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Fernandez‐Pozo N, Metz T, Chandler JO, Gramzow L, Mérai Z, Maumus F, Mittelsten Scheid O, Theißen G, Schranz ME, Leubner‐Metzger G, Rensing SA. Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:275-293. [PMID: 33453123 PMCID: PMC8641386 DOI: 10.1111/tpj.15161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/31/2020] [Accepted: 01/08/2021] [Indexed: 05/06/2023]
Abstract
Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA-seq libraries and 136 307 full-length PacBio Iso-seq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At-α polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS-box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of full-length transcripts related to ABA-mediated seed dormancy discovered a conserved isoform of PIF6-β and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni-marburg.de/aetar_db).
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Affiliation(s)
- Noe Fernandez‐Pozo
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
| | - Timo Metz
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
| | - Jake O. Chandler
- School of Biological SciencesRoyal Holloway University of LondonEghamSurreyUK
| | - Lydia Gramzow
- Matthias Schleiden Institute/GeneticsFriedrich Schiller University JenaJenaGermany
| | - Zsuzsanna Mérai
- Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | | | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
| | - Günter Theißen
- Matthias Schleiden Institute/GeneticsFriedrich Schiller University JenaJenaGermany
| | - M. Eric Schranz
- Biosystematics GroupWageningen UniversityWageningenThe Netherlands
| | - Gerhard Leubner‐Metzger
- School of Biological SciencesRoyal Holloway University of LondonEghamSurreyUK
- Laboratory of Growth RegulatorsCentre of the Region Haná for Biotechnological and Agricultural ResearchPalacký University and Institute of Experimental BotanyAcademy of Sciences of the Czech RepublicOlomoucCzech Republic
| | - Stefan A. Rensing
- Plant Cell BiologyDepartment of BiologyUniversity of MarburgMarburgGermany
- BIOSS Centre for Biological Signaling StudiesUniversity of FreiburgFreiburgGermany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO)University of MarburgMarburgGermany
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Regulation of DNA (de)Methylation Positively Impacts Seed Germination during Seed Development under Heat Stress. Genes (Basel) 2021; 12:genes12030457. [PMID: 33807066 PMCID: PMC8005211 DOI: 10.3390/genes12030457] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 12/15/2022] Open
Abstract
Seed development needs the coordination of multiple molecular mechanisms to promote correct tissue development, seed filling, and the acquisition of germination capacity, desiccation tolerance, longevity, and dormancy. Heat stress can negatively impact these processes and upon the increase of global mean temperatures, global food security is threatened. Here, we explored the impact of heat stress on seed physiology, morphology, gene expression, and methylation on three stages of seed development. Notably, Arabidopsis Col-0 plants under heat stress presented a decrease in germination capacity as well as a decrease in longevity. We observed that upon mild stress, gene expression and DNA methylation were moderately affected. Nevertheless, upon severe heat stress during seed development, gene expression was intensively modified, promoting heat stress response mechanisms including the activation of the ABA pathway. By analyzing candidate epigenetic markers using the mutants’ physiological assays, we observed that the lack of DNA demethylation by the ROS1 gene impaired seed germination by affecting germination-related gene expression. On the other hand, we also observed that upon severe stress, a large proportion of differentially methylated regions (DMRs) were located in the promoters and gene sequences of germination-related genes. To conclude, our results indicate that DNA (de)methylation could be a key regulatory process to ensure proper seed germination of seeds produced under heat stress.
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53
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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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Hu G, Huang B, Wang K, Frasse P, Maza E, Djari A, Benhamed M, Gallusci P, Li Z, Zouine M, Bouzayen M. Histone posttranslational modifications rather than DNA methylation underlie gene reprogramming in pollination-dependent and pollination-independent fruit set in tomato. THE NEW PHYTOLOGIST 2021; 229:902-919. [PMID: 32875585 PMCID: PMC7821339 DOI: 10.1111/nph.16902] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/10/2020] [Indexed: 05/10/2023]
Abstract
Fruit formation comprises a series of developmental transitions among which the fruit set process is essential in determining crop yield. Yet, our understanding of the epigenetic landscape remodelling associated with the flower-to-fruit transition remains poor. We investigated the epigenetic and transcriptomic reprogramming underlying pollination-dependent and auxin-induced flower-to-fruit transitions in the tomato (Solanum lycopersicum) using combined genomewide transcriptomic profiling, global ChIP-sequencing and whole genomic DNA bisulfite sequencing (WGBS). Variation in the expression of the overwhelming majority of genes was associated with change in histone mark distribution, whereas changes in DNA methylation concerned a minor fraction of differentially expressed genes. Reprogramming of genes involved in processes instrumental to fruit set correlated with their H3K9ac or H3K4me3 marking status but not with changes in cytosine methylation, indicating that histone posttranslational modifications rather than DNA methylation are associated with the remodelling of the epigenetic landscape underpinning the flower-to-fruit transition. Given the prominent role previously assigned to DNA methylation in reprogramming key genes of the transition to ripening, the outcome of the present study supports the idea that the two main developmental transitions in fleshy fruit and the underlying transcriptomic reprogramming are associated with different modes of epigenetic regulations.
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Affiliation(s)
- Guojian Hu
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Baowen Huang
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Keke Wang
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Pierre Frasse
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Elie Maza
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Anis Djari
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris‐SaclayCNRSINRAUniversity Paris‐SudUniversity of EvryUniversity Paris‐DiderotSorbonne Paris‐CiteUniversity of Paris‐SaclayBatiment 630Orsay91405France
| | - Philippe Gallusci
- UMR EGFVBordeaux Sciences AgroINRAUniversité de Bordeaux210 Chemin de Leysotte, CS 50008Villenave d’Ornon33882France
| | - Zhengguo Li
- Center of Plant Functional GenomicsInstitute of Advanced Interdisciplinary StudiesChongqing UniversityChongqing401331China
| | - Mohamed Zouine
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
| | - Mondher Bouzayen
- UMR990 Génomique et Biotechnologie des FruitsINRAe/INP ToulouseUniversité de ToulouseAvenue de l’AgrobiopoleCastanet‐TolosanCS32607, F‐31326France
- Center of Plant Functional GenomicsInstitute of Advanced Interdisciplinary StudiesChongqing UniversityChongqing401331China
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Borges F, Donoghue MTA, LeBlanc C, Wear EE, Tanurdžić M, Berube B, Brooks A, Thompson WF, Hanley-Bowdoin L, Martienssen RA. Loss of Small-RNA-Directed DNA Methylation in the Plant Cell Cycle Promotes Germline Reprogramming and Somaclonal Variation. Curr Biol 2020; 31:591-600.e4. [PMID: 33275892 DOI: 10.1016/j.cub.2020.10.098] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/24/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023]
Abstract
5-methyl cytosine is widespread in plant genomes in both CG and non-CG contexts. During replication, hemi-methylation on parental DNA strands guides symmetric CG methylation on nascent strands, but non-CG methylation requires modified histones and small RNA guides. Here, we used immortalized Arabidopsis cell suspensions to sort replicating nuclei and determine genome-wide cytosine methylation dynamics during the plant cell cycle. We find that symmetric mCG and mCHG are selectively retained in actively dividing cells in culture, whereas mCHH is depleted. mCG becomes transiently asymmetric during S phase but is rapidly restored in G2, whereas mCHG remains asymmetric throughout the cell cycle. Hundreds of loci gain ectopic CHG methylation, as well as 24-nt small interfering RNAs (siRNAs) and histone H3 lysine dimethylation (H3K9me2), without gaining CHH methylation. This suggests that spontaneous epialleles that arise in plant cell cultures are stably maintained by siRNA and H3K9me2 independent of the canonical RNA-directed DNA methylation (RdDM) pathway. In contrast, loci that fail to produce siRNA may be targeted for demethylation when the cell cycle arrests. Comparative analysis with methylomes of various tissues and cell types suggests that loss of small-RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones.
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Affiliation(s)
- Filipe Borges
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Mark T A Donoghue
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Emily E Wear
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Milos Tanurdžić
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Benjamin Berube
- Cold Spring Harbor Laboratory School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ashley Brooks
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - William F Thompson
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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Rymen B, Ferrafiat L, Blevins T. Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants. Transcription 2020; 11:172-191. [PMID: 33180661 PMCID: PMC7714444 DOI: 10.1080/21541264.2020.1825906] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multisubunit RNA polymerase (Pol) complexes are the core machinery for gene expression in eukaryotes. The enzymes Pol I, Pol II and Pol III transcribe distinct subsets of nuclear genes. This family of nuclear RNA polymerases expanded in terrestrial plants by the duplication of Pol II subunit genes. Two Pol II-related enzymes, Pol IV and Pol V, are highly specialized in the production of regulatory, non-coding RNAs. Pol IV and Pol V are the central players of RNA-directed DNA methylation (RdDM), an RNA interference pathway that represses transposable elements (TEs) and selected genes. Genetic and biochemical analyses of Pol IV/V subunits are now revealing how these enzymes evolved from ancestral Pol II to sustain non-coding RNA biogenesis in silent chromatin. Intriguingly, Pol IV-RdDM regulates genes that influence flowering time, reproductive development, stress responses and plant–pathogen interactions. Pol IV target genes vary among closely related taxa, indicating that these regulatory circuits are often species-specific. Data from crops like maize, rice, tomato and Brassicarapa suggest that dynamic repositioning of TEs, accompanied by Pol IV targeting to TE-proximal genes, leads to the reprogramming of plant gene expression over short evolutionary timescales.
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Affiliation(s)
- Bart Rymen
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
| | - Laura Ferrafiat
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
| | - Todd Blevins
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
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57
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Zhao X, Li C, Zhang H, Yan C, Sun Q, Wang J, Yuan C, Shan S. Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development. BMC PLANT BIOLOGY 2020; 20:488. [PMID: 33096983 PMCID: PMC7585205 DOI: 10.1186/s12870-020-02702-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/14/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, and the generation of pegs and formation of subterranean pods are essential processes in peanut reproductive development. However, little information has been reported about alternative splicing (AS) in peanut peg formation and development. RESULTS Herein, we presented a comprehensive full-length (FL) transcriptome profiling of AS isoforms during peanut peg and early pod development. We identified 1448, 1102, 832, and 902 specific spliced transcripts in aerial pegs, subterranean pegs, subterranean unswollen pegs, and early swelling pods, respectively. A total of 184 spliced transcripts related to gravity stimulation, light and mechanical response, hormone mediated signaling pathways, and calcium-dependent proteins were identified as possibly involved in peanut peg development. For aerial pegs, spliced transcripts we got were mainly involved in gravity stimulation and cell wall morphogenetic processes. The genes undergoing AS in subterranean peg were possibly involved in gravity stimulation, cell wall morphogenetic processes, and abiotic response. For subterranean unswollen pegs, spliced transcripts were predominantly related to the embryo development and root formation. The genes undergoing splice in early swelling pods were mainly related to ovule development, root hair cells enlargement, root apex division, and seed germination. CONCLUSION This study provides evidence that multiple genes are related to gravity stimulation, light and mechanical response, hormone mediated signaling pathways, and calcium-dependent proteins undergoing AS express development-specific spliced isoforms or exhibit an obvious isoform switch during the peanut peg development. AS isoforms in subterranean pegs and pods provides valuable sources to further understand post-transcriptional regulatory mechanisms of AS in the generation of pegs and formation of subterranean pods.
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Affiliation(s)
- Xiaobo Zhao
- Shandong Peanut Research Institute, Qingdao, China
| | - Chunjuan Li
- Shandong Peanut Research Institute, Qingdao, China
| | - Hao Zhang
- Shandong Peanut Research Institute, Qingdao, China
| | - Caixia Yan
- Shandong Peanut Research Institute, Qingdao, China
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao, China
| | - Juan Wang
- Shandong Peanut Research Institute, Qingdao, China
| | - Cuiling Yuan
- Shandong Peanut Research Institute, Qingdao, China
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao, China
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Conserved and Opposite Transcriptome Patterns during Germination in Hordeum vulgare and Arabidopsis thaliana. Int J Mol Sci 2020; 21:ijms21197404. [PMID: 33036486 PMCID: PMC7584043 DOI: 10.3390/ijms21197404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 11/16/2022] Open
Abstract
Seed germination is a critical process for completion of the plant life cycle and for global food production. Comparing the germination transcriptomes of barley (Hordeum vulgare) to Arabidopsis thaliana revealed the overall pattern was conserved in terms of functional gene ontology; however, many oppositely responsive orthologous genes were identified. Conserved processes included a set of approximately 6000 genes that peaked early in germination and were enriched in processes associated with RNA metabolism, e.g., pentatricopeptide repeat (PPR)-containing proteins. Comparison of orthologous genes revealed more than 3000 orthogroups containing almost 4000 genes that displayed similar expression patterns including functions associated with mitochondrial tricarboxylic acid (TCA) cycle, carbohydrate and RNA/DNA metabolism, autophagy, protein modifications, and organellar function. Biochemical and proteomic analyses indicated mitochondrial biogenesis occurred early in germination, but detailed analyses revealed the timing involved in mitochondrial biogenesis may vary between species. More than 1800 orthogroups representing 2000 genes displayed opposite patterns in transcript abundance, representing functions of energy (carbohydrate) metabolism, photosynthesis, protein synthesis and degradation, and gene regulation. Differences in expression of basic-leucine zippers (bZIPs) and Apetala 2 (AP2)/ethylene-responsive element binding proteins (EREBPs) point to differences in regulatory processes at a high level, which provide opportunities to modify processes in order to enhance grain quality, germination, and storage as needed for different uses.
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Hofmeister BT, Denkena J, Colomé-Tatché M, Shahryary Y, Hazarika R, Grimwood J, Mamidi S, Jenkins J, Grabowski PP, Sreedasyam A, Shu S, Barry K, Lail K, Adam C, Lipzen A, Sorek R, Kudrna D, Talag J, Wing R, Hall DW, Jacobsen D, Tuskan GA, Schmutz J, Johannes F, Schmitz RJ. A genome assembly and the somatic genetic and epigenetic mutation rate in a wild long-lived perennial Populus trichocarpa. Genome Biol 2020; 21:259. [PMID: 33023654 PMCID: PMC7539514 DOI: 10.1186/s13059-020-02162-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 09/02/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local adaption in an ecoevolutionary context, particularly in long-lived perennials. RESULTS Here, we generate a new high-quality reference genome from the oldest branch of a wild Populus trichocarpa tree with two dominant stems which have been evolving independently for 330 years. By sampling multiple, age-estimated branches of this tree, we use a multi-omics approach to quantify age-related somatic changes at the genetic, epigenetic, and transcriptional level. We show that the per-year somatic mutation and epimutation rates are lower than in annuals and that transcriptional variation is mainly independent of age divergence and cytosine methylation. Furthermore, a detailed analysis of the somatic epimutation spectrum indicates that transgenerationally heritable epimutations originate mainly from DNA methylation maintenance errors during mitotic rather than during meiotic cell divisions. CONCLUSION Taken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.
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Affiliation(s)
| | - Johanna Denkena
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - Maria Colomé-Tatché
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Yadollah Shahryary
- Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany
| | - Rashmi Hazarika
- Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany
- Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Sujan Mamidi
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Jerry Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | | | | | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Kathleen Lail
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Catherine Adam
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Anna Lipzen
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Rod Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - David W Hall
- Department of Genetics, University of Georgia, Athens, GA, USA
| | - Daniel Jacobsen
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Frank Johannes
- Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, Germany.
- Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany.
| | - Robert J Schmitz
- Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, Germany.
- Department of Genetics, University of Georgia, Athens, GA, USA.
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Grzybkowska D, Nowak K, Gaj MD. Hypermethylation of Auxin-Responsive Motifs in the Promoters of the Transcription Factor Genes Accompanies the Somatic Embryogenesis Induction in Arabidopsis. Int J Mol Sci 2020; 21:E6849. [PMID: 32961931 PMCID: PMC7555384 DOI: 10.3390/ijms21186849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 12/17/2022] Open
Abstract
The auxin-induced embryogenic reprogramming of plant somatic cells is associated with extensive modulation of the gene expression in which epigenetic modifications, including DNA methylation, seem to play a crucial role. However, the function of DNA methylation, including the role of auxin in epigenetic regulation of the SE-controlling genes, remains poorly understood. Hence, in the present study, we analysed the expression and methylation of the TF genes that play a critical regulatory role during SE induction (LEC1, LEC2, BBM, WUS and AGL15) in auxin-treated explants of Arabidopsis. The results showed that auxin treatment substantially affected both the expression and methylation patterns of the SE-involved TF genes in a concentration-dependent manner. The auxin treatment differentially modulated the methylation of the promoter (P) and gene body (GB) sequences of the SE-involved genes. Relevantly, the SE-effective auxin treatment (5.0 µM of 2,4-D) was associated with the stable hypermethylation of the P regions of the SE-involved genes and a significantly higher methylation of the P than the GB fragments was a characteristic feature of the embryogenic culture. The presence of auxin-responsive (AuxRE) motifs in the hypermethylated P regions suggests that auxin might substantially contribute to the DNA methylation-mediated control of the SE-involved genes.
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Affiliation(s)
| | | | - Małgorzata D. Gaj
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland; (D.G.); (K.N.)
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61
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Papareddy RK, Páldi K, Paulraj S, Kao P, Lutzmayer S, Nodine MD. Chromatin regulates expression of small RNAs to help maintain transposon methylome homeostasis in Arabidopsis. Genome Biol 2020; 21:251. [PMID: 32943088 PMCID: PMC7499886 DOI: 10.1186/s13059-020-02163-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Eukaryotic genomes are partitioned into euchromatic and heterochromatic domains to regulate gene expression and other fundamental cellular processes. However, chromatin is dynamic during growth and development and must be properly re-established after its decondensation. Small interfering RNAs (siRNAs) promote heterochromatin formation, but little is known about how chromatin regulates siRNA expression. RESULTS We demonstrate that thousands of transposable elements (TEs) produce exceptionally high levels of siRNAs in Arabidopsis thaliana embryos. TEs generate siRNAs throughout embryogenesis according to two distinct patterns depending on whether they are located in euchromatic or heterochromatic regions of the genome. siRNA precursors are transcribed in embryos, and siRNAs are required to direct the re-establishment of DNA methylation on TEs from which they are derived in the new generation. Decondensed chromatin also permits the production of 24-nt siRNAs from heterochromatic TEs during post-embryogenesis, and siRNA production from bipartite-classified TEs is controlled by their chromatin states. CONCLUSIONS Decondensation of heterochromatin in response to developmental, and perhaps environmental, cues promotes the transcription and function of siRNAs in plants. Our results indicate that chromatin-mediated siRNA transcription provides a cell-autonomous homeostatic control mechanism to help reconstitute pre-existing chromatin states during growth and development including those that ensure silencing of TEs in the future germ line.
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Affiliation(s)
- Ranjith K. Papareddy
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Katalin Páldi
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Subramanian Paulraj
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Ping Kao
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Stefan Lutzmayer
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael D. Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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62
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Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes. Proc Natl Acad Sci U S A 2020; 117:23991-24000. [PMID: 32879011 DOI: 10.1073/pnas.2010250117] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The genomic sequences of crops continue to be produced at a frenetic pace. It remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Chromatin accessibility assays enable discovery of functional elements; however, to uncover the full portfolio of cis-elements would require profiling of many combinations of cell types, tissues, developmental stages, and environments. Here, we explore the potential to use DNA methylation profiles to develop more complete annotations. Using leaf tissue in maize, we define ∼100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs are found greater than 2 kb from genes. UMRs are highly stable in multiple vegetative tissues, and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf, and these represent regions with potential to become accessible in specific cell types or developmental stages. These UMRs often occur near genes that are expressed in other tissues and are enriched for binding sites of transcription factors. The leaf-inaccessible UMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMR space in four additional monocots ranges from 80 to 120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures provide powerful filters to distill large genomes down to the small fraction of putative functional genes and regulatory elements.
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63
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Higo A, Saihara N, Miura F, Higashi Y, Yamada M, Tamaki S, Ito T, Tarutani Y, Sakamoto T, Fujiwara M, Kurata T, Fukao Y, Moritoh S, Terada R, Kinoshita T, Ito T, Kakutani T, Shimamoto K, Tsuji H. DNA methylation is reconfigured at the onset of reproduction in rice shoot apical meristem. Nat Commun 2020; 11:4079. [PMID: 32796936 PMCID: PMC7429860 DOI: 10.1038/s41467-020-17963-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 07/28/2020] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is an epigenetic modification that specifies the basic state of pluripotent stem cells and regulates the developmental transition from stem cells to various cell types. In flowering plants, the shoot apical meristem (SAM) contains a pluripotent stem cell population which generates the aerial part of plants including the germ cells. Under appropriate conditions, the SAM undergoes a developmental transition from a leaf-forming vegetative SAM to an inflorescence- and flower-forming reproductive SAM. While SAM characteristics are largely altered in this transition, the complete picture of DNA methylation remains elusive. Here, by analyzing whole-genome DNA methylation of isolated rice SAMs in the vegetative and reproductive stages, we show that methylation at CHH sites is kept high, particularly at transposable elements (TEs), in the vegetative SAM relative to the differentiated leaf, and increases in the reproductive SAM via the RNA-dependent DNA methylation pathway. We also show that half of the TEs that were highly methylated in gametes had already undergone CHH hypermethylation in the SAM. Our results indicate that changes in DNA methylation begin in the SAM long before germ cell differentiation to protect the genome from harmful TEs. The shoot apical meristem of flowering plants transitions from forming leaves to floral organs. Here Higo et al. show that DNA methylation of many transposons that are hypermethylated in gametes is established in the SAM before flowering, suggesting it protects against harmful transposition long before germ cell differentiation.
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Affiliation(s)
- Asuka Higo
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan
| | - Noriko Saihara
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan.,Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, 812-8582, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama, Japan
| | - Yoko Higashi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Megumi Yamada
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Shojiro Tamaki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Tasuku Ito
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan.,Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - Tomoaki Sakamoto
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.,Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-Ku, Kyoto, 603-8555, Japan
| | - Masayuki Fujiwara
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.,YANMAR HOLDINGS Co. Ltd., Chayamachi 1-32, Kita-ku, Osaka, 530-8311, Japan
| | - Tetsuya Kurata
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.,EditForce Inc., 4th Fl., Tenjin Fukuoka Seimei Bldg., Tenjin 1-9-17, Fukuoka, 810-0001, Japan
| | - Yoichiro Fukao
- Plant Global Education Project, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan.,Graduate School of Life Science, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Satoru Moritoh
- National Institute for Physiological Sciences, Okazaki, Aichi, 444-8585, Japan.,College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Rie Terada
- Graduate School of Agriculture, Meijo University, Nagoya, 468-8502, Japan
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8602, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, 812-8582, Japan
| | - Tetsuji Kakutani
- National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.,Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan.,Faculty of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ko Shimamoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, 244-0813, Japan.
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64
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A Molecular Signal Integration Network Underpinning Arabidopsis Seed Germination. Curr Biol 2020; 30:3703-3712.e4. [PMID: 32763174 PMCID: PMC7544511 DOI: 10.1016/j.cub.2020.07.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 06/22/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022]
Abstract
Seed dormancy is an adaptive trait defining where and when plants are established. Diverse signals from the environment are used to decide when to initiate seed germination, a process driven by the expansion of cells within the embryo. How these signals are integrated and transduced into the biomechanical changes that drive embryo growth remains poorly understood. Using Arabidopsis seeds, we demonstrate that cell-wall-loosening EXPANSIN (EXPA) genes promote gibberellic acid (GA)-mediated germination, identifying EXPAs as downstream molecular targets of this developmental phase transition. Molecular interaction screening identified transcription factors (TFs) that bind to both EXPA promoter fragments and DELLA GA-response regulators. A subset of these TFs is targeted each by nitric oxide (NO) and the phytochrome-interacting TF PIL5. This molecular interaction network therefore directly links the perception of an external environmental signal (light) and internal hormonal signals (GA and NO) with downstream germination-driving EXPA gene expression. Experimental validation of this network established that many of these TFs mediate GA-regulated germination, including TCP14/15, RAP2.2/2.3/2.12, and ZML1. The reduced germination phenotype of the tcp14 tcp15 mutant seed was partially rescued through ectopic expression of their direct target EXPA9. The GA-mediated control of germination by TCP14/15 is regulated through EXPA-mediated control of cell wall loosening, providing a mechanistic explanation for this phenotype and a previously undescribed role for TCPs in the control of cell expansion. This network reveals the paths of signal integration that culminate in seed germination and provides a resource to uncover links between the genetic and biomechanical bases of plant growth. The network linking integration of environmental signals to seed growth is mapped EXPANSIN gene expression is redundantly regulated and promotes GA-mediated germination The TCP14 transcription factor directly regulates EXPANSIN9 expression The tcp14/15 germination phenotype is complemented by EXPANSIN9 expression
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65
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Tognacca RS, Kubaczka MG, Servi L, Rodríguez FS, Godoy Herz MA, Petrillo E. Light in the transcription landscape: chromatin, RNA polymerase II and splicing throughout Arabidopsis thaliana's life cycle. Transcription 2020; 11:117-133. [PMID: 32748694 DOI: 10.1080/21541264.2020.1796473] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Plants have a high level of developmental plasticity that allows them to respond and adapt to changes in the environment. Among the environmental cues, light controls almost every aspect of A. thaliana's life cycle, including seed maturation, seed germination, seedling de-etiolation and flowering time. Light signals induce massive reprogramming of gene expression, producing changes in RNA polymerase II transcription, alternative splicing, and chromatin state. Since splicing reactions occur mainly while transcription takes place, the regulation of RNAPII transcription has repercussions in the splicing outcomes. This cotranscriptional nature allows a functional coupling between transcription and splicing, in which properties of the splicing reactions are affected by the transcriptional process. Chromatin landscapes influence both transcription and splicing. In this review, we highlight, summarize and discuss recent progress in the field to gain a comprehensive insight on the cross-regulation between chromatin state, RNAPII transcription and splicing decisions in plants, with a special focus on light-triggered responses. We also introduce several examples of transcription and splicing factors that could be acting as coupling factors in plants. Unravelling how these connected regulatory networks operate, can help in the design of better crops with higher productivity and tolerance.
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Affiliation(s)
- Rocío S Tognacca
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - M Guillermina Kubaczka
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Lucas Servi
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Florencia S Rodríguez
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina.,Departamento De Biodiversidad Y Biología Experimental, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Micaela A Godoy Herz
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
| | - Ezequiel Petrillo
- Departamento De Fisiología, Biología Molecular Y Celular, Facultad De Ciencias Exactas Y Naturales, Universidad De Buenos Aires , Buenos Aires, Argentina.,Instituto De Fisiología, Biología Molecular Y Neurociencias (IFIBYNE), CONICET-Universidad De Buenos Aires , Buenos Aires, Argentina
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66
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Yao M, Chen W, Kong J, Zhang X, Shi N, Zhong S, Ma P, Gallusci P, Jackson S, Liu Y, Hong Y. METHYLTRANSFERASE1 and Ripening Modulate Vivipary during Tomato Fruit Development. PLANT PHYSIOLOGY 2020; 183:1883-1897. [PMID: 32503901 PMCID: PMC7401104 DOI: 10.1104/pp.20.00499] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/26/2020] [Indexed: 05/04/2023]
Abstract
Vivipary, wherein seeds germinate prior to dispersal while still associated with the maternal plant, is an adaptation to extreme environments. It is normally inhibited by the establishment of dormancy. The genetic framework of vivipary has been well studied; however, the role of epigenetics in vivipary remains unknown. Here, we report that silencing of METHYLTRANSFERASE1 (SlMET1) promoted precocious seed germination and seedling growth within the tomato (Solanum lycopersicum) epimutant Colorless non-ripening (Cnr) fruits. This was associated with decreases in abscisic acid concentration and levels of mRNA encoding 9-cis-epoxycarotenoid-dioxygenase (SlNCED), which is involved in abscisic acid biosynthesis. Differentially methylated regions were identified in promoters of differentially expressed genes, including SlNCED SlNCED knockdown also induced viviparous seedling growth in Cnr fruits. Strikingly, Cnr ripening reversion suppressed vivipary. Moreover, neither SlMET1/SlNCED-virus-induced gene silencing nor transgenic SlMET1-RNA interference produced vivipary in wild-type tomatoes; the latter affected leaf architecture, arrested flowering, and repressed seed development. Thus, a dual pathway in ripening and SlMET1-mediated epigenetics coordinates the blockage of seed vivipary.
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Affiliation(s)
- Mengqin Yao
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Weiwei Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Junhua Kong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Xinlian Zhang
- Division of Biostatistics and Bioinformatics, University of California, San Diego, California 92093
- Department of Statistics, University of Georgia, Athens, Georgia 30602
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ping Ma
- Department of Statistics, University of Georgia, Athens, Georgia 30602
| | - Philippe Gallusci
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France
| | - Stephen Jackson
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
| | - Yule Liu
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom
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67
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The seed water content as a time-independent physiological trait during germination in wild tree species such as Ceiba aesculifolia. Sci Rep 2020; 10:10429. [PMID: 32591557 PMCID: PMC7319967 DOI: 10.1038/s41598-020-66759-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/26/2020] [Indexed: 12/26/2022] Open
Abstract
Seeds constitute a key physiological stage in plants life cycle. During seed germination, there is a spatial-temporal imbibition pattern that correlates with described physiological processes. However, only the moment of testa rupture has been described as a critical, discrete stage. Could a specific relative water content (RWC) value reflect a physiological stage useful for comparisons between seed batches? We tracked seed-by-seed imbibition during germination to homogenize sampling and selected a transcriptomic approach to analyse the physiological transitions that occur in seed batches collected in different years and with contrasting phenotypic responses to a priming treatment. The seed RWC reflected the transcriptional transitions that occur during germination, regardless of imbibition time or collection year, and revealed a set of biological processes that occur in the dry seed and during early germination are associated with the phenotypic response to priming. As climate shifts, so do the timing of developmental events important for determining organismal fitness, and poses another challenge to the comprehension of molecular and physiological processes driving the interaction between organisms and environment. In this study, we demonstrate that the use of physiological traits, specific to a particular developmental stage, is a reliable time-independent approach.
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68
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Park HJ, You YN, Lee A, Jung H, Jo SH, Oh N, Kim HS, Lee HJ, Kim JK, Kim YS, Jung C, Cho HS. OsFKBP20-1b interacts with the splicing factor OsSR45 and participates in the environmental stress response at the post-transcriptional level in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:992-1007. [PMID: 31925835 DOI: 10.1111/tpj.14682] [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: 05/27/2019] [Revised: 11/28/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
Sessile plants have evolved distinct mechanisms to respond and adapt to adverse environmental conditions through diverse mechanisms including RNA processing. While the role of RNA processing in the stress response is well understood for Arabidopsis thaliana, limited information is available for rice (Oryza sativa). Here, we show that OsFKBP20-1b, belonging to the immunophilin family, interacts with the splicing factor OsSR45 in both nuclear speckles and cytoplasmic foci, and plays an essential role in post-transcriptional regulation of abiotic stress response. The expression of OsFKBP20-1b was highly upregulated under various abiotic stresses. Moreover genetic analysis revealed that OsFKBP20-1b positively affected transcription and pre-mRNA splicing of stress-responsive genes under abiotic stress conditions. In osfkbp20-1b loss-of-function mutants, the expression of stress-responsive genes was downregulated, while that of their splicing variants was increased. Conversely, in plants overexpressing OsFKBP20-1b, the expression of the same stress-responsive genes was strikingly upregulated under abiotic stress. In vivo experiments demonstrated that OsFKBP20-1b directly maintains protein stability of OsSR45 splicing factor. Furthermore, we found that the plant-specific OsFKBP20-1b gene has uniquely evolved as a paralogue only in some Poaceae species. Together, our findings suggest that OsFKBP20-1b-mediated RNA processing contributes to stress adaptation in rice.
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Affiliation(s)
- Hyun J Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Young N You
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea
| | - Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea
| | - Seung H Jo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea
| | - Nuri Oh
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Ju-Kon Kim
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Youn S Kim
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Choonkyun Jung
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang, 25354, Republic of Korea
| | - Hye S Cho
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Korea
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69
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Carrera-Castaño G, Calleja-Cabrera J, Pernas M, Gómez L, Oñate-Sánchez L. An Updated Overview on the Regulation of Seed Germination. PLANTS 2020; 9:plants9060703. [PMID: 32492790 PMCID: PMC7356954 DOI: 10.3390/plants9060703] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/22/2020] [Accepted: 05/26/2020] [Indexed: 02/07/2023]
Abstract
The ability of a seed to germinate and establish a plant at the right time of year is of vital importance from an ecological and economical point of view. Due to the fragility of these early growth stages, their swiftness and robustness will impact later developmental stages and crop yield. These traits are modulated by a continuous interaction between the genetic makeup of the plant and the environment from seed production to germination stages. In this review, we have summarized the established knowledge on the control of seed germination from a molecular and a genetic perspective. This serves as a “backbone” to integrate the latest developments in the field. These include the link of germination to events occurring in the mother plant influenced by the environment, the impact of changes in the chromatin landscape, the discovery of new players and new insights related to well-known master regulators. Finally, results from recent studies on hormone transport, signaling, and biophysical and mechanical tissue properties are underscoring the relevance of tissue-specific regulation and the interplay of signals in this crucial developmental process.
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70
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Borg M, Jacob Y, Susaki D, LeBlanc C, Buendía D, Axelsson E, Kawashima T, Voigt P, Boavida L, Becker J, Higashiyama T, Martienssen R, Berger F. Targeted reprogramming of H3K27me3 resets epigenetic memory in plant paternal chromatin. Nat Cell Biol 2020; 22:621-629. [PMID: 32393884 PMCID: PMC7116658 DOI: 10.1038/s41556-020-0515-y] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 03/31/2020] [Indexed: 12/22/2022]
Abstract
Epigenetic marks are reprogrammed in the gametes to reset genomic potential in the next generation. In mammals, paternal chromatin is extensively reprogrammed through the global erasure of DNA methylation and the exchange of histones with protamines1,2. Precisely how the paternal epigenome is reprogrammed in flowering plants has remained unclear since DNA is not demethylated and histones are retained in sperm3,4. Here, we describe a multi-layered mechanism by which H3K27me3 is globally lost from histone-based sperm chromatin in Arabidopsis. This mechanism involves the silencing of H3K27me3 writers, activity of H3K27me3 erasers and deposition of a sperm-specific histone, H3.10 (ref. 5), which we show is immune to lysine 27 methylation. The loss of H3K27me3 facilitates the transcription of genes essential for spermatogenesis and pre-configures sperm with a chromatin state that forecasts gene expression in the next generation. Thus, plants have evolved a specific mechanism to simultaneously differentiate male gametes and reprogram the paternal epigenome.
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Affiliation(s)
- Michael Borg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Yannick Jacob
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York, NY, USA
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, USA
| | - Daichi Susaki
- Institute of Transformative Bio-Molecules (WPI-ITbM), Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Chantal LeBlanc
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT, USA
| | - Daniel Buendía
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
| | - Tomokazu Kawashima
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA
| | - Philipp Voigt
- Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Edinburgh, UK
| | - Leonor Boavida
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, USA
| | - Jörg Becker
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Robert Martienssen
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, New York, NY, USA
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.
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Lin W, Sun L, Huang RZ, Liang W, Liu X, He H, Fukuda H, He XQ, Qian W. Active DNA demethylation regulates tracheary element differentiation in Arabidopsis. SCIENCE ADVANCES 2020; 6:eaaz2963. [PMID: 32637594 PMCID: PMC7319731 DOI: 10.1126/sciadv.aaz2963] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 05/13/2020] [Indexed: 05/16/2023]
Abstract
DNA demethylation is important for the erasure of DNA methylation. The role of DNA demethylation in plant development remains poorly understood. Here, we found extensive DNA demethylation in the CHH context around pericentromeric regions and DNA demethylation in the CG, CHG, and CHH contexts at discrete genomic regions during ectopic xylem tracheary element (TE) differentiation. While loss of pericentromeric methylation occurs passively, DNA demethylation at a subset of regions relies on active DNA demethylation initiated by DNA glycosylases ROS1, DML2, and DML3. The ros1 and rdd mutations impair ectopic TE differentiation and xylem development in the young roots of Arabidopsis seedlings. Active DNA demethylation targets and regulates many genes for TE differentiation. The defect of xylem development in rdd is proposed to be caused by dysregulation of multiple genes. Our study identifies a role of active DNA demethylation in vascular development and reveals an epigenetic mechanism for TE differentiation.
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Affiliation(s)
- Wei Lin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Linhua Sun
- Academy for Advanced Interdisciplinary Studies, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Run-Zhou Huang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wenjie Liang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xinyu Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hiroo Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Xin-Qiang He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Corresponding author. (X.-Q.H.); (W.Q.)
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
- Corresponding author. (X.-Q.H.); (W.Q.)
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72
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Katsuya-Gaviria K, Caro E, Carrillo-Barral N, Iglesias-Fernández R. Reactive Oxygen Species (ROS) and Nucleic Acid Modifications During Seed Dormancy. PLANTS (BASEL, SWITZERLAND) 2020; 9:E679. [PMID: 32471221 PMCID: PMC7356579 DOI: 10.3390/plants9060679] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/24/2020] [Accepted: 05/26/2020] [Indexed: 12/15/2022]
Abstract
The seed is the propagule of higher plants and allows its dissemination and the survival of the species. Seed dormancy prevents premature germination under favourable conditions. Dormant seeds are only able to germinate in a narrow range of conditions. During after-ripening (AR), a mechanism of dormancy release, seeds gradually lose dormancy through a period of dry storage. This review is mainly focused on how chemical modifications of mRNA and genomic DNA, such as oxidation and methylation, affect gene expression during late stages of seed development, especially during dormancy. The oxidation of specific nucleotides produced by reactive oxygen species (ROS) alters the stability of the seed stored mRNAs, being finally degraded or translated into non-functional proteins. DNA methylation is a well-known epigenetic mechanism of controlling gene expression. In Arabidopsis thaliana, while there is a global increase in CHH-context methylation through embryogenesis, global DNA methylation levels remain stable during seed dormancy, decreasing when germination occurs. The biological significance of nucleic acid oxidation and methylation upon seed development is discussed.
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Affiliation(s)
- Kai Katsuya-Gaviria
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
| | - Néstor Carrillo-Barral
- Departamento de Fisiología Vegetal, Facultad de Ciencias, Universidad da Coruña (UdC), 15008-A Coruña, Spain;
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas-Severo Ochoa (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28223-Pozuelo de Alarcón, Spain; (K.K.-G.); (E.C.)
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, UPM, 28040-Madrid, Spain
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73
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Time Series RNA-seq in Pigeonpea Revealed the Core Genes in Metabolic Pathways under Aluminum Stress. Genes (Basel) 2020; 11:genes11040380. [PMID: 32244575 PMCID: PMC7230159 DOI: 10.3390/genes11040380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 02/18/2020] [Accepted: 03/12/2020] [Indexed: 11/17/2022] Open
Abstract
Pigeonpea is an important economic crop in the world and is mainly distributed in tropical and subtropical regions. In order to further expand the scope of planting, one of the problems that must be solved is the impact of soil acidity on plants in these areas. Based on our previous work, we constructed a time series RNA sequencing (RNA-seq) analysis under aluminum (Al) stress in pigeonpea. Through a comparison analysis, 11,425 genes were found to be differentially expressed among all the time points. After clustering these genes by their expression patterns, 12 clusters were generated. Many important functional pathways were identified by gene ontology (GO) analysis, such as biological regulation, localization, response to stimulus, metabolic process, detoxification, and so on. Further analysis showed that metabolic pathways played an important role in the response of Al stress. Thirteen out of the 23 selected genes related to flavonoids and phenols were downregulated in response to Al stress. In addition, we verified these key genes of flavonoid- and phenol-related metabolism pathways by qRT-PCR. Collectively, our findings not only revealed the regulation mechanism of pigeonpea under Al stress but also provided methodological support for further exploration of plant stress regulation mechanisms.
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Chow HT, Chakraborty T, Mosher RA. RNA-directed DNA Methylation and sexual reproduction: expanding beyond the seed. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:11-17. [PMID: 31881293 DOI: 10.1016/j.pbi.2019.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 05/12/2023]
Abstract
Two trends are changing our understanding of RNA-directed DNA methylation. In model systems like Arabidopsis, tissue-specific analysis of DNA methylation is uncovering dynamic changes in methylation during sexual reproduction and unraveling the contribution of maternal and paternal epigenomes to the developing embryo. These studies indicate that RNA-directed DNA Methylation might be important for mediating balance between maternal and paternal contributions to the endosperm. At the same time, researchers are moving beyond Arabidopsis to illuminate the ancestral role of RdDM in non-flowering plants that lack an endosperm, suggesting that RdDM might play a broader role in sexual reproduction.
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Affiliation(s)
- Hiu Tung Chow
- The School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, United States
| | - Tania Chakraborty
- The School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, United States
| | - Rebecca A Mosher
- The School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, United States.
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Hoai PTT, Tyerman SD, Schnell N, Tucker M, McGaughey SA, Qiu J, Groszmann M, Byrt CS. Deciphering aquaporin regulation and roles in seed biology. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1763-1773. [PMID: 32109278 DOI: 10.1093/jxb/erz555] [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: 08/12/2019] [Accepted: 02/26/2020] [Indexed: 05/25/2023]
Abstract
Seeds are the typical dispersal and propagation units of angiosperms and gymnosperms. Water movement into and out of seeds plays a crucial role from the point of fertilization through to imbibition and seed germination. A class of membrane intrinsic proteins called aquaporins (AQPs) assist with the movement of water and other solutes within seeds. These highly diverse and abundant proteins are associated with different processes in the development, longevity, imbibition, and germination of seed. However, there are many AQPs encoded in a plant's genome and it is not yet clear how, when, or which AQPs are involved in critical stages of seed biology. Here we review the literature to examine the evidence for AQP involvement in seeds and analyse Arabidopsis seed-related transcriptomic data to assess which AQPs are likely to be important in seed water relations and explore additional roles for AQPs in seed biology.
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Affiliation(s)
- Phan T T Hoai
- Australian Research Council Centre of Excellence in Plant Energy Biology, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
- School of Agriculture, Food and Wine, and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
- Faculty of Agriculture and Forestry, Tay Nguyen University, Dak Lak, Viet Nam
| | - Stephen D Tyerman
- Australian Research Council Centre of Excellence in Plant Energy Biology, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
- School of Agriculture, Food and Wine, and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
| | - Nicholas Schnell
- School of Agriculture, Food and Wine, and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
| | - Matthew Tucker
- School of Agriculture, Food and Wine, and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
| | - Samantha A McGaughey
- Australian Research Council Centre of Excellence in Plant Energy Biology, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
- School of Agriculture, Food and Wine, and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
| | - Jiaen Qiu
- Australian Research Council Centre of Excellence in Plant Energy Biology, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
- School of Agriculture, Food and Wine, and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
| | - Michael Groszmann
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT, Australia
| | - Caitlin S Byrt
- Australian Research Council Centre of Excellence in Plant Energy Biology, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
- School of Agriculture, Food and Wine, and Waite Research Institute, Waite Research Precinct, University of Adelaide, Glen Osmond, Australia
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Division of Plant Sciences, Research School of Biology, The Australian National University, Acton, ACT, Australia
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76
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Liew LC, Narsai R, Wang Y, Berkowitz O, Whelan J, Lewsey MG. Temporal tissue-specific regulation of transcriptomes during barley (Hordeum vulgare) seed germination. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:700-715. [PMID: 31628689 DOI: 10.1111/tpj.14574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/09/2019] [Accepted: 10/08/2019] [Indexed: 06/10/2023]
Abstract
The distinct functions of individual cell types require cells to express specific sets of genes. The germinating seed is an excellent model to study genome regulation between cell types since the majority of the transcriptome is differentially expressed in a short period, beginning from a uniform, metabolically inactive state. In this study, we applied laser-capture microdissection RNA-sequencing to small numbers of cells from the plumule, radicle tip and scutellum of germinating barley seeds every 8 h, over a 48 h time course. Tissue-specific gene expression was notably common; 25% (910) of differentially expressed transcripts in plumule, 34% (1876) in radicle tip and 41% (2562) in scutellum were exclusive to that organ. We also determined that tissue-specific storage of transcripts occurs during seed development and maturation. Co-expression of genes had strong spatiotemporal structure, with most co-expression occurring within one organ and at a subset of specific time points during germination. Overlapping and distinct enrichment of functional categories were observed in the tissue-specific profiles. We identified candidate transcription factors amongst these that may be regulators of spatiotemporal gene expression programs. Our findings contribute to the broader goal of generating an integrative model that describes the structure and function of individual cells within seeds during germination.
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Affiliation(s)
- Lim Chee Liew
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Reena Narsai
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Yan Wang
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - James Whelan
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
| | - Mathew G Lewsey
- Department of Animal, Plant and Soil Science, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, Vic., 3086, Australia
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77
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Trejo-Arellano MS, Mehdi S, de Jonge J, Dvorák Tomastíková E, Köhler C, Hennig L. Dark-Induced Senescence Causes Localized Changes in DNA Methylation. PLANT PHYSIOLOGY 2020; 182:949-961. [PMID: 31792150 PMCID: PMC6997673 DOI: 10.1104/pp.19.01154] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/14/2019] [Indexed: 05/04/2023]
Abstract
Senescence occurs in a programmed manner to dismantle the vegetative tissues and redirect nutrients towards metabolic pathways supporting reproductive success. External factors can trigger the senescence program as an adaptive strategy, indicating that this terminal program is controlled at different levels. It has been proposed that epigenetic factors accompany the reprogramming of the senescent genome; however, the mechanism and extent of this reprogramming remain unknown. Using bisulphite conversion followed by sequencing, we assessed changes in the methylome of senescent Arabidopsis (Arabidopsis thaliana) leaves induced by darkness and monitored their effect on gene and transposable element (TE) expression with transcriptome sequencing. Upon dark-induced senescence, genes controlling chromatin silencing were collectively down-regulated. As a consequence, the silencing of TEs was impaired, causing in particular young TEs to become preferentially reactivated. In parallel, heterochromatin at chromocenters was decondensed. Despite the disruption of the chromatin maintenance network, the global DNA methylation landscape remained highly stable, with localized changes mainly restricted to CHH methylation. Together, our data show that the terminal stage of plant life is accompanied by global changes in chromatin structure but only localized changes in DNA methylation, adding another example of the dynamics of DNA methylation during plant development.
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Affiliation(s)
- Minerva S Trejo-Arellano
- Swedish University of Agricultural Sciences, Department of Plant Biology and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Saher Mehdi
- Swedish University of Agricultural Sciences, Department of Plant Biology and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Jennifer de Jonge
- Swedish University of Agricultural Sciences, Department of Plant Biology and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Eva Dvorák Tomastíková
- Swedish University of Agricultural Sciences, Department of Plant Biology and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Claudia Köhler
- Swedish University of Agricultural Sciences, Department of Plant Biology and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Lars Hennig
- Swedish University of Agricultural Sciences, Department of Plant Biology and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
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78
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Kenchanmane Raju SK, Ritter EJ, Niederhuth CE. Establishment, maintenance, and biological roles of non-CG methylation in plants. Essays Biochem 2019; 63:743-755. [PMID: 31652316 PMCID: PMC6923318 DOI: 10.1042/ebc20190032] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/18/2022]
Abstract
Cytosine DNA methylation is prevalent throughout eukaryotes and prokaryotes. While most commonly thought of as being localized to dinucleotide CpG sites, non-CG sites can also be modified. Such non-CG methylation is widespread in plants, occurring at trinucleotide CHG and CHH (H = A, T, or C) sequence contexts. The prevalence of non-CG methylation in plants is due to the plant-specific CHROMOMETHYLASE (CMT) and RNA-directed DNA Methylation (RdDM) pathways. These pathways have evolved through multiple rounds of gene duplication and gene loss, generating epigenomic variation both within and between species. They regulate both transposable elements and genes, ensure genome integrity, and ultimately influence development and environmental responses. In these capacities, non-CG methylation influence and shape plant genomes.
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Affiliation(s)
| | | | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, U.S.A
- AgBioResearch, Michigan State University, East Lansing, MI 48824, U.S.A
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79
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Han Q, Bartels A, Cheng X, Meyer A, An YQC, Hsieh TF, Xiao W. Epigenetics Regulates Reproductive Development in Plants. PLANTS 2019; 8:plants8120564. [PMID: 31810261 PMCID: PMC6963493 DOI: 10.3390/plants8120564] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 11/23/2019] [Accepted: 11/27/2019] [Indexed: 12/20/2022]
Abstract
Seed, resulting from reproductive development, is the main nutrient source for human beings, and reproduction has been intensively studied through genetic, molecular, and epigenetic approaches. However, how different epigenetic pathways crosstalk and integrate to regulate seed development remains unknown. Here, we review the recent progress of epigenetic changes that affect chromatin structure, such as DNA methylation, polycomb group proteins, histone modifications, and small RNA pathways in regulating plant reproduction. In gametogenesis of flowering plants, epigenetics is dynamic between the companion cell and gametes. Cytosine DNA methylation occurs in CG, CHG, CHH contexts (H = A, C, or T) of genes and transposable elements, and undergoes dynamic changes during reproduction. Cytosine methylation in the CHH context increases significantly during embryogenesis, reaches the highest levels in mature embryos, and decreases as the seed germinates. Polycomb group proteins are important transcriptional regulators during seed development. Histone modifications and small RNA pathways add another layer of complexity in regulating seed development. In summary, multiple epigenetic pathways are pivotal in regulating seed development. It remains to be elucidated how these epigenetic pathways interplay to affect dynamic chromatin structure and control reproduction.
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Affiliation(s)
- Qiang Han
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Arthur Bartels
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Xi Cheng
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
| | - Angela Meyer
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Yong-Qiang Charles An
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, Donald Danforth Plant Science Center, MO 63132, USA;
| | - Tzung-Fu Hsieh
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA;
- Plants for Human Health Institute, North Carolina State University, North Carolina Research Campus, Kannapolis, NC 28081, USA
| | - Wenyan Xiao
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA (A.B.); (X.C.)
- Correspondence: ; Tel.: +1-314-977-2547
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Boter M, Calleja-Cabrera J, Carrera-Castaño G, Wagner G, Hatzig SV, Snowdon RJ, Legoahec L, Bianchetti G, Bouchereau A, Nesi N, Pernas M, Oñate-Sánchez L. An Integrative Approach to Analyze Seed Germination in Brassica napus. FRONTIERS IN PLANT SCIENCE 2019; 10:1342. [PMID: 31708951 PMCID: PMC6824160 DOI: 10.3389/fpls.2019.01342] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/26/2019] [Indexed: 05/23/2023]
Abstract
Seed germination is a complex trait determined by the interaction of hormonal, metabolic, genetic, and environmental components. Variability of this trait in crops has a big impact on seedling establishment and yield in the field. Classical studies of this trait in crops have focused mainly on the analyses of one level of regulation in the cascade of events leading to seed germination. We have carried out an integrative and extensive approach to deepen our understanding of seed germination in Brassica napus by generating transcriptomic, metabolic, and hormonal data at different stages upon seed imbibition. Deep phenotyping of different seed germination-associated traits in six winter-type B. napus accessions has revealed that seed germination kinetics, in particular seed germination speed, are major contributors to the variability of this trait. Metabolic profiling of these accessions has allowed us to describe a common pattern of metabolic change and to identify the levels of malate and aspartate metabolites as putative metabolic markers to estimate germination performance. Additionally, analysis of seed content of different hormones suggests that hormonal balance between ABA, GA, and IAA at crucial time points during this process might underlie seed germination differences in these accessions. In this study, we have also defined the major transcriptome changes accompanying the germination process in B. napus. Furthermore, we have observed that earlier activation of key germination regulatory genes seems to generate the differences in germination speed observed between accessions in B. napus. Finally, we have found that protein-protein interactions between some of these key regulator are conserved in B. napus, suggesting a shared regulatory network with other plant species. Altogether, our results provide a comprehensive and detailed picture of seed germination dynamics in oilseed rape. This new framework will be extremely valuable not only to evaluate germination performance of B. napus accessions but also to identify key targets for crop improvement in this important process.
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Affiliation(s)
- Marta Boter
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
| | - Julián Calleja-Cabrera
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
| | - Gerardo Carrera-Castaño
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
| | - Geoffrey Wagner
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Sarah Vanessa Hatzig
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Laurie Legoahec
- Joint Laboratory for Genetics, Institute for Genetics, Environment and Plant Protection (IGEPP), Le Rheu, France
| | - Grégoire Bianchetti
- Joint Laboratory for Genetics, Institute for Genetics, Environment and Plant Protection (IGEPP), Le Rheu, France
| | - Alain Bouchereau
- Joint Laboratory for Genetics, Institute for Genetics, Environment and Plant Protection (IGEPP), Le Rheu, France
| | - Nathalie Nesi
- Joint Laboratory for Genetics, Institute for Genetics, Environment and Plant Protection (IGEPP), Le Rheu, France
| | - Mónica Pernas
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
| | - Luis Oñate-Sánchez
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
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Gehring M. Epigenetic dynamics during flowering plant reproduction: evidence for reprogramming? THE NEW PHYTOLOGIST 2019; 224:91-96. [PMID: 31002174 PMCID: PMC6711810 DOI: 10.1111/nph.15856] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 04/05/2019] [Indexed: 05/08/2023]
Abstract
Over the last 10 yr there have been major advances in documenting and understanding dynamic changes to DNA methylation, small RNAs, chromatin modifications and chromatin structure that accompany reproductive development in flowering plants, from germline specification to seed maturation. Here I highlight recent advances in the field, mostly made possible by microscopic analysis of epigenetic states or by the ability to isolate specific cell types or tissues and apply omics approaches. I consider in which contexts there is potentially reprogramming vs maintenance or reinforcement of epigenetic states.
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Affiliation(s)
- Mary Gehring
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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82
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Ji L, Mathioni SM, Johnson S, Tucker D, Bewick AJ, Do Kim K, Daron J, Slotkin RK, Jackson SA, Parrott WA, Meyers BC, Schmitz RJ. Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean. THE PLANT CELL 2019; 31:2315-2331. [PMID: 31439802 PMCID: PMC6790092 DOI: 10.1105/tpc.19.00255] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/29/2019] [Accepted: 08/19/2019] [Indexed: 05/06/2023]
Abstract
Somatic embryogenesis is an important tissue culture technique that sometimes leads to phenotypic variation via genetic and/or epigenetic changes. To understand the genomic and epigenomic impacts of somatic embryogenesis, we characterized soybean (Glycine max) epigenomes sampled from embryos at 10 different stages ranging from 6 weeks to 13 years of continuous culture. We identified genome-wide increases in DNA methylation from cultured samples, especially at CHH sites. The hypermethylation almost exclusively occurred in regions previously possessing non-CG methylation and was accompanied by increases in the expression of genes encoding the RNA-directed DNA methylation (RdDM) machinery. The epigenomic changes were similar between somatic and zygotic embryogenesis. Following the initial global wave of hypermethylation, rare decay events of maintenance methylation were observed, and the extent of the decay increased with time in culture. These losses in DNA methylation were accompanied by downregulation of genes encoding the RdDM machinery and transcriptome reprogramming reminiscent of transcriptomes during late-stage seed development. These results reveal a process for reinforcing already silenced regions to maintain genome integrity during somatic embryogenesis over the short term, which eventually decays at certain loci over longer time scales.
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Affiliation(s)
- Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602
| | | | - Sarah Johnson
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Donna Tucker
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Adam J Bewick
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Josquin Daron
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - R Keith Slotkin
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Department of Molecular Genetics, Ohio State University, Columbus, Ohio 43210
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Wayne A Parrott
- Institute for Plant Breeding Genetics and Genomics, University of Georgia, Athens, Georgia 30602
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 63132
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia 30602
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83
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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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84
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Kawakatsu T, Ecker JR. Diversity and dynamics of DNA methylation: epigenomic resources and tools for crop breeding. BREEDING SCIENCE 2019; 69:191-204. [PMID: 31481828 PMCID: PMC6711733 DOI: 10.1270/jsbbs.19005] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 03/18/2019] [Indexed: 05/17/2023]
Abstract
DNA methylation is an epigenetic modification that can affect gene expression and transposable element (TE) activities. Because cytosine DNA methylation patterns are inherited through both mitotic and meiotic cell divisions, differences in these patterns can contribute to phenotypic variability. Advances in high-throughput sequencing technologies have enabled the generation of abundant DNA sequence data. Integrated analyses of genome-wide gene expression patterns and DNA methylation patterns have revealed the underlying mechanisms and functions of DNA methylation. Moreover, associations between DNA methylation and agronomic traits have also been uncovered. The resulting information may be useful for future applications of natural epigenomic variation, for crop breeding. Additionally, artificial epigenome editing may be an attractive new plant breeding technique for generating novel varieties with improved agronomic traits.
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Affiliation(s)
- Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization,
1-2 Owashi Tsukuba, Ibaraki 305-8634,
Japan
- Corresponding author (e-mail: )
| | - Joseph R. Ecker
- Howard Hughes Medical Institute,
10010 North Torrey Pines Road, La Jolla, CA 92037,
USA
- The Salk Institute for Biological Studies,
10010 North Torrey Pines Road, La Jolla, CA 92037,
USA
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85
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Genome-Wide DNA Methylation Profiling in the Lotus ( Nelumbo nucifera) Flower Showing its Contribution to the Stamen Petaloid. PLANTS 2019; 8:plants8050135. [PMID: 31137487 PMCID: PMC6572404 DOI: 10.3390/plants8050135] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 05/16/2019] [Accepted: 05/17/2019] [Indexed: 01/06/2023]
Abstract
DNA methylation is a vital epigenetic modification. Methylation has a significant effect on the gene expression influencing the regulation of different physiological processes. Current studies on DNA methylation have been conducted on model plants. Lotus (Nelumbo nucifera) is a basic eudicot exhibiting variations during development, especially in flower formation. DNA methylation profiling was conducted on different flower tissues of lotuses through whole genome bisulfite sequencing (WGBS) to investigate the effects of DNA methylation on its stamen petaloid. A map of methylated cytosines at the single base pair resolution for the lotus was constructed. When the stamen was compared with the stamen petaloid, the DNA methylation exhibited a global decrease. Genome-wide relationship analysis between DNA methylation and gene expression identified 31 different methylation region (DMR)-associated genes, which might play crucial roles in floral organ formation, especially in the stamen petaloid. One out of 31 DMR-associated genes, NNU_05638 was homolog with Plant U-box 33 (PUB33). The DNA methylation status of NNU_05638 promoter was distinct in three floral organs, which was confirmed by traditional bisulfite sequencing. These results provide further insights about the regulation of stamen petaloids at the epigenetic level in lotus.
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86
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Fan S, Gao X, Gao C, Yang Y, Zhu X, Feng W, Li R, Mobeen Tahir M, Zhang D, Han M, An N. Dynamic Cytosine DNA Methylation Patterns Associated with mRNA and siRNA Expression Profiles in Alternate Bearing Apple Trees. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:5250-5264. [PMID: 31008599 DOI: 10.1021/acs.jafc.9b00871] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Cytosine DNA methylation plays an important role in plants: it can mediate gene expression to affect plant growth and development. However, little is known about the potential involvement of cytosine DNA methylation in apple trees as well as in response to alternate bearing. Here, we performed whole-genome bisulfate sequencing to investigate genomic CG, CHG, and CHH methylation patterns, together with their global mRNA accumulation and small RNA expression in "Fuji" apple trees. Results showed that "Fuji" apple trees have a higher CHH methylation than Arabidopsis. Moreover, genomic methylation analysis revealed that CG and CHG methylation were robustly maintained at the early stage of flower induction. Additionally, differentially methylated regions (DMRs), including hypermethylated and hypomethylated DMRs, were also characterized in alternate bearing (AB) apple trees. Intriguingly, the DMRs were enriched in hormones, redox state, and starch and sucrose metabolism, which affected flowering. Further global gene expression evaluation based on methylome analysis revealed a negative correlation between gene body methylation and gene expression. Subsequent small RNA analyses showed that 24-nucleotide small interfering RNAs were activated and maintained in non-CG methylated apple trees. Our whole-genome DNA methylation analysis and RNA and small RNA expression profile construction provide valuable information for future studies.
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Affiliation(s)
- Sheng Fan
- College of Horticulture , Northwest A&F University , Yangling 712100 , Shaanxi , China
| | - Xiuhua Gao
- College of Horticulture , Northwest A&F University , Yangling 712100 , Shaanxi , China
| | - Cai Gao
- College of Horticulture , Northwest A&F University , Yangling 712100 , Shaanxi , China
| | - Yang Yang
- Innovation Experimental College , Northwest A&F University , Yangling 712100 , Shaanxi , China
| | - Xinzheng Zhu
- Innovation Experimental College , Northwest A&F University , Yangling 712100 , Shaanxi , China
| | - Wei Feng
- Innovation Experimental College , Northwest A&F University , Yangling 712100 , Shaanxi , China
| | - Ruimin Li
- College of Horticulture , Northwest A&F University , Yangling 712100 , Shaanxi , China
| | - Muhammad Mobeen Tahir
- College of Horticulture , Northwest A&F University , Yangling 712100 , Shaanxi , China
| | - Dong Zhang
- College of Horticulture , Northwest A&F University , Yangling 712100 , Shaanxi , China
| | - Mingyu Han
- College of Horticulture , Northwest A&F University , Yangling 712100 , Shaanxi , China
| | - Na An
- College of Horticulture , Northwest A&F University , Yangling 712100 , Shaanxi , China
- College of Life Science , Northwest A&F University , Yangling 712100 , Shaanxi , China
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87
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Johannes F, Schmitz RJ. Spontaneous epimutations in plants. THE NEW PHYTOLOGIST 2019; 221:1253-1259. [PMID: 30216456 DOI: 10.1111/nph.15434] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/01/2018] [Indexed: 05/22/2023]
Abstract
Contents Summary 1253 I. Introduction 1253 II. What is the rate and molecular spectrum of spontaneous epimutations? 1254 III. Do spontaneous epimutations have phenotypic consequences? 1257 IV. Conclusion and discussion 1258 Acknowledgements 1258 References 1258 SUMMARY: Heritable gains or losses of cytosine methylation can arise stochastically in plant genomes independently of DNA sequence changes. These so-called 'spontaneous epimutations' appear to be a byproduct of imperfect DNA methylation maintenance and epigenome reinforcement events that occur in specialized cell types. There is continued interest in the plant epigenetics community in trying to understand the broader implications of these stochastic events, as some have been shown to induce heritable gene expression changes, shape patterns of methylation diversity within and among plant populations, and appear to be responsive to multi-generational environmental stressors. In this paper we synthesized our current knowledge of the molecular basis and functional consequences of spontaneous epimutations in plants, discuss technical and conceptual challenges, and highlight emerging research directions.
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Affiliation(s)
- Frank Johannes
- Department of Plant Sciences, Technical University of Munich, Liesel-Beckmann-Str. 2, Freising, 85354, Germany
- Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, 85748, Germany
| | - Robert J Schmitz
- Institute for Advanced Study (IAS), Technical University of Munich, Lichtenbergstr. 2a, Garching, 85748, Germany
- Department of Genetics, The University of Georgia, 120 East Green Street, Athens, GA, 30602, USA
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88
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Mohanapriya G, Bharadwaj R, Noceda C, Costa JH, Kumar SR, Sathishkumar R, Thiers KLL, Santos Macedo E, Silva S, Annicchiarico P, Groot SP, Kodde J, Kumari A, Gupta KJ, Arnholdt-Schmitt B. Alternative Oxidase (AOX) Senses Stress Levels to Coordinate Auxin-Induced Reprogramming From Seed Germination to Somatic Embryogenesis-A Role Relevant for Seed Vigor Prediction and Plant Robustness. FRONTIERS IN PLANT SCIENCE 2019; 10:1134. [PMID: 31611888 PMCID: PMC6776121 DOI: 10.3389/fpls.2019.01134] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 08/16/2019] [Indexed: 05/21/2023]
Abstract
Somatic embryogenesis (SE) is the most striking and prominent example of plant plasticity upon severe stress. Inducing immature carrot seeds perform SE as substitute to germination by auxin treatment can be seen as switch between stress levels associated to morphophysiological plasticity. This experimental system is highly powerful to explore stress response factors that mediate the metabolic switch between cell and tissue identities. Developmental plasticity per se is an emerging trait for in vitro systems and crop improvement. It is supposed to underlie multi-stress tolerance. High plasticity can protect plants throughout life cycles against variable abiotic and biotic conditions. We provide proof of concepts for the existing hypothesis that alternative oxidase (AOX) can be relevant for developmental plasticity and be associated to yield stability. Our perspective on AOX as relevant coordinator of cell reprogramming is supported by real-time polymerase chain reaction (PCR) analyses and gross metabolism data from calorespirometry complemented by SHAM-inhibitor studies on primed, elevated partial pressure of oxygen (EPPO)-stressed, and endophyte-treated seeds. In silico studies on public experimental data from diverse species strengthen generality of our insights. Finally, we highlight ready-to-use concepts for plant selection and optimizing in vivo and in vitro propagation that do not require further details on molecular physiology and metabolism. This is demonstrated by applying our research & technology concepts to pea genotypes with differential yield performance in multilocation fields and chickpea types known for differential robustness in the field. By using these concepts and tools appropriately, also other marker candidates than AOX and complex genomics data can be efficiently validated for prebreeding and seed vigor prediction.
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Affiliation(s)
- Gunasekaran Mohanapriya
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Revuru Bharadwaj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Carlos Noceda
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- Cell and Molecular Biology of Plants (BPOCEMP)/Industrial Biotechnology and Bioproducts, Department of Sciences of the Vidaydela Agriculture, University of the Armed Forces-ESPE, Milagro, Ecuador
- Faculty of Engineering, State University of Milagro (UNEMI), Milagro, Ecuador
| | - José Hélio Costa
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Sarma Rajeev Kumar
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- *Correspondence: Birgit Arnholdt-Schmitt, ; Ramalingam Sathishkumar,
| | - Karine Leitão Lima Thiers
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Elisete Santos Macedo
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Sofia Silva
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
| | - Paolo Annicchiarico
- Council for Agricultural Research and Economics (CREA), Research Centre for Animal Production and Aquaculture, Lodi, Italy
| | - Steven P.C. Groot
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Jan Kodde
- Wageningen Plant Research, Wageningen University & Research, Wageningen, Netherlands
| | - Aprajita Kumari
- National Institute of Plant Genome Research, New Delhi, India
| | - Kapuganti Jagadis Gupta
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- National Institute of Plant Genome Research, New Delhi, India
| | - Birgit Arnholdt-Schmitt
- Functional Cell Reprogramming and Organism Plasticity (FunCROP), University of Évora, Évora, Portugal
- Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- CERNAS-Research Center for Natural Resources, Environment and Society, Department of Environment, Escola Superior Agrária de Coimbra, Coimbra, Portugal
- *Correspondence: Birgit Arnholdt-Schmitt, ; Ramalingam Sathishkumar,
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89
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Tognacca RS, Servi L, Hernando CE, Saura-Sanchez M, Yanovsky MJ, Petrillo E, Botto JF. Alternative Splicing Regulation During Light-Induced Germination of Arabidopsis thaliana Seeds. FRONTIERS IN PLANT SCIENCE 2019; 10:1076. [PMID: 31552074 PMCID: PMC6746916 DOI: 10.3389/fpls.2019.01076] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/07/2019] [Indexed: 05/17/2023]
Abstract
Seed dormancy and germination are relevant processes for a successful seedling establishment in the field. Light is one of the most important environmental factors involved in the relief of dormancy to promote seed germination. In Arabidopsis thaliana seeds, phytochrome photoreceptors tightly regulate gene expression at different levels. The contribution of alternative splicing (AS) regulation in the photocontrol of seed germination is still unknown. The aim of this work is to study gene expression modulated by light during germination of A. thaliana seeds, with focus on AS changes. Hence, we evaluated transcriptome-wide changes in stratified seeds irradiated with a pulse of red (Rp) or far-red (FRp) by RNA sequencing (RNA-seq). Our results show that the Rp changes the expression of ∼20% of the transcriptome and modifies the AS pattern of 226 genes associated with mRNA processing, RNA splicing, and mRNA metabolic processes. We further confirmed these effects for some of the affected AS events. Interestingly, the reverse transcriptase-polymerase chain reaction (RT-PCR) analyses show that the Rp modulates the AS of splicing-related factors (At-SR30, At-RS31a, At-RS31, and At-U2AF65A), a light-signaling component (At-PIF6), and a dormancy-related gene (At-DRM1). Furthermore, while the phytochrome B (phyB) is responsible for the AS pattern changes of At-U2AF65A and At-PIF6, the regulation of the other AS events is independent of this photoreceptor. We conclude that (i) Rp triggers AS changes in some splicing factors, light-signaling components, and dormancy/germination regulators; (ii) phyB modulates only some of these AS events; and (iii) AS events are regulated by R and FR light, but this regulation is not directly associated with the intensity of germination response. These data will help in boosting research in the splicing field and our understanding about the role of this mechanism during the photocontrol of seed germination.
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Affiliation(s)
- Rocío Soledad Tognacca
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | - Lucas Servi
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
| | | | - Maite Saura-Sanchez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | - Ezequiel Petrillo
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología Molecular y Celular and CONICET-UBA, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), Universidad de Buenos Aires (UBA), Buenos Aires, Argentina
- *Correspondence: Ezequiel Petrillo, ; Javier Francisco Botto,
| | - Javier Francisco Botto
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
- *Correspondence: Ezequiel Petrillo, ; Javier Francisco Botto,
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90
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Benoit M, Simon L, Desset S, Duc C, Cotterell S, Poulet A, Le Goff S, Tatout C, Probst AV. Replication-coupled histone H3.1 deposition determines nucleosome composition and heterochromatin dynamics during Arabidopsis seedling development. THE NEW PHYTOLOGIST 2019; 221:385-398. [PMID: 29897636 DOI: 10.1111/nph.15248] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/23/2023]
Abstract
Developmental phase transitions are often characterized by changes in the chromatin landscape and heterochromatin reorganization. In Arabidopsis, clustering of repetitive heterochromatic loci into so-called chromocenters is an important determinant of chromosome organization in nuclear space. Here, we investigated the molecular mechanisms involved in chromocenter formation during the switch from a heterotrophic to a photosynthetically competent state during early seedling development. We characterized the spatial organization and chromatin features at centromeric and pericentromeric repeats and identified mutant contexts with impaired chromocenter formation. We find that clustering of repetitive DNA loci into chromocenters takes place in a precise temporal window and results in reinforced transcriptional repression. Although repetitive sequences are enriched in H3K9me2 and linker histone H1 before repeat clustering, chromocenter formation involves increasing enrichment in H3.1 as well as H2A.W histone variants, hallmarks of heterochromatin. These processes are severely affected in mutants impaired in replication-coupled histone assembly mediated by CHROMATIN ASSEMBLY FACTOR 1 (CAF-1). We further reveal that histone deposition by CAF-1 is required for efficient H3K9me2 enrichment at repetitive sequences during chromocenter formation. Taken together, we show that chromocenter assembly during post-germination development requires dynamic changes in nucleosome composition and histone post-translational modifications orchestrated by the replication-coupled H3.1 deposition machinery.
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Affiliation(s)
- Matthias Benoit
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
- The Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Lauriane Simon
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden
| | - Sophie Desset
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Céline Duc
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Sylviane Cotterell
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Axel Poulet
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, 1518 Clifton Road NE, Atlanta, GA, 30322, USA
| | - Samuel Le Goff
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Christophe Tatout
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
| | - Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, BP 38, 63001, Clermont-Ferrand, France
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91
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Rodrigues AS, De Vega JJ, Miguel CM. Comprehensive assembly and analysis of the transcriptome of maritime pine developing embryos. BMC PLANT BIOLOGY 2018; 18:379. [PMID: 30594130 PMCID: PMC6310951 DOI: 10.1186/s12870-018-1564-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 11/22/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND There are clear differences in embryo development between angiosperm and gymnosperm species. Most of the current knowledge on gene expression and regulation during plant embryo development has derived from studies on angiosperms species, in particular from the model plant Arabidopsis thaliana. The few published studies on transcript profiling of conifer embryogenesis show the existence of many putative embryo-specific transcripts without an assigned function. In order to extend the knowledge on the transcriptomic expression during conifer embryogenesis, we sequenced the transcriptome of zygotic embryos for several developmental stages that cover most of Pinus pinaster (maritime pine) embryogenesis. RESULTS Total RNA samples collected from five zygotic embryo developmental stages were sequenced with Illumina technology. A de novo transcriptome was assembled as no genome sequence is yet published for Pinus pinaster. The transcriptome of reference for the period of zygotic embryogenesis in maritime pine contains 67,429 transcripts, which likely encode 58,527 proteins. The annotation shows a significant percentage, 31%, of predicted proteins exclusively present in pine embryogenesis. Functional categories and enrichment analysis of the differentially expressed transcripts evidenced carbohydrate transport and metabolism over-representation in early embryo stages, as highlighted by the identification of many putative glycoside hydrolases, possibly associated with cell wall modification, and carbohydrate transport transcripts. Moreover, the predominance of chromatin remodelling events was detected in early to middle embryogenesis, associated with an active synthesis of histones and their post-translational modifiers related to increased transcription, as well as silencing of transposons. CONCLUSIONS Our results extend the understanding of gene expression and regulation during zygotic embryogenesis in conifers and are a valuable resource to support further improvements in somatic embryogenesis for vegetative propagation of conifer species. Specific transcripts associated with carbohydrate metabolism, monosaccharide transport and epigenetic regulation seem to play an important role in pine early embryogenesis and may be a source of reliable molecular markers for early embryogenesis.
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Affiliation(s)
- Andreia S. Rodrigues
- Instituto de Biologia Experimental e Tecnológica (iBET), Apartado 12, 2780-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
| | - José J. De Vega
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK
| | - Célia M. Miguel
- Instituto de Biologia Experimental e Tecnológica (iBET), Apartado 12, 2780-901 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157 Oeiras, Portugal
- Universidade de Lisboa, Faculdade de Ciências, BioISI - Biosystems & Integrative Sciences Institute, Campo Grande, 1749-016 Lisbon, Portugal
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92
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Robinson AJ, Tamiru M, Salby R, Bolitho C, Williams A, Huggard S, Fisch E, Unsworth K, Whelan J, Lewsey MG. AgriSeqDB: an online RNA-Seq database for functional studies of agriculturally relevant plant species. BMC PLANT BIOLOGY 2018; 18:200. [PMID: 30231853 PMCID: PMC6146512 DOI: 10.1186/s12870-018-1406-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/30/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND The genome-wide expression profile of genes in different tissues/cell types and developmental stages is a vital component of many functional genomic studies. Transcriptome data obtained by RNA-sequencing (RNA-Seq) is often deposited in public databases that are made available via data portals. Data visualization is one of the first steps in assessment and hypothesis generation. However, these databases do not typically include visualization tools and establishing one is not trivial for users who are not computational experts. This, as well as the various formats in which data is commonly deposited, makes the processes of data access, sharing and utility more difficult. Our goal was to provide a simple and user-friendly repository that meets these needs for data-sets from major agricultural crops. DESCRIPTION AgriSeqDB ( https://expression.latrobe.edu.au/agriseqdb ) is a database for viewing, analysing and interpreting developmental and tissue/cell-specific transcriptome data from several species, including major agricultural crops such as wheat, rice, maize, barley and tomato. The disparate manner in which public transcriptome data is often warehoused and the challenge of visualizing raw data are both major hurdles to data reuse. The popular eFP browser does an excellent job of presenting transcriptome data in an easily interpretable view, but previous implementation has been mostly on a case-by-case basis. Here we present an integrated visualisation database of transcriptome data-sets from six species that did not previously have public-facing visualisations. We combine the eFP browser, for gene-by-gene investigation, with the Degust browser, which enables visualisation of all transcripts across multiple samples. The two visualisation interfaces launch from the same point, enabling users to easily switch between analysis modes. The tools allow users, even those without bioinformatics expertise, to mine into data-sets and understand the behaviour of transcripts of interest across samples and time. We have also incorporated an additional graphic download option to simplify incorporation into presentations or publications. CONCLUSION Powered by eFP and Degust browsers, AgriSeqDB is a quick and easy-to-use platform for data analysis and visualization in five crops and Arabidopsis. Furthermore, it provides a tool that makes it easy for researchers to share their data-sets, promoting research collaborations and data-set reuse.
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Affiliation(s)
| | - Muluneh Tamiru
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Rachel Salby
- Library, La Trobe University, Melbourne, Australia
| | | | | | | | - Eva Fisch
- Library, La Trobe University, Melbourne, Australia
| | | | - James Whelan
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Mathew G. Lewsey
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Australia
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93
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Lepiniec L, Devic M, Roscoe TJ, Bouyer D, Zhou DX, Boulard C, Baud S, Dubreucq B. Molecular and epigenetic regulations and functions of the LAFL transcriptional regulators that control seed development. PLANT REPRODUCTION 2018; 31:291-307. [PMID: 29797091 DOI: 10.1007/s00497-018-0337-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/10/2018] [Indexed: 05/20/2023]
Abstract
The LAFL (i.e. LEC1, ABI3, FUS3, and LEC2) master transcriptional regulators interact to form different complexes that induce embryo development and maturation, and inhibit seed germination and vegetative growth in Arabidopsis. Orthologous genes involved in similar regulatory processes have been described in various angiosperms including important crop species. Consistent with a prominent role of the LAFL regulators in triggering and maintaining embryonic cell fate, their expression appears finely tuned in different tissues during seed development and tightly repressed in vegetative tissues by a surprisingly high number of genetic and epigenetic factors. Partial functional redundancies and intricate feedback regulations of the LAFL have hampered the elucidation of the underpinning molecular mechanisms. Nevertheless, genetic, genomic, cellular, molecular, and biochemical analyses implemented during the last years have greatly improved our knowledge of the LALF network. Here we summarize and discuss recent progress, together with current issues required to gain a comprehensive insight into the network, including the emerging function of LEC1 and possibly LEC2 as pioneer transcription factors.
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Affiliation(s)
- L Lepiniec
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France.
| | - M Devic
- Régulations Epigénétiques et Développement de la Graine, ERL 5300 CNRS-IRD UMR DIADE, IRD centre de Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, Université Pierre et Marie Curie (Paris 06) & Centre National pour la Recherche Scientifique CNRS UMR 7621, 66650, Banyuls-sur-Mer, France
| | - T J Roscoe
- Régulations Epigénétiques et Développement de la Graine, ERL 5300 CNRS-IRD UMR DIADE, IRD centre de Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, Université Pierre et Marie Curie (Paris 06) & Centre National pour la Recherche Scientifique CNRS UMR 7621, 66650, Banyuls-sur-Mer, France
| | - D Bouyer
- Institut de Biologie de l'ENS, CNRS UMR8197, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France
| | - D-X Zhou
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Sud 11, Université Paris-Saclay, 91405, Orsay, France
| | - C Boulard
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
| | - S Baud
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
| | - B Dubreucq
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
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94
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Szakonyi D, Duque P. Alternative Splicing as a Regulator of Early Plant Development. FRONTIERS IN PLANT SCIENCE 2018; 9:1174. [PMID: 30158945 PMCID: PMC6104592 DOI: 10.3389/fpls.2018.01174] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/23/2018] [Indexed: 05/19/2023]
Abstract
Most plant genes are interrupted by introns and the corresponding transcripts need to undergo pre-mRNA splicing to remove these intervening sequences. Alternative splicing (AS) is an important posttranscriptional process that creates multiple mRNA variants from a single pre-mRNA molecule, thereby enhancing the coding and regulatory potential of genomes. In plants, this mechanism has been implicated in the response to environmental cues, including abiotic and biotic stresses, in the regulation of key developmental processes such as flowering, and in circadian timekeeping. The early plant development steps - from embryo formation and seed germination to skoto- and photomorphogenesis - are critical to both execute the correct body plan and initiate a new reproductive cycle. We review here the available evidence for the involvement of AS and various splicing factors in the initial stages of plant development, while highlighting recent findings as well as potential future challenges.
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Affiliation(s)
| | - Paula Duque
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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95
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Dynamic DNA Methylation in Plant Growth and Development. Int J Mol Sci 2018; 19:ijms19072144. [PMID: 30041459 PMCID: PMC6073778 DOI: 10.3390/ijms19072144] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/12/2018] [Accepted: 07/20/2018] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is an epigenetic modification required for transposable element (TE) silencing, genome stability, and genomic imprinting. Although DNA methylation has been intensively studied, the dynamic nature of methylation among different species has just begun to be understood. Here we summarize the recent progress in research on the wide variation of DNA methylation in different plants, organs, tissues, and cells; dynamic changes of methylation are also reported during plant growth and development as well as changes in response to environmental stresses. Overall DNA methylation is quite diverse among species, and it occurs in CG, CHG, and CHH (H = A, C, or T) contexts of genes and TEs in angiosperms. Moderately expressed genes are most likely methylated in gene bodies. Methylation levels decrease significantly just upstream of the transcription start site and around transcription termination sites; its levels in the promoter are inversely correlated with the expression of some genes in plants. Methylation can be altered by different environmental stimuli such as pathogens and abiotic stresses. It is likely that methylation existed in the common eukaryotic ancestor before fungi, plants and animals diverged during evolution. In summary, DNA methylation patterns in angiosperms are complex, dynamic, and an integral part of genome diversity after millions of years of evolution.
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96
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Heidorn-Czarna M, Domanski D, Kwasniak-Owczarek M, Janska H. Targeted Proteomics Approach Toward Understanding the Role of the Mitochondrial Protease FTSH4 in the Biogenesis of OXPHOS During Arabidopsis Seed Germination. FRONTIERS IN PLANT SCIENCE 2018; 9:821. [PMID: 29963070 PMCID: PMC6014109 DOI: 10.3389/fpls.2018.00821] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 05/28/2018] [Indexed: 05/23/2023]
Abstract
Seed germination provides an excellent model to study the process of mitochondrial biogenesis. It is a complex and strictly regulated process which requires a proper biogenesis of fully active organelles from existing promitochondrial structures. We have previously reported that the lack of the inner mitochondrial membrane protease FTSH4 delayed Arabidopsis seed germination. Here, we implemented a targeted mass spectrometry-based approach, Multiple Reaction Monitoring (MRM), with stable-isotope-labeled standard peptides for increased sensitivity, to quantify mitochondrial proteins in dry and germinating wild-type and ftsh4 mutant seeds, lacking the FTSH4 protease. Using total seed protein extracts we measured the abundance of the peptide targets belonging to the OXPHOS complexes, AOX1A, transport, and inner membrane scaffold as well as mitochondrial proteins that are highly specific to dry and germinating seeds. The MRM assay showed that the abundance of these proteins in ftsh4 did not differ substantially from that observed in wild-type at the level of dry seed and after stratification, but we observed a reduction in protein abundance in most of the examined OXPHOS subunits in the later stages of germination. These changes in OXPHOS protein levels in ftsh4 mutants were accompanied by a lower cytochrome pathway activity as well as an increased AOX1A amount at the transcript and protein level and alternative pathway activity. The analyses of the steady-state transcript levels of mitochondrial and nuclear genes encoding OXPHOS subunits did not show significant difference in their amount, indicating that the observed changes in the OXPHOS occurred at the post-transcriptional level. At the time when ftsh4 seeds were fully germinated, the abundance of the OXPHOS proteins in the mutant was either slightly lowered or comparable to these amounts in wild-type seeds at the similar developmental stage. By the implementation of an integrative approach combining targeted proteomics, quantitative transcriptomics, and physiological studies we have shown that the FTSH4 protease has an important role in the biogenesis of OXPHOS and thus biogenesis of mitochondria during germination of Arabidopsis seeds.
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Affiliation(s)
- Malgorzata Heidorn-Czarna
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Dominik Domanski
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Hanna Janska
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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97
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Anderson SN, Zynda GJ, Song J, Han Z, Vaughn MW, Li Q, Springer NM. Subtle Perturbations of the Maize Methylome Reveal Genes and Transposons Silenced by Chromomethylase or RNA-Directed DNA Methylation Pathways. G3 (BETHESDA, MD.) 2018; 8:1921-1932. [PMID: 29618467 PMCID: PMC5982821 DOI: 10.1534/g3.118.200284] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/03/2018] [Indexed: 01/17/2023]
Abstract
DNA methylation is a chromatin modification that can provide epigenetic regulation of gene and transposon expression. Plants utilize several pathways to establish and maintain DNA methylation in specific sequence contexts. The chromomethylase (CMT) genes maintain CHG (where H = A, C or T) methylation. The RNA-directed DNA methylation (RdDM) pathway is important for CHH methylation. Transcriptome analysis was performed in a collection of Zea mays lines carrying mutant alleles for CMT or RdDM-associated genes. While the majority of the transcriptome was not affected, we identified sets of genes and transposon families sensitive to context-specific decreases in DNA methylation in mutant lines. Many of the genes that are up-regulated in CMT mutant lines have high levels of CHG methylation, while genes that are differentially expressed in RdDM mutants are enriched for having nearby mCHH islands, implicating context-specific DNA methylation in the regulation of expression for a small number of genes. Many genes regulated by CMTs exhibit natural variation for DNA methylation and transcript abundance in a panel of diverse inbred lines. Transposon families with differential expression in the mutant genotypes show few defining features, though several families up-regulated in RdDM mutants show enriched expression in endosperm tissue, highlighting the potential importance for this pathway during reproduction. Taken together, our findings suggest that while the number of genes and transposon families whose expression is reproducibly affected by mild perturbations in context-specific methylation is small, there are distinct patterns for loci impacted by RdDM and CMT mutants.
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Affiliation(s)
- Sarah N Anderson
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108
| | - Gregory J Zynda
- Texas Advanced Computing Center, University of Texas, Austin, TX 78758
| | - Jawon Song
- Texas Advanced Computing Center, University of Texas, Austin, TX 78758
| | - Zhaoxue Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Matthew W Vaughn
- Texas Advanced Computing Center, University of Texas, Austin, TX 78758
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108
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98
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Brun G, Braem L, Thoiron S, Gevaert K, Goormachtig S, Delavault P. Seed germination in parasitic plants: what insights can we expect from strigolactone research? JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2265-2280. [PMID: 29281042 DOI: 10.1093/jxb/erx472] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/14/2017] [Indexed: 06/07/2023]
Abstract
Obligate root-parasitic plants belonging to the Orobanchaceae family are deadly pests for major crops all over the world. Because these heterotrophic plants severely damage their hosts even before emerging from the soil, there is an unequivocal need to design early and efficient methods for their control. The germination process of these species has probably undergone numerous selective pressure events in the course of evolution, in that the perception of host-derived molecules is a necessary condition for seeds to germinate. Although most of these molecules belong to the strigolactones, structurally different molecules have been identified. Since strigolactones are also classified as novel plant hormones that regulate several physiological processes other than germination, the use of autotrophic model plant species has allowed the identification of many actors involved in the strigolactone biosynthesis, perception, and signal transduction pathways. Nevertheless, many questions remain to be answered regarding the germination process of parasitic plants. For instance, how did parasitic plants evolve to germinate in response to a wide variety of molecules, while autotrophic plants do not? What particular features are associated with their lack of spontaneous germination? In this review, we attempt to illustrate to what extent conclusions from research into strigolactones could be applied to better understand the biology of parasitic plants.
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Affiliation(s)
- Guillaume Brun
- Laboratoire de Biologie et Pathologie Végétales, EA, Université de Nantes, BP Nantes Cedex, France
| | - Lukas Braem
- VIB-UGent Center for Plant Systems Biology, Technologiepark Zwijnaarde, Belgium
- VIB-UGent Center for Medical Biotechnology, Albert Baertsoenkaai Ghent, Belgium
| | - Séverine Thoiron
- Laboratoire de Biologie et Pathologie Végétales, EA, Université de Nantes, BP Nantes Cedex, France
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Albert Baertsoenkaai Ghent, Belgium
- Department of Biochemistry, Ghent University, Albert Baertsoenkaai Ghent, Belgium
| | - Sofie Goormachtig
- VIB-UGent Center for Plant Systems Biology, Technologiepark Zwijnaarde, Belgium
| | - Philippe Delavault
- Laboratoire de Biologie et Pathologie Végétales, EA, Université de Nantes, BP Nantes Cedex, France
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99
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Woloszynska M, Gagliardi O, Vandenbussche F, Van Lijsebettens M. Elongator promotes germination and early post-germination growth. PLANT SIGNALING & BEHAVIOR 2018; 13:e1422465. [PMID: 29286868 PMCID: PMC5790400 DOI: 10.1080/15592324.2017.1422465] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 12/19/2017] [Indexed: 06/07/2023]
Abstract
The Elongator complex interacts with RNA polymerase II and via histone acetylation and DNA demethylation facilitates epigenetically the transcription of genes involved in diverse processes in plants, including growth, development, and immune response. Recently, we have shown that the Elongator complex promotes hypocotyl elongation and photomorphogenesis in Arabidopsis thaliana by regulating the photomorphogenesis and growth-related gene network that converges on genes implicated in cell wall biogenesis and hormone signaling. Here, we report that germination in the elo mutant was delayed by 6 h in the dark when compared to the wild type in a time lapse and germination assay. A number of germination-correlated genes were down-regulated in the elo transcriptome, suggesting a transcriptional regulation by Elongator. We also show that the hypocotyl elongation defect observed in the elo mutants in darkness originates very early in the post-germination development and is independent from the germination delay.
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Affiliation(s)
- Magdalena Woloszynska
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Genetics, Faculty of Biology and Animal Sciences, Wroclaw University of Environmental and Life Sciences, Wroclaw, Poland
| | - Olimpia Gagliardi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Filip Vandenbussche
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Mieke Van Lijsebettens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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100
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Koch L. Development: Epigenome dynamics from seed to seedling. Nat Rev Genet 2017; 18:637. [PMID: 28944781 DOI: 10.1038/nrg.2017.78] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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