies on the functional analysis of allele-specific imprinted genes. RESULTS Here, we generated three reciprocal crosses among the B73, Mo17 and CAU5 inbred lines. Based on the transcriptome-wide analysis of allele-specific expression using RNA sequencing technology, 305 allele-specific imprinting genes (ASIGs) were identified in embryos, and 655 ASIGs were identified in endosperms from three maize F1 hybrids. Of these ASIGs, most did not show consistent maternal or paternal bias between the same tissue from different hybrids or different tissues from one hybrid cross. By gene ontology (GO) analysis, five and eight categories of GO exhibited significantly higher functional enrichments for ASIGs identified in embryo and endosperm, respectively. These functional categories indicated that ASIGs are involved in intercellular nutrient transport, signaling pathways, and transcriptional regulation of kernel development. Finally, the mutation and overexpression of one ASIG (Zm305) affected the length and width of the kernel. CONCLUSION In this study, our data will be helpful in gaining further knowledge of genes exhibiting allele-specific imprinting patterns in seeds. The gain- and loss-of-function phenotypes of ASIGs associated with agronomically important seed traits provide compelling evidence for ASIGs as crucial targets to optimize seed traits in crop plants.
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Affiliation(s)
- Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Haishan Luo
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Wenjing Bi
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Hanyu Chen
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Shuai Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Xiaoyu Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yuxin Dai
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Xipeng Cheng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Yupeng Xing
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, 110866, Liaoning, China
| | - Xiaoqin Fan
- Manas Agricultural Experimental Station of Xinjiang Academy of Agricultural Sciences, Changji, 832200, Xinjiang, China
| | - Yanbin Zhu
- National Key Laboratory of Maize Biological Breeding, Key Laboratory of Genetics and Breeding of Main Crops in Northeast Region, Ministry of Agriculture and Rural Affairs, Liaoning Dongya Seed Industry Co., Ltd, Shenyang, Liaoning, 110164, China
| | - Yanling Guo
- National Key Laboratory of Maize Biological Breeding, Key Laboratory of Genetics and Breeding of Main Crops in Northeast Region, Ministry of Agriculture and Rural Affairs, Liaoning Dongya Seed Industry Co., Ltd, Shenyang, Liaoning, 110164, China
| | - Dexuan Meng
- College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
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Peirats-Llobet M, Yi C, Liew L, Berkowitz O, Narsai R, Lewsey M, Whelan J. Spatially resolved transcriptomic analysis of the germinating barley grain. Nucleic Acids Res 2023; 51:7798-7819. [PMID: 37351575 PMCID: PMC10450182 DOI: 10.1093/nar/gkad521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/26/2023] [Accepted: 06/03/2023] [Indexed: 06/24/2023] Open
Abstract
Seeds are a vital source of calories for humans and a unique stage in the life cycle of flowering plants. During seed germination, the embryo undergoes major developmental transitions to become a seedling. Studying gene expression in individual seed cell types has been challenging due to the lack of spatial information or low throughput of existing methods. To overcome these limitations, a spatial transcriptomics workflow was developed for germinating barley grain. This approach enabled high-throughput analysis of spatial gene expression, revealing specific spatial expression patterns of various functional gene categories at a sub-tissue level. This study revealed over 14 000 genes differentially regulated during the first 24 h after imbibition. Individual genes, such as the aquaporin gene family, starch degradation, cell wall modification, transport processes, ribosomal proteins and transcription factors, were found to have specific spatial expression patterns over time. Using spatial autocorrelation algorithms, we identified auxin transport genes that had increasingly focused expression within subdomains of the embryo over time, suggesting their role in establishing the embryo axis. Overall, our study provides an unprecedented spatially resolved cellular map for barley germination and identifies specific functional genomics targets to better understand cellular restricted processes during germination. The data can be viewed at https://spatial.latrobe.edu.au/.
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Affiliation(s)
- Marta Peirats-Llobet
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Changyu Yi
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Lim Chee Liew
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - Reena Narsai
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Mathew G Lewsey
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia
- Research Centre for Engineering Biology, College of Life Science, Zhejiang University, 718 East Haizhou Road, Haining, Jiaxing, Zhejiang 314400, China
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10
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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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11
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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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12
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Zhang H, Gong Z, Zhu JK. Active DNA demethylation in plants: 20 years of discovery and beyond. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2217-2239. [PMID: 36478523 DOI: 10.1111/jipb.13423] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Maintaining proper DNA methylation levels in the genome requires active demethylation of DNA. However, removing the methyl group from a modified cytosine is chemically difficult and therefore, the underlying mechanism of demethylation had remained unclear for many years. The discovery of the first eukaryotic DNA demethylase, Arabidopsis thaliana REPRESSOR OF SILENCING 1 (ROS1), led to elucidation of the 5-methylcytosine base excision repair mechanism of active DNA demethylation. In the 20 years since ROS1 was discovered, our understanding of this active DNA demethylation pathway, as well as its regulation and biological functions in plants, has greatly expanded. These exciting developments have laid the groundwork for further dissecting the regulatory mechanisms of active DNA demethylation, with potential applications in epigenome editing to facilitate crop breeding and gene therapy.
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Affiliation(s)
- Heng Zhang
- State Key Laboratory of Molecular Plant Genetics, Shanghai Centre for Plant Stress Biology, Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Jian-Kang Zhu
- School of Life Sciences, Institute of Advanced Biotechnology, Southern University of Science and Technology, Shenzhen, 518055, China
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13
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Wan J, Wang Q, Zhao J, Zhang X, Guo Z, Hu D, Meng S, Lin Y, Qiu X, Mu L, Ding D, Tang J. Gene expression variation explains maize seed germination heterosis. BMC PLANT BIOLOGY 2022; 22:301. [PMID: 35718761 PMCID: PMC9208091 DOI: 10.1186/s12870-022-03690-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 06/07/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Heterosis has been extensively utilized in plant breeding, however, the underlying molecular mechanism remains largely elusive. Maize (Zea mays), which exhibits strong heterosis, is an ideal material for studying heterosis. RESULTS In this study, there is faster imbibition and development in reciprocal crossing Zhengdan958 hybrids than in their parent lines during seed germination. To investigate the mechanism of heterosis of maize germination, comparative transcriptomic analyses were conducted. The gene expression patterns showed that 1324 (47.27%) and 1592 (66.44%) of the differential expression genes between hybrids and either parental line display parental dominance up or higher levels in the reciprocal cross of Zhengdan958, respectively. Notably, these genes were mainly enriched in metabolic pathways, including carbon metabolism, glycolysis/gluconeogenesis, protein processing in endoplasmic reticulum, etc. CONCLUSION: Our results provide evidence for the higher expression level genes in hybrid involved in metabolic pathways acting as main contributors to maize seed germinating heterosis. These findings provide new insights into the gene expression variation of maize embryos and improve the understanding of maize seed germination heterosis.
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Affiliation(s)
- Jiong Wan
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qiyue Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jiawen Zhao
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhanyong Guo
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Desheng Hu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Shujun Meng
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yuan Lin
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiaoqian Qiu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Liqin Mu
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
- The Shennong Laboratory, Zhengzhou, 450002, China.
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14
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Iwasaki M, Penfield S, Lopez-Molina L. Parental and Environmental Control of Seed Dormancy in Arabidopsis thaliana. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:355-378. [PMID: 35138879 DOI: 10.1146/annurev-arplant-102820-090750] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Seed dormancy-the absence of seed germination under favorable germination conditions-is a plant trait that evolved to enhance seedling survival by avoiding germination under unsuitable environmental conditions. In Arabidopsis, dormancy levels are influenced by the seed coat composition, while the endosperm is essential to repress seed germination of dormant seeds upon their imbibition. Recent research has shown that the mother plant modulates its progeny seed dormancy in response to seasonal temperature changes by changing specific aspects of seed coat and endosperm development. This process involves genomic imprinting by means of epigenetic marks deposited in the seed progeny and regulators previously known to regulate flowering time. This review discusses and summarizes these discoveries and provides an update on our present understanding of the role of DOG1 and abscisic acid, two key contributors to dormancy.
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Affiliation(s)
- Mayumi Iwasaki
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland;
| | - Steven Penfield
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Luis Lopez-Molina
- Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland;
- Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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15
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Yu L, Sun Y, Zhang X, Chen M, Wu T, Zhang J, Xing Y, Tian J, Yao Y. ROS1 promotes low temperature-induced anthocyanin accumulation in apple by demethylating the promoter of anthocyanin-associated genes. HORTICULTURE RESEARCH 2022; 9:uhac007. [PMID: 35147161 PMCID: PMC9123231 DOI: 10.1093/hr/uhac007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 12/15/2021] [Indexed: 05/07/2023]
Abstract
Low temperature can affect the growth and development of plants through changes in DNA demethylation patterns. Another known effect of low temperature is the accumulation of anthocyanin pigments. However, it is not known whether the two phenomena are linked, specifically, whether DNA demethylation participates in anthocyanin accumulation in response to low-temperature stress. The ROS1 gene is involved in plant DNA demethylation and influences methylation levels in response to low temperature stress. In this study, using RNA sequencing, we detected that the transcription levels of MdROS1 correlate with the anthocyanin content, as well as with those of anthocyanin biosynthesis-related genes in apple (Malus domestica), at low temperatures. Genomic bisulfite sequencing showed that the methylation levels of the promoters of the anthocyanin related genes MdCHS, MdCHI, MdF3'H, MdANS, MdUFGT, and MdMYB10 decreased in apple leaves after low-temperature treatment. Similar expression and methylation results were also found in apple fruit. Transiently silencing MdROS1 in the leaves and fruit of apple cultivars inhibited the accumulation of anthocyanins and led to decreased expression of anthocyanin biosynthetic genes, and the opposite results were detected in MdROS1-overexpressing leaves and fruit. A promoter binding assay showed that the conserved RRD-DME domains of MdROS1 directly bind to the promoters of MdF3'H and MdUFGT. Taken together, these results suggest that ROS1 affects the anthocyanin biosynthetic pathway by decreasing the methylation level of anthocyanin-related gene promoters, thereby increasing their expression and increasing anthocyanin accumulation.
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Affiliation(s)
- Lujia Yu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yuying Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Xi Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Mengchen Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yifan Xing
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Ji Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Department of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
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16
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Lu D, Zhai J, Xi M. Regulation of DNA Methylation During Plant Endosperm Development. Front Genet 2022; 13:760690. [PMID: 35222527 PMCID: PMC8867698 DOI: 10.3389/fgene.2022.760690] [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: 08/18/2021] [Accepted: 01/17/2022] [Indexed: 11/21/2022] Open
Abstract
The endosperm is a vital storage tissue in plant seeds. It provides nutrients to the embryos or the seedlings during seed development and germination. Although the genetic information in the endosperm cannot be passed directly to the next generation, its inherited epigenetic marks affect gene expression and its development and, consequently, embryo and seed growth. DNA methylation is a major form of epigenetic modification that can be investigated to understand the epigenome changes during reproductive development. Therefore, it is of great significance to explore the effects of endosperm DNA methylation on crop yield and traits. In this review, we discuss the changes in DNA methylation and the resulting imprinted gene expression levels during plant endosperm development, as well as their effects on seed development.
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Affiliation(s)
- Dongdong Lu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Jixian Zhai
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
- *Correspondence: Jixian Zhai, ; Mengli Xi,
| | - Mengli Xi
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- *Correspondence: Jixian Zhai, ; Mengli Xi,
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17
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Plants' Epigenetic Mechanisms and Abiotic Stress. Genes (Basel) 2021; 12:genes12081106. [PMID: 34440280 PMCID: PMC8394019 DOI: 10.3390/genes12081106] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/28/2022] Open
Abstract
Plants are sessile organisms that need to adapt to constantly changing environmental conditions. Unpredictable climate change places plants under a variety of abiotic stresses. Studying the regulation of stress-responsive genes can help to understand plants’ ability to adapt to fluctuating environmental conditions. Changes in epigenetic marks such as histone modifications and DNA methylation are known to regulate gene expression by their dynamic variation in response to stimuli. This can then affect their phenotypic plasticity, which helps with the adaptation of plants to adverse conditions. Epigenetic marks may also provide a mechanistic basis for stress memory, which enables plants to respond more effectively and efficiently to recurring stress and prepare offspring for potential future stresses. Studying epigenetic changes in addition to genetic factors is important to better understand the molecular mechanisms underlying plant stress responses. This review summarizes the epigenetic mechanisms behind plant responses to some main abiotic stresses.
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18
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Nishiyama E, Nonogaki M, Yamazaki S, Nonogaki H, Ohshima K. Ancient and recent gene duplications as evolutionary drivers of the seed maturation regulators DELAY OF GERMINATION1 family genes. THE NEW PHYTOLOGIST 2021; 230:889-901. [PMID: 33454982 DOI: 10.1111/nph.17201] [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: 10/02/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
The DELAY OF GERMINATION1 (DOG1) family genes (DFGs) in Arabidopsis thaliana are involved in seed dormancy, reserve accumulation, and desiccation tolerance. Decoding the molecular evolution of DFGs is key to understanding how these seed programs evolved. This article demonstrates that DFGs have diverged in the four lineages DOG1, DOG1-LIKE4 (DOGL4), DOGL5 and DOGL6, whereas DOGL1, DOGL2 and DOGL3 arose separately within the DOG1 lineage. The systematic DFG nomenclature proposed in this article addresses the current issues of inconsistent DFG annotation and highlights DFG genomic synteny in angiosperms. DFG pseudogenes, or collapsed coding sequences, hidden in the genomes of early-diverging angiosperms are documented here. They suggest ancient birth and loss of DFGs over the course of angiosperm evolution. The proposed models suggest that the origin of DFG diversification dates back to the most recent common ancestor of living angiosperms. The presence of a single form of DFG in nonflowering plants is discussed. Phylogenetic analysis of gymnosperm, lycophyte, and liverwort DFGs and similar genes found in mosses and algae suggests that DFGs diverged from the TGACG motif-binding transcription factor genes before the divergence of the bryophyte lineage.
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Affiliation(s)
- Eri Nishiyama
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Mariko Nonogaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Satoru Yamazaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Hiroyuki Nonogaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Kazuhiko Ohshima
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
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19
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Luján-Soto E, Dinkova TD. Time to Wake Up: Epigenetic and Small-RNA-Mediated Regulation during Seed Germination. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10020236. [PMID: 33530470 PMCID: PMC7911344 DOI: 10.3390/plants10020236] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 05/03/2023]
Abstract
Plants make decisions throughout their lifetime based on complex networks. Phase transitions during seed growth are not an exception. From embryo development through seedling growth, several molecular pathways control genome stability, environmental signal transduction and the transcriptional landscape. Particularly, epigenetic modifications and small non-coding RNAs (sRNAs) have been extensively studied as significant handlers of these processes in plants. Here, we review key epigenetic (histone modifications and methylation patterns) and sRNA-mediated regulatory networks involved in the progression from seed maturation to germination, their relationship with seed traits and crosstalk with environmental inputs.
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20
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Kong X, Hong Y, Hsu YF, Huang H, Liu X, Song Z, Zhu JK. SIZ1-Mediated SUMOylation of ROS1 Enhances Its Stability and Positively Regulates Active DNA Demethylation in Arabidopsis. MOLECULAR PLANT 2020; 13:1816-1824. [PMID: 32927102 DOI: 10.1016/j.molp.2020.09.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/21/2020] [Accepted: 09/08/2020] [Indexed: 05/20/2023]
Abstract
The 5-methylcytosine DNA glycosylase/lyase REPRESSOR OF SILENCING 1 (ROS1)-mediated active DNA demethylation is critical for shaping the genomic DNA methylation landscape in Arabidopsis. Whether and how the stability of ROS1 may be regulated by post-translational modifications is unknown. Using a methylation-sensitive PCR (CHOP-PCR)-based forward genetic screen for Arabidopsis DNA hyper-methylation mutants, we identified the SUMO E3 ligase SIZ1 as a critical regulator of active DNA demethylation. Dysfunction of SIZ1 leads to hyper-methylation at approximately 1000 genomic regions. SIZ1 physically interacts with ROS1 and mediates the SUMOylation of ROS1. The SUMOylation of ROS1 is reduced in siz1 mutant plants. Compared with that in wild-type plants, the protein level of ROS1 is significantly decreased, whereas there is an increased level of ROS1 transcripts in siz1 mutant plants. Our results suggest that SIZ1-mediated SUMOylation of ROS1 promotes its stability and positively regulates active DNA demethylation.
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Affiliation(s)
- Xiangfeng Kong
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China; University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yechun Hong
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China; University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yi-Feng Hsu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China
| | - Huan Huang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China
| | - Xue Liu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China
| | - Zhe Song
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China; University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, People's Republic of China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.
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21
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Kim JS, Kidokoro S, Shinozaki K, Yamaguchi-Shinozaki K. DNA demethylase ROS1 prevents inheritable DREB1A/CBF3 repression by transgene-induced promoter methylation in the Arabidopsis ice1-1 mutant. PLANT MOLECULAR BIOLOGY 2020; 104:575-582. [PMID: 33000386 DOI: 10.1007/s11103-020-01061-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
In the ros1-defective mutant, DREB1A repression by the transgene-induced promoter methylation of ice1-1 became inheritable across generations even in the absence of the causative transgene NICE1. Transgene silencing (TGS) is a widely observed event during plant bioengineering, which is presented as a gradual decrease in ectopic gene expression across generations and occasionally coupled with endogenous gene silencing based on DNA sequence similarity. TGS is known to be established by guided DNA methylation machinery. However, the machinery underlying gene recovery from TGS has not been fully elucidated. We previously reported that in ice1-1 outcross descendants, the expressional repression and recovery of DREB1A/CBF3 were instantly achieved by a newly discovered NICE1 transgene, instead of the formerly proposed ice1-1 mutation in the ICE1 gene. The plants harboring NICE1 produced small RNAs targeting and causing the DREB1A promoter to be hypermethylated and silenced. To analyze the role of the plant-specific active DNA demethylase REPRESSOR OF SILENCING 1 (ROS1) in instant DREB1A recovery, we propagated the NICE1-segregating population upon ros1 dysfunction and evaluated the gene expression and DNA methylation levels of DREB1A through generations. Our results showed that the epigenetic DREB1A repression was substantially sustained in subsequent generations even without NICE1 and stably inherited across generations. Consistent with the gene expression results, only incomplete DNA methylation removal was detected in the same generations. These results indicate that a novel inheritable epiallele emerged by the ros1 dysfunction. Overall, our study reveals the important role of ROS1 in the inheritability of TGS-associated gene repression.
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Affiliation(s)
- June-Sik Kim
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki, 305-0074, Japan
| | - Satoshi Kidokoro
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kazuo Shinozaki
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, Ibaraki, 305-0074, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
- Research Institute for Agricultural and Life Sciences, Tokyo University of Agriculture, Setagaya-ku, Tokyo, 156-8502, Japan.
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22
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Zhou Y, Yang P, Zhang F, Luo X, Xie J. Histone deacetylase HDA19 interacts with histone methyltransferase SUVH5 to regulate seed dormancy in Arabidopsis. PLANT BIOLOGY (STUTTGART, GERMANY) 2020; 22:1062-1071. [PMID: 32643178 DOI: 10.1111/plb.13158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 05/10/2020] [Accepted: 06/30/2020] [Indexed: 05/22/2023]
Abstract
Seed dormancy controls the timing of germination and plays a significant role in adaptation and evolution of seed plants. In this study, a yeast two-hybrid, pull-down assay and co-immunoprecipitation assay were used to ascertain the protein relationship of SUVH5 and HDA19. Both qRT-PCR and ChIP-qPCR were used to examine the molecular mechanism of how HDA19 and SUVH5 regulate seed dormancy. The results demonstrated that histone methyltransferase SUVH5 interacted with histone deacetylase HDA19 in vivo and in vitro. In addition, they showed that mutants of HDA19 could deepen seed dormancy, and that SUVH5 had the same effect. The hda19 suvh5 double mutant displayed a higher level of seed dormancy than the single mutants hda19 or suvh5. Moreover, the expression of seed dormancy-related genes increased in hda19, suvh5 and in hda19 suvh5 double mutant plants, which was associated with increased histone H3 acetylation (H3ac), but decreased histone H3 Lys 9 dimethylation (H3K9me2). ChIP assays proved that HDA19 could directly integrate into the chromatin of genes regulating seed dormancy. Taken together, our results show that HDA19 and SUVH5 work together and have a negative role in seed dormancy.
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Affiliation(s)
- Y Zhou
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - P Yang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - F Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - X Luo
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - J Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
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Verma P, Tandon R, Yadav G, Gaur V. Structural Aspects of DNA Repair and Recombination in Crop Improvement. Front Genet 2020; 11:574549. [PMID: 33024442 PMCID: PMC7516265 DOI: 10.3389/fgene.2020.574549] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
The adverse effects of global climate change combined with an exponentially increasing human population have put substantial constraints on agriculture, accelerating efforts towards ensuring food security for a sustainable future. Conventional plant breeding and modern technologies have led to the creation of plants with better traits and higher productivity. Most crop improvement approaches (conventional breeding, genome modification, and gene editing) primarily rely on DNA repair and recombination (DRR). Studying plant DRR can provide insights into designing new strategies or improvising the present techniques for crop improvement. Even though plants have evolved specialized DRR mechanisms compared to other eukaryotes, most of our insights about plant-DRRs remain rooted in studies conducted in animals. DRR mechanisms in plants include direct repair, nucleotide excision repair (NER), base excision repair (BER), mismatch repair (MMR), non-homologous end joining (NHEJ) and homologous recombination (HR). Although each DRR pathway acts on specific DNA damage, there is crosstalk between these. Considering the importance of DRR pathways as a tool in crop improvement, this review focuses on a general description of each DRR pathway, emphasizing on the structural aspects of key DRR proteins. The review highlights the gaps in our understanding and the importance of studying plant DRR in the context of crop improvement.
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Affiliation(s)
- Prabha Verma
- National Institute of Plant Genome Research, New Delhi, India
| | - Reetika Tandon
- National Institute of Plant Genome Research, New Delhi, India
| | - Gitanjali Yadav
- National Institute of Plant Genome Research, New Delhi, India
| | - Vineet Gaur
- National Institute of Plant Genome Research, New Delhi, India
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24
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Nonogaki H, Nishiyama E, Ohshima K, Nonogaki M. Ancient Memories of Seeds: ABA-Dependent Growth Arrest and Reserve Accumulation. Trends Genet 2020; 36:464-473. [DOI: 10.1016/j.tig.2020.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 11/30/2022]
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Small RNA Function in Plants: From Chromatin to the Next Generation. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2020; 84:133-140. [PMID: 32518093 DOI: 10.1101/sqb.2019.84.040394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Small RNA molecules can target a particular virus, gene, or transposable element (TE) with a high degree of specificity. Their ability to move from cell to cell and recognize targets in trans also allows building networks capable of regulating a large number of related targets at once. In the case of epigenetic silencing, small RNA may use the widespread distribution of TEs in eukaryotic genomes to coordinate many loci across developmental and generational time. Here, we discuss the intriguing role of plant small RNA in targeting transposons and repeats in pollen and seeds. Epigenetic reprogramming in the germline and early seed development provides a mechanism to control genome dosage, imprinted gene expression, and incompatible hybridizations via the "triploid block."
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Lin W, Sun L, Huang RZ, Liang W, Liu X, He H, Fukuda H, He XQ, Qian W. Active DNA demethylation regulates tracheary element differentiation in Arabidopsis. SCIENCE ADVANCES 2020; 6:eaaz2963. [PMID: 32637594 PMCID: PMC7319731 DOI: 10.1126/sciadv.aaz2963] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 05/13/2020] [Indexed: 05/16/2023]
Abstract
DNA demethylation is important for the erasure of DNA methylation. The role of DNA demethylation in plant development remains poorly understood. Here, we found extensive DNA demethylation in the CHH context around pericentromeric regions and DNA demethylation in the CG, CHG, and CHH contexts at discrete genomic regions during ectopic xylem tracheary element (TE) differentiation. While loss of pericentromeric methylation occurs passively, DNA demethylation at a subset of regions relies on active DNA demethylation initiated by DNA glycosylases ROS1, DML2, and DML3. The ros1 and rdd mutations impair ectopic TE differentiation and xylem development in the young roots of Arabidopsis seedlings. Active DNA demethylation targets and regulates many genes for TE differentiation. The defect of xylem development in rdd is proposed to be caused by dysregulation of multiple genes. Our study identifies a role of active DNA demethylation in vascular development and reveals an epigenetic mechanism for TE differentiation.
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Affiliation(s)
- Wei Lin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Linhua Sun
- Academy for Advanced Interdisciplinary Studies, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Run-Zhou Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenjie Liang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xinyu Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Xin-Qiang He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Corresponding author. (X.-Q.H.); (W.Q.)
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Corresponding author. (X.-Q.H.); (W.Q.)
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27
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Katsuya-Gaviria K, Caro E, Carrillo-Barral N, Iglesias-Fernández R. Reactive Oxygen Species (ROS) and Nucleic Acid Modifications During Seed Dormancy. PLANTS (BASEL, SWITZERLAND) 2020; 9:E679. [PMID: 32471221 PMCID: PMC7356579 DOI: 10.3390/plants9060679] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022]
Abstract
The seed is the propagule of higher plants and allows its dissemination and the survival of the species. Seed dormancy prevents premature germination under favourable conditions. Dormant seeds are only able to germinate in a narrow range of conditions. During after-ripening (AR), a mechanism of dormancy release, seeds gradually lose dormancy through a period of dry storage. This review is mainly focused on how chemical modifications of mRNA and genomic DNA, such as oxidation and methylation, affect gene expression during late stages of seed development, especially during dormancy. The oxidation of specific nucleotides produced by reactive oxygen species (ROS) alters the stability of the seed stored mRNAs, being finally degraded or translated into non-functional proteins. DNA methylation is a well-known epigenetic mechanism of controlling gene expression. In Arabidopsis thaliana, while there is a global increase in CHH-context methylation through embryogenesis, global DNA methylation levels remain stable during seed dormancy, decreasing when germination occurs. The biological significance of nucleic acid oxidation and methylation upon seed development is discussed.
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Affiliation(s)
- Kai Katsuya-Gaviria
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
| | - Néstor Carrillo-Barral
- Departamento de Fisiología Vegetal, Facultad de Ciencias, Universidad da Coruña (UdC), 15008-A Coruña, Spain;
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
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Chang YN, Zhu C, Jiang J, Zhang H, Zhu JK, Duan CG. Epigenetic regulation in plant abiotic stress responses. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:563-580. [PMID: 31872527 DOI: 10.1111/jipb.12901] [Citation(s) in RCA: 217] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/20/2020] [Indexed: 05/18/2023]
Abstract
In eukaryotic cells, gene expression is greatly influenced by the dynamic chromatin environment. Epigenetic mechanisms, including covalent modifications to DNA and histone tails and the accessibility of chromatin, create various chromatin states for stress-responsive gene expression that is important for adaptation to harsh environmental conditions. Recent studies have revealed that many epigenetic factors participate in abiotic stress responses, and various chromatin modifications are changed when plants are exposed to stressful environments. In this review, we summarize recent progress on the cross-talk between abiotic stress response pathways and epigenetic regulatory pathways in plants. Our review focuses on epigenetic regulation of plant responses to extreme temperatures, drought, salinity, the stress hormone abscisic acid, nutrient limitations and ultraviolet stress, and on epigenetic mechanisms of stress memory.
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Affiliation(s)
- Ya-Nan Chang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jing Jiang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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29
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Liu R, Lang Z. The mechanism and function of active DNA demethylation in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:148-159. [PMID: 31628716 DOI: 10.1111/jipb.12879] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/16/2019] [Indexed: 05/26/2023]
Abstract
DNA methylation is a conserved and important epigenetic mark in both mammals and plants. DNA methylation can be dynamically established, maintained, and removed through different pathways. In plants, active DNA demethylation is initiated by the RELEASE OF SILENCING 1 (ROS1) family of bifunctional DNA glycosylases/lyases. Accumulating evidence suggests that DNA demethylation is important in many processes in plants. In this review, we summarize recent studies on the enzymes and regulatory factors that have been identified in the DNA demethylation pathway. We also review the functions of active DNA demethylation in plant development as well as biotic and abiotic stress responses. Finally, we highlight those aspects of DNA demethylation that require additional research.
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Affiliation(s)
- Ruie Liu
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
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30
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Sall K, Dekkers BJW, Nonogaki M, Katsuragawa Y, Koyari R, Hendrix D, Willems LAJ, Bentsink L, Nonogaki H. DELAY OF GERMINATION 1-LIKE 4 acts as an inducer of seed reserve accumulation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:7-19. [PMID: 31359518 DOI: 10.1111/tpj.14485] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/10/2019] [Accepted: 06/17/2019] [Indexed: 05/18/2023]
Abstract
More than 70% of global food supply depends on seeds. The major seed reserves, such as proteins, lipids, and polysaccharides, are produced during seed maturation. Here, we report that DELAY OF GERMINATION 1-LIKE 4 (DOGL4) is a major inducer of reserve accumulation during seed maturation. The DOGL family proteins are plant-specific proteins of largely unknown biochemical function. DOGL4 shares only limited homology in amino acid sequence with DOG1, a major regulator of seed dormancy. DOGL4 was identified as one of the outstanding abscisic acid (ABA)-induced genes in our RNA sequencing analysis, whereas DOG1 was not induced by ABA. Induction of DOGL4 caused the expression of 70 seed maturation-specific genes, even in germinating seeds, including the major seed reserves ALBUMIN, CRUCIFERIN and OLEOSIN. Although DOG1 affects the expression of many seed maturation genes, the major seed reserve genes induced by DOGL4 are not altered by the dog1 mutation. Furthermore, the reduced dormancy and longevity phenotypes observed in the dog1 seeds were not observed in the dogl4 mutants, suggesting that these two genes have limited functional overlap. Taken together, these results suggest that DOGL4 is a central factor mediating reserve accumulation in seeds, and that the two DOG1 family proteins have diverged over the course of evolution into independent regulators of seed maturation, but retain some overlapping function.
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Affiliation(s)
- Khadidiatou Sall
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - Bas J W Dekkers
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, Wageningen, the Netherlands
| | - Mariko Nonogaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | | | - Ryosuke Koyari
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
| | - David Hendrix
- Department of Biochemistry and Biophysics, School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Leo A J Willems
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, Wageningen, the Netherlands
| | - Leónie Bentsink
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, Wageningen, the Netherlands
| | - Hiroyuki Nonogaki
- Department of Horticulture, Oregon State University, Corvallis, OR, 97331, USA
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31
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Miao W, Dai J, La Y, Lu C, Zhang J, Hong X, Zhou S, Wang Q, Wang X, Rui Q, Tan F, La H. Characterization and fine mapping of Arabidopsis RLL3, a locus required for DNA demethylation pathway. Mol Genet Genomics 2019; 295:81-93. [PMID: 31486938 DOI: 10.1007/s00438-019-01605-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 08/13/2019] [Indexed: 01/06/2023]
Abstract
DNA methylation pattern is found to be established by the combined actions of DNA methylation and demethylation. Compared to the DNA methylation pathway, DNA demethylation pathway, however, remains largely unknown. To better understand the DNA demethylation pathway, we performed genetic screening for Arabidopsis mutants with increased genomic DNA methylation levels through a 2 × 35S:LUC (LUC, luciferase) reporter system. A mutant with reduced LUC luminescence was identified by such a system, therefore named rll3-1 (for reduced LUC luminescence 3-1). The rll3-1 mutant exhibited pleiotropic developmental defects, such as delayed bolting as well as flowering, more branches, etc. By map-based cloning approach, rll3 locus that contains a single nuclear recessive mutation as revealed by the genetic analysis was mapped to a region between molecular markers CL102_B1 M1 and CL102_B3M1, which are located in bacterial artificial chromosome (BAC) clones F9P14 and F12K11, respectively, on chromosome 1. Chop-PCR analysis indicated that a total of seven tested loci displayed elevated DNA methylation levels. Whole-genome bisulfite sequencing further revealed 1536 loci exhibiting increased DNA methylation levels relative to Col-LUC control, among which there are 507 such loci overlapping between the rll3-1 and ros1-7 mutants, suggestive of a functional association between RLL3 and REPRESSOR OF SILENCING 1 (ROS1). Further investigations demonstrated that the expression levels of a few genes (like ROS1, IDM1, etc.), which are involved in DNA demethylation pathway, remained unchanged in the rll3-1 mutant, indicating that the increased DNA methylation levels in rll3-1 mutant are not attributable to downregulation of such genes. Taken together, our studies provide a demonstration of the involvement of RLL3 in the DNA demethylation pathway.
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Affiliation(s)
- Wei Miao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jie Dai
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yumei La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Chong Lu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jianzhen Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xinyue Hong
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shaoxia Zhou
- College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qianqian Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiangyu Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Qi Rui
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Feng Tan
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Honggui La
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Nonogaki H. Seed germination and dormancy: The classic story, new puzzles, and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:541-563. [PMID: 30565406 DOI: 10.1111/jipb.12762] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/17/2018] [Indexed: 05/18/2023]
Abstract
This review highlights recent progresses in seed germination and dormancy research. Research on the weakening of the endosperm during germination, which is almost a classic theme in seed biology, was resumed by α-xylosidase studies. Strong genetic evidence was presented to suggest that the quality control of xyloglucan biosynthesis in the endosperm (and the embryo) plays a critical role in germination. Further analyses on the endosperm and the adjacent layers have suggested that the cutin coat in the endosperm-testa interphase negatively affects germination while the endosperm-embryo interphase produces a sheath that facilitates germination. These progresses significantly advanced our understanding of seed germination mechanisms. A breakthrough in dormancy research, on the other hand, revealed the unique abscisic acid signaling pathway that is regulated by DELAY OF GERMINATION1 (DOG1). The detailed analysis of DOG1 expression uncovered the intriguing story of reciprocal regulation of the sense-antisense pair, which generated new questions. Recent studies also suggested that the DOG1 function is not limited to dormancy but extended through general seed maturation, which provokes questions about the evolution of DOG1 family proteins. Seed biology is becoming more exciting with the classic stories being revitalized and new puzzles emerging from the frontier.
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33
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Zhao QQ, Lin RN, Li L, Chen S, He XJ. A methylated-DNA-binding complex required for plant development mediates transcriptional activation of promoter methylated genes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:120-139. [PMID: 30589221 DOI: 10.1111/jipb.12767] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 12/27/2018] [Indexed: 05/29/2023]
Abstract
Although the mechanism of DNA methylation-mediated gene silencing is extensively studied, relatively little is known about how promoter methylated genes are protected from transcriptional silencing. SUVH1, an Arabidopsis Su(var)3-9 homolog, was previously shown to be required for the expression of a few promoter methylated genes. By chromatin immunoprecipitation combined with sequencing, we demonstrate that SUVH1 binds to methylated genomic loci targeted by RNA-directed DNA methylation. SUVH1 and its homolog SUVH3 function partially redundantly and interact with three DNAJ domain-containing homologs, SDJ1, SDJ2, and SDJ3, thus forming a complex which we named SUVH-SDJ. The SUVH-SDJ complex components are co-localized in a large number of methylated promoters and are required for the expression of a subset of promoter methylated genes. We demonstrate that the SUVH-SDJ complex components have transcriptional activation activity. SUVH1 and SUVH3 function synergistically with SDJ1, SDJ2, and SDJ3 and are required for plant viability. This study reveals how the SUVH-SDJ complex protects promoter methylated genes from transcriptional silencing and suggests that the transcriptional activation of promoter methylated genes mediated by the SUVH-SDJ complex may play a critical role in plant growth and development.
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Affiliation(s)
- Qiang-Qiang Zhao
- National Institute of Biological Sciences, Beijing 102206, China
- Graduate School of Peking Union Medical College, Beijing 100730, China
| | - Rong-Nan Lin
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing 102206, China
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34
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Gu D, Ji R, He C, Peng T, Zhang M, Duan J, Xiong C, Liu X. Arabidopsis Histone Methyltransferase SUVH5 Is a Positive Regulator of Light-Mediated Seed Germination. FRONTIERS IN PLANT SCIENCE 2019; 10:841. [PMID: 31316539 PMCID: PMC6610342 DOI: 10.3389/fpls.2019.00841] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 06/12/2019] [Indexed: 05/20/2023]
Abstract
Plant lifecycle starts from seed germination, which is regulated by various environmental cues and endogenous hormones. Light promotes seed germination mainly by phytochrome B (PHYB) during the initial phase of imbibition, which involves genome-wide light-responsive transcription changes. Recent studies indicated an involvement of multiple epigenetic factors in the control of seed germination. However, few studies have been reported about the role of a histone methyltransferase in light-mediated seed germination process. Here, we identified SUVH5, a histone H3 lysine 9 methyltransferase, as a positive regulator in light-mediated seed germination in Arabidopsis. Loss of function of SUVH5 leads to decreased PHYB-dependent seed germination. RNA-sequencing analysis displayed that SUVH5 regulates 24.6% of light-responsive transcriptome in imbibed seeds, which mainly related to hormonal signaling pathways and developmental processes. Furthermore, SUVH5 represses the transcription of ABA biosynthesis and signal transduction-related genes, as well as a family of DELAY OF GERMINATION (DOG) genes via dimethylation of histone H3 at lysine 9 (H3K9me2) in imbibed seeds. Taken together, our findings revealed that SUVH5 is a novel positive regulator of light-mediated seed germination in Arabidopsis.
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Affiliation(s)
- Dachuan Gu
- 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
- Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Rujun Ji
- 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
- Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Chunmei He
- 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
- Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tao Peng
- 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
- Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Mingyong Zhang
- 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
- Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jun Duan
- 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
- Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Changyun Xiong
- College of Tropical Crops, Yunnan Agricultural University, Pu’er, China
- *Correspondence: Changyun Xiong,
| | - Xuncheng Liu
- 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
- Core Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Xuncheng Liu,
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