1
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Zhang H, Zhu JK. Epigenetic gene regulation in plants and its potential applications in crop improvement. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00769-1. [PMID: 39192154 DOI: 10.1038/s41580-024-00769-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2024] [Indexed: 08/29/2024]
Abstract
DNA methylation, also known as 5-methylcytosine, is an epigenetic modification that has crucial functions in plant growth, development and adaptation. The cellular DNA methylation level is tightly regulated by the combined action of DNA methyltransferases and demethylases. Protein complexes involved in the targeting and interpretation of DNA methylation have been identified, revealing intriguing roles of methyl-DNA binding proteins and molecular chaperones. Structural studies and in vitro reconstituted enzymatic systems have provided mechanistic insights into RNA-directed DNA methylation, the main pathway catalysing de novo methylation in plants. A better understanding of the regulatory mechanisms will enable locus-specific manipulation of the DNA methylation status. CRISPR-dCas9-based epigenome editing tools are being developed for this goal. Given that DNA methylation patterns can be stably transmitted through meiosis, and that large phenotypic variations can be contributed by epimutations, epigenome editing holds great promise in crop breeding by creating additional phenotypic variability on the same genetic material.
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Affiliation(s)
- Heng Zhang
- Department of Genetics and Developmental Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
| | - Jian-Kang Zhu
- Institute of Advanced Biotechnology and School of Medicine, Southern University of Science and Technology, Shenzhen, China.
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2
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Zhang Y, Jang H, Luo Z, Dong Y, Xu Y, Kantamneni Y, Schmitz RJ. Dynamic evolution of the heterochromatin sensing histone demethylase IBM1. PLoS Genet 2024; 20:e1011358. [PMID: 38991029 PMCID: PMC11265718 DOI: 10.1371/journal.pgen.1011358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 07/23/2024] [Accepted: 07/01/2024] [Indexed: 07/13/2024] Open
Abstract
Heterochromatin is critical for maintaining genome stability, especially in flowering plants, where it relies on a feedback loop involving the H3K9 methyltransferase, KRYPTONITE (KYP), and the DNA methyltransferase CHROMOMETHYLASE3 (CMT3). The H3K9 demethylase INCREASED IN BONSAI METHYLATION 1 (IBM1) counteracts the detrimental consequences of KYP-CMT3 activity in transcribed genes. IBM1 expression in Arabidopsis is uniquely regulated by methylation of the 7th intron, allowing it to monitor global H3K9me2 levels. We show the methylated intron is prevalent across flowering plants and its underlying sequence exhibits dynamic evolution. We also find extensive genetic and expression variations in KYP, CMT3, and IBM1 across flowering plants. We identify Arabidopsis accessions resembling weak ibm1 mutants and Brassicaceae species with reduced IBM1 expression or deletions. Evolution towards reduced IBM1 activity in some flowering plants could explain the frequent natural occurrence of diminished or lost CMT3 activity and loss of gene body DNA methylation, as cmt3 mutants in A. thaliana mitigate the deleterious effects of IBM1.
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Affiliation(s)
- Yinwen Zhang
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Hosung Jang
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Ziliang Luo
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Yinxin Dong
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Yangyang Xu
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Yamini Kantamneni
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
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3
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Wang J, Eulgem T. Growth deficiency and enhanced basal immunity in Arabidopsis thaliana mutants of EDM2, EDM3 and IBM2 are genetically interlinked. PLoS One 2024; 19:e0291705. [PMID: 38329997 PMCID: PMC10852260 DOI: 10.1371/journal.pone.0291705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/14/2024] [Indexed: 02/10/2024] Open
Abstract
Mutants of the Arabidopsis thaliana genes, EDM2 (Enhanced Downy Mildew 2), EDM3 (Enhanced Downy Mildew 3) and IBM2 (Increase in Bonsai Methylation 2) are known to show defects in a diverse set of defense and developmental processes. For example, they jointly exhibit enhanced levels of basal defense and stunted growth. Here we show that these two phenotypes are functionally connected by their dependency on the salicylic acid biosynthesis gene SID2 and the basal defense regulatory gene PAD4. Stunted growth of edm2, edm3 and ibm2 plants is a consequence of up-regulated basal defense. Constitutively enhanced activity of reactive oxygen species-generating peroxidases, we observed in these mutants, appears also to contribute to both, their enhanced basal defense and their growth retardation phenotypes. Furthermore, we found the histone H3 demethylase gene IBM1, a direct regulatory target of EDM2, EDM3 and IBM2, to be at least partially required for the basal defense and growth-related effects observed in these mutants. We recently reported that EDM2, EDM3 and IBM2 coordinate basal immunity with the timing of the floral transition by gradually reducing the extent of this defense mechanism prior to flowering. Together with these observations, data presented here show that at least some of the diverse phenotypic effects in edm2, edm3 and ibm2 mutants are genetically interlinked and functionally connected. Our new results show that repression of basal immunity by EDM2, EDM3 and IBM2 limits negative impact on growth and development.
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Affiliation(s)
- Jianqiang Wang
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
| | - Thomas Eulgem
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California, United States of America
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4
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Nakashima K, Yuhazu M, Mikuriya S, Kasai M, Abe J, Taneda A, Kanazawa A. Frequency of cytosine methylation in the adjacent regions of soybean retrotransposon SORE-1 depends on chromosomal location. Genome 2024; 67:1-12. [PMID: 37746933 DOI: 10.1139/gen-2023-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Mobilization of transposable elements (TEs) is suppressed by epigenetic mechanisms involving cytosine methylation. However, few studies have focused on clarifying relationships between epigenetic influences of TEs on the adjacent DNA regions and time after insertion of TEs into the genome and/or their chromosomal location. Here we addressed these issues using soybean retrotransposon SORE-1. We analyzed SORE-1, inserted in exon 1 of the GmphyA2 gene, one of the newest insertions in this family so far identified. Cytosine methylation was detected in this element but was barely present in the adjacent regions. These results were correlated, respectively, with the presence and absence of the production of short interfering RNAs. Cytosine methylation profiles of 74 SORE-1 elements in the Williams 82 reference genome indicated that methylation frequency in the adjacent regions of SORE-1 was profoundly higher in pericentromeric regions than in euchromatic chromosome arms and was only weakly correlated with the length of time after insertion into the genome. Notably, the higher level of methylation in the 5' adjacent regions of SORE-1 coincided with the presence of repetitive elements in pericentromeric regions. Together, these results suggest that epigenetic influence of SORE-1 on the adjacent regions is influenced by its location on the chromosome.
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Affiliation(s)
- Kenta Nakashima
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Mashiro Yuhazu
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Shun Mikuriya
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Megumi Kasai
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Akito Taneda
- Graduate School of Science and Technology, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Akira Kanazawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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5
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Kan Q, Li Q. Post-transcriptional and translational regulation of plant gene expression by transposons. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102438. [PMID: 37619514 DOI: 10.1016/j.pbi.2023.102438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/22/2023] [Accepted: 07/22/2023] [Indexed: 08/26/2023]
Abstract
Transposons are mobile DNA sequences that can move within the genome and integrate in new genomic locations. They are widespread in eukaryotes and prokaryotes and can influence gene expression when landing within or nearby a gene. Although transposon-induced regulation of gene expression at the transcriptional level has been extensively studied, there has been less focus on regulation at the post-transcriptional and translational levels. Recent studies in maize (Zea mays) and other plant species suggest that transposon insertions can affect RNA processing, RNA stability, protein translation and protein stability. We will describe the diverse mechanisms by which transposons can influence gene expression at the post-transcriptional and translational levels, and discuss the interactions between these mechanisms.
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Affiliation(s)
- Qiuxin Kan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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6
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Wang J, Eulgem T. The Arabidopsis RRM domain proteins EDM3 and IBM2 coordinate the floral transition and basal immune responses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:128-143. [PMID: 37347678 DOI: 10.1111/tpj.16364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
The transition from vegetative to reproductive development (floral transition) is a costly process in annual plants requiring increased investments in metabolic resources. The Arabidopsis thaliana (Arabidopsis) PHD finger protein EDM2 and RRM domain proteins EDM3 and IBM2 are known to form chromatin-associated complexes controlling transcript processing. We are reporting that distinct splice isoforms of EDM3 and IBM2 cooperate in the coordination of the floral transition with basal immune responses. These cooperating splice isoforms, termed EDM3L and IBM2L, control the intensity of basal immunity and, via a separate pathway, the timing of the floral transition. During the developmental phase prior to the floral transition expression of EDM3L and IBM2L strongly and gradually increases, while these isoforms simultaneously down-regulate expression of the floral suppressor gene FLC and promote the transition to reproductive growth. At the same time these accumulating EDM3 and IBM2 splice isoforms gradually suppress basal immunity against the virulent Noco2 isolate of the pathogenic oomycete Hyaloperonospora arabidopsidis and down-regulate expression of a set of defense-associated genes and immune receptor genes. We are providing clear evidence for a functional link between the floral transition and basal immunity in the annual plant Arabidopsis. Coordination of these two biological processes, which compete for metabolic resources, is likely critical for plant survival and reproductive success.
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Affiliation(s)
- Jianqiang Wang
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
| | - Thomas Eulgem
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, California, USA
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7
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Berthelier J, Furci L, Asai S, Sadykova M, Shimazaki T, Shirasu K, Saze H. Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana. Nat Commun 2023; 14:3248. [PMID: 37277361 DOI: 10.1038/s41467-023-38954-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 05/21/2023] [Indexed: 06/07/2023] Open
Abstract
Transposable elements (TEs) are accumulated in both intergenic and intragenic regions in plant genomes. Intragenic TEs often act as regulatory elements of associated genes and are also co-transcribed with genes, generating chimeric TE-gene transcripts. Despite the potential impact on mRNA regulation and gene function, the prevalence and transcriptional regulation of TE-gene transcripts are poorly understood. By long-read direct RNA sequencing and a dedicated bioinformatics pipeline, ParasiTE, we investigated the transcription and RNA processing of TE-gene transcripts in Arabidopsis thaliana. We identified a global production of TE-gene transcripts in thousands of A. thaliana gene loci, with TE sequences often being associated with alternative transcription start sites or transcription termination sites. The epigenetic state of intragenic TEs affects RNAPII elongation and usage of alternative poly(A) signals within TE sequences, regulating alternative TE-gene isoform production. Co-transcription and inclusion of TE-derived sequences into gene transcripts impact regulation of RNA stability and environmental responses of some loci. Our study provides insights into TE-gene interactions that contributes to mRNA regulation, transcriptome diversity, and environmental responses in plants.
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Grants
- JP20H02995 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP22H00364 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05909 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP20H05913 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
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Affiliation(s)
- Jérémy Berthelier
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
| | - Leonardo Furci
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Shuta Asai
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Munissa Sadykova
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Tomoe Shimazaki
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Ken Shirasu
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
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8
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Agius DR, Kapazoglou A, Avramidou E, Baranek M, Carneros E, Caro E, Castiglione S, Cicatelli A, Radanovic A, Ebejer JP, Gackowski D, Guarino F, Gulyás A, Hidvégi N, Hoenicka H, Inácio V, Johannes F, Karalija E, Lieberman-Lazarovich M, Martinelli F, Maury S, Mladenov V, Morais-Cecílio L, Pecinka A, Tani E, Testillano PS, Todorov D, Valledor L, Vassileva V. Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. FRONTIERS IN PLANT SCIENCE 2023; 14:1181039. [PMID: 37389288 PMCID: PMC10306282 DOI: 10.3389/fpls.2023.1181039] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/27/2023] [Indexed: 07/01/2023]
Abstract
Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.
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Affiliation(s)
- Dolores Rita Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
- Biology Department, Ġ.F.Abela Junior College, Msida, Malta
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Evangelia Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Miroslav Baranek
- Mendeleum-Insitute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czechia
| | - Elena Carneros
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Stefano Castiglione
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Angela Cicatelli
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Aleksandra Radanovic
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
| | - Jean-Paul Ebejer
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Francesco Guarino
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Andrea Gulyás
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Norbert Hidvégi
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Hans Hoenicka
- Genomic Research Department, Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Vera Inácio
- BioISI – BioSystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Frank Johannes
- Plant Epigenomics, Technical University of Munich (TUM), Freising, Germany
| | - Erna Karalija
- Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Michal Lieberman-Lazarovich
- Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Center, Institute of Plant Sciences, Rishon LeZion, Israel
| | | | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures EA1207 USC1328, INRAE, Université d’Orléans, Orléans, France
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Pilar S. Testillano
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Dimitar Todorov
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias, University of Oviedo, Oviedo, Spain
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
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9
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Zhang Q, Xie J, Zhu X, Ma X, Yang T, Khan NU, Zhang S, Liu M, Li L, Liang Y, Pan Y, Li D, Li J, Li Z, Zhang H, Zhang Z. Natural variation in Tiller Number 1 affects its interaction with TIF1 to regulate tillering in rice. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1044-1057. [PMID: 36705337 PMCID: PMC10106862 DOI: 10.1111/pbi.14017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/15/2022] [Accepted: 01/23/2023] [Indexed: 05/04/2023]
Abstract
Tiller number per plant-a cardinal component of ideal plant architecture-affects grain yield potential. Thus, alleles positively affecting tillering must be mined to promote genetic improvement. Here, we report a Tiller Number 1 (TN1) protein harbouring a bromo-adjacent homology domain and RNA recognition motifs, identified through genome-wide association study of tiller numbers. Natural variation in TN1 affects its interaction with TIF1 (TN1 interaction factor 1) to affect DWARF14 expression and negatively regulate tiller number in rice. Further analysis of variations in TN1 among indica genotypes according to geographical distribution revealed that low-tillering varieties with TN1-hapL are concentrated in Southeast Asia and East Asia, whereas high-tillering varieties with TN1-hapH are concentrated in South Asia. Taken together, these results indicate that TN1 is a tillering regulatory factor whose alleles present apparent preferential utilization across geographical regions. Our findings advance the molecular understanding of tiller development.
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Affiliation(s)
- Quan Zhang
- MOE Key Laboratory of Crop Heterosis and Utilization/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jianyin Xie
- MOE Key Laboratory of Crop Heterosis and Utilization/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xiaoyang Zhu
- MOE Key Laboratory of Crop Heterosis and Utilization/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xiaoqian Ma
- MOE Key Laboratory of Crop Heterosis and Utilization/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Tao Yang
- MOE Key Laboratory of Crop Heterosis and Utilization/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Najeeb Ullah Khan
- MOE Key Laboratory of Crop Heterosis and Utilization/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Shuyang Zhang
- MOE Key Laboratory of Crop Heterosis and Utilization/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Miaosong Liu
- MOE Key Laboratory of Crop Heterosis and Utilization/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Lin Li
- MOE Key Laboratory of Crop Heterosis and Utilization/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yuntao Liang
- Guangxi Key Laboratory of Rice Genetics and BreedingRice Research Institute of Guangxi Academy of Agricultural SciencesNanningGuangxiChina
| | - Yinghua Pan
- Guangxi Key Laboratory of Rice Genetics and BreedingRice Research Institute of Guangxi Academy of Agricultural SciencesNanningGuangxiChina
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and BreedingRice Research Institute of Guangxi Academy of Agricultural SciencesNanningGuangxiChina
| | - Jinjie Li
- MOE Key Laboratory of Crop Heterosis and Utilization/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Zichao Li
- MOE Key Laboratory of Crop Heterosis and Utilization/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
| | - Hongliang Zhang
- MOE Key Laboratory of Crop Heterosis and Utilization/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
- Sanya Institute of China Agricultural UniversitySanyaChina
- Sanya Nanfan Research Institute of Hainan UniversitySanyaChina
| | - Zhanying Zhang
- MOE Key Laboratory of Crop Heterosis and Utilization/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
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10
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Ooi SE, Sarpan N, Taranenko E, Feshah I, Nuraziyan A, Roowi SH, Burhan MN, Jayanthi N, Rahmah ARS, Teh OK, Ong-Abdullah M, Tatarinova TV. Small RNAs and Karma methylation in Elaeis guineensis mother palms are linked to high clonal mantling. PLANT MOLECULAR BIOLOGY 2023; 111:345-363. [PMID: 36609897 DOI: 10.1007/s11103-022-01330-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 12/08/2022] [Indexed: 06/17/2023]
Abstract
The mantled phenotype is an abnormal somaclonal variant arising from the oil palm cloning process and severe phenotypes lead to oil yield losses. Hypomethylation of the Karma retrotransposon within the B-type MADS-box EgDEF1 gene has been associated with this phenotype. While abnormal Karma-EgDEF1 hypomethylation was detected in mantled clones, we examined the methylation state of Karma in ortets that gave rise to high mantling rates in their clones. Small RNAs (sRNAs) were proposed to play a role in Karma hypomethylation as part of the RNA-directed DNA methylation process, hence differential expression analysis of sRNAs between the ortet groups was conducted. While no sRNA was differentially expressed at the Karma-EgDEF1 region, three sRNA clusters were differentially regulated in high-mantling ortets. The first two down-regulated clusters were possibly derived from long non-coding RNAs while the third up-regulated cluster was derived from the intron of a DnaJ chaperone gene. Several predicted mRNA targets for the first two sRNA clusters conversely displayed increased expression in high-mantling relative to low-mantling ortets. These predicted mRNA targets may be associated with defense or pathogenesis response. In addition, several differentially methylated regions (DMRs) were identified in Karma and its surrounding regions, mainly comprising subtle CHH hypomethylation in high-mantling ortets. Four of the 12 DMRs were located in a region corresponding to hypomethylated areas at the 3'end of Karma previously reported in mantled clones. Further investigations on these sRNAs and DMRs may indicate the predisposition of certain ortets towards mantled somaclonal variation.
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Affiliation(s)
- Siew-Eng Ooi
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
| | - Norashikin Sarpan
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Elizaveta Taranenko
- Department of Biology, University of La Verne, La Verne, CA, USA
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia, 660036
| | - Ishak Feshah
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Azimi Nuraziyan
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | | | | | - Nagappan Jayanthi
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Abdul Rahman Siti Rahmah
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia
| | - Ooi-Kock Teh
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd., Nankang, Taipei, Taiwan, R.O.C
| | - Meilina Ong-Abdullah
- Malaysian Palm Oil Board, 6 Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia.
| | - Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, CA, USA.
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia, 660036.
- Vavilov Institute for General Genetics, Moscow, Russia.
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
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11
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Sammarco I, Pieters J, Salony S, Toman I, Zolotarov G, Lafon Placette C. Epigenetic targeting of transposon relics: beating the dead horses of the genome? Epigenetics 2022; 17:1331-1344. [PMID: 36255200 PMCID: PMC9586680 DOI: 10.1080/15592294.2021.2022066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Transposable elements (TEs) have been seen as selfish genetic elements that can propagate in a host genome. Their propagation success is however hindered by a combination of mechanisms such as mutations, selection, and their epigenetic silencing by the host genome. As a result, most copies of TEs in a given genome are dead relics: their sequence is too degenerated to allow any transposition. Nevertheless, these TE relics often, but not always, remain epigenetically silenced, and if not to prevent transposition anymore, one can wonder the reason for this phenomenon. The mere self-perpetuating loop inherent to epigenetic silencing could alone explain that even when inactive, TE copies remain silenced. Beyond this process, nevertheless, antagonistic selective forces are likely to act on TE relic silencing. Especially, without the benefit of preventing transposition, TE relic silencing may prove deleterious to the host fitness, suggesting that the maintenance of TE relic silencing is the result of a fine, and perhaps case-by-case, evolutionary trade-off between beneficial and deleterious effects. Ultimately, the release of TE relics silencing may provide a 'safe' ground for adaptive epimutations to arise. In this review, we provide an overview of these questions in both plants and animals.
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Affiliation(s)
- Iris Sammarco
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic,Institute of Botany, Czech Academy of Sciences, Pruhonice, Czech Republic
| | - Janto Pieters
- Laboratory of Pollen Biology, Institute of Experimental Botany, Czech Academy of Science, Prague, Czech Republic,Department of Plant Experimental Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Susnata Salony
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Izabela Toman
- Department of Anthropology and Human Genetics, Faculty of Science, Charles University, Prague, Czech Republic
| | - Grygoriy Zolotarov
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Clément Lafon Placette
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic,CONTACT Clément Lafon Placette Department of Botany, Faculty of Science, Charles University, PragueCZ-128 01, Czech Republic
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12
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Plewiński P, Rychel-Bielska S, Kozak B, Maureira-Butler IJ, Iqbal MM, Nelson MN, Książkiewicz M. FLOWERING LOCUS T indel variants confer vernalization-independent and photoperiod-insensitive flowering of yellow lupin ( Lupinus luteus L.). HORTICULTURE RESEARCH 2022; 9:uhac180. [PMID: 36338848 PMCID: PMC9627521 DOI: 10.1093/hr/uhac180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023]
Abstract
Ongoing climate change has considerably reduced the seasonal window for crop vernalization, concurrently expanding cultivation area into northern latitudes with long-day photoperiod. To address these changes, cool season legume breeders need to understand molecular control of vernalization and photoperiod. A key floral transition gene integrating signals from these pathways is the Flowering locus T (FT). Here, a recently domesticated grain legume, yellow lupin (Lupinus luteus L.), was explored for potential involvement of FT homologues in abolition of vernalization and photoperiod requirements. Two FTa (LlutFTa1a and LlutFTa1b) and FTc (LlutFTc1 and LlutFTc2) homologues were identified and sequenced for two contrasting parents of a reference recombinant inbred line (RIL) population, an early-flowering cultivar Wodjil and a late-flowering wild-type P28213. Large deletions were detected in the 5' promoter regions of three FT homologues. Quantitative trait loci were identified for flowering time and vernalization response in the RIL population and in a diverse panel of wild and domesticated accessions. A 2227 bp deletion found in the LlutFTc1 promoter was linked with early phenology and vernalization independence, whereas LlutFTa1a and LlutFTc2 indels with photoperiod responsiveness. Comparative mapping highlighted convergence of FTc1 indel evolution in two Old World lupin species, addressing both artificial selection during domestication and natural adaptation to short season environmental conditions. We concluded that rapid flowering in yellow lupin is associated with the de-repression of the LlutFTc1 homologue from the juvenile phase, putatively due to the elimination of all binding sites in the promoter region for the AGAMOUS-like 15 transcription factor.
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Affiliation(s)
- Piotr Plewiński
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Bartosz Kozak
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Iván J Maureira-Butler
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Muhammad Munir Iqbal
- Centre for Plant Genetics and Breeding, The University of Western Australia, Perth, 6009, WA, Australia
- Genomics WA, Joint initiative of Telethon Kids Institute, Harry Perkins Institute of Medical Research and The University of Western Australia, QEII campus, Nedlands, 6009, Western Australia, Australia
| | - Matthew N Nelson
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia
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13
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DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development. Nat Commun 2022; 13:1335. [PMID: 35288562 PMCID: PMC8921224 DOI: 10.1038/s41467-022-28940-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/16/2022] [Indexed: 12/17/2022] Open
Abstract
A contribution of DNA methylation to defense against invading nucleic acids and maintenance of genome integrity is uncontested; however, our understanding of the extent of involvement of this epigenetic mark in genome-wide gene regulation and plant developmental control is incomplete. Here, we knock out all five known DNA methyltransferases in Arabidopsis, generating DNA methylation-free plants. This quintuple mutant exhibits a suite of developmental defects, unequivocally demonstrating that DNA methylation is essential for multiple aspects of plant development. We show that CG methylation and non-CG methylation are required for a plethora of biological processes, including pavement cell shape, endoreduplication, cell death, flowering, trichome morphology, vasculature and meristem development, and root cell fate determination. Moreover, we find that DNA methylation has a strong dose-dependent effect on gene expression and repression of transposable elements. Taken together, our results demonstrate that DNA methylation is dispensable for Arabidopsis survival but essential for the proper regulation of multiple biological processes. Our understanding of the extent of involvement of DNA methylation in genome-wide gene regulation and plant developmental control is incomplete. Here, the authors knock out all five known DNA methyltransferases and show the developmental and gene expression changes in the DNA methylation-free Arabidopsis plants.
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14
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Viviani A, Ventimiglia M, Fambrini M, Vangelisti A, Mascagni F, Pugliesi C, Usai G. Impact of transposable elements on the evolution of complex living systems and their epigenetic control. Biosystems 2021; 210:104566. [PMID: 34718084 DOI: 10.1016/j.biosystems.2021.104566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/21/2021] [Accepted: 10/21/2021] [Indexed: 10/20/2022]
Abstract
Transposable elements (TEs) contribute to genomic innovations, as well as genome instability, across a wide variety of species. Popular designations such as 'selfish DNA' and 'junk DNA,' common in the 1980s, may be either inaccurate or misleading, while a more enlightened view of the TE-host relationship covers a range from parasitism to mutualism. Both plant and animal hosts have evolved epigenetic mechanisms to reduce the impact of TEs, both by directly silencing them and by reducing their ability to transpose in the genome. However, TEs have also been co-opted by both plant and animal genomes to perform a variety of physiological functions, ranging from TE-derived proteins acting directly in normal biological functions to innovations in transcription factor activity and also influencing gene expression. Their presence, in fact, can affect a range of features at genome, phenotype, and population levels. The impact TEs have had on evolution is multifaceted, and many aspects still remain unexplored. In this review, the epigenetic control of TEs is contextualized according to the evolution of complex living systems.
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Affiliation(s)
- Ambra Viviani
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Maria Ventimiglia
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy.
| | - Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto, 80-56124, Pisa, Italy
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15
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The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation. Int J Mol Sci 2021; 22:ijms222111387. [PMID: 34768817 PMCID: PMC8583499 DOI: 10.3390/ijms222111387] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023] Open
Abstract
Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.
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16
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You L, Lin J, Xu H, Chen C, Chen J, Zhang J, Zhang J, Li Y, Ye C, Zhang H, Jiang J, Zhu J, Li QQ, Duan C. Intragenic heterochromatin-mediated alternative polyadenylation modulates miRNA and pollen development in rice. THE NEW PHYTOLOGIST 2021; 232:835-852. [PMID: 34289124 PMCID: PMC9292364 DOI: 10.1111/nph.17635] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/25/2021] [Indexed: 05/02/2023]
Abstract
Despite a much higher proportion of intragenic heterochromatin-containing genes in crop genomes, the importance of intragenic heterochromatin in crop development remains unclear. Intragenic heterochromatin can be recognised by a protein complex, ASI1-AIPP1-EDM2 (AAE) complex, to regulate alternative polyadenylation. Here, we investigated the impact of rice ASI1 on global poly(A) site usage through poly(A) sequencing and ASI1-dependent regulation on rice development. We found that OsASI1 is essential for rice pollen development and flowering. OsASI1 dysfunction has an important impact on global poly(A) site usage, which is closely related to heterochromatin marks. Intriguingly, OsASI1 interacts with the intronic heterochromatin of OsXRNL, a nuclear XRN family exonuclease gene involved in the processing of an miRNA precursor, to promote the processing of full-length OsXRNL and regulate miRNA abundance. We found that OsASI1-mediated regulation of pollen development partially depends on OsXRNL. Finally, we characterised the rice AAE complex and its involvement in alternative polyadenylation and pollen development. Our findings help to elucidate an epigenetic mechanism governing miRNA abundance and rice development, and provide a valuable resource for studying the epigenetic mechanisms of many important processes in crops.
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Affiliation(s)
- Li‐Yuan You
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
- University of Chinese Academy of SciencesBeijing100049China
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland EcosystemsCollege of the Environment and EcologyXiamen UniversityXiamenFujian361102China
| | - Hua‐Wei Xu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
- College of AgricultureHenan University of Science and TechnologyLuoyang471023China
| | - Chun‐Xiang Chen
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
- University of Chinese Academy of SciencesBeijing100049China
| | - Jun‐Yu Chen
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
- University of Chinese Academy of SciencesBeijing100049China
| | - Jinshan Zhang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
| | - Jian Zhang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
- University of Chinese Academy of SciencesBeijing100049China
| | - Ying‐Xin Li
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
- University of Chinese Academy of SciencesBeijing100049China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland EcosystemsCollege of the Environment and EcologyXiamen UniversityXiamenFujian361102China
| | - Hui Zhang
- College of Life ScienceShanghai Normal UniversityShanghai200234China
| | - Jing Jiang
- State Key Laboratory of Crop Stress Adaptation and ImprovementSchool of Life SciencesHenan UniversityKaifeng475004China
| | - Jian‐Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
| | - Qingshun Q. Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland EcosystemsCollege of the Environment and EcologyXiamen UniversityXiamenFujian361102China
- Graduate College of Biomedical SciencesWestern University of Health SciencesPomonaCA91766USA
| | - Cheng‐Guo Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant SciencesChinese Academy of ScienceShanghai201602China
- University of Chinese Academy of SciencesBeijing100049China
- State Key Laboratory of Crop Stress Adaptation and ImprovementSchool of Life SciencesHenan UniversityKaifeng475004China
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17
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De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree ( Bruguiera gymnorhiza). Int J Mol Sci 2021; 22:ijms22189874. [PMID: 34576037 PMCID: PMC8467813 DOI: 10.3390/ijms22189874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 12/13/2022] Open
Abstract
Their high adaptability to difficult coastal conditions makes mangrove trees a valuable resource and an interesting model system for understanding the molecular mechanisms underlying stress tolerance and adaptation of plants to the stressful environmental conditions. In this study, we used RNA sequencing (RNA-Seq) for de novo assembling and characterizing the Bruguiera gymnorhiza (L.) Lamk leaf transcriptome. B. gymnorhiza is one of the most widely distributed mangrove species from the biggest family of mangroves; Rhizophoraceae. The de novo assembly was followed by functional annotations and identification of individual transcripts and gene families that are involved in abiotic stress response. We then compared the genome-wide expression profiles between two populations of B. gymnorhiza, growing under different levels of stress, in their natural habitats. One population living in high salinity environment, in the shore of the Pacific Ocean- Japan, and the other population living about one kilometre farther from the ocean, and next to the estuary of a river; in less saline and more brackish condition. Many genes involved in response to salt and osmotic stress, showed elevated expression levels in trees growing next to the ocean in high salinity condition. Validation of these genes may contribute to future salt-resistance research in mangroves and other woody plants. Furthermore, the sequences and transcriptome data provided in this study are valuable scientific resources for future comparative transcriptome research in plants growing under stressful conditions.
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18
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Ritter EJ, Niederhuth CE. Intertwined evolution of plant epigenomes and genomes. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:101990. [PMID: 33445143 DOI: 10.1016/j.pbi.2020.101990] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
DNA methylation is found across eukaryotes; however, plants have evolved patterns and pathways of DNA methylation that are distinct from animals and fungi. DNA methylation shapes the evolution of genomes through its direct roles in transposon silencing, gene expression, genome stability, and its impact on mutation rates. In return the diversity of DNA methylation across species is shaped by genome sequence evolution. Extensive diversification of key DNA methylation pathways has continued in plants through gene duplication and loss. Meanwhile, frequent movement of transposons has altered local DNA methylation patterns and the genes affected. Only recently has the diversity and evolutionary history of plant DNA methylation become evident with the availability of increasing genomic and epigenomic data. However, much remains unresolved regarding the evolutionary forces that have shaped the dynamics of the complex and intertwined history of plant genome and epigenome evolution.
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Affiliation(s)
- Eleanore J Ritter
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; AgBioResearch, Michigan State University, East Lansing, MI 48824, USA.
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19
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Baduel P, Quadrana L. Jumpstarting evolution: How transposition can facilitate adaptation to rapid environmental changes. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102043. [PMID: 33932785 DOI: 10.1016/j.pbi.2021.102043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/10/2021] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
Because of their ability to replicate across genomes, transposable elements (TEs) represent major generators of large-effect mutations. As a result, chromatin-based mechanisms have evolved to control the mutational potential of TEs at multiple levels, from the epigenetic silencing of TE sequences, through the modulation of their integration space, up to the alleviation of the impact of new insertions. Although most TE insertions are highly deleterious, some can provide key adaptive variation. Together with their remarkable sensitivity to the environment and precise integration preferences, the unique characteristics of TEs place them as potent genomic engines of adaptive innovation. Herein, we review recent works exploring the regulation and impact of transposition in nature and discuss their implications for the evolutionary response of species to drastic environmental changes.
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Affiliation(s)
- Pierre Baduel
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France
| | - Leandro Quadrana
- Institut de Biologie de l'École Normale Supérieure, ENS, 46 rue d'Ulm, 75005, Paris, France.
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20
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Parker MT, Knop K, Zacharaki V, Sherwood AV, Tomé D, Yu X, Martin PGP, Beynon J, Michaels SD, Barton GJ, Simpson GG. Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA. eLife 2021; 10:e65537. [PMID: 33904405 PMCID: PMC8116057 DOI: 10.7554/elife.65537] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers of nucleotide-binding, leucine-rich repeat (NLR) genes are found in plant genomes and are required for disease resistance. However, NLRs can trigger autoimmunity, disrupt beneficial microbiota or reduce fitness. It is therefore crucial to understand how NLRs are controlled. Here, we show that the RNA-binding protein FPA mediates widespread premature cleavage and polyadenylation of NLR transcripts, thereby controlling their functional expression and impacting immunity. Using long-read Nanopore direct RNA sequencing, we resolved the complexity of NLR transcript processing and gene annotation. Our results uncover a co-transcriptional layer of NLR control with implications for understanding the regulatory and evolutionary dynamics of NLRs in the immune responses of plants.
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Affiliation(s)
- Matthew T Parker
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Katarzyna Knop
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | | | - Anna V Sherwood
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Daniel Tomé
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Xuhong Yu
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Pascal GP Martin
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Jim Beynon
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Scott D Michaels
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | | | - Gordon G Simpson
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
- The James Hutton InstituteInvergowrieUnited Kingdom
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21
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Zhang Z, Wang H, Wang Y, Xi F, Wang H, Kohnen MV, Gao P, Wei W, Chen K, Liu X, Gao Y, Han X, Hu K, Zhang H, Zhu Q, Zheng Y, Liu B, Ahmad A, Hsu YH, Jacobsen SE, Gu L. Whole-genome characterization of chronological age-associated changes in methylome and circular RNAs in moso bamboo (Phyllostachys edulis) from vegetative to floral growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:435-453. [PMID: 33506534 DOI: 10.1111/tpj.15174] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/30/2020] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
In mammals, DNA methylation is associated with aging. However, age-related DNA methylation changes during phase transitions largely remain unstudied in plants. Moso bamboo (Phyllostachys edulis) requires a very long time to transition from the vegetative to the floral phase. To comprehensively investigate the association of DNA methylation with aging, we present here single-base-resolution DNA methylation profiles using both high-throughput bisulfite sequencing and single-molecule nanopore-based DNA sequencing, covering the long period of vegetative growth and transition to flowering in moso bamboo. We discovered that CHH methylation gradually accumulates from vegetative to reproductive growth in a time-dependent fashion. Differentially methylated regions, correlating with chronological aging, occurred preferentially at both transcription start sites and transcription termination sites. Genes with CG methylation changes showed an enrichment of Gene Ontology (GO) categories in 'vegetative to reproductive phase transition of meristem'. Combining methylation data with mRNA sequencing revealed that DNA methylation in promoters, introns and exons may have different roles in regulating gene expression. Finally, circular RNA (circRNA) sequencing revealed that the flanking introns of circRNAs are hypermethylated and enriched in long terminal repeat (LTR) retrotransposons. Together, the observations in this study provide insights into the dynamic DNA methylation and circRNA landscapes, correlating with chronological age, which paves the way to study further the impact of epigenetic factors on flowering in moso bamboo.
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Affiliation(s)
- Zeyu Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongsheng Wang
- Basic Forestry and Proteomics Research Center, College of life science, Fuzhou, 350002, China
| | - Feihu Xi
- Basic Forestry and Proteomics Research Center, College of life science, Fuzhou, 350002, China
| | - Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Markus V Kohnen
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Pengfei Gao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wentao Wei
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kai Chen
- Basic Forestry and Proteomics Research Center, College of life science, Fuzhou, 350002, China
| | - Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yubang Gao
- Basic Forestry and Proteomics Research Center, College of life science, Fuzhou, 350002, China
| | - Ximei Han
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kaiqiang Hu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiang Zhu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yushan Zheng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bo Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ayaz Ahmad
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Steven E Jacobsen
- Department of Molecular, Cell & Developmental Biology, Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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22
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Zhang YZ, Lin J, Ren Z, Chen CX, Miki D, Xie SS, Zhang J, Chang YN, Jiang J, Yan J, Li QQ, Zhu JK, Duan CG. Genome-wide distribution and functions of the AAE complex in epigenetic regulation in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:707-722. [PMID: 33438356 DOI: 10.1111/jipb.13068] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/30/2020] [Indexed: 06/12/2023]
Abstract
Heterochromatin is widespread in eukaryotic genomes and has diverse impacts depending on its genomic context. Previous studies have shown that a protein complex, the ASI1-AIPP1-EDM2 (AAE) complex, participates in polyadenylation regulation of several intronic heterochromatin-containing genes. However, the genome-wide functions of AAE are still unknown. Here, we show that the ASI1 and EDM2 mostly target the common genomic regions on a genome-wide level and preferentially interacts with genetic heterochromatin. Polyadenylation (poly(A) sequencing reveals that AAE complex has a substantial influence on poly(A) site usage of heterochromatin-containing genes, including not only intronic heterochromatin-containing genes but also the genes showing overlap with heterochromatin. Intriguingly, AAE is also involved in the alternative splicing regulation of a number of heterochromatin-overlapping genes, such as the disease resistance gene RPP4. We provided evidence that genic heterochromatin is indispensable for the recruitment of AAE in polyadenylation and splicing regulation. In addition to conferring RNA processing regulation at genic heterochromatin-containing genes, AAE also targets some transposable elements (TEs) outside of genes (including TEs sandwiched by genes and island TEs) for epigenetic silencing. Our results reveal new functions of AAE in RNA processing and epigenetic silencing, and thus represent important advances in epigenetic regulation.
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Affiliation(s)
- Yi-Zhe Zhang
- Shanghai Center for Plant Stress Biology and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
| | - Zhizhong Ren
- Shanghai Center for Plant Stress Biology and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Chun-Xiang Chen
- Shanghai Center for Plant Stress Biology and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Si-Si Xie
- Shanghai Center for Plant Stress Biology and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Zhang
- Shanghai Center for Plant Stress Biology and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ya-Nan Chang
- Shanghai Center for Plant Stress Biology and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Jiang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Jun Yan
- School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, 91766, USA
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, 47907, USA
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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23
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Eskier D, Karakülah G. In Silico Identification of Stress-Associated Transposable Elements in Arabidopsis thaliana Using Public Transcriptome Data. Methods Mol Biol 2021; 2250:15-30. [PMID: 33900589 DOI: 10.1007/978-1-0716-1134-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Transposable elements (TEs) have been associated with stress response in many plants, making them a key target of study. However, the high variability, genomic repeat-heavy nature, and widely noncoding character of TEs have made them difficult to study using non-specialized methods, whether experimental or computational. In this chapter, we introduce two computational workflows to analyze transposable elements using publicly available transcriptome data. In the first of these methods, we identify TEs, which show differential expression under salt stress using sample transcriptome libraries that includes noncoding transcripts. In the second, we identify protein-coding genes with differential expression under the same conditions, and determine which TEs are enriched in the promoter regions of these stress-related genes.
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Affiliation(s)
- Doğa Eskier
- İzmir International Biomedicine and Genome Institute (iBG-İzmir), Dokuz Eylül University, İnciralti, İzmir, Turkey
- İzmir Biomedicine and Genome Center (IBG), İnciralti, İzmir, Turkey
| | - Gökhan Karakülah
- İzmir International Biomedicine and Genome Institute (iBG-İzmir), Dokuz Eylül University, İnciralti, İzmir, Turkey.
- İzmir Biomedicine and Genome Center (IBG), İnciralti, İzmir, Turkey.
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24
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Fambrini M, Usai G, Vangelisti A, Mascagni F, Pugliesi C. The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations. Genesis 2020; 58:e23399. [DOI: 10.1002/dvg.23399] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/07/2020] [Accepted: 11/10/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE) University of Pisa Pisa Italy
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25
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Lai Y, Lu XM, Daron J, Pan S, Wang J, Wang W, Tsuchiya T, Holub E, McDowell JM, Slotkin RK, Le Roch KG, Eulgem T. The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression. PLoS Genet 2020; 16:e1008993. [PMID: 32925902 PMCID: PMC7529245 DOI: 10.1371/journal.pgen.1008993] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/01/2020] [Accepted: 07/14/2020] [Indexed: 12/19/2022] Open
Abstract
Plant NLR-type receptors serve as sensitive triggers of host immunity. Their expression has to be well-balanced, due to their interference with various cellular processes and dose-dependency of their defense-inducing activity. A genetic “arms race” with fast-evolving pathogenic microbes requires plants to constantly innovate their NLR repertoires. We previously showed that insertion of the COPIA-R7 retrotransposon into RPP7 co-opted the epigenetic transposon silencing signal H3K9me2 to a new function promoting expression of this Arabidopsis thaliana NLR gene. Recruitment of the histone binding protein EDM2 to COPIA-R7-associated H3K9me2 is required for optimal expression of RPP7. By profiling of genome-wide effects of EDM2, we now uncovered additional examples illustrating effects of transposons on NLR gene expression, strongly suggesting that these mobile elements can play critical roles in the rapid evolution of plant NLR genes by providing the “raw material” for gene expression mechanisms. We further found EDM2 to have a global role in NLR expression control. Besides serving as a positive regulator of RPP7 and a small number of other NLR genes, EDM2 acts as a suppressor of a multitude of additional NLR genes. We speculate that the dual functionality of EDM2 in NLR expression control arose from the need to compensate for fitness penalties caused by high expression of some NLR genes by suppression of others. Moreover, we are providing new insights into functional relationships of EDM2 with its interaction partner, the RNA binding protein EDM3/AIPP1, and its target gene IBM1, encoding an H3K9-demethylase. We previously found the Arabidopsis thaliana PHD-finger protein EDM2 to serve as a chromatin-associated factor controlling expression of the NLR-type immune receptor gene RPP7. EDM2 binds to the transposon-silencing signal H3K9me2 and affects levels of this epigenetic mark at various loci. By genome-wide profiling of transcript- and H3K9me2-levels we now found EDM2 to have a broader role in controlling NLR gene expression. In order to mitigate fitness costs caused by its promoting effects on RPP7 expression and that of several other NLR genes, EDM2 seems to suppress expression of many additional members of this gene family. This observation is in line with multiple reports demonstrating the need for balanced expression of NLRs, which can substantially reduce overall plant fitness, but need to be present at certain minimal levels to confer sufficient immune protection. Our previous results demonstrated that the influence of EDM2 on RPP7 expression was co-opted to this immune receptor gene by the insertion of an EDM2-controlled transposon. Here, we are providing additional examples for transposon-associated effects on NLR gene expression, suggesting that these mobile elements play an important role for NLR genes by equipping members of this rapidly evolving gene family with regulatory mechanisms needed for balanced expression.
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Affiliation(s)
- Yan Lai
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, China
| | - Xueqing Maggie Lu
- Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, Department of Molecular, Cell and Systems Biology, University of California at Riverside, Riverside, CA, United States of America
| | - Josquin Daron
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Songqin Pan
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
| | - Jianqiang Wang
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
| | - Wei Wang
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States of America
| | - Tokuji Tsuchiya
- College of Bioresource Sciences, Nihon University, Kanagawa, Japan
| | - Eric Holub
- School of Life Sciences, University of Warwick, Wellesbourne campus, United Kingdom
| | - John M. McDowell
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, United States of America
| | - R. Keith Slotkin
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, United States of America
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
- Division of Biological Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Karine G. Le Roch
- Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, Department of Molecular, Cell and Systems Biology, University of California at Riverside, Riverside, CA, United States of America
- * E-mail: (KGLR); (TE)
| | - Thomas Eulgem
- Center for Plant Cell Biology, Institute of Integrative Genome Biology, Department of Botany and Plan Sciences, University of California at Riverside, Riverside, CA, United States of America
- * E-mail: (KGLR); (TE)
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26
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Zavallo D, Crescente JM, Gantuz M, Leone M, Vanzetti LS, Masuelli RW, Asurmendi S. Genomic re-assessment of the transposable element landscape of the potato genome. PLANT CELL REPORTS 2020; 39:1161-1174. [PMID: 32435866 DOI: 10.1007/s00299-020-02554-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/07/2020] [Indexed: 05/14/2023]
Abstract
We provide a comprehensive and reliable potato TE landscape, based on a wide variety of identification tools and integrative approaches, producing clear and ready-to-use outputs for the scientific community. Transposable elements (TEs) are DNA sequences with the ability to autoreplicate and move throughout the host genome. TEs are major drivers in stress response and genome evolution. Given their significance, the development of clear and efficient TE annotation pipelines has become essential for many species. The latest de novo TE discovery tools, along with available TEs from Repbase and sRNA-seq data, allowed us to perform a reliable potato TEs detection, classification and annotation through an open-source and freely available pipeline ( https://github.com/DiegoZavallo/TE_Discovery ). Using a variety of tools, approaches and rules, we were able to provide a clearly annotated of characterized TEs landscape. Additionally, we described the distribution of the different types of TEs across the genome, where LTRs and MITEs present a clear clustering pattern in pericentromeric and subtelomeric/telomeric regions respectively. Finally, we analyzed the insertion age and distribution of LTR retrotransposon families which display a distinct pattern between the two major superfamilies. While older Gypsy elements concentrated around heterochromatic regions, younger Copia elements located predominantly on euchromatic regions. Overall, we delivered not only a reliable, ready-to-use potato TE annotation files, but also all the necessary steps to perform de novo detection for other species.
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Affiliation(s)
- Diego Zavallo
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repeto, Hurlingham, Argentina.
| | - Juan Manuel Crescente
- Grupo Biotecnologia y Recursos Genéticos, EEA INTA Marcos Juárez, Ruta 12 Km 3, 2580, Marcos Juárez, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Magdalena Gantuz
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Melisa Leone
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repeto, Hurlingham, Argentina
- Agencia Nacional de Promocion Científica y Tecnológica (ANPCyT), Buenos Aires, Argentina
| | - Leonardo Sebastian Vanzetti
- Grupo Biotecnologia y Recursos Genéticos, EEA INTA Marcos Juárez, Ruta 12 Km 3, 2580, Marcos Juárez, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ricardo Williams Masuelli
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Sebastian Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repeto, Hurlingham, Argentina.
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27
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Zhang J, Zhang YZ, Jiang J, Duan CG. The Crosstalk Between Epigenetic Mechanisms and Alternative RNA Processing Regulation. Front Genet 2020; 11:998. [PMID: 32973889 PMCID: PMC7472560 DOI: 10.3389/fgene.2020.00998] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/05/2020] [Indexed: 12/19/2022] Open
Abstract
As a co-transcriptional process, RNA processing, including alternative splicing and alternative polyadenylation, is crucial for the generation of multiple mRNA isoforms. RNA processing mechanisms are widespread across all higher eukaryotes and play critical roles in cell differentiation, organ development and disease response. Recently, significant progresses have been made in understanding the mechanism of RNA processing. RNA processing is regulated by trans-acting factors such as splicing factors, RNA-binding proteins and cis-sequences in pre-mRNA, and increasing evidence suggests that epigenetic mechanisms, which are important for the dynamic regulation and state of specific chromatic regions, are also involved in co-transcriptional RNA processing. In contrast, recent studies also suggest that alternative RNA processing also has a feedback regulation on epigenetic mechanisms. In this review, we discuss recent studies and summarize the current knowledge on the epigenetic regulation of alternative RNA processing. In addition, a feedback regulation of RNA processing on epigenetic regulators is also discussed.
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Affiliation(s)
- Jian Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yi-Zhe Zhang
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jing Jiang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
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28
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Quadrana L. The contribution of transposable elements to transcriptional novelty in plants: the FLC affair. Transcription 2020; 11:192-198. [PMID: 32783496 PMCID: PMC7714446 DOI: 10.1080/21541264.2020.1803031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Transposable elements (TEs) are repetitive DNA sequences with the ability to replicate across genomes and generate mutations with major transcriptional effects. Epigenetic silencing mechanisms that target TEs to limit their activity, including DNA methylation, add to the range of gene expression variants generated by TEs. Here, using the iconic gene flowering locus C (FLC) as a case study I discuss the multiple ways by which TEs can affect the expression of genes and contribute to the adaptation of plants to changing environments
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Affiliation(s)
- Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University , Paris, France
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29
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Le NT, Harukawa Y, Miura S, Boer D, Kawabe A, Saze H. Epigenetic regulation of spurious transcription initiation in Arabidopsis. Nat Commun 2020; 11:3224. [PMID: 32591528 PMCID: PMC7319988 DOI: 10.1038/s41467-020-16951-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/01/2020] [Indexed: 01/01/2023] Open
Abstract
In plants, epigenetic regulation is critical for silencing transposons and maintaining proper gene expression. However, its impact on the genome-wide transcription initiation landscape remains elusive. By conducting a genome-wide analysis of transcription start sites (TSSs) using cap analysis of gene expression (CAGE) sequencing, we show that thousands of TSSs are exclusively activated in various epigenetic mutants of Arabidopsis thaliana and referred to as cryptic TSSs. Many have not been identified in previous studies, of which up to 65% are contributed by transposons. They possess similar genetic features to regular TSSs and their activation is strongly associated with the ectopic recruitment of RNAPII machinery. The activation of cryptic TSSs significantly alters transcription of nearby TSSs, including those of genes important for development and stress responses. Our study, therefore, sheds light on the role of epigenetic regulation in maintaining proper gene functions in plants by suppressing transcription from cryptic TSSs. Epigenetic regulation can silence transposons and maintain gene expression. Here the authors survey Arabidopsis mutants defective in epigenetic regulation and show ectopic activation of thousands of cryptic TSSs and altered expression of nearby genes demonstrating the importance of suppressing spurious transcription.
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Affiliation(s)
- Ngoc Tu Le
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Yoshiko Harukawa
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Saori Miura
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan
| | - Damian Boer
- Wageningen University & Research, Droevendaalsesteeg 4, 6708 PB Wageningen, Netherlands
| | - Akira Kawabe
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, 603-8555, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
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30
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Zhou J, Liu L, Li Q, Xu W, Li K, Wang ZW, Sun Q. Intronic heterochromatin prevents cryptic transcription initiation in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1185-1197. [PMID: 31647592 DOI: 10.1111/tpj.14584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 10/06/2019] [Accepted: 10/17/2019] [Indexed: 06/10/2023]
Abstract
Intronic transposable elements (TEs) comprise a large proportion in eukaryotic genomes, but how they regulate the host genes remains to be explored. Our forward genetic screen disclosed the plant-specific RNA polymerases IV and V in suppressing intronic TE-mediated cryptic transcription initiation of a chimeric transcripts at FLC (FLCTE ). Initiation of FLCTE transcription is blocked by the locally formed intronic heterochromatin, which is directly associated with RNA Pol V to inhibit the entry of RNA Pol II and the occupancy of H3K4 methylation. Genome-wide Pol II Ser5p native elongation transcription sequencing revealed that a significant number of intronic heterochromatin-containing genes undergo this mechanism. This study sheds light on deeply understanding the function of intronic heterochromatin on host genes expression in eukaryotic genome.
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Affiliation(s)
- Jincong Zhou
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Liangyu Liu
- Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing Municipal Government, College of Life Sciences, Capital Normal University, Beijing, China
| | - Qin Li
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wei Xu
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Kuan Li
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhi-Wei Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Qianwen Sun
- Tsinghua-Peking Joint Center for Life Sciences and Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
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31
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Espinas NA, Tu LN, Furci L, Shimajiri Y, Harukawa Y, Miura S, Takuno S, Saze H. Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome. PLoS Genet 2020; 16:e1008637. [PMID: 32187179 PMCID: PMC7145194 DOI: 10.1371/journal.pgen.1008637] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 04/09/2020] [Accepted: 01/28/2020] [Indexed: 11/18/2022] Open
Abstract
Intronic regions of eukaryotic genomes accumulate many Transposable Elements (TEs). Intronic TEs often trigger the formation of transcriptionally repressive heterochromatin, even within transcription-permissive chromatin environments. Although TE-bearing introns are widely observed in eukaryotic genomes, their epigenetic states, impacts on gene regulation and function, and their contributions to genetic diversity and evolution, remain poorly understood. In this study, we investigated the genome-wide distribution of intronic TEs and their epigenetic states in the Oryza sativa genome, where TEs comprise 35% of the genome. We found that over 10% of rice genes contain intronic heterochromatin, most of which are associated with TEs and repetitive sequences. These heterochromatic introns are longer and highly enriched in promoter-proximal positions. On the other hand, introns also accumulate hypomethylated short TEs. Genes with heterochromatic introns are implicated in various biological functions. Transcription of genes bearing intronic heterochromatin is regulated by an epigenetic mechanism involving the conserved factor OsIBM2, mutation of which results in severe developmental and reproductive defects. Furthermore, we found that heterochromatic introns evolve rapidly compared to non-heterochromatic introns. Our study demonstrates that heterochromatin is a common epigenetic feature associated with actively transcribed genes in the rice genome.
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Affiliation(s)
- Nino A. Espinas
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama city, Kanagawa, Japan
| | - Le Ngoc Tu
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Leonardo Furci
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Yasuka Shimajiri
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
- EditForce, Fukuoka, Japan
| | - Yoshiko Harukawa
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Saori Miura
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
| | - Shohei Takuno
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Hidetoshi Saze
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, Onna-son, Okinawa, Japan
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Zhu C, Zhang S, Zhou C, Chen L, Fu H, Li X, Lin Y, Lai Z, Guo Y. Genome-wide investigation and transcriptional analysis of cytosine-5 DNA methyltransferase and DNA demethylase gene families in tea plant ( Camellia sinensis) under abiotic stress and withering processing. PeerJ 2020; 8:e8432. [PMID: 31976183 PMCID: PMC6968495 DOI: 10.7717/peerj.8432] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is a highly conserved epigenetic modification involved in many biological processes, including growth and development, stress response, and secondary metabolism. In the plant kingdom, cytosine-5 DNA methyltransferase (C5-MTase) and DNA demethylase (dMTase) genes have been identified in some plant species. However, to the best of our knowledge, no investigator has focused on the identification and analysis of C5-MTase and dMTase genes in tea plants (Camellia sinensis) based on genome-wide levels. In this study, eight CsC5-MTases and four dMTases were identified in tea plants. These CsC5-MTase genes were divided into four subfamilies, including CsMET, CsCMT, CsDRM and CsDNMT2. The CsdMTase genes can be classified into CsROS, CsDME and CsDML. Based on conserved domain analysis of these genes, the gene loss and duplication events occurred during the evolution of CsC5-MTase and CsdMTase. Furthermore, multiple cis-acting elements were observed in the CsC5-MTase and CsdMTase, including light responsiveness, phytohormone responsiveness, stress responsiveness, and plant growth and development-related elements. Then, we investigated the transcript abundance of CsC5-MTase and CsdMTase under abiotic stress (cold and drought) and withering processing (white tea and oolong tea). Notably, most CsC5-MTases, except for CsCMT1 and CsCMT2, were significantly downregulated under abiotic stress, while the transcript abundance of all four CsdMTase genes was significantly induced. Similarly, the same transcript abundance of CsC5-MTase and CsdMTase was found during withering processing of white tea and oolong tea, respectively. In total, our findings will provide a basis for the roles of CsC5-MTase and CsdMTase in response to abiotic stress and the potential functions of these two gene families in affecting tea flavor during tea withering processing.
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Affiliation(s)
- Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Lan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Haifeng Fu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaozhen Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Alvarez JM, Moyano TC, Zhang T, Gras DE, Herrera FJ, Araus V, O'Brien JA, Carrillo L, Medina J, Vicente-Carbajosa J, Jiang J, Gutiérrez RA. Local Changes in Chromatin Accessibility and Transcriptional Networks Underlying the Nitrate Response in Arabidopsis Roots. MOLECULAR PLANT 2019; 12:1545-1560. [PMID: 31526863 DOI: 10.1016/j.molp.2019.09.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/27/2019] [Accepted: 09/05/2019] [Indexed: 05/13/2023]
Abstract
Transcriptional regulation, determined by the chromatin structure and regulatory elements interacting at promoter regions, is a key step in plant responses to environmental cues. Nitrate (NO3-) is a nutrient signal that regulates the expression of hundreds of genes in Arabidopsis thaliana. Here, we integrate mRNA sequencing, genome-wide RNA polymerase II (RNPII), chromatin immunoprecipitation sequencing, and DNase sequencing datasets to establish the relationship between RNPII occupancy and chromatin accessibility in response to NO3- treatments in Arabidopsis roots. Genomic footprinting allowed us to identify in vivo regulatory elements controlling gene expression in response to NO3- treatments. NO3--modulated transcription factor (TF) footprints are important for a rapid increase in RNPII occupancy and transcript accumulation over time. We mapped key TF regulatory interactions and functionally validated the role of NAP, an NAC-domain containing TF, as a new regulatory factor in NO3- transport. Taken together, our study provides a comprehensive view of transcriptional networks in response to a nutrient signal in Arabidopsis roots.
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Affiliation(s)
- José M Alvarez
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Tomás C Moyano
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Tao Zhang
- Yangzhou University, Yangzhou, China
| | - Diana E Gras
- Instituto de Agrobiotecnologia del Litoral, CONICET, Santa Fe, Argentina
| | - Francisco J Herrera
- University of California, Berkeley, CA, USA; Trancura Biosciences, Inc., San Francisco, CA 94158, USA
| | - Viviana Araus
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - José A O'Brien
- Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Laura Carrillo
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Joaquín Medina
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Jesús Vicente-Carbajosa
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, 28223-Pozuelo de Alarcón, Madrid, Spain
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Plant Biology and Horticulture, Michigan State University, MI 48824, USA
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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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35
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Pontier D, Picart C, El Baidouri M, Roudier F, Xu T, Lahmy S, Llauro C, Azevedo J, Laudié M, Attina A, Hirtz C, Carpentier MC, Shen L, Lagrange T. The m 6A pathway protects the transcriptome integrity by restricting RNA chimera formation in plants. Life Sci Alliance 2019; 2:2/3/e201900393. [PMID: 31142640 PMCID: PMC6545605 DOI: 10.26508/lsa.201900393] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 11/24/2022] Open
Abstract
This study reveals that an m6A-assisted polyadenylation pathway comprising conserved m6A writer proteins and a plant-specific m6A reader contributes to transcriptome integrity in Arabidopsis thaliana by restricting RNA chimera formation at rearranged loci. Global, segmental, and gene duplication–related processes are driving genome size and complexity in plants. Despite their evolutionary potentials, those processes can also have adverse effects on genome regulation, thus implying the existence of specialized corrective mechanisms. Here, we report that an N6-methyladenosine (m6A)–assisted polyadenylation (m-ASP) pathway ensures transcriptome integrity in Arabidopsis thaliana. Efficient m-ASP pathway activity requires the m6A methyltransferase-associated factor FIP37 and CPSF30L, an m6A reader corresponding to an YT512-B Homology Domain-containing protein (YTHDC)-type domain containing isoform of the 30-kD subunit of cleavage and polyadenylation specificity factor. Targets of the m-ASP pathway are enriched in recently rearranged gene pairs, displayed an atypical chromatin signature, and showed transcriptional readthrough and mRNA chimera formation in FIP37- and CPSF30L-deficient plants. Furthermore, we showed that the m-ASP pathway can also restrict the formation of chimeric gene/transposable-element transcript, suggesting a possible implication of this pathway in the control of transposable elements at specific locus. Taken together, our results point to selective recognition of 3′-UTR m6A as a safeguard mechanism ensuring transcriptome integrity at rearranged genomic loci in plants.
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Affiliation(s)
- Dominique Pontier
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Claire Picart
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Moaine El Baidouri
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - François Roudier
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon1, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Lyon, France
| | - Tao Xu
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Sylvie Lahmy
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Christel Llauro
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Jacinthe Azevedo
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Michèle Laudié
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Aurore Attina
- Platform SMART/Laboratoire de Biochimie et Protéomique Clinique/Plateforme de Protéomique Clinique, University of Montpellier, Institut de Médecine Régénérative et de Biothérapie , Centre Hospitalier Universitaire Montpellier, Institut national de la santé et de la Recherche Médicale, Montpeller, France
| | - Christophe Hirtz
- Platform SMART/Laboratoire de Biochimie et Protéomique Clinique/Plateforme de Protéomique Clinique, University of Montpellier, Institut de Médecine Régénérative et de Biothérapie , Centre Hospitalier Universitaire Montpellier, Institut national de la santé et de la Recherche Médicale, Montpeller, France
| | - Marie-Christine Carpentier
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France.,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
| | - Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, NUS, Singapore
| | - Thierry Lagrange
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, UMR 5096, Perpignan, France .,Univ. Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, Perpignan, France
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36
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Liu X, Zhao J, Guo HS. IBM1-dependent H3K9 demethylation enables self-silencing of an exogenous silencer for the non-cell autonomous silencing of an endogenous target gene. J Genet Genomics 2019; 46:149-153. [PMID: 30935857 DOI: 10.1016/j.jgg.2019.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 02/19/2019] [Indexed: 11/18/2022]
Affiliation(s)
- Xiaolan Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianhua Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hui-Shan Guo
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China; College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China.
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37
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Genome defense against integrated organellar DNA fragments from plastids into plant nuclear genomes through DNA methylation. Sci Rep 2019; 9:2060. [PMID: 30765781 PMCID: PMC6376042 DOI: 10.1038/s41598-019-38607-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 12/31/2018] [Indexed: 01/09/2023] Open
Abstract
Nuclear genomes are always faced with the modification of themselves by insertions and integrations of foreign DNAs and intrinsic parasites such as transposable elements. There is also substantial number of integrations from symbiotic organellar genomes to their host nuclear genomes. Such integration might have acted as a beneficial mutation during the evolution of symbiosis, while most of them have more or less deleterious effects on the stability of current genomes. Here we report the pattern of DNA substitution and methylation on organellar DNA fragments integrated from plastid into plant nuclear genomes. The genome analyses of 17 plants show homology–dependent DNA substitution bias. A certain number of these sequences are DNA methylated in the nuclear genome. The intensity of DNA methylation also decays according to the increase of relative evolutionary times after being integrated into nuclear genomes. The methylome data of epigenetic mutants shows that the DNA methylation of organellar DNA fragments in nuclear genomes are mainly dependent on the methylation maintenance machinery, while other mechanisms may also affect on the DNA methylation level. The DNA methylation on organellar DNA fragments may contribute to maintaining the genome stability and evolutionary dynamics of symbiotic organellar and their host’s genomes.
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38
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Lai Y, Cuzick A, Lu XM, Wang J, Katiyar N, Tsuchiya T, Le Roch K, McDowell JM, Holub E, Eulgem T. The Arabidopsis RRM domain protein EDM3 mediates race-specific disease resistance by controlling H3K9me2-dependent alternative polyadenylation of RPP7 immune receptor transcripts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:646-660. [PMID: 30407670 PMCID: PMC7138032 DOI: 10.1111/tpj.14148] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/27/2018] [Accepted: 10/26/2018] [Indexed: 05/18/2023]
Abstract
The NLR-receptor RPP7 mediates race-specific immunity in Arabidopsis. Previous screens for enhanced downy mildew (edm) mutants identified the co-chaperone SGT1b (EDM1) and the PHD-finger protein EDM2 as critical regulators of RPP7. Here, we describe a third edm mutant compromised in RPP7 immunity, edm3. EDM3 encodes a nuclear-localized protein featuring an RNA-recognition motif. Like EDM2, EDM3 promotes histone H3 lysine 9 dimethylation (H3K9me2) at RPP7. Global profiling of H3K9me2 showed EDM3 to affect this silencing mark at a large set of loci. Importantly, both EDM3 and EDM2 co-associate in vivo with H3K9me2-marked chromatin and transcripts at a critical proximal polyadenylation site of RPP7, where they suppress proximal transcript polyadeylation/termination. Our results highlight the complexity of plant NLR gene regulation, and establish a functional and physical link between a histone mark and NLR-transcript processing.
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Affiliation(s)
- Yan Lai
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
- College of Life Sciences, Fujian Agricultural and Forestry University, Fuzhou, Fujian, 350002, China
| | - Alayne Cuzick
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick, CV35 9EF, UK
- Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Xueqing M Lu
- Department of Molecular, Cell and Systems Biology, Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
| | - Jianqiang Wang
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
| | - Neerja Katiyar
- Institute of Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
| | - Tokuji Tsuchiya
- College of Bioresource Sciences, Nihon University, Kanagawa, 252-0880, Japan
| | - Karine Le Roch
- Department of Molecular, Cell and Systems Biology, Center for Infectious Disease and Vector Research, Institute of Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
| | - John M McDowell
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, Blacksburg, VA, 24060-0329, USA
| | - Eric Holub
- School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick, CV35 9EF, UK
| | - Thomas Eulgem
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California at Riverside, Riverside, CA, 92521, USA
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Yadav NS, Khadka J, Domb K, Zemach A, Grafi G. CMT3 and SUVH4/KYP silence the exonic Evelknievel retroelement to allow for reconstitution of CMT1 mRNA. Epigenetics Chromatin 2018; 11:69. [PMID: 30446008 PMCID: PMC6238269 DOI: 10.1186/s13072-018-0240-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/09/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The Chromomethylase 1 (CMT1) has long been considered a nonessential gene because, in certain Arabidopsis ecotypes, the CMT1 gene is disrupted by the Evelknievel (EK) retroelement, inserted within exon 13, or contains frameshift mutations, resulting in a truncated, non-functional protein. In contrast to other transposable elements, no transcriptional activation of EK was observed under stress conditions (e.g., protoplasting). RESULTS We wanted to explore the regulatory pathway responsible for EK silencing in the Ler ecotype and its effect on CMT1 transcription. Methylome databases confirmed that EK retroelement is heavily methylated and methylation is extended toward CMT1 downstream region. Strong transcriptional activation of EK accompanied by significant reduction in non-CG methylation was found in cmt3 and kyp2, but not in ddm1 or RdDM mutants. EK activation in cmt3 and kyp2 did not interfere with upstream CMT1 expression but abolish transcription through the EK. We identified, in wild-type Ler, three spliced variants in which the entire EK is spliced out; one variant (25% of splicing incidents) facilitates proper reconstitution of an intact CMT1 mRNA. We could recover very low amount of the full-length CMT1 mRNA from WT Ler and Col, but not from cmt3 mutant. CONCLUSIONS Our findings highlight CMT3-SUVH4/KYP as the major pathway silencing the intragenic EK via inducing non-CG methylation. Furthermore, retroelement insertion within exons (e.g., CMT1) may not lead to a complete abolishment of the gene product when the element is kept silent. Rather the element can be spliced out to bring about reconstruction of an intact, functional mRNA and possibly retrieval of an active protein.
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Affiliation(s)
- Narendra Singh Yadav
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Midreshet Ben Gurion, Israel
| | - Janardan Khadka
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Midreshet Ben Gurion, Israel
| | - Katherine Domb
- The School of Plant Sciences and Food Security, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Assaf Zemach
- The School of Plant Sciences and Food Security, Tel-Aviv University, 69978, Tel Aviv, Israel
| | - Gideon Grafi
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 84990, Midreshet Ben Gurion, Israel.
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40
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Duan CG, Zhu JK, Cao X. Retrospective and perspective of plant epigenetics in China. J Genet Genomics 2018; 45:621-638. [PMID: 30455036 DOI: 10.1016/j.jgg.2018.09.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/25/2018] [Accepted: 09/30/2018] [Indexed: 01/21/2023]
Abstract
Epigenetics refers to the study of heritable changes in gene function that do not involve changes in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors or be part of normal developmental program. In eukaryotes, DNA wraps on a histone octamer (two copies of H2A, H2B, H3 and H4) to form nucleosome, the fundamental unit of chromatin. The structure of chromatin is subjected to a dynamic regulation through multiple epigenetic mechanisms, including DNA methylation, histone posttranslational modifications (PTMs), chromatin remodeling and noncoding RNAs. As conserved regulatory mechanisms in gene expression, epigenetic mechanisms participate in almost all the important biological processes ranging from basal development to environmental response. Importantly, all of the major epigenetic mechanisms in mammalians also occur in plants. Plant studies have provided numerous important contributions to the epigenetic research. For example, gene imprinting, a mechanism of parental allele-specific gene expression, was firstly observed in maize; evidence of paramutation, an epigenetic phenomenon that one allele acts in a single locus to induce a heritable change in the other allele, was firstly reported in maize and tomato. Moreover, some unique epigenetic mechanisms have been evolved in plants. For example, the 24-nt siRNA-involved RNA-directed DNA methylation (RdDM) pathway is plant-specific because of the involvements of two plant-specific DNA-dependent RNA polymerases, Pol IV and Pol V. A thorough study of epigenetic mechanisms is of great significance to improve crop agronomic traits and environmental adaptability. In this review, we make a brief summary of important progress achieved in plant epigenetics field in China over the past several decades and give a brief outlook on future research prospects. We focus our review on DNA methylation and histone PTMs, the two most important aspects of epigenetic mechanisms.
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Affiliation(s)
- Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA.
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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41
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Čermák V, Fischer L. Pervasive read-through transcription of T-DNAs is frequent in tobacco BY-2 cells and can effectively induce silencing. BMC PLANT BIOLOGY 2018; 18:252. [PMID: 30348096 PMCID: PMC6196474 DOI: 10.1186/s12870-018-1482-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 10/12/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Plant transformation via Agrobacterium tumefaciens is characterized by integration of commonly low number of T-DNAs at random positions in the genome. When integrated into an active gene region, promoterless reporter genes placed near the T-DNA border sequence are frequently transcribed and even translated to reporter proteins, which is the principle of promoter- and gene-trap lines. RESULTS Here we show that even internal promotorless regions of T-DNAs are often transcribed. Such spontaneous transcription was observed in the majority of independently transformed tobacco BY-2 lines (over 65%) and it could effectively induce silencing if an inverted repeat was present within the T-DNA. We documented that the transcription often occurred in both directions. It was not directly connected with any regulatory elements present within the T-DNAs and at least some of the transcripts were initiated outside of the T-DNA. The likeliness of this read-through transcription seemed to increase in lines with higher T-DNA copy number. Splicing and presence of a polyA tail in the transcripts indicated involvement of Pol II, but surprisingly, the transcription was able to run across two transcription terminators present within the T-DNA. Such pervasive transcription was observed with three different T-DNAs in BY-2 cells and with lower frequency was also detected in Arabidopsis thaliana. CONCLUSIONS Our results demonstrate unexpected pervasive read-through transcription of T-DNAs. We hypothesize that it was connected with a specific chromatin state of newly integrated DNA, possibly affected by the adjacent genomic region. Although this phenomenon can be easily overlooked, it can have significant consequences when working with highly sensitive systems like RNAi induction using an inverted repeat construct, so it should be generally considered when interpreting results obtained with the transgenic technology.
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Affiliation(s)
- Vojtěch Čermák
- Department of Experimental Plant Biology, Charles University, Faculty of Science, Viničná 5, 128 44 Prague 2, Czech Republic
| | - Lukáš Fischer
- Department of Experimental Plant Biology, Charles University, Faculty of Science, Viničná 5, 128 44 Prague 2, Czech Republic
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42
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Tan LM, Zhang CJ, Hou XM, Shao CR, Lu YJ, Zhou JX, Li YQ, Li L, Chen S, He XJ. The PEAT protein complexes are required for histone deacetylation and heterochromatin silencing. EMBO J 2018; 37:embj.201798770. [PMID: 30104406 DOI: 10.15252/embj.201798770] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 06/27/2018] [Accepted: 06/28/2018] [Indexed: 01/26/2023] Open
Abstract
In eukaryotes, heterochromatin regions are typically subjected to transcriptional silencing. DNA methylation has an important role in such silencing and has been studied extensively. However, little is known about how methylated heterochromatin regions are subjected to silencing. We conducted a genetic screen and identified an epcr (enhancer of polycomb-related) mutant that releases heterochromatin silencing in Arabidopsis thaliana We demonstrated that EPCR1 functions redundantly with its paralog EPCR2 and interacts with PWWP domain-containing proteins (PWWPs), AT-rich interaction domain-containing proteins (ARIDs), and telomere repeat binding proteins (TRBs), thus forming multiple functionally redundant protein complexes named PEAT (PWWPs-EPCRs-ARIDs-TRBs). The PEAT complexes mediate histone deacetylation and heterochromatin condensation and thereby facilitate heterochromatin silencing. In heterochromatin regions, the production of small interfering RNAs (siRNAs) and DNA methylation is repressed by the PEAT complexes. The study reveals how histone deacetylation, heterochromatin condensation, siRNA production, and DNA methylation interplay with each other and thereby maintain heterochromatin silencing.
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Affiliation(s)
- Lian-Mei Tan
- National Institute of Biological Sciences, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Cui-Jun Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Xiao-Mei Hou
- National Institute of Biological Sciences, Beijing, China
| | | | - Yu-Jia Lu
- National Institute of Biological Sciences, Beijing, China
| | - Jin-Xing Zhou
- National Institute of Biological Sciences, Beijing, China
| | - Yong-Qiang Li
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, China .,Graduate School of Peking Union Medical College, Beijing, China
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43
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Lai Y, Eulgem T. Transcript-level expression control of plant NLR genes. MOLECULAR PLANT PATHOLOGY 2018; 19:1267-1281. [PMID: 28834153 PMCID: PMC6638128 DOI: 10.1111/mpp.12607] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/14/2017] [Accepted: 08/15/2017] [Indexed: 05/20/2023]
Abstract
Plant NLR genes encode sensitive immune receptors that can mediate the specific recognition of pathogen avirulence effectors and activate a strong defence response, termed effector-triggered immunity. The expression of NLRs requires strict regulation, as their ability to trigger immunity is dependent on their dose, and overexpression of NLRs results in autoimmunity and massive fitness costs. An elaborate interplay of different mechanisms controlling NLR transcript levels allows plants to maximize their defence capacity, whilst limiting negative impact on their fitness. Global suppression of NLR transcripts may be a prerequisite for the fast evolution of new NLR variants and the expansion of this gene family. Here, we summarize recent progress made towards a comprehensive understanding of NLR transcript-level expression control. Multiple mechanistic steps, including transcription as well as co-/post-transcriptional processing and transcript turn-over, contribute to balanced base levels of NLR transcripts and allow for dynamic adjustments to defence situations.
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Affiliation(s)
- Yan Lai
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome BiologyUniversity of California at RiversideRiversideCA 92521USA
- College of Life SciencesFujian Agricultural and Forestry UniversityFuzhouFujian 350002China
| | - Thomas Eulgem
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome BiologyUniversity of California at RiversideRiversideCA 92521USA
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44
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Sahebi M, Hanafi MM, van Wijnen AJ, Rice D, Rafii MY, Azizi P, Osman M, Taheri S, Bakar MFA, Isa MNM, Noor YM. Contribution of transposable elements in the plant's genome. Gene 2018; 665:155-166. [PMID: 29684486 DOI: 10.1016/j.gene.2018.04.050] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 04/04/2018] [Accepted: 04/18/2018] [Indexed: 12/26/2022]
Abstract
Plants maintain extensive growth flexibility under different environmental conditions, allowing them to continuously and rapidly adapt to alterations in their environment. A large portion of many plant genomes consists of transposable elements (TEs) that create new genetic variations within plant species. Different types of mutations may be created by TEs in plants. Many TEs can avoid the host's defense mechanisms and survive alterations in transposition activity, internal sequence and target site. Thus, plant genomes are expected to utilize a variety of mechanisms to tolerate TEs that are near or within genes. TEs affect the expression of not only nearby genes but also unlinked inserted genes. TEs can create new promoters, leading to novel expression patterns or alternative coding regions to generate alternate transcripts in plant species. TEs can also provide novel cis-acting regulatory elements that act as enhancers or inserts within original enhancers that are required for transcription. Thus, the regulation of plant gene expression is strongly managed by the insertion of TEs into nearby genes. TEs can also lead to chromatin modifications and thereby affect gene expression in plants. TEs are able to generate new genes and modify existing gene structures by duplicating, mobilizing and recombining gene fragments. They can also facilitate cellular functions by sharing their transposase-coding regions. Hence, TE insertions can not only act as simple mutagens but can also alter the elementary functions of the plant genome. Here, we review recent discoveries concerning the contribution of TEs to gene expression in plant genomes and discuss the different mechanisms by which TEs can affect plant gene expression and reduce host defense mechanisms.
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Affiliation(s)
- Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohamed M Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | | | - David Rice
- Department of Molecular Biology & Biotecnology, University of Sheffield, United Kingdom
| | - M Y Rafii
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Parisa Azizi
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Mohamad Osman
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
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45
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Hosaka A, Kakutani T. Transposable elements, genome evolution and transgenerational epigenetic variation. Curr Opin Genet Dev 2018. [DOI: 10.1016/j.gde.2018.02.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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46
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A protein complex regulates RNA processing of intronic heterochromatin-containing genes in Arabidopsis. Proc Natl Acad Sci U S A 2017; 114:E7377-E7384. [PMID: 28808009 DOI: 10.1073/pnas.1710683114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In several eukaryotic organisms, heterochromatin (HC) in the introns of genes can regulate RNA processing, including polyadenylation, but the mechanism underlying this regulation is poorly understood. By promoting distal polyadenylation, the bromo-adjacent homology (BAH) domain-containing and RNA recognition motif-containing protein ASI1 and the H3K9me2-binding protein EDM2 are required for the expression of functional full-length transcripts of intronic HC-containing genes in Arabidopsis Here we report that ASI1 and EDM2 form a protein complex in vivo via a bridge protein, ASI1-Immunoprecipitated Protein 1 (AIPP1), which is another RNA recognition motif-containing protein. The complex also may contain the Pol II CTD phosphatase CPL2, the plant homeodomain-containing protein AIPP2, and another BAH domain protein, AIPP3. As is the case with dysfunction of ASI1 and EDM2, dysfunction of AIPP1 impedes the use of distal polyadenylation sites at tested intronic HC-containing genes, such as the histone demethylase gene IBM1, resulting in a lack of functional full-length transcripts. A mutation in AIPP1 causes silencing of the 35S-SUC2 transgene and genome-wide CHG hypermethylation at gene body regions, consistent with the lack of full-length functional IBM1 transcripts in the mutant. Interestingly, compared with asi1, edm2, and aipp1 mutations, mutations in CPL2, AIPP2, and AIPP3 cause the opposite effects on the expression of intronic HC-containing genes and other genes, suggesting that CPL2, AIPP2, and AIPP3 may form a distinct subcomplex. These results advance our understanding of the interplay between heterochromatic epigenetic modifications and RNA processing in higher eukaryotes.
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47
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Zheng X, Zhou J, Tan DX, Wang N, Wang L, Shan D, Kong J. Melatonin Improves Waterlogging Tolerance of Malus baccata (Linn.) Borkh. Seedlings by Maintaining Aerobic Respiration, Photosynthesis and ROS Migration. FRONTIERS IN PLANT SCIENCE 2017; 8:483. [PMID: 28424730 PMCID: PMC5380759 DOI: 10.3389/fpls.2017.00483] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 03/20/2017] [Indexed: 05/18/2023]
Abstract
Waterlogging, one of the notorious abiotic stressors, retards the growth of apple plants and reduces their production. Thus, it is an urgent agenda for scientists to identify the suitable remedies for this problem. In the current study, we found that melatonin significantly improved the tolerance of apple seedlings against waterlogging stress. This was indicated by the reduced chlorosis and wilting of the seedlings after melatonin applications either by leaf spray or root irrigation. The mechanisms involve in that melatonin functions to maintain aerobic respiration, preserves photosynthesis and reduces oxidative damage of the plants which are under waterlogging stress. Melatonin application also enhances the gene expression of its synthetic enzymes (MbT5H1, MbAANAT3, MbASMT9) and increases melatonin production. This is the first report of a positive feedback that exogenous melatonin application promotes the melatonin synthesis in plants. A post-transcriptional regulation apparently participated in this regulation. When exogenous melatonin meets the requirement of the plants it is found that the protein synthesis of MbASMT9 was suppressed. Taken together, the results showed that melatonin was an effective molecule to protect plant, particularly apple plant, against waterlogging stress.
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Affiliation(s)
- Xiaodong Zheng
- College of Horticulture, China Agricultural UniversityBeijing, China
| | - Jingzhe Zhou
- Beijing Soil and Fertilizer Work StationBeijing, China
| | - Dun-Xian Tan
- Department of Cellular and Structural Biology, UT Health Science Center San Antonio, San AntonioTX, USA
| | - Na Wang
- College of Horticulture, China Agricultural UniversityBeijing, China
| | - Lin Wang
- College of Horticulture, China Agricultural UniversityBeijing, China
| | - Dongqian Shan
- College of Horticulture, China Agricultural UniversityBeijing, China
| | - Jin Kong
- College of Horticulture, China Agricultural UniversityBeijing, China
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48
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Epigenetic Regulation of Intronic Transgenes in Arabidopsis. Sci Rep 2017; 7:45166. [PMID: 28338020 PMCID: PMC5364540 DOI: 10.1038/srep45166] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/20/2017] [Indexed: 11/23/2022] Open
Abstract
Defense mechanisms of plant genomes can epigenetically inactivate repetitive sequences and exogenous transgenes. Loss of mutant phenotypes in intronic T-DNA insertion lines by interaction with another T-DNA locus, termed T-DNA suppression, has been observed in Arabidopsis thaliana, although the molecular basis of establishment and maintenance of T-DNA suppression is poorly understood. Here we show that maintenance of T-DNA suppression requires heterochromatinisation of T-DNA sequences and the nuclear proteins, INCREASED IN BONSAI METHYLATION 2 (IBM2) and ENHANCED DOWNY MILDEW 2 (EDM2), which prevent ectopic 3′ end processing of mRNA in atypically long introns containing T-DNA sequences. Initiation of T-DNA suppression is mediated by the canonical RdDM pathway after hybridisation of two T-DNA strains, accompanied by DNA hypermethylation of T-DNA sequences in the F1 generation. Our results reveal the presence of a genome surveillance mechanism through genome hybridisation that masks repetitive DNAs intruding into transcription units.
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49
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Masuta Y, Nozawa K, Takagi H, Yaegashi H, Tanaka K, Ito T, Saito H, Kobayashi H, Matsunaga W, Masuda S, Kato A, Ito H. Inducible Transposition of a Heat-Activated Retrotransposon in Tissue Culture. PLANT & CELL PHYSIOLOGY 2017; 58:375-384. [PMID: 28013279 DOI: 10.1093/pcp/pcw202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/14/2016] [Indexed: 06/06/2023]
Abstract
A transposition of a heat-activated retrotransposon named ONSEN required compromise of a small RNA-mediated epigenetic regulation that includes RNA-directed DNA methylation (RdDM) machinery after heat treatment. In the current study, we analyzed the transcriptional and transpositional activation of ONSEN to better understand the underlying molecular mechanism involved in the maintenance and/or induction of transposon activation in plant tissue culture. We found the transposition of heat-primed ONSEN during tissue culture independently of RdDM mutation. The heat activation of ONSEN transcripts was not significantly up-regulated in tissue culture compared with that in heat-stressed seedlings, indicating that the transposition of ONSEN was regulated independently of the transcript level. RdDM-related genes were up-regulated by heat stress in both tissue culture and seedlings. The level of DNA methylation of ONSEN did not show any change in tissue culture, and the amount of ONSEN-derived small RNAs was not affected by heat stress. The results indicated that the transposition of ONSEN was regulated by an alternative mechanism in addition to the RdDM-mediated epigenetic regulation in tissue culture. We applied the tissue culture-induced transposition of ONSEN to Japanese radish, an important breeding species of the family Brassicaceae. Several new insertions were detected in a regenerated plant derived from heat-stressed tissues and its self-fertilized progeny, revealing the possibility of molecular breeding without genetic modification.
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Affiliation(s)
- Yukari Masuta
- Faculty of Science, Hokkaido University, Sappor, Japan
| | - Kosuke Nozawa
- Faculty of Science, Hokkaido University, Sappor, Japan
| | | | | | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Tasuku Ito
- Center for Ecological Research, Kyoto University, Otsu, Japan
| | - Hideyuki Saito
- Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | | | - Seiji Masuda
- Faculty of Science, Hokkaido University, Sappor, Japan
| | - Atsushi Kato
- Faculty of Science, Hokkaido University, Sappor, Japan
| | - Hidetaka Ito
- Faculty of Science, Hokkaido University, Sappor, Japan
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50
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Inagaki S, Takahashi M, Hosaka A, Ito T, Toyoda A, Fujiyama A, Tarutani Y, Kakutani T. Gene-body chromatin modification dynamics mediate epigenome differentiation in Arabidopsis. EMBO J 2017; 36:970-980. [PMID: 28100676 DOI: 10.15252/embj.201694983] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 12/14/2016] [Accepted: 12/16/2016] [Indexed: 11/09/2022] Open
Abstract
Heterochromatin is marked by methylation of lysine 9 on histone H3 (H3K9me). A puzzling feature of H3K9me is that this modification localizes not only in promoters but also in internal regions (bodies) of silent transcription units. Despite its prevalence, the biological significance of gene-body H3K9me remains enigmatic. Here we show that H3K9me-associated removal of H3K4 monomethylation (H3K4me1) in gene bodies mediates transcriptional silencing. Mutations in an Arabidopsis H3K9 demethylase gene IBM1 induce ectopic H3K9me2 accumulation in gene bodies, with accompanying severe developmental defects. Through suppressor screening of the ibm1-induced developmental defects, we identified the LDL2 gene, which encodes a homolog of conserved H3K4 demethylases. The ldl2 mutation suppressed the developmental defects, without suppressing the ibm1-induced ectopic H3K9me2. The ectopic H3K9me2 mark directed removal of gene-body H3K4me1 and caused transcriptional repression in an LDL2-dependent manner. Furthermore, mutations of H3K9 methylases increased the level of H3K4me1 in the gene bodies of various transposable elements, and this H3K4me1 increase is a prerequisite for their transcriptional derepression. Our results uncover an unexpected role of gene-body H3K9me2/H3K4me1 dynamics as a mediator of heterochromatin silencing and epigenome differentiation.
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Affiliation(s)
- Soichi Inagaki
- National Institute of Genetics, Mishima, Shizuoka, Japan .,Department of Genetics, School of Life science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | | | - Aoi Hosaka
- National Institute of Genetics, Mishima, Shizuoka, Japan.,Department of Genetics, School of Life science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Tasuku Ito
- National Institute of Genetics, Mishima, Shizuoka, Japan.,Faculty of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Atsushi Toyoda
- National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Asao Fujiyama
- National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Yoshiaki Tarutani
- National Institute of Genetics, Mishima, Shizuoka, Japan.,Department of Genetics, School of Life science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan
| | - Tetsuji Kakutani
- National Institute of Genetics, Mishima, Shizuoka, Japan .,Department of Genetics, School of Life science, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, Japan.,Faculty of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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