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Wang W, Zhang T, Liu C, Liu C, Jiang Z, Zhang Z, Ali S, Li Z, Wang J, Sun S, Chen Q, Zhang Q, Xie L. A DNA demethylase reduces seed size by decreasing the DNA methylation of AT-rich transposable elements in soybean. Commun Biol 2024; 7:613. [PMID: 38773248 PMCID: PMC11109123 DOI: 10.1038/s42003-024-06306-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024] Open
Abstract
Understanding how to increase soybean yield is crucial for global food security. The genetic and epigenetic factors influencing seed size, a major crop yield determinant, are not fully understood. We explore the role of DNA demethylase GmDMEa in soybean seed size. Our research indicates that GmDMEa negatively correlates with soybean seed size. Using CRISPR-Cas9, we edited GmDMEa in the Dongnong soybean cultivar, known for small seeds. Modified plants had larger seeds and greater yields without altering plant architecture or seed nutrition. GmDMEa preferentially demethylates AT-rich transposable elements, thus activating genes and transcription factors associated with the abscisic acid pathway, which typically decreases seed size. Chromosomal substitution lines confirm that these modifications are inheritable, suggesting a stable epigenetic method to boost seed size in future breeding. Our findings provide insights into epigenetic seed size control and suggest a strategy for improving crop yields through the epigenetic regulation of crucial genes. This work implies that targeted epigenetic modification has practical agricultural applications, potentially enhancing food production without compromising crop quality.
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Affiliation(s)
- Wanpeng Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Chunyu Liu
- College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhenfeng Jiang
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Zhaohan Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Shahid Ali
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Zhuozheng Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Jiang Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Shanwen Sun
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, China.
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, Heilongjiang, China.
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China.
- College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China.
| | - Linan Xie
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, Heilongjiang, China.
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, Heilongjiang, China.
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2
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Suguiyama VF, Rodriguez JDP, Dos Santos TCN, Lira BS, de Haro LA, Silva JPN, Borba EL, Purgatto E, da Silva EA, Bellora N, Carrari F, Centeno DDC, Bermúdez LF, Rossi M, de Setta N. Regulatory mechanisms behind the phenotypic plasticity associated with Setaria italica water deficit tolerance. PLANT MOLECULAR BIOLOGY 2022; 109:761-780. [PMID: 35524936 DOI: 10.1007/s11103-022-01273-w] [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: 12/20/2021] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Drought is one of the main environmental stresses that negatively impacts vegetative and reproductive yield. Water deficit responses are determined by the duration and intensity of the stress, which, together with plant genotype, will define the chances of plant survival. The metabolic adjustments in response to water deficit are complex and involve gene expression modulation regulated by DNA-binding proteins and epigenetic modifications. This last mechanism may also regulate the activity of transposable elements, which in turn impact the expression of nearby loci. Setaria italica plants submitted to five water deficit regimes were analyzed through a phenotypical approach, including growth, physiological, RNA-seq and sRNA-seq analyses. The results showed a progressive reduction in yield as a function of water deficit intensity associated with signaling pathway modulation and metabolic adjustments. We identified a group of loci that were consistently associated with drought responses, some of which were related to water deficit perception, signaling and regulation. Finally, an analysis of the transcriptome and sRNAome allowed us to identify genes putatively regulated by TE- and sRNA-related mechanisms and an intriguing positive correlation between transcript levels and sRNA accumulation in gene body regions. These findings shed light on the processes that allow S. italica to overcome drought and survive under water restrictive conditions.
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Affiliation(s)
- Vanessa Fuentes Suguiyama
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | | | | | - Bruno Silvestre Lira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Luis Alejandro de Haro
- Departament of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - João Paulo Naldi Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - Eduardo Leite Borba
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Eduardo Purgatto
- Departamento de Alimentos e Nutrição Experimental, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Emerson Alves da Silva
- Instituto de Botânica da Secretaria do Meio Ambiente do Estado de São Paulo, São Paulo, SP, Brazil
| | - Nicolas Bellora
- Institute of Nuclear Technologies for Health (Intecnus), National Scientific and Technical Research Council (CONICET), 8400, Bariloche, Argentina
| | - Fernando Carrari
- Instituto de Agrobiotecnología Y Biología Molecular (IABIMO), CICVYA, INTA-CONICET, Hurlingham, Argentina
- Cátedra de Genética, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Danilo da Cruz Centeno
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - Luisa Fernanda Bermúdez
- Instituto de Agrobiotecnología Y Biología Molecular (IABIMO), CICVYA, INTA-CONICET, Hurlingham, Argentina
- Cátedra de Genética, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Nathalia de Setta
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil.
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3
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Plant DNA Methylation: An Epigenetic Mark in Development, Environmental Interactions, and Evolution. Int J Mol Sci 2022; 23:ijms23158299. [PMID: 35955429 PMCID: PMC9368846 DOI: 10.3390/ijms23158299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/21/2022] [Accepted: 07/24/2022] [Indexed: 01/06/2023] Open
Abstract
DNA methylation is an epigenetic modification of the genome involved in the regulation of gene expression and modulation of chromatin structure. Plant genomes are widely methylated, and the methylation generally occurs on the cytosine bases through the activity of specific enzymes called DNA methyltransferases. On the other hand, methylated DNA can also undergo demethylation through the action of demethylases. The methylation landscape is finely tuned and assumes a pivotal role in plant development and evolution. This review illustrates different molecular aspects of DNA methylation and some plant physiological processes influenced by this epigenetic modification in model species, crops, and ornamental plants such as orchids. In addition, this review aims to describe the relationship between the changes in plant DNA methylation levels and the response to biotic and abiotic stress. Finally, we discuss the possible evolutionary implications and biotechnological applications of DNA methylation.
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Bianchetti R, Bellora N, de Haro LA, Zuccarelli R, Rosado D, Freschi L, Rossi M, Bermudez L. Phytochrome-Mediated Light Perception Affects Fruit Development and Ripening Through Epigenetic Mechanisms. FRONTIERS IN PLANT SCIENCE 2022; 13:870974. [PMID: 35574124 PMCID: PMC9096621 DOI: 10.3389/fpls.2022.870974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Phytochrome (PHY)-mediated light and temperature perception has been increasingly implicated as important regulator of fruit development, ripening, and nutritional quality. Fruit ripening is also critically regulated by chromatin remodeling via DNA demethylation, though the molecular basis connecting epigenetic modifications in fruits and environmental cues remains largely unknown. Here, to unravel whether the PHY-dependent regulation of fruit development involves epigenetic mechanisms, an integrative analysis of the methylome, transcriptome and sRNAome of tomato fruits from phyA single and phyB1B2 double mutants was performed in immature green (IG) and breaker (BK) stages. The transcriptome analysis showed that PHY-mediated light perception regulates more genes in BK than in the early stages of fruit development (IG) and that PHYB1B2 has a more substantial impact than PHYA in the fruit transcriptome, in both analyzed stages. The global profile of methylated cytosines revealed that both PHYA and PHYB1B2 affect the global methylome, but PHYB1B2 has a greater impact on ripening-associated methylation reprogramming across gene-rich genomic regions in tomato fruits. Remarkably, promoters of master ripening-associated transcription factors (TF) (RIN, NOR, CNR, and AP2a) and key carotenoid biosynthetic genes (PSY1, PDS, ZISO, and ZDS) remained highly methylated in phyB1B2 from the IG to BK stage. The positional distribution and enrichment of TF binding sites were analyzed over the promoter region of the phyB1B2 DEGs, exposing an overrepresentation of binding sites for RIN as well as the PHY-downstream effectors PIFs and HY5/HYH. Moreover, phyA and phyB1B2 mutants showed a positive correlation between the methylation level of sRNA cluster-targeted genome regions in gene bodies and mRNA levels. The experimental evidence indicates that PHYB1B2 signal transduction is mediated by a gene expression network involving chromatin organization factors (DNA methylases/demethylases, histone-modifying enzymes, and remodeling factors) and transcriptional regulators leading to altered mRNA profile of ripening-associated genes. This new level of understanding provides insights into the orchestration of epigenetic mechanisms in response to environmental cues affecting agronomical traits.
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Affiliation(s)
- Ricardo Bianchetti
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Nicolas Bellora
- Institute of Nuclear Technologies for Health (Intecnus), National Scientific and Technical Research Council (CONICET), Bariloche, Argentina
| | - Luis A. de Haro
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Rafael Zuccarelli
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Daniele Rosado
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Luisa Bermudez
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, INTA-CONICET, Castelar, Argentina
- Cátedra de Genética, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
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5
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Lu D, Zhai J, Xi M. Regulation of DNA Methylation During Plant Endosperm Development. Front Genet 2022; 13:760690. [PMID: 35222527 PMCID: PMC8867698 DOI: 10.3389/fgene.2022.760690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/17/2022] [Indexed: 11/21/2022] Open
Abstract
The endosperm is a vital storage tissue in plant seeds. It provides nutrients to the embryos or the seedlings during seed development and germination. Although the genetic information in the endosperm cannot be passed directly to the next generation, its inherited epigenetic marks affect gene expression and its development and, consequently, embryo and seed growth. DNA methylation is a major form of epigenetic modification that can be investigated to understand the epigenome changes during reproductive development. Therefore, it is of great significance to explore the effects of endosperm DNA methylation on crop yield and traits. In this review, we discuss the changes in DNA methylation and the resulting imprinted gene expression levels during plant endosperm development, as well as their effects on seed development.
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Affiliation(s)
- Dongdong Lu
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
| | - Jixian Zhai
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
- Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology, Shenzhen, China
- *Correspondence: Jixian Zhai, ; Mengli Xi,
| | - Mengli Xi
- Key Laboratory of Forest Genetics and Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, China
- *Correspondence: Jixian Zhai, ; Mengli Xi,
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6
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Ding X, Jia X, Xiang Y, Jiang W. Histone Modification and Chromatin Remodeling During the Seed Life Cycle. FRONTIERS IN PLANT SCIENCE 2022; 13:865361. [PMID: 35548305 PMCID: PMC9083068 DOI: 10.3389/fpls.2022.865361] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/21/2022] [Indexed: 05/16/2023]
Abstract
Seeds are essential for the reproduction and dispersion of spermatophytes. The seed life cycle from seed development to seedling establishment proceeds through a series of defined stages regulated by distinctive physiological and biochemical mechanisms. The role of histone modification and chromatin remodeling in seed behavior has been intensively studied in recent years. In this review, we summarize progress in elucidating the regulatory network of these two kinds of epigenetic regulation during the seed life cycle, especially in two model plants, rice and Arabidopsis. Particular emphasis is placed on epigenetic effects on primary tissue formation (e.g., the organized development of embryo and endosperm), pivotal downstream gene expression (e.g., transcription of DOG1 in seed dormancy and repression of seed maturation genes in seed-to-seedling transition), and environmental responses (e.g., seed germination in response to different environmental cues). Future prospects for understanding of intricate interplay of epigenetic pathways and the epigenetic mechanisms in other commercial species are also proposed.
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Affiliation(s)
- Xiali Ding
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Xuhui Jia
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Yong Xiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
| | - Wenhui Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, China
- *Correspondence: Wenhui Jiang,
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7
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Garewal N, Goyal N, Pathania S, Kaur J, Singh K. Gauging the trends of pseudogenes in plants. Crit Rev Biotechnol 2021; 41:1114-1129. [PMID: 33993808 DOI: 10.1080/07388551.2021.1901648] [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: 12/21/2022]
Abstract
Pseudogenes, the debilitated parts of ancient genes, were previously scrapped off as junk or discarded genes with no functional significance. Pseudogenes have come under scrutiny for their functionality, since recent studies have unveiled their importance in the regulation of their corresponding parent genes and various biological mechanisms. Despite the enormous occurrence of pseudogenes in plants, the lack of experimental validation has contributed toward their unresolved roles in gene regulation. Contrarily, most of the studies associated with gene regulation have been mainly reported for humans, mice, and other mammalian genomes. Consequently, in order to present a cumulative report on plant-based pseudogenes research, an attempt has been made to assemble multiple studies presenting the pseudogene classification, the prediction and the determination of comparative accuracies of various computational pipelines, and recent trends in analyzing their biological functions, and regulatory mechanisms. This review represents the classical, as well as the recent advances on pseudogene identification and their potential roles in transcriptional regulation, which could possibly invigorate the quality of genome annotation, evolutionary analysis, and complexity surrounding the regulatory pathways in plants. Thus, when the ambiguous boundary girdling the pseudogenes eventually recedes on account of their explicit orchestration role, research in flora would no longer saunter compared to that on fauna.
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Affiliation(s)
- Naina Garewal
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Neetu Goyal
- Department of Biotechnology, Panjab University, Chandigarh, India
| | | | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Kashmir Singh
- Department of Biotechnology, Panjab University, Chandigarh, India
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Luján-Soto E, Dinkova TD. Time to Wake Up: Epigenetic and Small-RNA-Mediated Regulation during Seed Germination. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10020236. [PMID: 33530470 PMCID: PMC7911344 DOI: 10.3390/plants10020236] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 05/03/2023]
Abstract
Plants make decisions throughout their lifetime based on complex networks. Phase transitions during seed growth are not an exception. From embryo development through seedling growth, several molecular pathways control genome stability, environmental signal transduction and the transcriptional landscape. Particularly, epigenetic modifications and small non-coding RNAs (sRNAs) have been extensively studied as significant handlers of these processes in plants. Here, we review key epigenetic (histone modifications and methylation patterns) and sRNA-mediated regulatory networks involved in the progression from seed maturation to germination, their relationship with seed traits and crosstalk with environmental inputs.
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Genome-Wide Differential DNA Methylation and miRNA Expression Profiling Reveals Epigenetic Regulatory Mechanisms Underlying Nitrogen-Limitation-Triggered Adaptation and Use Efficiency Enhancement in Allotetraploid Rapeseed. Int J Mol Sci 2020; 21:ijms21228453. [PMID: 33182819 PMCID: PMC7697602 DOI: 10.3390/ijms21228453] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/05/2020] [Accepted: 11/08/2020] [Indexed: 12/15/2022] Open
Abstract
Improving crop nitrogen (N) limitation adaptation (NLA) is a core approach to enhance N use efficiency (NUE) and reduce N fertilizer application. Rapeseed has a high demand for N nutrients for optimal plant growth and seed production, but it exhibits low NUE. Epigenetic modification, such as DNA methylation and modification from small RNAs, is key to plant adaptive responses to various stresses. However, epigenetic regulatory mechanisms underlying NLA and NUE remain elusive in allotetraploid B. napus. In this study, we identified overaccumulated carbohydrate, and improved primary and lateral roots in rapeseed plants under N limitation, which resulted in decreased plant nitrate concentrations, enhanced root-to-shoot N translocation, and increased NUE. Transcriptomics and RT-qPCR assays revealed that N limitation induced the expression of NRT1.1, NRT1.5, NRT1.7, NRT2.1/NAR2.1, and Gln1;1, and repressed the transcriptional levels of CLCa, NRT1.8, and NIA1. High-resolution whole genome bisulfite sequencing characterized 5094 differentially methylated genes involving ubiquitin-mediated proteolysis, N recycling, and phytohormone metabolism under N limitation. Hypermethylation/hypomethylation in promoter regions or gene bodies of some key N-metabolism genes might be involved in their transcriptional regulation by N limitation. Genome-wide miRNA sequencing identified 224 N limitation-responsive differentially expressed miRNAs regulating leaf development, amino acid metabolism, and plant hormone signal transduction. Furthermore, degradome sequencing and RT-qPCR assays revealed the miR827-NLA pathway regulating limited N-induced leaf senescence as well as the miR171-SCL6 and miR160-ARF17 pathways regulating root growth under N deficiency. Our study provides a comprehensive insight into the epigenetic regulatory mechanisms underlying rapeseed NLA, and it will be helpful for genetic engineering of NUE in crop species through epigenetic modification of some N metabolism-associated genes.
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Chu S, Zhang X, Yu K, Lv L, Sun C, Liu X, Zhang J, Jiao Y, Zhang D. Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress. Int J Mol Sci 2020; 21:E6817. [PMID: 32957498 PMCID: PMC7555642 DOI: 10.3390/ijms21186817] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/12/2020] [Accepted: 09/15/2020] [Indexed: 01/23/2023] Open
Abstract
Low-phosphorus (low-P) stress has a significant limiting effect on crop yield and quality. Although the molecular mechanisms of the transcriptional level responsible for the low-P stress response have been studied in detail, the underlying epigenetic mechanisms in gene regulation remain largely unknown. In this study, we evaluated the changes in DNA methylation, gene expression and small interfering RNAs (siRNAs) abundance genome-wide in response to low-P stress in two representative soybean genotypes with different P-efficiencies. The DNA methylation levels were slightly higher under low-P stress in both genotypes. Integrative methylation and transcription analysis suggested a complex regulatory relationship between DNA methylation and gene expression that may be associated with the type, region, and extent of methylation. Association analysis of low-P-induced differential methylation and gene expression showed that transcriptional alterations of a small part of genes were associated with methylation changes. Dynamic methylation alterations in transposable element (TE) regions in the CHH methylation context correspond with changes in the amount of siRNA under low-P conditions, indicating an important role of siRNAs in modulating TE activity by guiding CHH methylation in TE regions. Together, these results could help to elucidate the epigenetic regulation mechanisms governing the responses of plants to abiotic stresses.
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Affiliation(s)
- Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Xiangqian Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Kaiye Yu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Lingling Lv
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Chongyuan Sun
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Xiaoqian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Jinyu Zhang
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang 453003, China;
| | - Yongqing Jiao
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (S.C.); (X.Z.); (K.Y.); (L.L.); (C.S.); (X.L.); (Y.J.)
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11
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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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12
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Liu R, Lang Z. The mechanism and function of active DNA demethylation in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:148-159. [PMID: 31628716 DOI: 10.1111/jipb.12879] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/16/2019] [Indexed: 05/26/2023]
Abstract
DNA methylation is a conserved and important epigenetic mark in both mammals and plants. DNA methylation can be dynamically established, maintained, and removed through different pathways. In plants, active DNA demethylation is initiated by the RELEASE OF SILENCING 1 (ROS1) family of bifunctional DNA glycosylases/lyases. Accumulating evidence suggests that DNA demethylation is important in many processes in plants. In this review, we summarize recent studies on the enzymes and regulatory factors that have been identified in the DNA demethylation pathway. We also review the functions of active DNA demethylation in plant development as well as biotic and abiotic stress responses. Finally, we highlight those aspects of DNA demethylation that require additional research.
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Affiliation(s)
- Ruie Liu
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 200032, China
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14
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Junaid A, Kumar H, Rao AR, Patil AN, Singh NK, Gaikwad K. Unravelling the epigenomic interactions between parental inbreds resulting in an altered hybrid methylome in pigeonpea. DNA Res 2018; 25:361-373. [PMID: 29566130 PMCID: PMC6105106 DOI: 10.1093/dnares/dsy008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/21/2018] [Indexed: 12/15/2022] Open
Abstract
DNA methylation is an important heritable landmark conferring epigenetic changes in hybrids and has fascinated biologists and plant-breeders over the years. Although epigenetic changes have been documented in rice and maize hybrids, such investigations have not been reported in pigeonpea. Here, we report genome-wide methylation profiles of pigeonpea sterile and fertile inbred lines and their fertile F1 hybrid at single base resolution. We found that pigeonpea genome is relatively enriched in CG methylation. Identification of differentially methylated regions (DMRs) in the sterile and fertile parent revealed remarkable differences between their methylation patterns. Investigation of methylation status of parental DMRs in hybrid revealed non-additive methylation patterns resulting from trans-chromosomal methylation and trans-chromosomal demethylation events. Furthermore, we discovered several DMRs negatively associated with gene expression in the hybrid and fertile parent. Interestingly, many of those DMRs belonged to transposable elements and genes encoding pentatricopeptide repeats associated proteins, which may mediate a role in modulating the genes impacting pollen fertility. Overall, our findings provide an understanding of two parental epigenomes interacting to give rise to an altered methylome in pigeonpea hybrids, from genome-wide point of view.
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Affiliation(s)
- Alim Junaid
- National Research Centre on Plant Biotechnology, LBS Centre, PUSA Campus, New Delhi, India
| | - Himanshu Kumar
- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - A R Rao
- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - A N Patil
- Pulse Reaserch Unit, Dr. Panjabrao Deshmukh Krishi Vidyapeeth, P.O. Krishi Nagar, Akola, Maharashtra, India
| | - N K Singh
- National Research Centre on Plant Biotechnology, LBS Centre, PUSA Campus, New Delhi, India
| | - Kishor Gaikwad
- National Research Centre on Plant Biotechnology, LBS Centre, PUSA Campus, New Delhi, India
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15
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Yaish MW, Al-Lawati A, Al-Harrasi I, Patankar HV. Genome-wide DNA Methylation analysis in response to salinity in the model plant caliph medic (Medicago truncatula). BMC Genomics 2018; 19:78. [PMID: 29361906 PMCID: PMC5781308 DOI: 10.1186/s12864-018-4484-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 01/16/2018] [Indexed: 11/10/2022] Open
Abstract
Background DNA methylation has a potential role in controlling gene expression and may, therefore, contribute to salinity adaptation in plants. Caliph medic (Medicago truncatula) is a model legume of moderate salinity tolerance capacity; however, a base-resolution DNA methylome map is not yet available for this plant. Results In this report, a differential whole-genome bisulfite sequencing (WGBS) was carried out using DNA samples extracted from root tissues exposed to either control or saline conditions. Around 50 million differentially methylated sites (DMSs) were recognized, 7% of which were significantly (p < 0.05, FDR < 0.05) altered in response to salinity. This analysis showed that 77.0% of the contexts of DMSs were mCHH, while only 9.1% and 13.9% were mCHG and mCG, respectively. The average change in methylation level was increased in all sequence contexts, ranging from 3.8 to 10.2% due to salinity stress. However, collectively, the level of the DNA methylation in the gene body slightly decreased in response to salinity treatment. The global increase in DNA methylation due to salinity was confirmed by mass spectrometry analysis. Gene expression analysis using qPCR did not reveal a constant relationship between the level of mCG methylation and the transcription abundance of some genes of potential importance in salinity tolerance, such as the potassium channel KAT3, the vacuolar H+-pyrophosphatase (V-PPase), and the AP2/ERF and bZIP transcription factors, implying the involvement of other epigenetic gene expression controllers. Computational functional prediction of the annotated genes that embrace DMSs revealed the presence of enzymes with potential cellular functions in biological processes associated with salinity tolerance mechanisms. Conclusions The information obtained from this study illustrates the effect of salinity on DNA methylation and shows how plants can remodel the landscape of 5-methylcytosine nucleotide (5-mC) in the DNA across gene structures, in response to salinity. This remodeling varies between gene regions and between 5-mC sequence contexts. The mCG has a vague impact on the expression levels of a few selected potentially important genes in salt tolerant mechanisms. Electronic supplementary material The online version of this article (10.1186/s12864-018-4484-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mahmoud W Yaish
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman.
| | - Abbas Al-Lawati
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Ibtisam Al-Harrasi
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
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Al-Harrasi I, Al-Yahyai R, Yaish MW. Differential DNA methylation and transcription profiles in date palm roots exposed to salinity. PLoS One 2018; 13:e0191492. [PMID: 29352281 PMCID: PMC5774813 DOI: 10.1371/journal.pone.0191492] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 01/05/2018] [Indexed: 12/31/2022] Open
Abstract
As a salt-adaptive plant, the date palm (Phoenix dactylifera L.) requires a suitable mechanism to adapt to the stress of saline soils. There is growing evidence that DNA methylation plays an important role in regulating gene expression in response to abiotic stresses, including salinity. Thus, the present study sought to examine the differential methylation status that occurs in the date palm genome when plants are exposed to salinity, and to identify salinity responsive genes that are regulated by DNA methylation. To achieve these, whole-genome bisulfite sequencing (WGBS) was employed and mRNA was sequenced from salinity-treated and untreated roots. The WGBS analysis included 324,987,795 and 317,056,091 total reads of the control and the salinity-treated samples, respectively. The analysis covered about 81% of the total genomic DNA with about 40% of mapping efficiency of the sequenced reads and an average read depth of 17-fold coverage per DNA strand, and with a bisulfite conversion rate of around 99%. The level of methylation within the differentially methylated regions (DMRs) was significantly (p < 0.05, FDR ≤ 0.05) increased in response to salinity specifically at the mCHG and mCHH sequence contexts. Consistently, the mass spectrometry and the enzyme-linked immunosorbent assay (ELISA) showed that there was a significant (p < 0.05) increase in the global DNA methylation in response to salinity. mRNA sequencing revealed the presence of 6,405 differentially regulated genes with a significant value (p < 0.001, FDR ≤ 0.05) in response to salinity. Integration of high-resolution methylome and transcriptome analyses revealed a negative correlation between mCG methylation located within the promoters and the gene expression, while a positive correlation was noticed between mCHG/mCHH methylation rations and gene expression specifically when plants grew under control conditions. Therefore, the methylome and transcriptome relationships vary based on the methylated sequence context, the methylated region within the gene, the protein-coding ability of the gene, and the salinity treatment. These results provide insights into interplay among DNA methylation and gene expression, and highlight the effect of salinity on the nature of this relationship, which may involve other genetic and epigenetic players under salt stress conditions. The results obtained from this project provide the first draft map of the differential methylome and transcriptome of date palm when exposed to an abiotic stress.
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MESH Headings
- Adaptation, Physiological/genetics
- DNA Methylation
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Epigenesis, Genetic
- Gene Expression Profiling
- Genes, Plant
- Molecular Sequence Annotation
- Phoeniceae/genetics
- Phoeniceae/growth & development
- Phoeniceae/metabolism
- Photosynthesis
- Plant Roots/genetics
- Plant Roots/growth & development
- Plant Roots/metabolism
- Promoter Regions, Genetic
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Salinity
- Whole Genome Sequencing
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Affiliation(s)
- Ibtisam Al-Harrasi
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
| | - Rashid Al-Yahyai
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Mahmoud W. Yaish
- Department of Biology, College of Science, Sultan Qaboos University, Muscat, Oman
- * E-mail:
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Banerjee A, Roychoudhury A. The gymnastics of epigenomics in rice. PLANT CELL REPORTS 2018; 37:25-49. [PMID: 28866772 DOI: 10.1007/s00299-017-2192-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/01/2017] [Indexed: 05/21/2023]
Abstract
Epigenomics is represented by the high-throughput investigations of genome-wide epigenetic alterations, which ultimately dictate genomic, transcriptomic, proteomic and metabolomic dynamism. Rice has been accepted as the global staple crop. As a result, this model crop deserves significant importance in the rapidly emerging field of plant epigenomics. A large number of recently available data reveal the immense flexibility and potential of variable epigenomic landscapes. Such epigenomic impacts and variability are determined by a number of epigenetic regulators and several crucial inheritable epialleles, respectively. This article highlights the correlation of the epigenomic landscape with growth, flowering, reproduction, non-coding RNA-mediated post-transcriptional regulation, transposon mobility and even heterosis in rice. We have also discussed the drastic epigenetic alterations which are reported in rice plants grown from seeds exposed to the extraterrestrial environment. Such abiotic conditions impose stress on the plants leading to epigenomic modifications in a genotype-specific manner. Some significant bioinformatic databases and in silico approaches have also been explained in this article. These softwares provide important interfaces for comparative epigenomics. The discussion concludes with a unified goal of developing epigenome editing to promote biological hacking of the rice epigenome. Such a cutting-edge technology if properly standardized, can integrate genomics and epigenomics together with the generation of high-yielding trait in several cultivars of rice.
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Affiliation(s)
- Aditya Banerjee
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, West Bengal, India
| | - Aryadeep Roychoudhury
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700016, West Bengal, India.
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18
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Yan H, Bombarely A, Xu B, Frazier TP, Wang C, Chen P, Chen J, Hasing T, Cui C, Zhang X, Zhao B, Huang L. siRNAs regulate DNA methylation and interfere with gene and lncRNA expression in the heterozygous polyploid switchgrass. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:208. [PMID: 30061930 PMCID: PMC6058383 DOI: 10.1186/s13068-018-1202-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/10/2018] [Indexed: 05/14/2023]
Abstract
BACKGROUND Understanding the DNA methylome and its relationship with non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), is essential for elucidating the molecular mechanisms underlying key biological processes in plants. Few studies have examined the functional roles of the DNA methylome in grass species with highly heterozygous polyploid genomes. RESULTS We performed genome-wide DNA methylation profiling in the tetraploid switchgrass (Panicum virgatum L.) cultivar 'Alamo' using bisulfite sequencing. Single-base-resolution methylation patterns were observed in switchgrass leaf and root tissues, which allowed for characterization of the relationship between DNA methylation and mRNA, miRNA, and lncRNA populations. The results of this study revealed that siRNAs positively regulate DNA methylation of the mCHH sites surrounding genes, and that DNA methylation interferes with gene and lncRNA expression in switchgrass. Ninety-six genes covered by differentially methylated regions (DMRs) were annotated by GO analysis as being involved in stimulus-related processes. Functionally, 82% (79/96) of these genes were found to be hypomethylated in switchgrass root tissue. Sequencing analysis of lncRNAs identified two lncRNAs that are potential precursors of miRNAs, which are predicted to target genes that function in cellulose biosynthesis, stress regulation, and stem and root development. CONCLUSIONS This study characterized the DNA methylome in switchgrass and elucidated its relevance to gene and non-coding RNAs. These results provide valuable genomic resources and references that will aid further epigenetic research in this important biofuel crop.
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Affiliation(s)
- Haidong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | | | - Bin Xu
- College of Grassland Science, Nanjing Agricultural University, Nanjing, 210095 China
| | - Taylor P. Frazier
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Chengran Wang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Peilin Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jing Chen
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Tomas Hasing
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | - Chenming Cui
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA 24061 USA
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Bingyu Zhao
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
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Doll NM, Depège-Fargeix N, Rogowsky PM, Widiez T. Signaling in Early Maize Kernel Development. MOLECULAR PLANT 2017; 10:375-388. [PMID: 28267956 DOI: 10.1016/j.molp.2017.01.008] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 01/18/2017] [Accepted: 01/19/2017] [Indexed: 05/26/2023]
Abstract
Developing the next plant generation within the seed requires the coordination of complex programs driving pattern formation, growth, and differentiation of the three main seed compartments: the embryo (future plant), the endosperm (storage compartment), representing the two filial tissues, and the surrounding maternal tissues. This review focuses on the signaling pathways and molecular players involved in early maize kernel development. In the 2 weeks following pollination, functional tissues are shaped from single cells, readying the kernel for filling with storage compounds. Although the overall picture of the signaling pathways regulating embryo and endosperm development remains fragmentary, several types of molecular actors, such as hormones, sugars, or peptides, have been shown to be involved in particular aspects of these developmental processes. These molecular actors are likely to be components of signaling pathways that lead to transcriptional programming mediated by transcriptional factors. Through the integrated action of these components, multiple types of information received by cells or tissues lead to the correct differentiation and patterning of kernel compartments. In this review, recent advances regarding the four types of molecular actors (hormones, sugars, peptides/receptors, and transcription factors) involved in early maize development are presented.
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Affiliation(s)
- Nicolas M Doll
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Nathalie Depège-Fargeix
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Peter M Rogowsky
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France
| | - Thomas Widiez
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France.
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Epigenetic Control of Gene Expression in Maize. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 328:25-48. [DOI: 10.1016/bs.ircmb.2016.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Yong WS, Hsu FM, Chen PY. Profiling genome-wide DNA methylation. Epigenetics Chromatin 2016; 9:26. [PMID: 27358654 PMCID: PMC4926291 DOI: 10.1186/s13072-016-0075-3] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 06/17/2016] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is an epigenetic modification that plays an important role in regulating gene expression and therefore a broad range of biological processes and diseases. DNA methylation is tissue-specific, dynamic, sequence-context-dependent and trans-generationally heritable, and these complex patterns of methylation highlight the significance of profiling DNA methylation to answer biological questions. In this review, we surveyed major methylation assays, along with comparisons and biological examples, to provide an overview of DNA methylation profiling techniques. The advances in microarray and sequencing technologies make genome-wide profiling possible at a single-nucleotide or even a single-cell resolution. These profiling approaches vary in many aspects, such as DNA input, resolution, genomic region coverage, and bioinformatics analysis, and selecting a feasible method requires knowledge of these methods. We first introduce the biological background of DNA methylation and its pattern in plants, animals and fungi. We present an overview of major experimental approaches to profiling genome-wide DNA methylation and hydroxymethylation and then extend to the single-cell methylome. To evaluate these methods, we outline their strengths and weaknesses and perform comparisons across the different platforms. Due to the increasing need to compute high-throughput epigenomic data, we interrogate the computational pipeline for bisulfite sequencing data and also discuss the concept of identifying differentially methylated regions (DMRs). This review summarizes the experimental and computational concepts for profiling genome-wide DNA methylation, followed by biological examples. Overall, this review provides researchers useful guidance for the selection of a profiling method suited to specific research questions.
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Affiliation(s)
- Wai-Shin Yong
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan, ROC
| | - Fei-Man Hsu
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561 Japan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529 Taiwan, ROC
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22
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Xu W, Yang T, Dong X, Li DZ, Liu A. Genomic DNA Methylation Analyses Reveal the Distinct Profiles in Castor Bean Seeds with Persistent Endosperms. PLANT PHYSIOLOGY 2016; 171:1242-58. [PMID: 27208275 PMCID: PMC4902593 DOI: 10.1104/pp.16.00056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/27/2016] [Indexed: 05/21/2023]
Abstract
Investigations of genomic DNA methylation in seeds have been restricted to a few model plants. The endosperm genomic DNA hypomethylation has been identified in angiosperm, but it is difficult to dissect the mechanism of how this hypomethylation is established and maintained because endosperm is ephemeral and disappears with seed development in most dicots. Castor bean (Ricinus communis), unlike Arabidopsis (Arabidopsis thaliana), endosperm is persistent throughout seed development, providing an excellent model in which to dissect the mechanism of endosperm genomic hypomethylation in dicots. We characterized the DNA methylation-related genes encoding DNA methyltransferases and demethylases and analyzed their expression profiles in different tissues. We examined genomic methylation including CG, CHG, and CHH contexts in endosperm and embryo tissues using bisulfite sequencing and revealed that the CHH methylation extent in endosperm and embryo was, unexpectedly, substantially higher than in previously studied plants, irrespective of the CHH percentage in their genomes. In particular, we found that the endosperm exhibited a global reduction in CG and CHG methylation extents relative to the embryo, markedly switching global gene expression. However, CHH methylation occurring in endosperm did not exhibit a significant reduction. Combining with the expression of 24-nucleotide small interfering RNAs (siRNAs) mapped within transposable element (TE) regions and genes involved in the RNA-directed DNA methylation pathway, we demonstrate that the 24-nucleotide siRNAs played a critical role in maintaining CHH methylation and repressing the activation of TEs in persistent endosperm development. This study discovered a novel genomic DNA methylation pattern and proposes the potential mechanism occurring in dicot seeds with persistent endosperm.
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Affiliation(s)
- Wei Xu
- Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources (W.X., X.D., A.L.), the Germplasm Bank of Wild Species (D.-Z.L.), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China;University of the Chinese Academy of Sciences, Beijing 100049, China (W.X., T.Y.);College of Life Sciences, Yunnan University, 650091 Kunming, China (W.X.); andKey Laboratory of Tropical Plant Resource Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China (T.Y.)
| | - Tianquan Yang
- Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources (W.X., X.D., A.L.), the Germplasm Bank of Wild Species (D.-Z.L.), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China;University of the Chinese Academy of Sciences, Beijing 100049, China (W.X., T.Y.);College of Life Sciences, Yunnan University, 650091 Kunming, China (W.X.); andKey Laboratory of Tropical Plant Resource Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China (T.Y.)
| | - Xue Dong
- Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources (W.X., X.D., A.L.), the Germplasm Bank of Wild Species (D.-Z.L.), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China;University of the Chinese Academy of Sciences, Beijing 100049, China (W.X., T.Y.);College of Life Sciences, Yunnan University, 650091 Kunming, China (W.X.); andKey Laboratory of Tropical Plant Resource Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China (T.Y.)
| | - De-Zhu Li
- Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources (W.X., X.D., A.L.), the Germplasm Bank of Wild Species (D.-Z.L.), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China;University of the Chinese Academy of Sciences, Beijing 100049, China (W.X., T.Y.);College of Life Sciences, Yunnan University, 650091 Kunming, China (W.X.); andKey Laboratory of Tropical Plant Resource Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China (T.Y.)
| | - Aizhong Liu
- Department of Economic Plants and Biotechnology, and Yunnan Key Laboratory for Wild Plant Resources (W.X., X.D., A.L.), the Germplasm Bank of Wild Species (D.-Z.L.), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China;University of the Chinese Academy of Sciences, Beijing 100049, China (W.X., T.Y.);College of Life Sciences, Yunnan University, 650091 Kunming, China (W.X.); andKey Laboratory of Tropical Plant Resource Science, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650223, China (T.Y.)
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