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Wang Z, Xia A, Wang Q, Cui Z, Lu M, Ye Y, Wang Y, He Y. Natural polymorphisms in ZMET2 encoding a DNA methyltransferase modulate the number of husk layers in maize. PLANT PHYSIOLOGY 2024; 195:2129-2142. [PMID: 38431291 PMCID: PMC11213254 DOI: 10.1093/plphys/kiae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/30/2024] [Accepted: 02/08/2024] [Indexed: 03/05/2024]
Abstract
DNA methylation affects agronomic traits and the environmental adaptability of crops, but the natural polymorphisms in DNA methylation-related genes and their contributions to phenotypic variation in maize (Zea mays) remain elusive. Here, we show that a polymorphic 10-bp insertion/deletion variant in the 3'UTR of Zea methyltransferase2 (ZMET2) alters its transcript level and accounts for variation in the number of maize husk layers. ZMET2 encodes a chromomethylase and is required for maintaining genome-wide DNA methylation in the CHG sequence context. Disruption of ZMET2 increased the number of husk layers and resulted in thousands of differentially methylated regions, a proportion of which were also distinguishable in natural ZMET2 alleles. Population genetic analyses indicated that ZMET2 was a target of selection and might play a role in the spread of maize from tropical to temperate regions. Our results provide important insights into the natural variation of ZMET2 that confers both global and locus-specific effects on DNA methylation, which contribute to phenotypic diversity in maize.
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Affiliation(s)
- Zi Wang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Aiai Xia
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Qi Wang
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Zhenhai Cui
- Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang Agricultural University, Shenyang 110866, China
| | - Ming Lu
- Maize Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Yusheng Ye
- Maize Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110065, China
| | - Yanbo Wang
- Maize Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110065, China
| | - Yan He
- State Key Laboratory of Maize Bio-breeding, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
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2
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Fan Y, Sun C, Yan K, Li P, Hein I, Gilroy EM, Kear P, Bi Z, Yao P, Liu Z, Liu Y, Bai J. Recent Advances in Studies of Genomic DNA Methylation and Its Involvement in Regulating Drought Stress Response in Crops. PLANTS (BASEL, SWITZERLAND) 2024; 13:1400. [PMID: 38794470 PMCID: PMC11125032 DOI: 10.3390/plants13101400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024]
Abstract
As global arid conditions worsen and groundwater resources diminish, drought stress has emerged as a critical impediment to plant growth and development globally, notably causing declines in crop yields and even the extinction of certain cultivated species. Numerous studies on drought resistance have demonstrated that DNA methylation dynamically interacts with plant responses to drought stress by modulating gene expression and developmental processes. However, the precise mechanisms underlying these interactions remain elusive. This article consolidates the latest research on the role of DNA methylation in plant responses to drought stress across various species, focusing on methods of methylation detection, mechanisms of methylation pattern alteration (including DNA de novo methylation, DNA maintenance methylation, and DNA demethylation), and overall responses to drought conditions. While many studies have observed significant shifts in genome-wide or gene promoter methylation levels in drought-stressed plants, the identification of specific genes and pathways involved remains limited. This review aims to furnish a reference for detailed research into plant responses to drought stress through epigenetic approaches, striving to identify drought resistance genes regulated by DNA methylation, specific signaling pathways, and their molecular mechanisms of action.
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Affiliation(s)
- Youfang Fan
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Kan Yan
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China;
| | - Pengcheng Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Ingo Hein
- The James Hutton Institute, Dundee DD2 5DA, UK; (I.H.); (E.M.G.)
| | | | - Philip Kear
- International Potato Center (CIP), CIP China Center for Asia Pacific (CCCAP), Beijing 102199, China;
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Panfeng Yao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Zhen Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (Y.F.); (P.L.); (Z.B.); (P.Y.); (Z.L.); (Y.L.)
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Zhang D, Gan Y, Le L, Pu L. Epigenetic variation in maize agronomical traits for breeding and trait improvement. J Genet Genomics 2024:S1673-8527(24)00028-6. [PMID: 38310944 DOI: 10.1016/j.jgg.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/28/2024] [Accepted: 01/29/2024] [Indexed: 02/06/2024]
Abstract
Epigenetics-mediated breeding (Epibreeding) involves engineering crop traits and stress responses through the targeted manipulation of key epigenetic features to enhance agricultural productivity. While conventional breeding methods raise concerns about reduced genetic diversity, epibreeding propels crop improvement through epigenetic variations that regulate gene expression, ultimately impacting crop yield. Epigenetic regulation in crops encompasses various modes, including histone modification, DNA modification, RNA modification, non-coding RNA, and chromatin remodeling. This review summarizes the epigenetic mechanisms underlying major agronomic traits in maize and identifies candidate epigenetic landmarks in the maize breeding process. We propose a valuable strategy for improving maize yield through epibreeding, combining CRISPR/Cas-based epigenome editing technology and Synthetic Epigenetics (SynEpi). Finally, we discuss the challenges and opportunities associated with maize trait improvement through epibreeding.
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Affiliation(s)
- Daolei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; School of Life Science, Inner Mongolia University, Hohhot, Inner Mongolia 010021, China
| | - Yujun Gan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liang Le
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Simko I. Differentially methylated genomic regions of lettuce seeds relate to divergence across morphologically distinct horticultural types. AOB PLANTS 2023; 15:plad060. [PMID: 37680204 PMCID: PMC10482144 DOI: 10.1093/aobpla/plad060] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 08/22/2023] [Indexed: 09/09/2023]
Abstract
Heritable cytosine methylation plays a role in shaping plant phenotypes; however, no information is available about DNA methylation in cultivated lettuce (Lactuca sativa), one of the most important leafy vegetables. Whole-genome bisulfite sequencing (WGBS) performed on seeds of 95 accessions from eight morphologically distinct horticultural types (Batavia, butterhead, iceberg, Latin, leaf, oilseed, romaine and stem) revealed a high level of methylation in lettuce genome with an average methylation of 90.6 % in the CG context, 72.9 % in the CHG context and 7.5 % in the CHH context. Although WGBS did not show substantial differences in overall methylation levels across eight horticultural types, 350 differentially methylated regions (DMR) were identified. Majority of the 41 pivotal DMR overlapped with genomic features predicted or confirmed to be involved in plant growth and development. These results provide the first insight into lettuce DNA methylation and indicate a potential role for heritable variation in cytosine methylation in lettuce morphology. The results reveal that differences in methylation profiles of morphologically distinct horticultural types are already detectable in seeds. Identified DMR can be a focus of the future functional studies.
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Affiliation(s)
- Ivan Simko
- Crop Improvement and Protection Research Unit, US Department of Agriculture, Agricultural Research Service, Salinas, CA 93905, USA
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Li J, Li C, Deng Y, Wei H, Lu S. Characteristics of Salvia miltiorrhiza methylome and the regulatory mechanism of DNA methylation in tanshinone biosynthesis. HORTICULTURE RESEARCH 2023; 10:uhad114. [PMID: 37577393 PMCID: PMC10419789 DOI: 10.1093/hr/uhad114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/21/2023] [Indexed: 08/15/2023]
Abstract
Salvia miltiorrhiza is a model medicinal plant with significant economic and medicinal value. Its roots produce a group of diterpenoid lipophilic bioactive components, termed tanshinones. Biosynthesis and regulation of tanshinones has attracted widespread interest. However, the methylome of S. miltiorrhiza has not been analysed and the regulatory mechanism of DNA methylation in tanshinone production is largely unknown. Here we report single-base resolution DNA methylomes from roots and leaves. Comparative analysis revealed differential methylation patterns for CG, CHG, and CHH contexts and the association between DNA methylation and the expression of genes and small RNAs. Lowly methylated genes always had higher expression levels and 24-nucleotide sRNAs could be key players in the RdDM pathway in S. miltiorrhiza. DNA methylation variation analysis showed that CHH methylation contributed mostly to the difference. Go enrichment analysis showed that diterpenoid biosynthetic process was significantly enriched for genes with downstream overlapping with hypoCHHDMR in July_root when comparing with those in March_root. Tanshinone biosynthesis-related enzyme genes, such as DXS2, CMK, IDI1, HMGR2, DXR, MDS, CYP76AH1, 2OGD25, and CYP71D373, were less CHH methylated in gene promoters or downstream regions in roots collected in July than those collected in March. Consistently, gene expression was up-regulated in S. miltiorrhiza roots collected in July compared with March and the treatment of DNA methylation inhibitor 5-azacytidine significantly promoted tanshinone production. It suggests that DNA methylation plays a significant regulatory role in tanshinone biosynthesis in S. miltiorrhiza through changing the levels of CHH methylation in promoters or downstreams of key enzyme genes.
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Affiliation(s)
- Jiang Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Caili Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Yuxing Deng
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Shanfa Lu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
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Zhu J, Wang Y, Wang Q, Li B, Wang X, Zhou X, Zhang H, Xu W, Li S, Wang L. The combination of DNA methylation and positive regulation of anthocyanin biosynthesis by MYB and bHLH transcription factors contributes to the petal blotch formation in Xibei tree peony. HORTICULTURE RESEARCH 2023; 10:uhad100. [PMID: 37427034 PMCID: PMC10327543 DOI: 10.1093/hr/uhad100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 05/05/2023] [Indexed: 07/11/2023]
Abstract
Xibei tree peony is a distinctive cultivar group that features red-purple blotches in petals. Interestingly, the pigmentations of blotches and non-blotches are largely independent of one another. The underlying molecular mechanism had attracted lots of attention from investigators, but was still uncertain. Our present work demonstrates the factors that are closely related to blotch formation in Paeonia rockii 'Shu Sheng Peng Mo'. Non-blotch pigmentation is prevented by the silencing of anthocyanin structural genes, among which PrF3H, PrDFR, and PrANS are the three major genes. We characterized two R2R3-MYBs as the key transcription factors that control the early and late anthocyanin biosynthetic pathways. PrMYBa1, which belongs to MYB subgroup 7 (SG7) was found to activate the early biosynthetic gene (EBG) PrF3H by interacting with SG5 member PrMYBa2 to form an 'MM' complex. The SG6 member PrMYBa3 interacts with two SG5 (IIIf) bHLHs to synergistically activate the late biosynthetic genes (LBGs) PrDFR and PrANS, which is essential for anthocyanin accumulation in petal blotches. The comparison of methylation levels of the PrANS and PrF3H promoters between blotch and non-blotch indicated a correlation between hypermethylation and gene silencing. The methylation dynamics of PrANS promoter during flower development revealed a potential early demethylating reaction, which may have contributed to the particular expression of PrANS solely in the blotch area. We suggest that the formation of petal blotch may be highly associated with the cooperation of transcriptional activation and DNA methylation of structural gene promoters.
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Affiliation(s)
- Jin Zhu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yizhou Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianyu Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaohan Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xian Zhou
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hechen Zhang
- Horticulture Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Wenzhong Xu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanshan Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangsheng Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Song J, Wang X, Huang L, Li Z, Ren H, Wang J. Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses. FRONTIERS IN PLANT SCIENCE 2022; 13:1017672. [PMID: 36479521 PMCID: PMC9721362 DOI: 10.3389/fpls.2022.1017672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
Plant height affects crop production and breeding practices, while genetic control of dwarfism draws a broad interest of researchers. Dwarfism in soybean (Glycine max) is mainly unexplored. Here, we characterized a dwarf mutant dm screened from ethyl methanesulfonate (EMS) mutated seeds of the soybean cultivar Zhongpin 661(ZP). Phenotypically, dm showed shorter and thinner stems, smaller leaves, and more nodes than ZP under greenhouse conditions. Genetically, whole-genome sequencing and comparison revealed that 210K variants of SNPs and InDel in ZP relative to the soybean reference genome Williams82, and EMS mutagenesis affected 636 genes with variants predicted to have a large impact on protein function in dm. Whole-genome methylation sequencing found 704 differentially methylated regions in dm. Further whole-genome RNA-Seq based transcriptomic comparison between ZP and dm leaves revealed 687 differentially expressed genes (DEGs), including 263 up-regulated and 424 down-regulated genes. Integrated omics analyses revealed 11 genes with both differential expressions and DNA variants, one gene with differential expression and differential methylation, and three genes with differential methylation and sequence variation, worthy of future investigation. Genes in cellulose, fatty acids, and energy-associated processes could be the key candidate genes for the dwarf phenotype. This study provides genetic clues for further understanding of the genetic control of dwarfism in soybean. The genetic resources could help to inbreed new cultivars with a desirable dwarf characteristic.
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Affiliation(s)
- Jian Song
- College of Life Science, Yangtze University, Jingzhou, China
- National Key Facility for Gene Resources and Genetic Improvement (NFCRI)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, AB, United States
| | - Lan Huang
- Department of Computer Science, Yangtze University, Jingzhou, China
| | - Zhongfeng Li
- National Key Facility for Gene Resources and Genetic Improvement (NFCRI)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honglei Ren
- National Key Facility for Gene Resources and Genetic Improvement (NFCRI)/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jun Wang
- College of Agriculture, Yangtze University, Jingzhou, China
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Sakamoto Y, Kawamura A, Suzuki T, Segami S, Maeshima M, Polyn S, De Veylder L, Sugimoto K. Transcriptional activation of auxin biosynthesis drives developmental reprogramming of differentiated cells. THE PLANT CELL 2022; 34:4348-4365. [PMID: 35922895 PMCID: PMC9614439 DOI: 10.1093/plcell/koac218] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/19/2022] [Indexed: 05/26/2023]
Abstract
Plant cells exhibit remarkable plasticity of their differentiation states, enabling regeneration of whole plants from differentiated somatic cells. How they revert cell fate and express pluripotency, however, remains unclear. In this study, we demonstrate that transcriptional activation of auxin biosynthesis is crucial for reprogramming differentiated Arabidopsis (Arabidopsis thaliana) leaf cells. Our data show that interfering with the activity of histone acetyltransferases dramatically reduces callus formation from leaf mesophyll protoplasts. Histone acetylation permits transcriptional activation of PLETHORAs, leading to the induction of their downstream YUCCA1 gene encoding an enzyme for auxin biosynthesis. Auxin biosynthesis is in turn required to accomplish initial cell division through the activation of G2/M phase genes mediated by MYB DOMAIN PROTEIN 3-RELATED (MYB3Rs). We further show that the AUXIN RESPONSE FACTOR 7 (ARF7)/ARF19 and INDOLE-3-ACETIC ACID INDUCIBLE 3 (IAA3)/IAA18-mediated auxin signaling pathway is responsible for cell cycle reactivation by transcriptionally upregulating MYB3R4. These findings provide a mechanistic model of how differentiated plant cells revert their fate and reinitiate the cell cycle to become pluripotent.
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Affiliation(s)
- Yuki Sakamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
| | - Ayako Kawamura
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
| | - Takamasa Suzuki
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan
| | - Shoji Segami
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan
| | - Masayoshi Maeshima
- Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan
| | - Stefanie Polyn
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
| | - Lieven De Veylder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent B-9052, Belgium
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Yu KMJ, Oliver J, McKinley B, Weers B, Fabich HT, Evetts N, Conradi MS, Altobelli SA, Marshall-Colon A, Mullet J. Bioenergy sorghum stem growth regulation: intercalary meristem localization, development, and gene regulatory network analysis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:476-492. [PMID: 36038985 DOI: 10.1111/tpj.15960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Bioenergy sorghum is a highly productive drought tolerant C4 grass that accumulates 80% of its harvestable biomass in approximately 4 m length stems. Stem internode growth is regulated by development, shading, and hormones that modulate cell proliferation in intercalary meristems (IMs). In this study, sorghum stem IMs were localized above the pulvinus at the base of elongating internodes using magnetic resonance imaging, microscopy, and transcriptome analysis. A change in cell morphology/organization occurred at the junction between the pulvinus and internode where LATERAL ORGAN BOUNDARIES (SbLOB), a boundary layer gene, was expressed. Inactivation of an AGCVIII kinase in DDYM (dw2) resulted in decreased SbLOB expression, disrupted IM localization, and reduced internode cell proliferation. Transcriptome analysis identified approximately 1000 genes involved in cell proliferation, hormone signaling, and other functions selectively upregulated in the IM compared with a non-meristematic stem tissue. This cohort of genes is expressed in apical dome stem tissues before localization of the IM at the base of elongating internodes. Gene regulatory network analysis identified connections between genes involved in hormone signaling and cell proliferation. The results indicate that gibberellic acid induces accumulation of growth regulatory factors (GRFs) known to interact with ANGUSTIFOLIA (SbAN3), a master regulator of cell proliferation. GRF:AN3 was predicted to induce SbARF3/ETT expression and regulate SbAN3 expression in an auxin-dependent manner. GRFs and ARFs regulate genes involved in cytokinin and brassinosteroid signaling and cell proliferation. The results provide a molecular framework for understanding how hormone signaling regulates the expression of genes involved in cell proliferation in the stem IM.
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Affiliation(s)
- Ka Man Jasmine Yu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843-2128, USA
| | - Joel Oliver
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843-2128, USA
| | - Brian McKinley
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843-2128, USA
| | - Brock Weers
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843-2128, USA
| | - Hilary T Fabich
- ABQMR, Inc., 2301 Yale Blvd. SE, Suite C2, Albuquerque, New Mexico, 87106, USA
| | - Nathan Evetts
- ABQMR, Inc., 2301 Yale Blvd. SE, Suite C2, Albuquerque, New Mexico, 87106, USA
| | - Mark S Conradi
- ABQMR, Inc., 2301 Yale Blvd. SE, Suite C2, Albuquerque, New Mexico, 87106, USA
| | - Stephen A Altobelli
- ABQMR, Inc., 2301 Yale Blvd. SE, Suite C2, Albuquerque, New Mexico, 87106, USA
| | - Amy Marshall-Colon
- Department of Plant Biology, University of Illinois, Champaign-Urbana, Illinois, 61801, USA
| | - John Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843-2128, USA
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Chowdhury S, Mukherjee A, Basak S, Das R, Mandal A, Kundu P. Disruption of tomato TGS machinery by ToLCNDV causes reprogramming of vascular tissue-specific TORNADO1 gene expression. PLANTA 2022; 256:78. [PMID: 36094622 DOI: 10.1007/s00425-022-03985-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
Vascular development-related TRN1 transcription is suppressed by cytosine methylation in fully developed leaves of tomato. ToLCNDV infection disrupts methylation machinery and reactivates TRN1 expression - likely causing abnormal leaf growth pattern. Leaf curl disease of tomato caused by tomato leaf curl New Delhi virus (ToLCNDV) inflicts huge economical loss. Disease symptoms resemble leaf developmental defects including abnormal vein architecture. Leaf vein patterning-related TORNADO1 gene's (SlTRN1) transcript level is augmented in virus-infected leaves. To elucidate the molecular mechanism of the upregulation of SlTRN1 in vivo, we have deployed SlTRN1 promoter-reporter transgenic tomato plants and investigated the gene's dynamic expression pattern in leaf growth stages and infection. Expression of the gene was delimited in the vascular tissues and suppressed in fully developed leaves. WRKY16 transcription factor readily activated SlTRN1 promoter in varied sized leaves and upon virus infection, while silencing of WRKY16 gene resulted in dampened promoter activity. Methylation-sensitive PCR analyses confirmed the accumulation of CHH methylation at multiple locations in the SlTRN1 promoter in older leaves. However, ToLCNDV infection reverses the methylation status and restores expression level in the leaf vascular bundle. The virus dampens the level of key maintenance and de novo DNA methyltransferases SlDRM5, SlMET1, SlCMT2 with concomitant augmentation of two DNA demethylases, SlDML1 and SlDML2 levels in SlTRN1 promoter-reporter transgenics. Transient overexpression of SlDML2 mimics the virus-induced hypomethylation state of the SlTRN1 promoter in mature leaves, while silencing of SlDML2 lessens promoter activity. Furthermore, in line with the previous studies, we confirm the crucial role of viral suppressors of RNA silencing AC2 and AC4 proteins in promoting DNA demethylation and directing it to restore activated transcription of SlTRN1. Unusually elevated expression of SlTRN1 may negatively impact normal growth of leaves.
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Affiliation(s)
- Shreya Chowdhury
- Division of Plant Biology, Bose Institute, EN Block, Sector V, Bidhan Nagar, Kolkata, 700091, West Bengal, India
| | - Ananya Mukherjee
- Division of Plant Biology, Bose Institute, EN Block, Sector V, Bidhan Nagar, Kolkata, 700091, West Bengal, India
| | - Shrabani Basak
- Division of Plant Biology, Bose Institute, EN Block, Sector V, Bidhan Nagar, Kolkata, 700091, West Bengal, India
| | - Rohit Das
- Division of Plant Biology, Bose Institute, EN Block, Sector V, Bidhan Nagar, Kolkata, 700091, West Bengal, India
| | - Arunava Mandal
- Division of Plant Biology, Bose Institute, EN Block, Sector V, Bidhan Nagar, Kolkata, 700091, West Bengal, India
- Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Pallob Kundu
- Division of Plant Biology, Bose Institute, EN Block, Sector V, Bidhan Nagar, Kolkata, 700091, West Bengal, India.
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11
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Guo Y, Chen Y, Zhang J, Li J, Fan K, Chen R, Liu Y, Zheng J, Fu J, Gu R, Wang G, Cui Y, Du X, Wang J. Epigenetic Mutation in a Tubulin-Folding Cofactor B (ZmTFCB) Gene Arrests Kernel Development in Maize. PLANT & CELL PHYSIOLOGY 2022; 63:1156-1167. [PMID: 35771678 DOI: 10.1093/pcp/pcac092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/26/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Epialleles, the heritable epigenetic variants that are not caused by changes in DNA sequences, can broaden genetic and phenotypic diversity and benefit to crop breeding, but very few epialleles related to agricultural traits have been identified in maize. Here, we cloned a small kernel mutant, smk-wl10, from maize, which encoded a tubulin-folding cofactor B (ZmTFCB) protein. Expression of the ZmTFCB gene decreased in the smk-wl10 mutant, which arrested embryo, endosperm and basal endosperm transfer layer developments. Overexpression of ZmTFCB could complement the defective phenotype of smk-wl10. No nucleotide sequence variation in ZmTFCB could be found between smk-wl10 and wild type (WT). Instead, we detected hypermethylation of nucleotide CHG (where H is A, C or T nucleotide) sequence contexts and increased level of histone H3K9me2 methylation in the upstream sequence of ZmTFCB in smk-wl10 compared with WT, which might respond to the attenuating transcription of ZmTFCB. In addition, yeast two-hybrid and bimolecular fluorescence complementation assays identified a strong interaction between ZmTFCB and its homolog ZmTFCE. Thus, our work identifies a novel epiallele of the maize ZmTFCB gene, which might represent a common phenomenon in the epigenetic regulation of important traits such as kernel development in maize.
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Affiliation(s)
- Yingmei Guo
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Yan Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Jie Zhang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jiankun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kaijian Fan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rongrong Chen
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yunjun Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jun Zheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junjie Fu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Riliang Gu
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yu Cui
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xuemei Du
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Jianhua Wang
- Beijing Innovation Center for Crop Seed Technology, Ministry of Agriculture and Rural Affairs, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
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12
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Dong T, Song S, Wang Y, Yang R, Chen P, Su J, Ding X, Liu Y, Duan H. Effects of 5-azaC on Iridoid Glycoside Accumulation and DNA Methylation in Rehmannia glutinosa. FRONTIERS IN PLANT SCIENCE 2022; 13:913717. [PMID: 35812974 PMCID: PMC9260266 DOI: 10.3389/fpls.2022.913717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Iridoid glycoside is the important secondary metabolite and the main active component in Rehmannia glutinosa. However, the mechanisms that underlie the regulation of iridoid glycoside biosynthesis remain poorly understood in R. glutinosa. Herein, the analysis of RNA-seq data revealed that 3,394 unigenes related to the biosynthesis of secondary metabolites were identified in R. glutinosa. A total of 357 unigenes were involved in iridoid glycoside synthesis, in which the highly conservative genes, such as DXS, DXR, GPPS, G10H, and 10HGO, in organisms were overexpressed. The analysis of the above genes confirmed that the co-occurrence ratio of DXS, DXR, and GPPS was high in plants. Further, our results showed that under normal and 5-azacytidine (5-azaC) treatment, the expression levels of DXS, DXR, GPPS, G10H, and 10HGO were consistent with the iridoid glycoside accumulation in R. glutinosa, in which the application of the different concentrations of 5-azaC, especially 50 μM 5-azaC, could significantly upregulate the expression of five genes above and iridoid glycoside content. In addition, the changes in the spatiotemporal specificity of degree and levels of DNA methylation were observed in R. glutinosa, in which the hemi-methylation was the main reason for the change in DNA methylation levels. Similar to the changes in 5-methyl cytosine (5mC) content, the DNA demethylation could be induced by 5-azaC and responded in a dose-dependent manner to 15, 50, and 100 μM 5-azaC. Taken together, the expression of iridoid glycoside synthesis gene was upregulated by the demethylation in R. glutinosa, followed by triggering the iridoid glycoside accumulation. These findings not only identify the key genes of iridoid glycoside synthesis from R. glutinosa, but also expand our current knowledge of the function of methylation in iridoid glycoside accumulation.
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Affiliation(s)
- Tianyu Dong
- College of Life Sciences, Henan Normal University, Xinxiang, China
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang, China
| | - Shanglin Song
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Ying Wang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Ruixue Yang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Peilei Chen
- College of Life Sciences, Henan Normal University, Xinxiang, China
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang, China
| | - Jiuchang Su
- College of Life Sciences, Henan Normal University, Xinxiang, China
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang, China
| | - Xinru Ding
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Yongkang Liu
- Agricultural Research Institute of Wenxian County, Wenxian, China
| | - Hongying Duan
- College of Life Sciences, Henan Normal University, Xinxiang, China
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang, China
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13
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Skirycz A, Fernie AR. Past accomplishments and future challenges of the multi-omics characterization of leaf growth. PLANT PHYSIOLOGY 2022; 189:473-489. [PMID: 35325227 PMCID: PMC9157134 DOI: 10.1093/plphys/kiac136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The advent of omics technologies has revolutionized biology and advanced our understanding of all biological processes, including major developmental transitions in plants and animals. Here, we review the vast knowledge accumulated concerning leaf growth in terms of transcriptional regulation before turning our attention to the historically less well-characterized alterations at the protein and metabolite level. We will then discuss how the advent of biochemical methods coupled with metabolomics and proteomics can provide insight into the protein-protein and protein-metabolite interactome of the growing leaves. We finally highlight the substantial challenges in detection, spatial resolution, integration, and functional validation of the omics results, focusing on metabolomics as a prerequisite for a comprehensive understanding of small-molecule regulation of plant growth.
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Affiliation(s)
- Aleksandra Skirycz
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
- Boyce Thompson Institute, Ithaca, New York 14853, USA
- Cornell University, Ithaca, New York 14853, USA
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
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14
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Kumari P, Khan S, Wani IA, Gupta R, Verma S, Alam P, Alaklabi A. Unravelling the Role of Epigenetic Modifications in Development and Reproduction of Angiosperms: A Critical Appraisal. Front Genet 2022; 13:819941. [PMID: 35664328 PMCID: PMC9157814 DOI: 10.3389/fgene.2022.819941] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 12/28/2022] Open
Abstract
Epigenetics are the heritable changes in gene expression patterns which occur without altering DNA sequence. These changes are reversible and do not change the sequence of the DNA but can alter the way in which the DNA sequences are read. Epigenetic modifications are induced by DNA methylation, histone modification, and RNA-mediated mechanisms which alter the gene expression, primarily at the transcriptional level. Such alterations do control genome activity through transcriptional silencing of transposable elements thereby contributing toward genome stability. Plants being sessile in nature are highly susceptible to the extremes of changing environmental conditions. This increases the likelihood of epigenetic modifications within the composite network of genes that affect the developmental changes of a plant species. Genetic and epigenetic reprogramming enhances the growth and development, imparts phenotypic plasticity, and also ensures flowering under stress conditions without changing the genotype for several generations. Epigenetic modifications hold an immense significance during the development of male and female gametophytes, fertilization, embryogenesis, fruit formation, and seed germination. In this review, we focus on the mechanism of epigenetic modifications and their dynamic role in maintaining the genomic integrity during plant development and reproduction.
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Affiliation(s)
- Priyanka Kumari
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Sajid Khan
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Ishfaq Ahmad Wani
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Renu Gupta
- Division of Soil Sciences & Agricultural Chemistry, Faculty of Agriculture Sher e Kashmir University of Agricultural Sciences and Technology, Chatha, India
| | - Susheel Verma
- Department of Botany, University of Jammu, Jammu, India
- *Correspondence: Susheel Verma,
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University (PSAU), Alkharj, Saudi Arabia
| | - Abdullah Alaklabi
- Department of Biology, College of Science, University of Bisha, Bisha, Saudi Arabia
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15
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Lin X, Zhou M, Yao J, Li QQ, Zhang YY. Phenotypic and Methylome Responses to Salt Stress in Arabidopsis thaliana Natural Accessions. FRONTIERS IN PLANT SCIENCE 2022; 13:841154. [PMID: 35310665 PMCID: PMC8931716 DOI: 10.3389/fpls.2022.841154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Salt stress threatens plant growth, development and crop yields, and has become a critical global environmental issue. Increasing evidence has suggested that the epigenetic mechanism such as DNA methylation can mediate plant response to salt stress through transcriptional regulation and transposable element (TE) silencing. However, studies exploring genome-wide methylation dynamics under salt stress remain limited, in particular, for studies on multiple genotypes. Here, we adopted four natural accessions of the model species Arabidopsis thaliana and investigated the phenotypic and genome-wide methylation responses to salt stress through whole-genome bisulfite sequencing (WGBS). We found that salt stress significantly changed plant phenotypes, including plant height, rosette diameter, fruit number, and aboveground biomass, and the change in biomass tended to depend on accessions. Methylation analysis revealed that genome-wide methylation patterns depended primarily on accessions, and salt stress caused significant methylation changes in ∼ 0.1% cytosines over the genomes. About 33.5% of these salt-induced differential methylated cytosines (DMCs) were located to transposable elements (TEs). These salt-induced DMCs were mainly hypermethylated and accession-specific. TEs annotated to have DMCs (DMC-TEs) across accessions were found mostly belonged to the superfamily of Gypsy, a type II transposon, indicating a convergent DMC dynamic on TEs across different genetic backgrounds. Moreover, 8.0% of salt-induced DMCs were located in gene bodies and their proximal regulatory regions. These DMCs were also accession-specific, and genes annotated to have DMCs (DMC-genes) appeared to be more accession-specific than DMC-TEs. Intriguingly, both accession-specific DMC-genes and DMC-genes shared by multiple accessions were enriched in similar functions, including methylation, gene silencing, chemical homeostasis, polysaccharide catabolic process, and pathways relating to shifts between vegetative growth and reproduction. These results indicate that, across different genetic backgrounds, methylation changes may have convergent functions in post-transcriptional, physiological, and phenotypic modulation under salt stress. These convergent methylation dynamics across accession may be autonomous from genetic variation or due to convergent genetic changes, which requires further exploration. Our study provides a more comprehensive picture of genome-wide methylation dynamics under salt stress, and highlights the importance of exploring stress response mechanisms from diverse genetic backgrounds.
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Affiliation(s)
- Xiaohe Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ming Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Jing Yao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qingshun Q. Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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16
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Exploration of the Potential Transcriptional Regulatory Mechanisms of DNA Methyltransferases and MBD Genes in Petunia Anther Development and Multi-Stress Responses. Genes (Basel) 2022; 13:genes13020314. [PMID: 35205359 PMCID: PMC8872020 DOI: 10.3390/genes13020314] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 02/01/2023] Open
Abstract
Cytosine-5 DNA methyltransferases (C5-MTases) and methyl-CpG-binding-domain (MBD) genes can be co-expressed. They directly control target gene expression by enhancing their DNA methylation levels in humans; however, the presence of this kind of cooperative relationship in plants has not been determined. A popular garden plant worldwide, petunia (Petunia hybrida) is also a model plant in molecular biology. In this study, 9 PhC5-MTase and 11 PhMBD proteins were identified in petunia, and they were categorized into four and six subgroups, respectively, on the basis of phylogenetic analyses. An expression correlation analysis was performed to explore the co-expression relationships between PhC5-MTases and PhMBDs using RNA-seq data, and 11 PhC5-MTase/PhMBD pairs preferentially expressed in anthers were identified as having the most significant correlations (Pearson’s correlation coefficients > 0.9). Remarkably, the stability levels of the PhC5-MTase and PhMBD pairs significantly decreased in different tissues and organs compared with that in anthers, and most of the selected PhC5-MTases and PhMBDs responded to the abiotic and hormonal stresses. However, highly correlated expression relationships between most pairs were not observed under different stress conditions, indicating that anther developmental processes are preferentially influenced by the co-expression of PhC5-MTases and PhMBDs. Interestingly, the nuclear localization genes PhDRM2 and PhMBD2 still had higher correlations under GA treatment conditions, implying that they play important roles in the GA-mediated development of petunia. Collectively, our study suggests a regulatory role for DNA methylation by C5-MTase and MBD genes in petunia anther maturation processes and multi-stress responses, and it provides a framework for the functional characterization of C5-MTases and MBDs in the future.
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17
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Pei L, Huang X, Liu Z, Tian X, You J, Li J, Fang DD, Lindsey K, Zhu L, Zhang X, Wang M. Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation. Genome Biol 2022; 23:45. [PMID: 35115029 PMCID: PMC8812185 DOI: 10.1186/s13059-022-02616-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/20/2022] [Indexed: 11/10/2022] Open
Abstract
Background Despite remarkable advances in our knowledge of epigenetically mediated transcriptional programming of cell differentiation in plants, little is known about chromatin topology and its functional implications in this process. Results To interrogate its significance, we establish the dynamic three-dimensional (3D) genome architecture of the allotetraploid cotton fiber, representing a typical single cell undergoing staged development in plants. We show that the subgenome-relayed switching of the chromatin compartment from active to inactive is coupled with the silencing of developmentally repressed genes, pinpointing subgenome-coordinated contribution to fiber development. We identify 10,571 topologically associating domain-like (TAD-like) structures, of which 25.6% are specifically organized in different stages and 75.23% are subject to partition or fusion between two subgenomes. Notably, dissolution of intricate TAD-like structure cliques showing long-range interactions represents a prominent characteristic at the later developmental stage. Dynamic chromatin loops are found to mediate the rewiring of gene regulatory networks that exhibit a significant difference between the two subgenomes, implicating expression bias of homologous genes. Conclusions This study sheds light on the spatial-temporal asymmetric chromatin structures of two subgenomes in the cotton fiber and offers a new insight into the regulatory orchestration of cell differentiation in plants. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02616-y.
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Affiliation(s)
- Liuling Pei
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianhui Huang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xuehan Tian
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jiaqi You
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Jianying Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - David D Fang
- Cotton Fiber Bioscience Research Unit, USDA-ARS, Southern Regional Research Center, New Orleans, LA, 70124, USA
| | - Keith Lindsey
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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18
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Kakoulidou I, Avramidou EV, Baránek M, Brunel-Muguet S, Farrona S, Johannes F, Kaiserli E, Lieberman-Lazarovich M, Martinelli F, Mladenov V, Testillano PS, Vassileva V, Maury S. Epigenetics for Crop Improvement in Times of Global Change. BIOLOGY 2021; 10:766. [PMID: 34439998 PMCID: PMC8389687 DOI: 10.3390/biology10080766] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Epigenetics has emerged as an important research field for crop improvement under the on-going climatic changes. Heritable epigenetic changes can arise independently of DNA sequence alterations and have been associated with altered gene expression and transmitted phenotypic variation. By modulating plant development and physiological responses to environmental conditions, epigenetic diversity-naturally, genetically, chemically, or environmentally induced-can help optimise crop traits in an era challenged by global climate change. Beyond DNA sequence variation, the epigenetic modifications may contribute to breeding by providing useful markers and allowing the use of epigenome diversity to predict plant performance and increase final crop production. Given the difficulties in transferring the knowledge of the epigenetic mechanisms from model plants to crops, various strategies have emerged. Among those strategies are modelling frameworks dedicated to predicting epigenetically controlled-adaptive traits, the use of epigenetics for in vitro regeneration to accelerate crop breeding, and changes of specific epigenetic marks that modulate gene expression of traits of interest. The key challenge that agriculture faces in the 21st century is to increase crop production by speeding up the breeding of resilient crop species. Therefore, epigenetics provides fundamental molecular information with potential direct applications in crop enhancement, tolerance, and adaptation within the context of climate change.
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Affiliation(s)
- Ioanna Kakoulidou
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
| | - Evangelia V. Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-Dimitra (ELGO-DIMITRA), 11528 Athens, Greece;
| | - Miroslav Baránek
- Faculty of Horticulture, Mendeleum—Institute of Genetics, Mendel University in Brno, Valtická 334, 69144 Lednice, Czech Republic;
| | - Sophie Brunel-Muguet
- UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, UNICAEN, INRAE, Normandie Université, CEDEX, F-14032 Caen, France;
| | - Sara Farrona
- Plant and AgriBiosciences Centre, Ryan Institute, National University of Ireland (NUI) Galway, H91 TK33 Galway, Ireland;
| | - Frank Johannes
- Department of Molecular Life Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, 85354 Freising, Germany; (I.K.); (F.J.)
- Institute for Advanced Study, Technical University of Munich, Lichtenberg Str. 2a, 85748 Garching, Germany
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow G12 8QQ, UK;
| | - Michal Lieberman-Lazarovich
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion 7505101, Israel;
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Sq. Dositeja Obradovića 8, 21000 Novi Sad, Serbia;
| | - Pilar S. Testillano
- Pollen Biotechnology of Crop Plants Group, Centro de Investigaciones Biológicas Margarita Salas-(CIB-CSIC), Ramiro Maeztu 9, 28040 Madrid, Spain;
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bldg. 21, 1113 Sofia, Bulgaria;
| | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, INRAE, EA1207 USC1328, Université d’Orléans, F-45067 Orléans, France
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19
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Fedoreyeva LI, Vanyushin BF. Gly, GlyGly, and GlyAsp Modulate Expression of Genes of the SNF2 Family and DNA Methyltransferases in Regenerants from Calluses of Tobacco Nicotiana tabacum. BIOL BULL+ 2021. [DOI: 10.1134/s1062359021040087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Xu G, Lyu J, Li Q, Liu H, Wang D, Zhang M, Springer NM, Ross-Ibarra J, Yang J. Evolutionary and functional genomics of DNA methylation in maize domestication and improvement. Nat Commun 2020; 11:5539. [PMID: 33139747 PMCID: PMC7606521 DOI: 10.1038/s41467-020-19333-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 10/08/2020] [Indexed: 12/23/2022] Open
Abstract
DNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines in the maize genome, but variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here, we leverage whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to estimate epimutation rates and selection coefficients. We find weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) are identified population-wide that are correlated with recent selection. For two trait-associated DMRs, vgt1-DMR and tb1-DMR, HiChIP data indicate that the interactive loops between DMRs and respective downstream genes are present in B73, a modern maize line, but absent in teosinte. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution. Variation and evolution of DNA methylation during maize domestication remain largely unknown. Here, the authors generate genome and methylome sequencing data as well as HiChIP-based interactome data to investigate the adaptive and phenotypic consequences of methylation variations in maize.
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Affiliation(s)
- Gen Xu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.,Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Jing Lyu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.,Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Qing Li
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA.,National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Han Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Dafang Wang
- Division of Math and Sciences, Delta State University, Cleveland, MS, 38733, USA
| | - Mei Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, China
| | - Nathan M Springer
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jeffrey Ross-Ibarra
- Department of Evolution and Ecology, Center for Population Biology and Genome Center, University of California, Davis, CA, 95616, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA. .,Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
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21
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Malinowska M, Nagy I, Wagemaker CAM, Ruud AK, Svane SF, Thorup-Kristensen K, Jensen CS, Eriksen B, Krusell L, Jahoor A, Jensen J, Eriksen LB, Asp T. The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth. THE PLANT GENOME 2020; 13:e20049. [PMID: 33217208 DOI: 10.1002/tpg2.20049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/14/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
Patterns and level of cytosine methylation vary widely among plant species and are associated with genome size as well as the proportion of transposons and other repetitive elements in the genome. We explored epigenetic patterns and diversity in a representative proportion of the spring barley (Hordeum vulgare L.) genome across several commercial and historical cultivars. This study adapted a genotyping-by-sequencing (GBS) approach for the detection of methylated cytosines in genomic DNA. To analyze the data, we developed WellMeth, a complete pipeline for analysis of reduced representation bisulfite sequencing. WellMeth enabled quantification of context-specific DNA methylation at the single-base resolution as well as identification of differentially methylated sites (DMCs) and regions (DMRs). On average, DNA methylation levels were significantly higher than what is commonly observed in many plants species, reaching over 10-fold higher levels than those in Arabidopsis thaliana (L.) Heynh. in the CHH methylation. Preferential methylation was observed within and at the edges of long-terminal repeats (LTR) retrotransposons Gypsy and Copia. From a pairwise comparison of cultivars, numerous DMRs could be identified of which more than 5,000 were conserved within the analyzed set of barley cultivars. The subset of regions overlapping with genes showed enrichment in gene ontology (GO) categories associated with chromatin and cellular structure and organization. A significant correlation between genetic and epigenetic distances suggests that a considerable portion of methylated regions is under strict genetic control in barley. The data presented herein represents the first step in efforts toward a better understanding of genome-level structural and functional aspects of methylation in barley.
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Affiliation(s)
- Marta Malinowska
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
- Center for Quantitative Genetics & Genomics, Aarhus University, Slagelse, Denmark
| | - Istvan Nagy
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
- Center for Quantitative Genetics & Genomics, Aarhus University, Slagelse, Denmark
| | | | - Anja K Ruud
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
- Center for Quantitative Genetics & Genomics, Aarhus University, Slagelse, Denmark
| | - Simon F Svane
- Department of Plant and Environmental Science, University of Copenhagen, Frederiksberg, Denmark
| | | | | | | | | | | | | | - Lars Bonde Eriksen
- Landbrug & Fødevarer, SEGES, Aarhus, Denmark
- LIMAGRAIN A/S, Horsens, Denmark
| | - Torben Asp
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
- Center for Quantitative Genetics & Genomics, Aarhus University, Slagelse, Denmark
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22
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AbdElgawad H, Avramova V, Baggerman G, Van Raemdonck G, Valkenborg D, Van Ostade X, Guisez Y, Prinsen E, Asard H, Van den Ende W, Beemster GTS. Starch biosynthesis contributes to the maintenance of photosynthesis and leaf growth under drought stress in maize. PLANT, CELL & ENVIRONMENT 2020; 43:2254-2271. [PMID: 32488892 DOI: 10.1111/pce.13813] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
To understand the growth response to drought, we performed a proteomics study in the leaf growth zone of maize (Zea mays L.) seedlings and functionally characterized the role of starch biosynthesis in the regulation of growth, photosynthesis and antioxidant capacity, using the shrunken-2 mutant (sh2), defective in ADP-glucose pyrophosphorylase. Drought altered the abundance of 284 proteins overrepresented for photosynthesis, amino acid, sugar and starch metabolism, and redox-regulation. Changes in protein levels correlated with enzyme activities (increased ATP synthase, cysteine synthase, starch synthase, RuBisCo, peroxiredoxin, glutaredoxin, thioredoxin and decreased triosephosphate isomerase, ferredoxin, cellulose synthase activities, respectively) and metabolite concentrations (increased ATP, cysteine, glycine, serine, starch, proline and decreased cellulose levels). The sh2 mutant showed a reduced increase of starch levels under drought conditions, leading to soluble sugar starvation at the end of the night and correlating with an inhibition of leaf growth rates. Increased RuBisCo activity and pigment concentrations observed in WT, in response to drought, were lacking in the mutant, which suffered more oxidative damage and recovered more slowly after re-watering. These results demonstrate that starch biosynthesis contributes to maintaining leaf growth under drought stress and facilitates enhanced carbon acquisition upon recovery.
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Affiliation(s)
- Hamada AbdElgawad
- Research group for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
- Department of Botany, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Viktoriya Avramova
- Research group for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Geert Baggerman
- Applied Bio & molecular Systems, VITO, Mol, Belgium
- Center for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Geert Van Raemdonck
- Center for Proteomics, University of Antwerp, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Dirk Valkenborg
- Applied Bio & molecular Systems, VITO, Mol, Belgium
- Center for Proteomics, University of Antwerp, Antwerp, Belgium
| | - Xaveer Van Ostade
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Yves Guisez
- Research group for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Els Prinsen
- Research group for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Han Asard
- Research group for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, KU Leuven, Leuven, Belgium
| | - Gerrit T S Beemster
- Research group for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium
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23
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Kitavi M, Cashell R, Ferguson M, Lorenzen J, Nyine M, McKeown PC, Spillane C. Heritable epigenetic diversity for conservation and utilization of epigenetic germplasm resources of clonal East African Highland banana (EAHB) accessions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2605-2625. [PMID: 32719910 PMCID: PMC7419381 DOI: 10.1007/s00122-020-03620-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 05/20/2020] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE Genetically identical East African Highland banana (EAHB) clones are epigenetically diverse with heritable epialleles that can contribute to morphological diversity. Heritable epigenetic variation can contribute to agronomic traits in crops and should be considered in germplasm conservation. Despite the genetic uniformity arising from a genetic bottleneck of one ancestral clone, followed by subsequent vegetative propagation, East African Highland bananas (EAHBs) display significant phenotypic diversity potentially arising from somatic mutations, heritable epialleles and/or genotype-by-environment interactions. Here, we use DNA methylation profiling across EAHB accessions representing most of the primary EAHB genepool to demonstrate that the genetically uniform EAHB genepool harbours significant epigenetic diversity. By analysing 724 polymorphic DNA methylation sites by methylation-sensitive AFLP across 90 EAHB cultivars, we could differentiate the EAHB varieties according to their regions (Kenya and Uganda). In contrast, there was minimal association of DNA methylation variation with the five morphological groups that are used to classify EAHBs. We further analysed DNA methylation patterns in parent-offspring cohort, which were maintained in offspring generated by sexual (seed) and asexual (vegetative) propagation, with higher levels of altered DNA methylation observed in vegetatively generated offspring. Our results indicate that the phenotypic diversity of near-isogenic EAHBs is mirrored by considerable DNA methylation variation, which is transmitted between generations by both vegetative reproduction and seed reproduction. Genetically uniform vegetatively propagated crops such as EAHBs harbour considerable heritable epigenetic variation, where heritable epialleles could arise in offspring and contribute to functional traits. This study provides a basis for developing strategies for conservation of epigenetic resources and for integration of epimarkers into crop breeding programmes.
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Affiliation(s)
- M Kitavi
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
- International Institute for Tropical Agriculture (IITA), P.O. Box 30709-00100, Nairobi, Kenya
| | - R Cashell
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - M Ferguson
- International Institute for Tropical Agriculture (IITA), P.O. Box 30709-00100, Nairobi, Kenya
| | - J Lorenzen
- International Institute for Tropical Agriculture (IITA), P.O. Box 30709-00100, Nairobi, Kenya
- Crop R&D, Agricultural Development, Bill & Melinda Gates Foundation, PO Box 23350, Seattle, WA, 98102, USA
| | - M Nyine
- International Institute for Tropical Agriculture (IITA), P.O. Box 30709-00100, Nairobi, Kenya
| | - P C McKeown
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland
| | - C Spillane
- Genetics and Biotechnology Lab, Plant and AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, University Road, Galway, H91 REW4, Ireland.
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24
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Dugé de Bernonville T, Maury S, Delaunay A, Daviaud C, Chaparro C, Tost J, O’Connor SE, Courdavault V. Developmental Methylome of the Medicinal Plant Catharanthus roseus Unravels the Tissue-Specific Control of the Monoterpene Indole Alkaloid Pathway by DNA Methylation. Int J Mol Sci 2020; 21:E6028. [PMID: 32825765 PMCID: PMC7503379 DOI: 10.3390/ijms21176028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/06/2020] [Accepted: 08/18/2020] [Indexed: 02/07/2023] Open
Abstract
Catharanthus roseus produces a wide spectrum of monoterpene indole alkaloids (MIAs). MIA biosynthesis requires a tightly coordinated pathway involving more than 30 enzymatic steps that are spatio-temporally and environmentally regulated so that some MIAs specifically accumulate in restricted plant parts. The first regulatory layer involves a complex network of transcription factors from the basic Helix Loop Helix (bHLH) or AP2 families. In the present manuscript, we investigated whether an additional epigenetic layer could control the organ-, developmental- and environmental-specificity of MIA accumulation. We used Whole-Genome Bisulfite Sequencing (WGBS) together with RNA-seq to identify differentially methylated and expressed genes among nine samples reflecting different plant organs and experimental conditions. Tissue specific gene expression was associated with specific methylation signatures depending on cytosine contexts and gene parts. Some genes encoding key enzymatic steps from the MIA pathway were found to be simultaneously differentially expressed and methylated in agreement with the corresponding MIA accumulation. In addition, we found that transcription factors were strikingly concerned by DNA methylation variations. Altogether, our integrative analysis supports an epigenetic regulation of specialized metabolisms in plants and more likely targeting transcription factors which in turn may control the expression of enzyme-encoding genes.
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Affiliation(s)
- Thomas Dugé de Bernonville
- Faculté des Sciences et Techniques, Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, F-37200 Tours, France;
| | - Stéphane Maury
- INRA, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, F-45067 Orléans, France;
| | - Alain Delaunay
- INRA, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, F-45067 Orléans, France;
| | - Christian Daviaud
- Laboratoire Epigénétique et Environnement, LEE, Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, F-92265 Evry, France; (C.D.); (J.T.)
| | - Cristian Chaparro
- CNRS, IFREMER, UMR5244 Interactions Hôtes-Pathogènes-Environnments, Université de Montpellier, Université de Perpignan Via Domitia, F-66860 Perpignan, France;
| | - Jörg Tost
- Laboratoire Epigénétique et Environnement, LEE, Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, F-92265 Evry, France; (C.D.); (J.T.)
| | - Sarah Ellen O’Connor
- Max Planck Institute for Chemical Ecology, Department of Natural Product Biosynthesis, 07745 Jena, Germany;
| | - Vincent Courdavault
- Faculté des Sciences et Techniques, Université de Tours, EA2106 Biomolécules et Biotechnologies Végétales, F-37200 Tours, France;
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25
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Ning YQ, Liu N, Lan KK, Su YN, Li L, Chen S, He XJ. DREAM complex suppresses DNA methylation maintenance genes and precludes DNA hypermethylation. NATURE PLANTS 2020; 6:942-956. [PMID: 32661276 DOI: 10.1038/s41477-020-0710-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 05/27/2020] [Indexed: 05/27/2023]
Abstract
The DNA methyltransferases MET1 and CMT3 are known to be responsible for maintenance of DNA methylation at symmetric CG and CHG sites, respectively, in Arabidopsis thaliana. However, it is unknown how the expression of methyltransferase genes is regulated in different cell states and whether change in expression affects DNA methylation at the whole-genome level. Using a reverse genetic screen, we identified TCX5, a tesmin/TSO1-like CXC domain-containing protein, and demonstrated that it is a transcriptional repressor of genes required for maintenance of DNA methylation, which include MET1, CMT3, DDM1, KYP and VIMs. TCX5 functions redundantly with its paralogue TCX6 in repressing the expression of these genes. In the tcx5 tcx6 double mutant, expression of these genes is markedly increased, thereby leading to markedly increased DNA methylation at CHG sites and, to a lesser extent, at CG sites at the whole-genome level. Furthermore, our whole-genome DNA methylation analysis indicated that the CG and CHG methylation level is lower in differentiated quiescent cells than in dividing cells in the wild type but is comparable in the tcx5/6 mutant, suggesting that TCX5/6 are required for maintenance of the difference in DNA methylation between the two cell types. We identified TCX5/6-containing multi-subunit complexes, which are known as DREAM in other eukaryotes, and demonstrated that the Arabidopsis DREAM components function as a whole to preclude DNA hypermethylation. Given that the DREAM complexes are conserved from plants to animals, the preclusion of DNA hypermethylation by DREAM complexes may represent a conserved mechanism in eukaryotes.
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Affiliation(s)
- Yong-Qiang Ning
- National Institute of Biological Sciences, Beijing, China
- The College of Life Sciences, Northwest University, Xi'an, China
| | - Na Liu
- National Institute of Biological Sciences, Beijing, China
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ke-Ke Lan
- National Institute of Biological Sciences, Beijing, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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26
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Responsive changes of DNA methylation in wheat (Triticum aestivum) under water deficit. Sci Rep 2020; 10:7938. [PMID: 32404881 PMCID: PMC7220947 DOI: 10.1038/s41598-020-64660-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/07/2020] [Indexed: 12/17/2022] Open
Abstract
DNA methylation plays an important role in the growth and development of plant, and would change under different environments. In this study, 5-methyl cytosine (5mC) content and methylation level exhibited tissue specificity in genomic DNA of wheat seedling, and increased significantly in leaf along with the increase of water deficit, which was especially significant in leaf of wheat AK58. Full-methylation might dominate in genomic DNA of wheat seedling, the increase of full-methylation level under water deficit was significantly higher than that of hemi-methylation level. Under water deficit, DNA methylation of wheat seedling showed significant polymorphism, this polymorphism was always higher in root, especially was higher in root of wheat AK58. Further analysis appeared that changes of DNA methylation in wheat seedling took methylation as principle and demethylation as supplement under water deficit. Therefore, under water deficit, the degree, level and polymorphism of DNA methylation in wheat seedling showed tissue specificity and species specificity, and were higher in wheat AK58 compared with those of wheat XM13, perhaps wheat AK58 could more rapidly respond to water deficit by changes of DNA methylation, which would contribute to reveal molecular mechanism of wheat adapting to water deficit.
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27
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Yu J, Xu F, Wei Z, Zhang X, Chen T, Pu L. Epigenomic landscape and epigenetic regulation in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1467-1489. [PMID: 31965233 DOI: 10.1007/s00122-020-03549-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 01/14/2020] [Indexed: 05/12/2023]
Abstract
Epigenetic regulation has been implicated in the control of multiple agronomic traits in maize. Here, we review current advances in our understanding of epigenetic regulation, which has great potential for improving agronomic traits and the environmental adaptability of crops. Epigenetic regulation plays vital role in the control of complex agronomic traits. Epigenetic variation could contribute to phenotypic diversity and can be used to improve the quality and productivity of crops. Maize (Zea mays L.), one of the most widely cultivated crops for human food, animal feed, and ethanol biofuel, is a model plant for genetic studies. Recent advances in high-throughput sequencing technology have made possible the study of epigenetic regulation in maize on a genome-wide scale. In this review, we discuss recent epigenetic studies in maize many achieved by Chinese research groups. These studies have explored the roles of DNA methylation, posttranslational modifications of histones, chromatin remodeling, and noncoding RNAs in the regulation of gene expression in plant development and environment response. We also provide our future prospects for manipulating epigenetic regulation to improve crops.
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Affiliation(s)
- Jia Yu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziwei Wei
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xiangxiang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.
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28
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Method for Bisulfite Sequencing Data Analysis for Whole-Genome Level DNA Methylation Detection in Legumes. Methods Mol Biol 2020; 2107:127-145. [PMID: 31893445 DOI: 10.1007/978-1-0716-0235-5_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Methylation of cytosines in DNA is the most stable type of epigenetic modification that is established and maintained by different enzymes. In plants, DNA methylation is inherited from one generation to another leaving an epigenetic mark as a memory of previous state, which may include encounter with stress or pathogen. Advancement in the next generation sequencing technologies has enabled the profiling of methylation marks. Whole-genome bisulfite sequencing (WGBS) has the potential to unravel the patterns of DNA methylation at single-base resolution. Though the sequencing technologies have evolved drastically, analysis of WGBS data still remains challenging. Here, we provide a methodology for performing WGBS data analysis along with critical steps for identification of methylation marks in plant genomes including legumes.
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29
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Abstract
Cytosine methylation as a reversible chromatin mark has been investigated extensively for its influence on gene silencing and the regulation of its dynamic association-disassociation at specific sites within a eukaryotic genome. With the remarkable reductions in cost and time associated with whole-genome DNA sequence analysis, coupled with the high fidelity of bisulfite-treated DNA sequencing, single nucleotide resolution of cytosine methylation repatterning within even very large genomes is increasingly achievable. What remains a challenge is the analysis of genome-wide methylome datasets and, consequently, a clear understanding of the overall influence of methylation repatterning on gene expression or vice versa. Reported data have sometimes been subject to stringent data filtering methods that can serve to skew downstream biological interpretation. These complications derive from methylome analysis procedures that vary widely in method and parameter setting. DNA methylation as a chromatin feature that influences DNA stability can be dynamic and rapidly responsive to environmental change. Consequently, methods to discriminate background "noise" of the system from biological signal in response to specific perturbation is essential in some types of experiments. We describe numerous aspects of whole-genome bisulfite sequence data that must be contemplated as well as the various steps of methylome data analysis which impact the biological interpretation of the final output.
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30
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Di Marsico M, Cerruti E, Comino C, Porceddu A, Acquadro A, Capomaccio S, Marconi G, Albertini E. MCSeEd (Methylation Context Sensitive Enzyme ddRAD): A New Method to Analyze DNA Methylation. Methods Mol Biol 2020; 2093:47-64. [PMID: 32088888 DOI: 10.1007/978-1-0716-0179-2_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Methylation context sensitive enzyme ddRAD (MCSeEd) is a NGS-based method for genome-wide investigations of DNA methylation at different contexts requiring only low to moderate sequencing depth. It is particularly useful for identifying methylation changes in experimental systems challenged by biotic or abiotic stresses or at different developmental stages.
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Affiliation(s)
- Marco Di Marsico
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Elisa Cerruti
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Cinzia Comino
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Andrea Porceddu
- Department of Agriculture, University of Sassari, Sassari, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Stefano Capomaccio
- Department of Veterinary Medicine, University of Perugia, Perugia, Italy
| | - Gianpiero Marconi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy.
| | - Emidio Albertini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
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31
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Li WF, Ning GX, Mao J, Guo ZG, Zhou Q, Chen BH. Whole-genome DNA methylation patterns and complex associations with gene expression associated with anthocyanin biosynthesis in apple fruit skin. PLANTA 2019; 250:1833-1847. [PMID: 31471637 DOI: 10.1007/s00425-019-03266-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 08/20/2019] [Indexed: 05/22/2023]
Abstract
DNA methylation of anthocyanin biosynthesis-related genes and MYB/bHLH transcription factors was associated with apple fruit skin color revealed by whole-genome bisulfite sequencing. DNA methylation is a common feature of epigenetic regulation and is associated with various biological processes. Anthocyanins are among the secondary metabolites that contribute to fruit colour, which is a key appearance and nutrition quality attribute of apple fruit. Although few studies reported that DNA methylation in the promoter of MYB transcription factor was associated with fruit skin color, there is a general lack of understanding of the dynamics of global and genic DNA methylation in apple fruit. Here, whole-genome bisulfite sequencing was carried out in fruit skin of apple (Malus domestica Borkh.) cv. 'Red Delicious' (G0) and its four-generation bud sport mutants, including 'Starking Red' (G1), 'Starkrimson' (G2), 'Campbell Redchief' (G3) and 'Vallee spur' (G4) at color break stage. Correlation and linear-regression analysis between DNA methylation level and anthocyanin content, as well as the transcription levels of genes related to anthocyanin biosynthesis were carried out. The results showed that the number of differentially methylated regions (DMRs) and differentially methylated genes (DMGs) was considerably increased from G1 to G4 versus the number observed in G0. The mCHH context was dominant in apple, but the levels of mCG and mCHG of DMGs were significantly higher than that of the mCHH. Genetic variation of bud sport mutants from 'Red Delicious' was associated with differential DNA methylation. Additionally, hypomethylation of mCG and mCHG contexts in flavonoid biosynthesis pathway genes (PAL, 4CL, CYP98A, PER, CCoAOMT, CHS, and F3'H), mCHG context in MYB10 at upstream, led to transcriptional activation and was conductive to anthocyanin accumulation. However, hypermethylation of mCG context in bHLH74 at upstream led to transcriptional inhibition, inhibiting anthocyanin accumulation.
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Affiliation(s)
- Wen-Fang Li
- College of Horticulture, Gansu Agricultural University, 730070, Lanzhou, People's Republic of China
| | - Gai-Xing Ning
- College of Horticulture, Gansu Agricultural University, 730070, Lanzhou, People's Republic of China
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, 730070, Lanzhou, People's Republic of China
| | - Zhi-Gang Guo
- College of Horticulture, Gansu Agricultural University, 730070, Lanzhou, People's Republic of China
| | - Qi Zhou
- College of Horticulture, Gansu Agricultural University, 730070, Lanzhou, People's Republic of China
| | - Bai-Hong Chen
- College of Horticulture, Gansu Agricultural University, 730070, Lanzhou, People's Republic of China.
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32
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Wojtasik W, Boba A, Preisner M, Kostyn K, Szopa J, Kulma A. DNA Methylation Profile of β-1,3-Glucanase and Chitinase Genes in Flax Shows Specificity Towards Fusarium Oxysporum Strains Differing in Pathogenicity. Microorganisms 2019; 7:E589. [PMID: 31757035 PMCID: PMC6956085 DOI: 10.3390/microorganisms7120589] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 11/16/2022] Open
Abstract
Most losses in flax (Linum usitatissimum L.) crops are caused by fungal infections. The new epigenetic approach to improve plant resistance requires broadening the knowledge about the influence of pathogenic and non-pathogenic Fusarium oxysporum strains on changes in the profile of DNA methylation. Two contrasting effects on the levels of methylation in flax have been detected for both types of Fusarium strain infection: Genome-wide hypermethylation and hypomethylation of resistance-related genes (β-1,3-glucanase and chitinase). Despite the differences in methylation profile, the expression of these genes increased. Plants pretreated with the non-pathogenic strain memorize the hypomethylation pattern and then react more efficiently upon pathogen infection. The peak of demethylation correlates with the alteration in gene expression induced by the non-pathogenic strain. In the case of pathogen infection, the expression peak lags behind the gene demethylation. Dynamic changes in tetramer methylation induced by both pathogenic and non-pathogenic Fusarium strains are dependent on the ratio between the level of methyltransferase and demethylase gene expression. Infection with both Fusarium strains suppressed methyltransferase expression and increased the demethylase (demeter) transcript level. The obtained results provide important new information about changes in methylation profile and thus expression regulation of pathogenesis-related genes in the flax plant response to stressors.
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Affiliation(s)
- Wioleta Wojtasik
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, 51-148 Wroclaw, Poland; (A.B.); (M.P.); (K.K.); (J.S.); (A.K.)
| | - Aleksandra Boba
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, 51-148 Wroclaw, Poland; (A.B.); (M.P.); (K.K.); (J.S.); (A.K.)
| | - Marta Preisner
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, 51-148 Wroclaw, Poland; (A.B.); (M.P.); (K.K.); (J.S.); (A.K.)
- Department of Genetics, Plant Breeding and Seed Production, Faculty of Life Sciences and Technology, Wroclaw University of Environmental and Plant Sciences, pl. Grunwaldzki 24A, 50-363 Wroclaw, Poland
| | - Kamil Kostyn
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, 51-148 Wroclaw, Poland; (A.B.); (M.P.); (K.K.); (J.S.); (A.K.)
- Department of Genetics, Plant Breeding and Seed Production, Faculty of Life Sciences and Technology, Wroclaw University of Environmental and Plant Sciences, pl. Grunwaldzki 24A, 50-363 Wroclaw, Poland
| | - Jan Szopa
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, 51-148 Wroclaw, Poland; (A.B.); (M.P.); (K.K.); (J.S.); (A.K.)
- Department of Genetics, Plant Breeding and Seed Production, Faculty of Life Sciences and Technology, Wroclaw University of Environmental and Plant Sciences, pl. Grunwaldzki 24A, 50-363 Wroclaw, Poland
| | - Anna Kulma
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, 51-148 Wroclaw, Poland; (A.B.); (M.P.); (K.K.); (J.S.); (A.K.)
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Moglia A, Gianoglio S, Acquadro A, Valentino D, Milani AM, Lanteri S, Comino C. Identification of DNA methyltransferases and demethylases in Solanum melongena L., and their transcription dynamics during fruit development and after salt and drought stresses. PLoS One 2019; 14:e0223581. [PMID: 31596886 PMCID: PMC6785084 DOI: 10.1371/journal.pone.0223581] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/24/2019] [Indexed: 12/21/2022] Open
Abstract
DNA methylation through the activity of cytosine-5-methyltransferases (C5-MTases) and DNA demethylases plays important roles in genome protection as well as in regulating gene expression during plant development and plant response to environmental stresses. In this study, we report on a genome-wide identification of six C5-MTases (SmelMET1, SmelCMT2, SmelCMT3a, SmelCMT3b, SmelDRM2, SmelDRM3) and five demethylases (SmelDemethylase_1, SmelDemethylase_2, SmelDemethylase_3, SmelDemethylase_4, SmelDemethylase_5) in eggplant. Gene structural characteristics, chromosomal localization and phylogenetic analyses are also described. The transcript profiling of both C5-MTases and demethylases was assessed at three stages of fruit development in three eggplant commercial F1 hybrids: i.e. 'Clara', 'Nite Lady' and 'Bella Roma', representative of the eggplant berry phenotypic variation. The trend of activation of C5-MTases and demethylase genes varied in function of the stage of fruit development and was genotype dependent. The transcription pattern of C5MTAses and demethylases was also assessed in leaves of the F1 hybrid 'Nite Lady' subjected to salt and drought stresses. A marked up-regulation and down-regulation of some C5-MTases and demethylases was detected, while others did not vary in their expression profile. Our results suggest a role for both C5-MTases and demethylases during fruit development, as well as in response to abiotic stresses in eggplant, and provide a starting framework for supporting future epigenetic studies in the species.
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Affiliation(s)
- Andrea Moglia
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Silvia Gianoglio
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Danila Valentino
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Anna Maria Milani
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Sergio Lanteri
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Cinzia Comino
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
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Abstract
DNA methylation is a conserved epigenetic modification that is important for gene regulation and genome stability. Aberrant patterns of DNA methylation can lead to plant developmental abnormalities. A specific DNA methylation state is an outcome of dynamic regulation by de novo methylation, maintenance of methylation and active demethylation, which are catalysed by various enzymes that are targeted by distinct regulatory pathways. In this Review, we discuss DNA methylation in plants, including methylating and demethylating enzymes and regulatory factors, and the coordination of methylation and demethylation activities by a so-called methylstat mechanism; the functions of DNA methylation in regulating transposon silencing, gene expression and chromosome interactions; the roles of DNA methylation in plant development; and the involvement of DNA methylation in plant responses to biotic and abiotic stress conditions.
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You WJ, Feng YR, Shen YH, Chen YR, Chen TY, Fu SF. Silencing of NbCMT3s has Pleiotropic Effects on Development by Interfering with Autophagy-Related Genes in Nicotiana benthamiana. PLANT & CELL PHYSIOLOGY 2019; 60:1120-1135. [PMID: 30785195 DOI: 10.1093/pcp/pcz034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/14/2019] [Indexed: 05/25/2023]
Abstract
DNA methylation is a chromatin mark that has a crucial role in regulating gene expression. The chromomethylase (CMT) protein family is a plant-specific DNA methyltransferase that mediates growth and development. However, the roles of CMT3 in autophagy remain to be elucidated. Here, we identified the potential targets of CMT3 in Nicotiana benthamiana (NbCMT3) during developmental programs. Virus-induced gene silencing of NbCMT3/3-2 in N. benthamiana had pleiotropic effects on plant morphology, which indicates its indispensible role in development. Genome-wide transcriptome analysis of NbCMT3/3-2-silenced plants revealed interference with genes related to autophagy and ubiquitination. The expression of NbBeclin 1 and NbHRD1B was higher in NbCMT3/3-2-silenced than control plants. The formation of autophagosomes and starch degradation was disrupted in NbCMT3/3-2-silenced plants, which implies a perturbed autophagic processes. We further generated transgenic N. benthamiana plants carrying a chimeric promoter-reporter construct linking the NbBeclin 1 promoter region and β-glucuronidase (GUS) reporter (pNbBeclin::GUS). NbBeclin 1 promoter activity was significantly enhanced in NbCMT3/3-2-silenced plants. Thus, NbCMT3/3-2 silencing had pleiotropic effects on development by interfering with NbBeclin 1 expression and autophagy-related processes.
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Affiliation(s)
- Wen-Jing You
- Department of Biology, National Changhua University of Education, No.1, Jin-De Road, Changhua, Taiwan
| | - Yun-Ru Feng
- Department of Biology, National Changhua University of Education, No.1, Jin-De Road, Changhua, Taiwan
| | - Ya-Han Shen
- Department of Biology, National Changhua University of Education, No.1, Jin-De Road, Changhua, Taiwan
| | - Yi-Ru Chen
- Department of Biology, National Changhua University of Education, No.1, Jin-De Road, Changhua, Taiwan
| | - Tzy-Yi Chen
- Department of Biology, National Changhua University of Education, No.1, Jin-De Road, Changhua, Taiwan
| | - Shih-Feng Fu
- Department of Biology, National Changhua University of Education, No.1, Jin-De Road, Changhua, Taiwan
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Forgione I, Wołoszyńska M, Pacenza M, Chiappetta A, Greco M, Araniti F, Abenavoli MR, Van Lijsebettens M, Bitonti MB, Bruno L. Hypomethylated drm1 drm2 cmt3 mutant phenotype of Arabidopsis thaliana is related to auxin pathway impairment. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 280:383-396. [PMID: 30824017 DOI: 10.1016/j.plantsci.2018.12.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/27/2018] [Accepted: 12/29/2018] [Indexed: 05/28/2023]
Abstract
DNA methylation carried out by different methyltransferase classes is a relevant epigenetic modification of DNA which plays a relevant role in the development of eukaryotic organisms. Accordingly, in Arabidopsis thaliana loss of DNA methylation due to combined mutations in genes encoding for DNA methyltransferases causes several developmental abnormalities. The present study describes novel growth disorders in the drm1 drm2 cmt3 triple mutant of Arabidopsis thaliana, defective both in maintenance and de novo DNA methylation, and highlights the correlation between DNA methylation and the auxin hormone pathway. By using an auxin responsive reporter gene, we discovered that auxin accumulation and distribution were affected in the mutant compared to the wild type, from embryo to adult plant stage. In addition, we demonstrated that the defective methylation status also affected the expression of genes that regulate auxin hormone pathways from synthesis to transport and signalling and a direct relationship between differentially expressed auxin-related genes and altered auxin accumulation and distribution in embryo, leaf and root was observed. Finally, we provided evidence of the direct and organ-specific modulation of auxin-related genes through the DNA methylation process.
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Affiliation(s)
- Ivano Forgione
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Magdalena Wołoszyńska
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Marianna Pacenza
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy
| | - Adriana Chiappetta
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy
| | - Maria Greco
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy; The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Fabrizio Araniti
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Maria Rosa Abenavoli
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, 89124 Reggio Calabria, Italy
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Maria Beatrice Bitonti
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy
| | - Leonardo Bruno
- Dipartimento di Biologia, Ecologia e Scienze della Terra, Università della Calabria, Arcavacata di Rende (CS), 87036 Arcavacata di Rende, CS, Italy.
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Aydinoglu F, Lucas SJ. Identification and expression profiles of putative leaf growth related microRNAs in maize (Zea mays L.) hybrid ADA313. Gene 2018; 690:57-67. [PMID: 30597233 DOI: 10.1016/j.gene.2018.12.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 10/17/2018] [Accepted: 12/13/2018] [Indexed: 02/06/2023]
Abstract
Throughout the plant life cycle, growth of new leaves is governed by cell division and cell expansion. During steady-state growth of the maize leaf, these processes are spatially separated between the meristem zone, consisting of dividing cells at the leaf base, the elongation zone, consisting of expanding cells moving upwards from the meristem, and the mature zone containing differentiated mature cells. Increased leaf size can be achieved through increasing cell number or cell size, for example by manipulating the genes controlling the transition between those zones. In this study, microRNA (miRNA) genes, which are a class of endogenous small, non-coding gene regulatory RNAs, were investigated in the growth zones, to gain insight into their role in the transition between cell division and cell expansion. A genome-wide survey was conducted using a miRNA-microarray and 59 miRNA genes were detected to be differentially expressed between the growth zones. miR160, miR166, miR168, miR172, miR319 and miR390 families were significantly up-regulated in the meristem relative to the elongation and mature zones. In contrast, expression of the miR167 and miR396 families was lower in the meristem and higher in the mature zone. Therefore, these were considered to be candidate growth-regulated miRNAs that control cell division processes indirectly by repressing target genes. The miR156, miR166, miR167, miR399, miR408 and miR2275 families were expressed most highly in the elongation zone, and so were classified as elongation-specific, with possible roles in switching from cell division to cell elongation during leaf differentiation. In silico target prediction analysis showed that these miRNAs target several transcription factors and metabolic genes, and a reciprocal relationship between the expression levels of miR319 and miR396 and their targets was confirmed by qRT-PCR. Furthermore, 12 candidate novel miRNAs were identified from the microarray data and computationally verified. Three out of twelve were also validated by qRT-PCR. These findings provide important information regarding the regulatory functions of miRNAs in controlling progression of growth mechanisms.
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Affiliation(s)
- Fatma Aydinoglu
- Gebze Technical University, Molecular Biology and Genetics Department, Kocaeli, Turkey.
| | - Stuart James Lucas
- Sabanci University Nanotechnology Research & Application Center (SUNUM), Istanbul, Turkey
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Beltramino M, Ercoli MF, Debernardi JM, Goldy C, Rojas AML, Nota F, Alvarez ME, Vercruyssen L, Inzé D, Palatnik JF, Rodriguez RE. Robust increase of leaf size by Arabidopsis thaliana GRF3-like transcription factors under different growth conditions. Sci Rep 2018; 8:13447. [PMID: 30194309 PMCID: PMC6128883 DOI: 10.1038/s41598-018-29859-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 07/17/2018] [Indexed: 02/03/2023] Open
Abstract
An increase in crop yield is essential to reassure food security to meet the accelerating global demand. Several genetic modifications can increase organ size, which in turn might boost crop yield. Still, only in a few cases their performance has been evaluated under stress conditions. MicroRNA miR396 repress the expression of GROWTH-REGULATING FACTOR (GRF) genes that codes for transcription factors that promote organ growth. Here, we show that both Arabidopsis thaliana At-GRF2 and At-GRF3 genes resistant to miR396 activity (rGRF2 and rGRF3) increased organ size, but only rGRF3 can produce this effect without causing morphological defects. Furthermore, introduction of At-rGRF3 in Brassica oleracea can increase organ size, and when At-rGRF3 homologs from soybean and rice are introduced in Arabidopsis, leaf size is also increased. This suggests that regulation of GRF3 activity by miR396 is important for organ growth in a broad range of species. Plants harboring rGRF3 have larger leaves also under drought stress, a condition that stimulates miR396 accumulation. These plants also showed an increase in the resistance to virulent bacteria, suggesting that the size increment promoted by rGRF3 occurs without an obvious cost on plant defenses. Our findings indicate that rGRF3 can increase plant organ size under both normal and stress conditions and is a valuable tool for biotechnological applications.
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Affiliation(s)
- Matías Beltramino
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, Argentina
| | - María Florencia Ercoli
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, Argentina
| | - Juan Manuel Debernardi
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, Argentina
| | - Camila Goldy
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, Argentina
| | - Arantxa M L Rojas
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, Argentina
| | - Florencia Nota
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina
| | - María Elena Alvarez
- CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
- Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica Ranwel Caputto, Córdoba, Argentina
| | - Liesbeth Vercruyssen
- VIB-UGent Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Dirk Inzé
- VIB-UGent Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Javier F Palatnik
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, Argentina.
- Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario, Argentina.
| | - Ramiro E Rodriguez
- IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario, Argentina.
- Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario, Argentina.
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Bhatia H, Khemka N, Jain M, Garg R. Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea. Sci Rep 2018; 8:9704. [PMID: 29946142 PMCID: PMC6018830 DOI: 10.1038/s41598-018-27979-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 05/30/2018] [Indexed: 12/31/2022] Open
Abstract
DNA methylation is widely known to regulate gene expression in eukaryotes. Here, we unraveled DNA methylation patterns in cultivated chickpea to understand the regulation of gene expression in different organs. We analyzed the methylation pattern in leaf tissue of wild chickpea too, and compared it with cultivated chickpea. Our analysis indicated abundant CG methylation within gene-body and CHH methylation in intergenic regions of the chickpea genome in all the organs examined. Analysis of differentially methylated regions (DMRs) demonstrated a higher number of CG context DMRs in wild chickpea and CHH context DMRs in cultivated chickpea. We observed increased preponderance of hypermethylated DMRs in the promoter regions and hypomethylated DMRs in the genic regions in cultivated chickpea. Genomic location and context of the DMRs correlated well with expression of proximal genes. Our results put forth a positive correlation of promoter hypermethylation with increased transcript abundance via identification of DMR-associated genes involved in flower development in cultivated chickpea. The atypical correlation observed between promoter hypermethylation and increased transcript abundance might be dependent on 24-nt small RNAs and transcription factors binding to the promoter region. This study provides novel insights into DNA methylation patterns in chickpea and their role in regulation of gene expression.
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Affiliation(s)
- Himanshi Bhatia
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Niraj Khemka
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.,National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, 201314, India.
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Monir MM, Zhu J. Dominance and Epistasis Interactions Revealed as Important Variants for Leaf Traits of Maize NAM Population. FRONTIERS IN PLANT SCIENCE 2018; 9:627. [PMID: 29967625 PMCID: PMC6015889 DOI: 10.3389/fpls.2018.00627] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/20/2018] [Indexed: 05/26/2023]
Abstract
Leaf orientation traits of maize (Zea mays) are complex traits controlling by multiple loci with additive, dominance, epistasis, and environmental interaction effects. In this study, an attempt was made for identifying the causal loci, and estimating the additive, non-additive, environmental specific genetic effects underpinning leaf traits (leaf length, leaf width, and upper leaf angle) of maize NAM population. Leaf traits were analyzed by using full genetic model and additive model of multiple loci. Analysis with full genetic model identified 38∼47 highly significant loci (-log10PEW > 5), while estimated total heritability were 64.32∼79.06% with large contributions due to dominance and dominance related epistasis effects (16.00∼56.91%). Analysis with additive model obtained smaller total heritability ( hT2 ≙ 18.68∼29.56%) and detected fewer loci (30∼36) as compared to the full genetic model. There were 12 pleiotropic loci identified for the three leaf traits: eight loci for leaf length and leaf width, and four loci for leaf length and leaf angle. Optimal genotype combinations of superior line (SL) and superior hybrid (SH) were predicted for each of the traits under four different environments based on estimated genotypic effects to facilitate maker-assisted selection for the leaf traits.
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Huang F, Peng M, Chen X, Li G, Di J, Zhao Y, Jiang T, Chang R, Yang L, Chen Y. Comparison of DNA methylation in developing seeds of Ricinus communis L. using MSAP analysis. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2018.1470034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Fenglan Huang
- Department of Biotechnology, College of Life Science, Inner Mongolia University for the Nationalities, Tongliao, PR China
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao, PR China
- Inner Mongolia Key Laboratory of Castor Breeding, Tongliao, PR China
- Inner Mongolia Collaborate Innovation Cultivate Center for Castor, Tongliao, PR China
| | - Mu Peng
- Department of Biotechnology, College of Life Science, Inner Mongolia University for the Nationalities, Tongliao, PR China
- Department of Genetics, College of Life Science, Northeast Forestry University, Harbin, PR China
| | - Xiaofeng Chen
- Department of Biotechnology, College of Life Science, Inner Mongolia University for the Nationalities, Tongliao, PR China
| | - Guorui Li
- Department of Biotechnology, College of Life Science, Inner Mongolia University for the Nationalities, Tongliao, PR China
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao, PR China
- Inner Mongolia Key Laboratory of Castor Breeding, Tongliao, PR China
- Inner Mongolia Collaborate Innovation Cultivate Center for Castor, Tongliao, PR China
| | - Jianjun Di
- Department of Biotechnology, College of Life Science, Inner Mongolia University for the Nationalities, Tongliao, PR China
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao, PR China
- Inner Mongolia Key Laboratory of Castor Breeding, Tongliao, PR China
- Inner Mongolia Collaborate Innovation Cultivate Center for Castor, Tongliao, PR China
| | - Yong Zhao
- Department of Biotechnology, College of Life Science, Inner Mongolia University for the Nationalities, Tongliao, PR China
| | - Tongtong Jiang
- Department of Biotechnology, College of Life Science, Inner Mongolia University for the Nationalities, Tongliao, PR China
| | - Ruihui Chang
- Department of Biotechnology, College of Life Science, Inner Mongolia University for the Nationalities, Tongliao, PR China
| | - Lifeng Yang
- Department of Biotechnology, College of Life Science, Inner Mongolia University for the Nationalities, Tongliao, PR China
| | - Yongshen Chen
- Department of Biotechnology, College of Life Science, Inner Mongolia University for the Nationalities, Tongliao, PR China
- Inner Mongolia Industrial Engineering Research Center of Universities for Castor, Tongliao, PR China
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Li J, Li C, Lu S. Identification and characterization of the cytosine-5 DNA methyltransferase gene family in Salvia miltiorrhiza. PeerJ 2018. [PMID: 29527415 PMCID: PMC5842782 DOI: 10.7717/peerj.4461] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Cytosine DNA methylation is highly conserved epigenetic modification involved in a wide range of biological processes in eukaryotes. It was established and maintained by cytosine-5 DNA methyltransferases (C5-MTases) in plants. Through genome-wide identification, eight putative SmC5-MTase genes were identified from the genome of Salvia miltiorrhiza, a well-known traditional Chinese medicine material and an emerging model medicinal plant. Based on conserved domains and phylogenetic analysis, eight SmC5-MTase genes were divided into four subfamilies, including MET, CMT, DRM and DNMT2. Genome-wide comparative analysis of the C5-MTase gene family in S. miltiorrhiza and Arabidopsis thaliana, including gene structure, sequence features, sequence alignment and conserved motifs, was carried out. The results showed conservation and divergence of the members of each subfamily in plants. The length of SmC5-MTase open reading frames ranges widely from 1,152 (SmDNMT2) to 5,034 bp (SmMET1). The intron number of SmC5-MTases varies between 7 (SmDRM1) and 20 (SmCMT1 and SmCMT2b). These features were similar to their counterparts from Arabidopsis. Sequence alignment and conserved motif analysis showed the existence of highly conserved and subfamily-specific motifs in the C5-MTases analyzed. Differential transcript abundance was detected for SmC5-MTases, implying genome-wide variance of DNA methylation in different organs and tissues. Transcriptome-wide analysis showed that the transcript levels of all SmC5-MTase genes was slightly changed under yeast extract and methyl jasmonate treatments. Six SmC5-MTases, including SmMET1, SmCMT1, SmCMT2a, SmCMT2b, SmCMT3 and SmDRM1, were salicylic acid-responsive, suggesting the involvement of SmC5-MTases in salicylic acid-dependent immunity. These results provide useful information for demonstrating the role of DNA methylation in bioactive compound biosynthesis and Dao-di herb formation in medicinal plants.
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Affiliation(s)
- Jiang Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Shanfa Lu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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43
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Lee K, Seo PJ. Dynamic Epigenetic Changes during Plant Regeneration. TRENDS IN PLANT SCIENCE 2018; 23:235-247. [PMID: 29338924 DOI: 10.1016/j.tplants.2017.11.009] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 05/18/2023]
Abstract
Plants have the remarkable ability to drive cellular dedifferentiation and regeneration. Changes in epigenetic landscapes accompany the cell fate transition. Notably, modifications of chromatin structure occur primarily during callus formation via an in vitro tissue culture process and, thus, pluripotent callus cells have unique epigenetic signatures. Here, we highlight the latest progress in epigenetic regulation of callus formation in plants, which addresses fundamental questions related to cell fate changes and pluripotency establishment. Global and local modifications of chromatin structure underlie callus formation, and the combination and sequence of epigenetic modifications further shape intricate cell fate changes. This review illustrates how a series of chromatin marks change dynamically during callus formation and their biological relevance in plant regeneration.
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Affiliation(s)
- Kyounghee Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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44
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Gianoglio S, Moglia A, Acquadro A, Comino C, Portis E. The genome-wide identification and transcriptional levels of DNA methyltransferases and demethylases in globe artichoke. PLoS One 2017; 12:e0181669. [PMID: 28746368 PMCID: PMC5529103 DOI: 10.1371/journal.pone.0181669] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/05/2017] [Indexed: 11/19/2022] Open
Abstract
Changes to the cytosine methylation status of DNA, driven by the activity of C5 methyltransferases (C5-MTases) and demethylases, exert an important influence over development, transposon movement, gene expression and imprinting. Three groups of C5-MTase enzymes have been identified in plants, namely MET (methyltransferase 1), CMT (chromomethyltransferases) and DRM (domains rearranged methyltransferases). Here the repertoire of genes encoding C5-MTase and demethylase by the globe artichoke (Cynara cardunculus var. scolymus) is described, based on sequence homology, a phylogenetic analysis and a characterization of their functional domains. A total of ten genes encoding C5-MTase (one MET, five CMTs and four DRMs) and five demethylases was identified. An analysis of their predicted product's protein structure suggested an extensive level of conservation has been retained by the C5-MTases. Transcriptional profiling based on quantitative real time PCR revealed a number of differences between the genes encoding maintenance and de novo methyltransferases, sometimes in a tissue- or development-dependent manner, which implied a degree of functional specialization.
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Affiliation(s)
- Silvia Gianoglio
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Andrea Moglia
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Cinzia Comino
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy
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45
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Turco GM, Kajala K, Kunde‐Ramamoorthy G, Ngan C, Olson A, Deshphande S, Tolkunov D, Waring B, Stelpflug S, Klein P, Schmutz J, Kaeppler S, Ware D, Wei C, Etchells JP, Brady SM. DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor. THE NEW PHYTOLOGIST 2017; 214:1213-1229. [PMID: 28186631 PMCID: PMC5655736 DOI: 10.1111/nph.14448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 12/19/2016] [Indexed: 05/23/2023]
Abstract
Plant secondary cell walls constitute the majority of plant biomass. They are predominantly found in xylem cells, which are derived from vascular initials during vascularization. Little is known about these processes in grass species despite their emerging importance as biomass feedstocks. The targeted biofuel crop Sorghum bicolor has a sequenced and well-annotated genome, making it an ideal monocot model for addressing vascularization and biomass deposition. Here we generated tissue-specific transcriptome and DNA methylome data from sorghum shoots, roots and developing root vascular and nonvascular tissues. Many genes associated with vascular development in other species show enriched expression in developing vasculature. However, several transcription factor families varied in vascular expression in sorghum compared with Arabidopsis and maize. Furthermore, differential expression of genes associated with DNA methylation were identified between vascular and nonvascular tissues, implying that changes in DNA methylation are a feature of sorghum root vascularization, which we confirmed using tissue-specific DNA methylome data. Roots treated with a DNA methylation inhibitor also showed a significant decrease in root length. Tissues and organs can be discriminated based on their genomic methylation patterns and methylation context. Consequently, tissue-specific changes in DNA methylation are part of the normal developmental process.
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Affiliation(s)
- Gina M. Turco
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
| | - Kaisa Kajala
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
| | | | - Chew‐Yee Ngan
- DOE Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory1 Bungtown RoadCold Spring HarborNY11724USA
| | | | - Denis Tolkunov
- DOE Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - Barbara Waring
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
| | - Scott Stelpflug
- Department of Agronomy and Great Lakes Bioenergy Research CenterUniversity of Wisconsin1575 Linden DriveMadisonWI53706USA
| | - Patricia Klein
- Institute for Plant Genomics and Biotechnology and Department of Horticultural SciencesTexas A and M UniversityCollege StationTX77843USA
| | - Jeremy Schmutz
- DOE Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
- HudsonAlpha Institute for Biotechnology601 Genome Way NWHuntsvilleAL35806USA
| | - Shawn Kaeppler
- Department of Agronomy and Great Lakes Bioenergy Research CenterUniversity of Wisconsin1575 Linden DriveMadisonWI53706USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory1 Bungtown RoadCold Spring HarborNY11724USA
- USDA‐ARSIthacaNY14853USA
| | - Chia‐Lin Wei
- DOE Joint Genome Institute2800 Mitchell DriveWalnut CreekCA94598USA
| | - J. Peter Etchells
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
- School of Biological and Biomedical SciencesDurham UniversitySouth RoadDurhamDH3 1LEUK
| | - Siobhan M. Brady
- Department of Plant Biology and Genome CenterUC DavisDavisCA95616USA
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Giovannoni J, Nguyen C, Ampofo B, Zhong S, Fei Z. The Epigenome and Transcriptional Dynamics of Fruit Ripening. ANNUAL REVIEW OF PLANT BIOLOGY 2017; 68:61-84. [PMID: 28226232 DOI: 10.1146/annurev-arplant-042916-040906] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Fruit has evolved myriad forms that facilitate seed dispersal in varied environmental and ecological contexts. Because fleshy fruits become attractive and nutritious to seed-dispersing animals, the transition from unripe to ripe fruit represents a dramatic shift in survival strategy-from protecting unripe fruit against damaging animals to making it appealing to those same animals once ripened. For optimal fitness, ripening therefore must be tightly controlled and coordinated with seed development. Fruits, like many vegetative tissues of plants that contribute to human diets, are also subject to decay, which is enhanced as a consequence of the ripening transition. As such, ripening control has enormous relevance for both plant biology and food security. Here, we review the complex interactions of hormones and transcription factors during fleshy-fruit ripening, with an emphasis on the recent discovery that epigenome dynamics are a critical and early regulator of the cascade of molecular events that ultimately contribute to fruit maturation and ripening.
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Affiliation(s)
- James Giovannoni
- Robert W. Holley Center, US Department of Agriculture-Agricultural Research Service, Ithaca, New York 14853;
- Boyce Thompson Institute, Ithaca, New York 14853;
- School of Integrated Plant Sciences, Cornell University, Ithaca, New York 14853; ,
| | - Cuong Nguyen
- School of Integrated Plant Sciences, Cornell University, Ithaca, New York 14853; ,
| | - Betsy Ampofo
- School of Integrated Plant Sciences, Cornell University, Ithaca, New York 14853; ,
| | - Silin Zhong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China;
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, New York 14853;
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Liu X, Li X, Zhang C, Dai C, Zhou J, Ren C, Zhang J. Phosphoenolpyruvate carboxylase regulation in C4-PEPC-expressing transgenic rice during early responses to drought stress. PHYSIOLOGIA PLANTARUM 2017; 159:178-200. [PMID: 27592839 DOI: 10.1111/ppl.12506] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 07/14/2016] [Accepted: 08/05/2016] [Indexed: 05/11/2023]
Abstract
Phosphoenolpyruvate carboxylase (PEPC; EC 4.1.1.31) has important functions in C4 photosynthesis and biosynthesis of intermediate metabolites. In this study, the drought resistance of C4-PEPC-expressing transgenic rice (Oryza sativa, line PC) plants was assessed using simulated drought conditions [i.e. polyethylene glycol (PEG)-6000 treatment]. The dry weight of PC plants was higher than that of wild-type (WT) plants following treatment with 15% PEG-6000 for 16 days. Furthermore, the water use efficiency, relative water content and proline content in PC plants were higher than those of WT plants, as were C4-PEPC activity and transcript levels following treatment with 5% PEG-6000 for 2 h. The protein kinase activities and transcript levels of sucrose non-fermenting-1-related protein kinases (SnRKs) genes, such as SnRK1a, OsK24 and OsK35 were also higher in PC plants than in WT plants following treatment with 5% PEG-6000 for 2 h. Additionally, phosphoenolpyruvate carboxylase kinase (PPCK, EC 4.1.1.32) activities and transcript levels (e.g. PPCK1 and PPCK2) increased following drought treatment. These changes were regulated by signaling molecules, such as calcium, nitric oxide and hydrogen peroxide. Furthermore, the -1095 to -416 region of the C4-PEPC promoter in PC plants was demethylated following exposure to drought conditions for 1 h. The demethylation coincided with an increase in C4-PEPC expression. Our data suggest that the demethylation of the C4-PEPC promoter and the phosphorylation catalyzed by PPCK have key roles in conferring drought tolerance to the transgenic rice plants.
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Affiliation(s)
- Xiaolong Liu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xia Li
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
| | - Chen Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
| | - Chuanchao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jiayu Zhou
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Chenggang Ren
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
| | - Jinfei Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Jiangsu High Quality Rice Research and Development Center, Nanjing Branch, China National Center for Rice Improvement, Nanjing, 210014, China
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48
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Inácio V, Barros PM, Costa A, Roussado C, Gonçalves E, Costa R, Graça J, Oliveira MM, Morais-Cecílio L. Differential DNA Methylation Patterns Are Related to Phellogen Origin and Quality of Quercus suber Cork. PLoS One 2017; 12:e0169018. [PMID: 28045988 PMCID: PMC5207400 DOI: 10.1371/journal.pone.0169018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/09/2016] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is thought to influence Quercus suber cork quality, which is the main constraint for its economic valorisation. However, a deep knowledge of the cytosine methylation patterns disclosing the epigenetic variability of trees with different cork quality types is totally missing. This study investigates the hypothesis that variations in DNA methylation contribute to differences in cork cellular characteristics directly related to original or traumatic phellogen activity. We used MSAPs (Methylation Sensitive Amplified Polymorphism) to assess DNA methylation patterns of cork and leaf tissues of Q. suber adult trees growing in three cork oak stands. The relationship between the detected polymorphisms and the diversity of cork quality traits was explored by a marker-trait analysis focusing on the most relevant quality characteristics. Populations differed widely in cork quality, but only slightly in degree of epigenetic differentiation. Four MSAP markers (1.3% of the total) were significantly associated with the most noteworthy quality traits: wood inclusions (nails) and porosity. This evidence supports the potential role of cytosine methylation in the modulation of differential phellogen activity either involved in localized cell death or in pore production, resulting in different cork qualities. Although, the underlying basis of the methylation polymorphism of loci affecting cork quality traits remain unclear, the disclosure of markers statistically associated with cork quality strengthens the potential role of DNA methylation in the regulation of these traits, namely at the phellogen level.
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Affiliation(s)
- Vera Inácio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Pedro M. Barros
- Genomics of Plant Stress Unit, ITQB NOVA—Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Augusta Costa
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Oeiras, Portugal
- Center for Environmental and Sustainability Research (CENSE), Environmental Sciences and Engineering Department, Faculty of Science and Technology, NOVA University of Lisbon, Caparica, Portugal
| | - Cristóvão Roussado
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Elsa Gonçalves
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Rita Costa
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Oeiras, Portugal
| | - José Graça
- Forest Research Center, Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - M. Margarida Oliveira
- Genomics of Plant Stress Unit, ITQB NOVA—Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- * E-mail: (LM-C); (MMO)
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
- * E-mail: (LM-C); (MMO)
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Guevara MÁ, de María N, Sáez-Laguna E, Vélez MD, Cervera MT, Cabezas JA. Analysis of DNA Cytosine Methylation Patterns Using Methylation-Sensitive Amplification Polymorphism (MSAP). Methods Mol Biol 2017; 1456:99-112. [PMID: 27770361 DOI: 10.1007/978-1-4899-7708-3_9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Different molecular techniques have been developed to study either the global level of methylated cytosines or methylation at specific gene sequences. One of them is the methylation-sensitive amplified polymorphism technique (MSAP) which is a modification of amplified fragment length polymorphism (AFLP). It has been used to study methylation of anonymous CCGG sequences in different fungi, plants, and animal species. The main variation of this technique resides on the use of isoschizomers with different methylation sensitivity (such as HpaII and MspI) as a frequent-cutter restriction enzyme. For each sample, MSAP analysis is performed using both EcoRI/HpaII- and EcoRI/MspI-digested samples. A comparative analysis between EcoRI/HpaII and EcoRI/MspI fragment patterns allows the identification of two types of polymorphisms: (1) methylation-insensitive polymorphisms that show common EcoRI/HpaII and EcoRI/MspI patterns but are detected as polymorphic amplified fragments among samples and (2) methylation-sensitive polymorphisms which are associated with the amplified fragments that differ in their presence or absence or in their intensity between EcoRI/HpaII and EcoRI/MspI patterns. This chapter describes a detailed protocol of this technique and discusses the modifications that can be applied to adjust the technology to different species of interest.
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Affiliation(s)
- María Ángeles Guevara
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - Nuria de María
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - Enrique Sáez-Laguna
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - María Dolores Vélez
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain
| | - María Teresa Cervera
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain.
| | - José Antonio Cabezas
- Department of Forest Ecology and Genetic, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de InvestigaciónForestal (INIA-CIFOR), Ctra. de La Coruña Km 7,5, Madrid, 28040, Spain.
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50
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Chwialkowska K, Korotko U, Kosinska J, Szarejko I, Kwasniewski M. Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq)-A Method for High-Throughput Analysis of Differentially Methylated CCGG Sites in Plants with Large Genomes. FRONTIERS IN PLANT SCIENCE 2017; 8:2056. [PMID: 29250096 PMCID: PMC5714927 DOI: 10.3389/fpls.2017.02056] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/16/2017] [Indexed: 05/14/2023]
Abstract
Epigenetic mechanisms, including histone modifications and DNA methylation, mutually regulate chromatin structure, maintain genome integrity, and affect gene expression and transposon mobility. Variations in DNA methylation within plant populations, as well as methylation in response to internal and external factors, are of increasing interest, especially in the crop research field. Methylation Sensitive Amplification Polymorphism (MSAP) is one of the most commonly used methods for assessing DNA methylation changes in plants. This method involves gel-based visualization of PCR fragments from selectively amplified DNA that are cleaved using methylation-sensitive restriction enzymes. In this study, we developed and validated a new method based on the conventional MSAP approach called Methylation Sensitive Amplification Polymorphism Sequencing (MSAP-Seq). We improved the MSAP-based approach by replacing the conventional separation of amplicons on polyacrylamide gels with direct, high-throughput sequencing using Next Generation Sequencing (NGS) and automated data analysis. MSAP-Seq allows for global sequence-based identification of changes in DNA methylation. This technique was validated in Hordeum vulgare. However, MSAP-Seq can be straightforwardly implemented in different plant species, including crops with large, complex and highly repetitive genomes. The incorporation of high-throughput sequencing into MSAP-Seq enables parallel and direct analysis of DNA methylation in hundreds of thousands of sites across the genome. MSAP-Seq provides direct genomic localization of changes and enables quantitative evaluation. We have shown that the MSAP-Seq method specifically targets gene-containing regions and that a single analysis can cover three-quarters of all genes in large genomes. Moreover, MSAP-Seq's simplicity, cost effectiveness, and high-multiplexing capability make this method highly affordable. Therefore, MSAP-Seq can be used for DNA methylation analysis in crop plants with large and complex genomes.
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Affiliation(s)
- Karolina Chwialkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Urszula Korotko
- Department of Genetics, University of Silesia in Katowice, Katowice, Poland
| | - Joanna Kosinska
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Iwona Szarejko
- Department of Genetics, University of Silesia in Katowice, Katowice, Poland
| | - Miroslaw Kwasniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
- *Correspondence: Miroslaw Kwasniewski
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