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An J, Brik Chaouche R, Pereyra-Bistraín LI, Zalzalé H, Wang Q, Huang Y, He X, Dias Lopes C, Antunez-Sanchez J, Bergounioux C, Boulogne C, Dupas C, Gillet C, Pérez-Pérez JM, Mathieu O, Bouché N, Fragkostefanakis S, Zhang Y, Zheng S, Crespi M, Mahfouz MM, Ariel F, Gutierrez-Marcos J, Raynaud C, Latrasse D, Benhamed M. An atlas of the tomato epigenome reveals that KRYPTONITE shapes TAD-like boundaries through the control of H3K9ac distribution. Proc Natl Acad Sci U S A 2024; 121:e2400737121. [PMID: 38968127 PMCID: PMC11252963 DOI: 10.1073/pnas.2400737121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/21/2024] [Indexed: 07/07/2024] Open
Abstract
In recent years, the exploration of genome three-dimensional (3D) conformation has yielded profound insights into the regulation of gene expression and cellular functions in both animals and plants. While animals exhibit a characteristic genome topology defined by topologically associating domains (TADs), plants display similar features with a more diverse conformation across species. Employing advanced high-throughput sequencing and microscopy techniques, we investigated the landscape of 26 histone modifications and RNA polymerase II distribution in tomato (Solanum lycopersicum). Our study unveiled a rich and nuanced epigenetic landscape, shedding light on distinct chromatin states associated with heterochromatin formation and gene silencing. Moreover, we elucidated the intricate interplay between these chromatin states and the overall topology of the genome. Employing a genetic approach, we delved into the role of the histone modification H3K9ac in genome topology. Notably, our investigation revealed that the ectopic deposition of this chromatin mark triggered a reorganization of the 3D chromatin structure, defining different TAD-like borders. Our work emphasizes the critical role of H3K9ac in shaping the topology of the tomato genome, providing valuable insights into the epigenetic landscape of this agriculturally significant crop species.
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Affiliation(s)
- Jing An
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Rim Brik Chaouche
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Leonardo I. Pereyra-Bistraín
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-YvetteF-91190, France
| | - Hugo Zalzalé
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-YvetteF-91190, France
| | - Qingyi Wang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Xiaoning He
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Chloé Dias Lopes
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | | | - Catherine Bergounioux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Claire Boulogne
- Imagerie-Gif, Electron Microscopy Facility, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette91198, France
| | - Cynthia Dupas
- Imagerie-Gif, Electron Microscopy Facility, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette91198, France
| | - Cynthia Gillet
- Imagerie-Gif, Electron Microscopy Facility, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette91198, France
| | | | - Olivier Mathieu
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, Clermont-FerrandF-63000, France
| | - Nicolas Bouché
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles78000, France
| | | | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai200438, China
| | - Shaojian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Martin Crespi
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Magdy M. Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal23955-6900, Saudi Arabia
| | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, Universidad Nacional del Litoral, SantaFe 3000, Argentina
| | | | - Cécile Raynaud
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay91405, France
- Université de Paris Cité, Institute of Plant Sciences Paris-Saclay (IPS2), Gif-sur-YvetteF-91190, France
- Institut Universitaire de France, Orsay, Gif-sur-Yvette91190, France
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Li A, Wang F, Ding T, Li K, Liu H, Zhang Q, Mu Q, Zhao H, Shan S, Wang P. Genome-wide DNA methylation dynamics and RNA-seq analysis during grape (cv. 'Cabernet Franc') skin coloration. Genomics 2024; 116:110810. [PMID: 38402913 DOI: 10.1016/j.ygeno.2024.110810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/18/2024] [Accepted: 02/19/2024] [Indexed: 02/27/2024]
Abstract
This study generated whole genome DNA methylation maps to characterize DNA methylomes of grape (cv. 'Cabernet Franc') skins and examine their functional significance during grape skin coloration. We sampled grape skin tissues at three key stages (the early stage of grape berry swelling, the late stage of grape berry swelling and the veraison) during which the color of grape berries changed from green to red. DNA methylation levels of grape skins at the three stages were higher in transposable element regions than in the genic regions, and the CG and CHG DNA methylation levels of the genic region were higher than the CHH DNA methylation levels. We identified differentially methylated regions (DMRs) in S2_vs_S1 and S3_vs_S1. The results indicated that DMRs predominantly occurred within the CHH context during grape skin coloration. Many gene ontology (GO)-enriched DMR-related genes were involved in "nucleotide binding," "catalytic activity" and "ribonucleotide binding" terms; however, many KEGG-enriched DMR-related genes were involved in the "flavonoid biosynthesis" pathway. Our results could provide an important foundation for future research on the development mechanism of grape berries.
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Affiliation(s)
- Ao Li
- Shandong Academy of Grape, Jinan 250100, China
| | | | | | - Ke Li
- Shandong Academy of Grape, Jinan 250100, China
| | - Huiping Liu
- Shandong Academy of Grape, Jinan 250100, China
| | | | - Qian Mu
- Shandong Academy of Grape, Jinan 250100, China
| | | | - Shouming Shan
- College of Enology and Horticulture, Ningxia University, Ningxia 750021, China.
| | - Pengfei Wang
- Shandong Academy of Grape, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture and Rural Affairs, Jinan 250100, China.
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3
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Hung FY, Feng YR, Hsin KT, Shih YH, Chang CH, Zhong W, Lai YC, Xu Y, Yang S, Sugimoto K, Cheng YS, Wu K. Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2. Commun Biol 2023; 6:219. [PMID: 36828846 PMCID: PMC9958104 DOI: 10.1038/s42003-023-04607-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/16/2023] [Indexed: 02/26/2023] Open
Abstract
The Arabidopsis H3K9 methyltransferases KRYPTONITE/SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 4 (KYP/SUVH4), SUVH5 and SUVH6 are redundantly involved in silencing of transposable elements (TEs). Our recent study indicated that KYP/SUVH5/6 can directly interact with the histone deacetylase HDA6 to synergistically regulate TE expression. However, the function of KYP/SUVH5/6 in plant development is still unclear. The transcriptional factors ASYMMETRIC LEAVES1 (AS1) and AS2 form a transcription complex, which is involved in leaf development by repressing the homeobox genes KNOTTED-LIKE FROM ARABIDOPSIS THALIANA 1 (KNAT1) and KNAT2. In this study, we found that KYP and SUVH5/6 directly interact with AS1-AS2 to repress KNAT1 and KNAT2 by altering histone H3 acetylation and H3K9 dimethylation levels. In addition, KYP can directly target the promoters of KNAT1 and KNAT2, and the binding of KYP depends on AS1. Furthermore, the genome-wide occupancy profile of KYP indicated that KYP is enriched in the promoter regions of coding genes, and the binding of KYP is positively correlated with that of AS1 and HDA6. Together, these results indicate that Arabidopsis H3K9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to alter histone H3 acetylation and H3K9 dimethylation from KNAT1 and KNAT2 loci.
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Affiliation(s)
- Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
- RIKEN, Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Yun-Ru Feng
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Kuan-Ting Hsin
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Yuan-Hsin Shih
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Chung-Han Chang
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Wenjian Zhong
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - You-Cheng Lai
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
| | - Yingchao Xu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Songguang Yang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Keiko Sugimoto
- RIKEN, Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Yi-Sheng Cheng
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan.
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Read A, Weiss T, Crisp PA, Liang Z, Noshay J, Menard CC, Wang C, Song M, Hirsch CN, Springer NM, Zhang F. Genome-wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:103-116. [PMID: 35436373 PMCID: PMC9541237 DOI: 10.1111/tpj.15781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/12/2022] [Indexed: 05/17/2023]
Abstract
The DOMAINS REARRANGED METHYLTRANSFERASEs (DRMs) are crucial for RNA-directed DNA methylation (RdDM) in plant species. Setaria viridis is a model monocot species with a relatively compact genome that has limited transposable element (TE) content. CRISPR-based genome editing approaches were used to create loss-of-function alleles for the two putative functional DRM genes in S. viridis to probe the role of RdDM. Double mutant (drm1ab) plants exhibit some morphological abnormalities but are fully viable. Whole-genome methylation profiling provided evidence for the widespread loss of methylation in CHH sequence contexts, particularly in regions with high CHH methylation in wild-type plants. Evidence was also found for the locus-specific loss of CG and CHG methylation, even in some regions that lack CHH methylation. Transcriptome profiling identified genes with altered expression in the drm1ab mutants. However, the majority of genes with high levels of CHH methylation directly surrounding the transcription start site or in nearby promoter regions in wild-type plants do not have altered expression in the drm1ab mutant, even when this methylation is lost, suggesting limited regulation of gene expression by RdDM. Detailed analysis of the expression of TEs identified several transposons that are transcriptionally activated in drm1ab mutants. These transposons are likely to require active RdDM for the maintenance of transcriptional repression.
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Affiliation(s)
- Andrew Read
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Trevor Weiss
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- Center for Precision Plant GenomicsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Peter A. Crisp
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- School of Agriculture and Food SciencesThe University of QueenslandBrisbaneQueensland4072Australia
| | - Zhikai Liang
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Jaclyn Noshay
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Claire C. Menard
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Chunfang Wang
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- Center for Precision Plant GenomicsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Meredith Song
- Department of Genetics, Cell Biology and DevelopmentUniversity of MinnesotaMinneapolisMinnesota55108USA
| | - Candice N. Hirsch
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Nathan M. Springer
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- Center for Precision Plant GenomicsUniversity of MinnesotaSaint PaulMinnesota55108USA
| | - Feng Zhang
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMinnesota55108USA
- Center for Precision Plant GenomicsUniversity of MinnesotaSaint PaulMinnesota55108USA
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Lei Z, Wang L, Kim EY, Cho J. Phase separation of chromatin and small RNA pathways in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1256-1265. [PMID: 34585805 DOI: 10.1111/tpj.15517] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/18/2021] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
Gene expression can be modulated by epigenetic mechanisms, including chromatin modifications and small regulatory RNAs. These pathways are unevenly distributed within a cell and usually take place in specific intracellular regions. Unfortunately, the fundamental driving force and biological relevance of such spatial differentiation is largely unknown. Liquid-liquid phase separation (LLPS) is a natural propensity of demixing liquid phases and has been recently suggested to mediate the formation of biomolecular condensates that are relevant to diverse cellular processes. LLPS provides a mechanistic explanation for the self-assembly of subcellular structures by which the efficiency and specificity of certain cellular reactions are achieved. In plants, LLPS has been observed for several key factors in the chromatin and small RNA pathways. For example, the formation of facultative and obligate heterochromatin involves the LLPS of multiple relevant factors. In addition, phase separation is observed in a set of proteins acting in microRNA biogenesis and the small interfering RNA pathway. In this Focused Review, we highlight and discuss the recent findings regarding phase separation in the epigenetic mechanisms of plants.
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Affiliation(s)
- Zhen Lei
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ling Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Eun Yu Kim
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jungnam Cho
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Chinese Academy of Sciences, Shanghai, 200032, China
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6
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The diversity of post-transcriptional gene silencing mediated by small silencing RNAs in plants. Essays Biochem 2021; 64:919-930. [PMID: 32885814 DOI: 10.1042/ebc20200006] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/11/2020] [Accepted: 08/14/2020] [Indexed: 12/31/2022]
Abstract
In plants, post-transcriptional gene silencing (PTGS) tightly regulates development, maintains genome stability and protects plant against foreign genes. PTGS can be triggered by virus infection, transgene, and endogenous transcript, thus commonly serves as an RNA-based immune mechanism. Accordingly, based on the initiating factors, PTGS can be divided into viral-PTGS, transgene-PTGS, and endo-gene-PTGS. Unlike the intensely expressed invading transgenes and viral genes that frequently undergo PTGS, most endogenous genes do not trigger PTGS, except for a few that can produce endogenous small RNAs (sRNAs), including microRNA (miRNA) and small interfering RNA (siRNA). Different lengths of miRNA and siRNA, mainly 21-, 22- or 24-nucleotides (nt) exert diverse functions, ranging from target mRNA degradation, translational inhibition, or DNA methylation and chromatin modifications. The abundant 21-nt miRNA or siRNA, processed by RNase-III enzyme DICER-LIKE 1 (DCL1) and DCL4, respectively, have been well studied in the PTGS pathways. By contrast, the scarceness of endogenous 22-nt sRNAs that are primarily processed by DCL2 limits their research, although a few encouraging studies have been reported recently. Therefore, we review here our current understanding of diverse PTGS pathways triggered by a variety of sRNAs and summarize the distinct features of the 22-nt sRNA mediated PTGS.
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Wang Y, Liu L, Li M, Lin L, Su P, Tang H, Fan X, Li X. Chicken cecal DNA methylome alteration in the response to Salmonella enterica serovar Enteritidis inoculation. BMC Genomics 2020; 21:814. [PMID: 33225883 PMCID: PMC7681971 DOI: 10.1186/s12864-020-07174-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 10/21/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Salmonella enterica serovar Enteritidis (SE) is one of the pathogenic bacteria, which affects poultry production and poses a severe threat to public health. Chicken meat and eggs are the main sources of human salmonellosis. DNA methylation is involved in regulatory processes including gene expression, chromatin structure and genomic imprinting. To understand the methylation regulation in the response to SE inoculation in chicken, the genome-wide DNA methylation profile following SE inoculation was analyzed through whole-genome bisulfite sequencing in the current study. RESULTS There were 185,362,463 clean reads and 126,098,724 unique reads in the control group, and 180,530,750 clean reads and 126,782,896 unique reads in the inoculated group. The methylation density in the gene body was higher than that in the upstream and downstream regions of the gene. There were 8946 differentially methylated genes (3639 hypo-methylated genes, 5307 hyper-methylated genes) obtained between inoculated and control groups. Methylated genes were mainly enriched in immune-related Gene Ontology (GO) terms and metabolic process terms. Cytokine-cytokine receptor interaction, TGF-beta signaling pathway, FoxO signaling pathway, Wnt signaling pathway and several metabolism-related pathways were significantly enriched. The density of differentially methylated cytosines in miRNAs was the highest. HOX genes were widely methylated. CONCLUSIONS The genome-wide DNA methylation profile in the response to SE inoculation in chicken was analyzed. SE inoculation promoted the DNA methylation in the chicken cecum and caused methylation alteration in immune- and metabolic- related genes. Wnt signal pathway, miRNAs and HOX gene family may play crucial roles in the methylation regulation of SE inoculation in chicken. The findings herein will deepen the understanding of epigenetic regulation in the response to SE inoculation in chicken.
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Affiliation(s)
- Yuanmei Wang
- College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Liying Liu
- College of Life Science, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Min Li
- College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Lili Lin
- College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Pengcheng Su
- College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Hui Tang
- College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Xinzhong Fan
- College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Xianyao Li
- College of Animal Science and Technology, Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Tai’an, 271018 Shandong China
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8
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Hummel G, Berr A, Graindorge S, Cognat V, Ubrig E, Pflieger D, Molinier J, Drouard L. Epigenetic silencing of clustered tRNA genes in Arabidopsis. Nucleic Acids Res 2020; 48:10297-10312. [PMID: 32941623 PMCID: PMC7544208 DOI: 10.1093/nar/gkaa766] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/21/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
Beyond their key role in translation, cytosolic transfer RNAs (tRNAs) are involved in a wide range of other biological processes. Nuclear tRNA genes (tDNAs) are transcribed by the RNA polymerase III (RNAP III) and cis-elements, trans-factors as well as genomic features are known to influence their expression. In Arabidopsis, besides a predominant population of dispersed tDNAs spread along the 5 chromosomes, some clustered tDNAs have been identified. Here, we demonstrate that these tDNA clusters are transcriptionally silent and that pathways involved in the maintenance of DNA methylation play a predominant role in their repression. Moreover, we show that clustered tDNAs exhibit repressive chromatin features whilst their dispersed counterparts contain permissive euchromatic marks. This work demonstrates that both genomic and epigenomic contexts are key players in the regulation of tDNAs transcription. The conservation of most of these regulatory processes suggests that this pioneering work in Arabidopsis can provide new insights into the regulation of RNA Pol III transcription in other organisms, including vertebrates.
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Affiliation(s)
- Guillaume Hummel
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Alexandre Berr
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Stéfanie Graindorge
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Valérie Cognat
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Elodie Ubrig
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Jean Molinier
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes-CNRS, Université de Strasbourg, 12 rue du Général Zimmer, F-67084 Strasbourg, France
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Parrilla-Doblas JT, Roldán-Arjona T, Ariza RR, Córdoba-Cañero D. Active DNA Demethylation in Plants. Int J Mol Sci 2019; 20:E4683. [PMID: 31546611 PMCID: PMC6801703 DOI: 10.3390/ijms20194683] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/17/2019] [Accepted: 09/19/2019] [Indexed: 02/06/2023] Open
Abstract
Methylation of cytosine (5-meC) is a critical epigenetic modification in many eukaryotes, and genomic DNA methylation landscapes are dynamically regulated by opposed methylation and demethylation processes. Plants are unique in possessing a mechanism for active DNA demethylation involving DNA glycosylases that excise 5-meC and initiate its replacement with unmodified C through a base excision repair (BER) pathway. Plant BER-mediated DNA demethylation is a complex process involving numerous proteins, as well as additional regulatory factors that avoid accumulation of potentially harmful intermediates and coordinate demethylation and methylation to maintain balanced yet flexible DNA methylation patterns. Active DNA demethylation counteracts excessive methylation at transposable elements (TEs), mainly in euchromatic regions, and one of its major functions is to avoid methylation spreading to nearby genes. It is also involved in transcriptional activation of TEs and TE-derived sequences in companion cells of male and female gametophytes, which reinforces transposon silencing in gametes and also contributes to gene imprinting in the endosperm. Plant 5-meC DNA glycosylases are additionally involved in many other physiological processes, including seed development and germination, fruit ripening, and plant responses to a variety of biotic and abiotic environmental stimuli.
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Affiliation(s)
- Jara Teresa Parrilla-Doblas
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071 Córdoba, Spain.
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain.
- Reina Sofía University Hospital, 14071 Córdoba, Spain.
| | - Teresa Roldán-Arjona
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071 Córdoba, Spain.
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain.
- Reina Sofía University Hospital, 14071 Córdoba, Spain.
| | - Rafael R Ariza
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071 Córdoba, Spain.
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain.
- Reina Sofía University Hospital, 14071 Córdoba, Spain.
| | - Dolores Córdoba-Cañero
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), 14071 Córdoba, Spain.
- Department of Genetics, University of Córdoba, 14071 Córdoba, Spain.
- Reina Sofía University Hospital, 14071 Córdoba, Spain.
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10
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Wang P, Shi S, Ma J, Song H, Zhang Y, Gao C, Zhao C, Zhao S, Hou L, Lopez-Baltazar J, Fan S, Xia H, Wang X. Global Methylome and gene expression analysis during early Peanut pod development. BMC PLANT BIOLOGY 2018; 18:352. [PMID: 30545288 PMCID: PMC6293580 DOI: 10.1186/s12870-018-1546-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 11/20/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Early peanut pod development is an important process of peanut reproductive development. Modes of DNA methylation during early peanut pod development are still unclear, possibly because its allotetraploid genome may cause difficulty for the methylome analysis. RESULTS To investigate the functions of the dynamic DNA methylation during the early development of the peanut pod, global methylome and gene expression analyses were carried out by Illumina high throughput sequencing. A novel mapping strategy of reads was developed and used for methylome and gene expression analysis. Differentially methylated genes, such as nodulin, cell number regulator-like protein, and senescence-associated genes, were identified during the early developmental stages of the peanut pod. The expression levels of gibberellin-related genes changed during this period of pod development. From the stage one (S1) gynophore to the stage two (S2) gynophore, the expression levels of two key methyltransferase genes, DRM2 and MET1, were up-regulated, which may lead to global DNA methylation changes between these two stages. The differentially methylated and expressed genes identified in the S1, S2, and stage 3 (S3) gynophore are involved in different biological processes such as stem cell fate determination, response to red, blue, and UV light, post-embryonic morphogenesis, and auxin biosynthesis. The expression levels of many genes were co-related by their DNA methylation levels. In addition, our results showed that the abundance of some 24-nucleotide siRNAs and miRNAs were positively associated with DNA methylation levels of their target loci in peanut pods. CONCLUSION A novel mapping strategy of reads was described and verified in this study. Our results suggest that the methylated modes of the S1, S2, and S3 gynophore are different. The methylation changes that were identified during early peanut pod development provide useful information for understanding the roles of epigenetic regulation in peanut pod development.
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Affiliation(s)
- Pengfei Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Shandong Academy of Grape, Jinan, 250100 People’s Republic of China
| | - Suhua Shi
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Junjie Ma
- Life Science College of Shandong University, Jinan, 250100 People’s Republic of China
| | - Hui Song
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | - Ye Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | - Chao Gao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | - Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Shuzhen Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | | | - Shoujin Fan
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
- Life Science College of Shandong University, Jinan, 250100 People’s Republic of China
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11
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Zhao T, Tao X, Feng S, Wang L, Hong H, Ma W, Shang G, Guo S, He Y, Zhou B, Guan X. LncRNAs in polyploid cotton interspecific hybrids are derived from transposon neofunctionalization. Genome Biol 2018; 19:195. [PMID: 30419941 PMCID: PMC6233382 DOI: 10.1186/s13059-018-1574-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/23/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Interspecific hybridization and whole genome duplication are driving forces of genomic and organism diversification. But the effect of interspecific hybridization and whole genome duplication on the non-coding portion of the genome in particular remains largely unknown. In this study, we examine the profile of long non-coding RNAs (lncRNAs), comparing them with that of coding genes in allotetraploid cotton (Gossypium hirsutum), its putative diploid ancestors (G. arboreum; G. raimondii), and an F1 hybrid (G. arboreum × G. raimondii, AD). RESULTS We find that most lncRNAs (80%) that were allelic expressed in the allotetraploid genome. Moreover, the genome shock of hybridization reprograms the non-coding transcriptome in the F1 hybrid. Interestingly, the activated lncRNAs are predominantly transcribed from demethylated TE regions, especially from long interspersed nuclear elements (LINEs). The DNA methylation dynamics in the interspecies hybridization are predominantly associated with the drastic expression variation of lncRNAs. Similar trends of lncRNA bursting are also observed in the progress of polyploidization. Additionally, we find that a representative novel lncRNA XLOC_409583 activated after polyploidization from a LINE in the A subgenome of allotetraploid cotton was involved in control of cotton seedling height. CONCLUSION Our results reveal that the processes of hybridization and polyploidization enable the neofunctionalization of lncRNA transcripts, acting as important sources of increased plasticity for plants.
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Affiliation(s)
- Ting Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China
| | - Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China
| | - Shouli Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Luyao Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Hui Hong
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wei Ma
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China
| | - Guandong Shang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shisong Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yuxin He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Xueying Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China.
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12
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Raza MA, Yu N, Wang D, Cao L, Gan S, Chen L. Differential DNA methylation and gene expression in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium. DNA Res 2018; 24:597-607. [PMID: 28679169 PMCID: PMC5726463 DOI: 10.1093/dnares/dsx028] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/27/2017] [Indexed: 12/22/2022] Open
Abstract
Wide hybridization is a common and efficient breeding strategy for enhancing crop yield and quality. An interesting phenomenon is that the reciprocal hybrids usually show different phenotypes, and its underlying mechanism is not well understood. Here, we reported our comparative analysis of the DNA methylation patterns in Solanum lycopersicum, Solanum pimpinellifolium and their reciprocal hybrids by methylated DNA immunoprecipitation sequencing. The reciprocal hybrids had lower levels of DNA methylation in CpG islands and LTR retroelements when compared with those of their parents. Importantly, remarkable differences in DNA methylation patterns, mainly in introns and CDS regions, were revealed between the reciprocal hybrids. These different methylated regions were mapped to 79 genes, 14 of which were selected for analysis of gene expression levels. While there was an inverse correlation between DNA methylation and gene expression in promoter regions, the relationship was complicated in gene body regions. Further association analysis revealed that there were 15 differentially methylated genes associated with siRNAs, and that the methylation levels of these genes were inversely correlated with respective siRNAs. All these data raised the possibility that the direction of hybridization induced the divergent epigenomes leading to changes in the transcription levels of reciprocal hybrids.
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Affiliation(s)
- Muhammad Ammar Raza
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, P. R. China
| | - Ningning Yu
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, P. R. China
| | - Dan Wang
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, P. R. China
| | - Liwen Cao
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, P. R. China
| | - Susheng Gan
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, P. R. China.,Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Liping Chen
- Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, P. R. China
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13
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Morgado L, Preite V, Oplaat C, Anava S, Ferreira de Carvalho J, Rechavi O, Johannes F, Verhoeven KJF. Small RNAs Reflect Grandparental Environments in Apomictic Dandelion. Mol Biol Evol 2018; 34:2035-2040. [PMID: 28472380 PMCID: PMC5850771 DOI: 10.1093/molbev/msx150] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Plants can show long-term effects of environmental stresses and in some cases a stress “memory” has been reported to persist across generations, potentially mediated by epigenetic mechanisms. However, few documented cases exist of transgenerational effects that persist for multiple generations and it remains unclear if or how epigenetic mechanisms are involved. Here, we show that the composition of small regulatory RNAs in apomictic dandelion lineages reveals a footprint of drought stress and salicylic acid treatment experienced two generations ago. Overall proportions of 21 and 24 nt RNA pools were shifted due to grandparental treatments. While individual genes did not show strong up- or downregulation of associated sRNAs, the subset of genes that showed the strongest shifts in sRNA abundance was significantly enriched for several GO terms including stress-specific functions. This suggests that a stress-induced signal was transmitted across multiple unexposed generations leading to persistent changes in epigenetic gene regulation.
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Affiliation(s)
- Lionel Morgado
- Groningen Bioinformatics Centre, University of Groningen, AG Groningen, The Netherlands
| | - Veronica Preite
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Carla Oplaat
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Sarit Anava
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Julie Ferreira de Carvalho
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Frank Johannes
- Population Epigenetics and Epigenomics, Technical University of Munich, Freising, Germany.,Institute for Advanced Study, Technical University of Munich, Garching, Germany
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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14
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Abstract
Our understanding of the epigenetic mechanisms that regulate gene expression has been largely increased in recent years by the development and refinement of different techniques. This has revealed that gene transcription is highly influenced by epigenetic mechanisms, i.e., those that do not involve changes in the genome sequence, but rather in nuclear architecture, chromosome conformation and histone and DNA modifications. Our understanding of how these different levels of epigenetic regulation interact with each other and with classical transcription-factor based gene regulation to influence gene transcription has just started to emerge. This review discusses the latest advances in unraveling the complex interactions between different types of epigenetic regulation and transcription factor activity, with special attention to the approaches that can be used to study these interactions.
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Affiliation(s)
- Marian Bemer
- Department of Molecular Biology, Wageningen University & Research, Droevendaalsesteeg 1, 6708, PB, Wageningen, The Netherlands.
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15
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Cho J. Transposon-Derived Non-coding RNAs and Their Function in Plants. FRONTIERS IN PLANT SCIENCE 2018; 9:600. [PMID: 29774045 PMCID: PMC5943564 DOI: 10.3389/fpls.2018.00600] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/16/2018] [Indexed: 05/03/2023]
Abstract
Transposable elements (TEs) are often regarded as harmful genomic factors and indeed they are strongly suppressed by the epigenetic silencing mechanisms. On the other hand, the mobilization of TEs brings about variability of genome and transcriptome which are essential in the survival and evolution of the host species. The vast majority of such controlling TEs influence the neighboring genes in cis by either promoting or repressing the transcriptional activities. Although TEs are highly repetitive in the genomes and transcribed in specific stress conditions or developmental stages, the trans-acting regulatory roles of TE-derived RNAs have been rarely studied. It was only recently that TEs were investigated for their regulatory roles as a form of RNA. Particularly in plants, TEs are ample source of small RNAs such as small interfering (si) RNAs and micro (mi) RNAs. Those TE-derived small RNAs have potentials to affect non-TE transcripts by sequence complementarity, thereby generating novel gene regulatory networks including stress resistance and hybridization barrier. Apart from the small RNAs, a number of long non-coding RNAs (lncRNAs) are originated from TEs in plants. For example, a retrotransposon-derived lncRNA expressed in rice root acts as a decoy RNA or miRNA target mimic which negatively controls miRNA171. The post-transcriptional suppression of miRNA171 in roots ensures the stabilization of the target transcripts encoding SCARECROW-LIKE transcription factors, the key regulators of root development. In this review article, the recent discoveries of the regulatory roles of TE-derived RNAs in plants will be highlighted.
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16
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Forestan C, Farinati S, Aiese Cigliano R, Lunardon A, Sanseverino W, Varotto S. Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription. BMC PLANT BIOLOGY 2017; 17:161. [PMID: 29025411 PMCID: PMC5639751 DOI: 10.1186/s12870-017-1108-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 10/04/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND RNA-directed DNA methylation (RdDM) is a plant-specific epigenetic process that relies on the RNA polymerase IV (Pol IV) for the production of 24 nucleotide small interfering RNAs (siRNA) that guide the cytosine methylation and silencing of genes and transposons. Zea mays RPD1/RMR6 gene encodes the largest subunit of Pol IV and is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs) and transcriptional regulation of specific alleles. RESULTS In this study we applied a total RNA-Seq approach to compare the B73 and rpd1/rmr6 leaf transcriptomes. Although previous studies indicated that loss of siRNAs production in RdDM mutants provokes a strong loss of CHH DNA methylation but not massive gene or TEs transcriptional activation in both Arabidopsis and maize, our total RNA-Seq analysis of rpd1/rmr6 transcriptome reveals that loss of Pol IV activity causes a global increase in the transcribed fraction of the maize genome. Our results point to the genes with nearby TE insertions as being the most strongly affected by Pol IV-mediated gene silencing. TEs modulation of nearby gene expression is linked to alternative methylation profiles on gene flanking regions, and these profiles are strictly dependent on specific characteristics of the TE member inserted. Although Pol IV is essential for the biogenesis of siRNAs, the genes with associated siRNA loci are less affected by the pol IV mutation. CONCLUSIONS This deep and integrated analysis of gene expression, TEs distribution, smallRNA targeting and DNA methylation levels, reveals that loss of Pol IV activity globally affects genome regulation, pointing at TEs as modulator of nearby gene expression and indicating the existence of multiple level epigenetic silencing mechanisms. Our results also suggest a predominant role of the Pol IV-mediated RdDM pathway in genome dominance regulation, and subgenome stability and evolution in maize.
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Affiliation(s)
- Cristian Forestan
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro, PD Italy
| | - Silvia Farinati
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro, PD Italy
| | | | - Alice Lunardon
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro, PD Italy
- Present Address: Department of Biology and Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, PA 16802 USA
| | | | - Serena Varotto
- Department of Agronomy, Food, Natural resources, Animals and Environment, University of Padova, Viale dell’Università 16, 35020 Legnaro, PD Italy
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17
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Khan A, Yadav NS, Morgenstern Y, Zemach A, Grafi G. Activation of Tag1 transposable elements in Arabidopsis dedifferentiating cells and their regulation by CHROMOMETHYLASE 3-mediated CHG methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1289-98. [PMID: 27475038 DOI: 10.1016/j.bbagrm.2016.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 07/13/2016] [Accepted: 07/25/2016] [Indexed: 12/11/2022]
Abstract
Dedifferentiation, that is, the acquisition of stem cell-like state, commonly induced by stress (e.g., protoplasting), is characterized by open chromatin conformation, a chromatin state that could lead to activation of transposable elements (TEs). Here, we studied the activation of the Arabidopsis class II TE Tag1, in which two copies, situated close to each other (near genes) on chromosome 1 are found in Landsberg erecta (Ler) but not in Columbia (Col). We first transformed protoplasts with a construct in which a truncated Tag1 (ΔTag1 non-autonomous) blocks the expression of a reporter gene AtMBD5-GFP and found a relatively high ectopic excision of ΔTag1 accompanied by expression of AtMBD5-GFP in protoplasts derived from Ler compared to Col; further increase was observed in ddm1 (decrease in DNA methylation1) protoplasts (Ler background). Ectopic excision was associated with transcription of the endogenous Tag1 and changes in histone H3 methylation at the promoter region. Focusing on the endogenous Tag1 elements we found low level of excision in Ler protoplasts, which was slightly and strongly enhanced in ddm1 and cmt3 (chromomethylase3) protoplasts, respectively, concomitantly with reduction in Tag1 gene body (GB) CHG methylation and increased Tag1 transcription; strong activation of Tag1 was also observed in cmt3 leaves. Notably, in cmt3, but not in ddm1, Tag1 elements were excised out from their original sites and transposed elsewhere in the genome. Our results suggest that dedifferentiation is associated with Tag1 activation and that CMT3 rather than DDM1 plays a central role in restraining Tag1 activation via inducing GB CHG methylation.
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Affiliation(s)
- Asif Khan
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel
| | - Narendra Singh Yadav
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel
| | - Yaakov Morgenstern
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben Gurion 84990, Israel
| | - Assaf Zemach
- Department of Molecular Biology and Ecology of Plants, 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, Midreshet Ben Gurion 84990, Israel.
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18
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Tan F, Zhou C, Zhou Q, Zhou S, Yang W, Zhao Y, Li G, Zhou DX. Analysis of Chromatin Regulators Reveals Specific Features of Rice DNA Methylation Pathways. PLANT PHYSIOLOGY 2016; 171:2041-54. [PMID: 27208249 PMCID: PMC4936571 DOI: 10.1104/pp.16.00393] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 05/11/2016] [Indexed: 05/18/2023]
Abstract
Plant DNA methylation that occurs at CG, CHG, and CHH sites (H = A, C, or T) is a hallmark of the repression of repetitive sequences and transposable elements (TEs). The rice (Oryza sativa) genome contains about 40% repetitive sequence and TEs and displays specific patterns of genome-wide DNA methylation. The mechanism responsible for the specific methylation patterns is unclear. Here, we analyzed the function of OsDDM1 (Deficient in DNA Methylation 1) and OsDRM2 (Deficient in DNA Methylation 1) in genome-wide DNA methylation, TE repression, small RNA accumulation, and gene expression. We show that OsDDM1 is essential for high levels of methylation at CHG and, to a lesser extent, CG sites in heterochromatic regions and also is required for CHH methylation that mainly locates in the genic regions of the genome. In addition to a large member of TEs, loss of OsDDM1 leads to hypomethylation and up-regulation of many protein-coding genes, producing very severe growth phenotypes at the initial generation. Importantly, we show that OsDRM2 mutation results in a nearly complete loss of CHH methylation and derepression of mainly small TE-associated genes and that OsDDM1 is involved in facilitating OsDRM2-mediated CHH methylation. Thus, the function of OsDDM1 and OsDRM2 defines distinct DNA methylation pathways in the bulk of DNA methylation of the genome, which is possibly related to the dispersed heterochromatin across chromosomes in rice and suggests that DNA methylation mechanisms may vary among different plant species.
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Affiliation(s)
- Feng Tan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
| | - Chao Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
| | - Qiangwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
| | - Shaoli Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
| | - Wenjing Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
| | - Yu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
| | - Dao-Xiu Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China (F.T., C.Z., Q.Z., S.Z., W.Y., Y.Z., G.L., D.-X.Z.); andInstitute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, Université Paris-Saclay, Université Paris-sud 11, 91405 Orsay, France (D.-X.Z.)
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Mahmood K, Højland DH, Asp T, Kristensen M. Transcriptome Analysis of an Insecticide Resistant Housefly Strain: Insights about SNPs and Regulatory Elements in Cytochrome P450 Genes. PLoS One 2016; 11:e0151434. [PMID: 27019205 PMCID: PMC4809514 DOI: 10.1371/journal.pone.0151434] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 02/28/2016] [Indexed: 11/25/2022] Open
Abstract
Background Insecticide resistance in the housefly, Musca domestica, has been investigated for more than 60 years. It will enter a new era after the recent publication of the housefly genome and the development of multiple next generation sequencing technologies. The genetic background of the xenobiotic response can now be investigated in greater detail. Here, we investigate the 454-pyrosequencing transcriptome of the spinosad-resistant 791spin strain in relation to the housefly genome with focus on P450 genes. Results The de novo assembly of clean reads gave 35,834 contigs consisting of 21,780 sequences of the spinosad resistant strain. The 3,648 sequences were annotated with an enzyme code EC number and were mapped to 124 KEGG pathways with metabolic processes as most highly represented pathway. One hundred and twenty contigs were annotated as P450s covering 44 different P450 genes of housefly. Eight differentially expressed P450s genes were identified and investigated for SNPs, CpG islands and common regulatory motifs in promoter and coding regions. Functional annotation clustering of metabolic related genes and motif analysis of P450s revealed their association with epigenetic, transcription and gene expression related functions. The sequence variation analysis resulted in 12 SNPs and eight of them found in cyp6d1. There is variation in location, size and frequency of CpG islands and specific motifs were also identified in these P450s. Moreover, identified motifs were associated to GO terms and transcription factors using bioinformatic tools. Conclusion Transcriptome data of a spinosad resistant strain provide together with genome data fundamental support for future research to understand evolution of resistance in houseflies. Here, we report for the first time the SNPs, CpG islands and common regulatory motifs in differentially expressed P450s. Taken together our findings will serve as a stepping stone to advance understanding of the mechanism and role of P450s in xenobiotic detoxification.
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Affiliation(s)
- Khalid Mahmood
- Department of Agroecology, Aarhus University, Slagelse, Denmark
| | | | - Torben Asp
- Department of Molecular Biology and Genetics, Aarhus University, Slagelse, Denmark
| | - Michael Kristensen
- Department of Agroecology, Aarhus University, Slagelse, Denmark
- * E-mail:
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Cheng C, Tarutani Y, Miyao A, Ito T, Yamazaki M, Sakai H, Fukai E, Hirochika H. Loss of function mutations in the rice chromomethylase OsCMT3a cause a burst of transposition. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:1069-1081. [PMID: 26243209 DOI: 10.1111/tpj.12952] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/21/2015] [Indexed: 06/04/2023]
Abstract
Methylation patterns of plants are unique as, in addition to the methylation at CG dinucleotides that occurs in mammals, methylation also occurs at non-CG sites. Genes are methylated at CG sites, but transposable elements (TEs) are methylated at both CG and non-CG sites. The role of non-CG methylation in transcriptional silencing of TEs is being extensively studied at this time, but only very rare transpositions have been reported when non-CG methylation machineries have been compromised. To understand the role of non-CG methylation in TE suppression and in plant development, we characterized rice mutants with changes in the chromomethylase gene, OsCMT3a. oscmt3a mutants exhibited a dramatic decrease in CHG methylation, changes in the expression of some genes and TEs, and pleiotropic developmental abnormalities. Genome resequencing identified eight TE families mobilized in oscmt3a during normal propagation. These TEs included tissue culture-activated copia retrotransposons Tos17 and Tos19 (Lullaby), a pericentromeric clustered high-copy-number non-autonomous gypsy retrotransposon Dasheng, two copia retrotransposons Osr4 and Osr13, a hAT-tip100 transposon DaiZ, a MITE transposon mPing, and a LINE element LINE1-6_OS. We confirmed the transposition of these TEs by polymerase chain reaction (PCR) and/or Southern blot analysis, and showed that transposition was dependent on the oscmt3a mutation. These results demonstrated that OsCMT3a-mediated non-CG DNA methylation plays a critical role in development and in the suppression of a wide spectrum of TEs. These in planta mobile TEs are important for studying the interaction between TEs and the host genome, and for rice functional genomics.
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Affiliation(s)
- Chaoyang Cheng
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yoshiaki Tarutani
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Akio Miyao
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Tasuku Ito
- National Institute of Genetics, Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Muneo Yamazaki
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Hiroaki Sakai
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Eigo Fukai
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Hirohiko Hirochika
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
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Du J, Johnson LM, Jacobsen SE, Patel DJ. DNA methylation pathways and their crosstalk with histone methylation. Nat Rev Mol Cell Biol 2015; 16:519-32. [PMID: 26296162 PMCID: PMC4672940 DOI: 10.1038/nrm4043] [Citation(s) in RCA: 622] [Impact Index Per Article: 69.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Methylation of DNA and of histone 3 at Lys 9 (H3K9) are highly correlated with gene silencing in eukaryotes from fungi to humans. Both of these epigenetic marks need to be established at specific regions of the genome and then maintained at these sites through cell division. Protein structural domains that specifically recognize methylated DNA and methylated histones are key for targeting enzymes that catalyse these marks to appropriate genome sites. Genetic, genomic, structural and biochemical data reveal connections between these two epigenetic marks, and these domains mediate much of the crosstalk.
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Affiliation(s)
- Jiamu Du
- Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Lianna M Johnson
- Howard Hughes Medical Institute and Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Steven E Jacobsen
- Howard Hughes Medical Institute and Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Dinshaw J Patel
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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Abstract
Arabidopsis thaliana serves as a very good model organism to investigate the control of transposable elements (TEs) by genetic and genomic approaches. As TE movements are potentially deleterious to the hosts, hosts silence TEs by epigenetic mechanisms, such as DNA methylation. DNA methylation is controlled by DNA methyltransferases and other regulators, including histone modifiers and chromatin remodelers. RNAi machinery directs DNA methylation to euchromatic TEs, which is under developmental control. In addition to the epigenetic controls, some TEs are controlled by environmental factors. TEs often affect expression of nearby genes, providing evolutionary sources for epigenetic, developmental, and environmental gene controls, which could even be beneficial for the host.
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FT-like proteins induce transposon silencing in the shoot apex during floral induction in rice. Proc Natl Acad Sci U S A 2015; 112:E901-10. [PMID: 25675495 DOI: 10.1073/pnas.1417623112] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Floral induction is a crucial developmental step in higher plants. Florigen, a mobile floral activator that is synthesized in the leaf and transported to the shoot apex, was recently identified as a protein encoded by FLOWERING LOCUS T (FT) and its orthologs; the rice florigen is Heading date 3a (Hd3a) protein. The 14-3-3 proteins mediate the interaction of Hd3a with the transcription factor OsFD1 to form a ternary structure called the florigen activation complex on the promoter of OsMADS15, a rice APETALA1 ortholog. However, crucial information, including the spatiotemporal overlap among FT-like proteins and the components of florigen activation complex and downstream genes, remains unclear. Here, we confirm that Hd3a coexists, in the same regions of the rice shoot apex, with the other components of the florigen activation complex and its transcriptional targets. Unexpectedly, however, RNA-sequencing analysis of shoot apex from wild-type and RNA-interference plants depleted of florigen activity revealed that 4,379 transposable elements (TEs; 58% of all classifiable rice TEs) were expressed collectively in the vegetative and reproductive shoot apex. Furthermore, in the reproductive shoot apex, 214 TEs were silenced by florigen. Our results suggest a link between floral induction and regulation of TEs.
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Wang P, Xia H, Zhang Y, Zhao S, Zhao C, Hou L, Li C, Li A, Ma C, Wang X. Genome-wide high-resolution mapping of DNA methylation identifies epigenetic variation across embryo and endosperm in Maize (Zea may). BMC Genomics 2015; 16:21. [PMID: 25612809 PMCID: PMC4316406 DOI: 10.1186/s12864-014-1204-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/24/2014] [Indexed: 12/26/2022] Open
Abstract
Background Epigenetic modifications play important roles in plant and animal development. DNA methylation impacts the transposable element (TE) silencing, gene imprinting and expression regulation. Results Through a genome-wide analysis, DNA methylation peaks were characterized and mapped in maize embryo and endosperm genome, respectively. Distinct methylation level was observed across maize embryo and endosperm. The maize embryo genome contained more DNA methylation than endosperm. Totally, 985,478 CG islands (CGIs) were identified and most of them were unmethylated. More CGI shores were methylated than CGIs in maize suggested that DNA methylation level was not positively correlated with CpG density. The promoter sequence and transcriptional termination region (TTR) were more methylated than the gene body (intron and exon) region based on peak number and methylated depth. Result showed that 99% TEs were methylated in maize embryo, but a large portion of them (34.8%) were not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated region between embryo and endosperm are CGI shores. Our results indicated that DNA methylation is associated with both gene silencing and gene activation in maize. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 41.5% imprinting genes were similarly methylated and 58.5% imprinting genes were differentially methylated between embryo and endosperm. Methylation level was associated with allelic silencing of only a small number of imprinting genes. The expression of maize DEMETER-like (DME-like) gene and MBD101 gene (MBD4 homolog) were higher in endosperm than in embryo. These two genes may be associated with distinct methylation levels across maize embryo and endosperm. Conclusions Through MeDIP-seq we systematically analyzed the methylomes of maize embryo and endosperm and results indicated that the global methylation status of embryo was more than that of the endosperm. Differences could be observed at the total number of methylation peaks, DMRs and specific methylated genes which were tightly associated with development of embryo and endosperm. Our results also revealed that many DNA methylation regions didn’t affect transcription of the corresponding genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-014-1204-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pengfei Wang
- Agricultural College, Anhui Agricultural University, Hefei, 230036, PR China. .,Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Han Xia
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Ye Zhang
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Shuzhen Zhao
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Chuanzhi Zhao
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Lei Hou
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Changsheng Li
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Aiqin Li
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
| | - Chuanxi Ma
- Agricultural College, Anhui Agricultural University, Hefei, 230036, PR China.
| | - Xingjun Wang
- Bio-Tech Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, PR China.
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Matzke MA, Kanno T, Matzke AJM. RNA-Directed DNA Methylation: The Evolution of a Complex Epigenetic Pathway in Flowering Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:243-67. [PMID: 25494460 DOI: 10.1146/annurev-arplant-043014-114633] [Citation(s) in RCA: 284] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
RNA-directed DNA methylation (RdDM) is an epigenetic process in plants that involves both short and long noncoding RNAs. The generation of these RNAs and the induction of RdDM rely on complex transcriptional machineries comprising two plant-specific, RNA polymerase II (Pol II)-related RNA polymerases known as Pol IV and Pol V, as well as a host of auxiliary factors that include both novel and refashioned proteins. We present current views on the mechanism of RdDM with a focus on evolutionary innovations that occurred during the transition from a Pol II transcriptional pathway, which produces mRNA precursors and numerous noncoding RNAs, to the Pol IV and Pol V pathways, which are specialized for RdDM and gene silencing. We describe recently recognized deviations from the canonical RdDM pathway, discuss unresolved issues, and speculate on the biological significance of RdDM for flowering plants, which have a highly developed Pol V pathway.
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Affiliation(s)
- Marjori A Matzke
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan; , ,
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Luo GH, Li XH, Han ZJ, Guo HF, Yang Q, Wu M, Zhang ZC, Liu BS, Qian L, Fang JC. Molecular characterization of the piggyBac-like element, a candidate marker for phylogenetic research of Chilo suppressalis (Walker) in China. BMC Mol Biol 2014; 15:28. [PMID: 25515331 PMCID: PMC4273485 DOI: 10.1186/s12867-014-0028-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 12/08/2014] [Indexed: 01/24/2023] Open
Abstract
Background Transposable elements (TEs, transposons) are mobile genetic DNA sequences. TEs can insert copies of themselves into new genomic locations and they have the capacity to multiply. Therefore, TEs have been crucial in the shaping of hosts’ current genomes. TEs can be utilized as genetic markers to study population genetic diversity. The rice stem borer Chilo suppressalis Walker is one of the most important insect pests of many subtropical and tropical paddy fields. This insect occurs in all the rice-growing areas in China. This research was carried out in order to find diversity between C. suppressalis field populations and detect the original settlement of C. suppressalis populations based on the piggyBac-like element (PLE). We also aim to provide insights into the evolution of PLEs in C. suppressalis and the phylogeography of C. suppressalis. Results Here we identify a new piggyBac-like element (PLE) in the rice stem borer Chilo suppressalis Walker, which is called CsuPLE1.1 (GenBank accession no. JX294476). CsuPLE1.1 is transcriptionally active. Additionally, the CsuPLE1.1 sequence varied slightly between field populations, with polymorphic indels (insertion/deletion) and hyper-variable regions including the identification of the 3′ region outside the open reading frame (ORF). CsuPLE1.1 insertion frequency varied between field populations. Sequences variation was found between CsuPLE1 copies and varied within and among field populations. Twenty-one different insertion sites for CsuPLE1 copies were identified with at least two insertion loci found in all populations. Conclusions Our results indicate that the initial invasion of CsuPLE1 into C. suppressalis occurred before C. suppressalis populations spread throughout China, and suggest that C. suppressalis populations have a common ancestor in China. Additionally, the lower reaches of the Yangtze River are probably the original settlement of C. suppressalis in China. Finally, the CsuPLE1 insertion site appears to be a candidate marker for phylogenetic research of C. suppressalis. Electronic supplementary material The online version of this article (doi:10.1186/s12867-014-0028-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guang-Hua Luo
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Xiao-Huan Li
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Zhao-Jun Han
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Hui-Fang Guo
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Qiong Yang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Min Wu
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Zhi-Chun Zhang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Bao-Sheng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Lu Qian
- Jiangsu Entry-Exit Inspection and Quarantine Bureau, Nanjing, 210001, China.
| | - Ji-Chao Fang
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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Dinh TT, Gao L, Liu X, Li D, Li S, Zhao Y, O'Leary M, Le B, Schmitz RJ, Manavella P, Li S, Weigel D, Pontes O, Ecker JR, Chen X. DNA topoisomerase 1α promotes transcriptional silencing of transposable elements through DNA methylation and histone lysine 9 dimethylation in Arabidopsis. PLoS Genet 2014; 10:e1004446. [PMID: 24992598 PMCID: PMC4080997 DOI: 10.1371/journal.pgen.1004446] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Accepted: 05/05/2014] [Indexed: 11/18/2022] Open
Abstract
RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) are related transcriptional silencing mechanisms that target transposable elements (TEs) and repeats to maintain genome stability in plants. RdDM is mediated by small and long noncoding RNAs produced by the plant-specific RNA polymerases Pol IV and Pol V, respectively. Through a chemical genetics screen with a luciferase-based DNA methylation reporter, LUCL, we found that camptothecin, a compound with anti-cancer properties that targets DNA topoisomerase 1α (TOP1α) was able to de-repress LUCL by reducing its DNA methylation and H3K9me2 levels. Further studies with Arabidopsis top1α mutants showed that TOP1α silences endogenous RdDM loci by facilitating the production of Pol V-dependent long non-coding RNAs, AGONAUTE4 recruitment and H3K9me2 deposition at TEs and repeats. This study assigned a new role in epigenetic silencing to an enzyme that affects DNA topology. DNA topoisomerase is an enzyme that releases the torsional stress in DNA generated during DNA replication or transcription. Here, we uncovered an unexpected role of DNA topoisomerase 1α (TOP1α) in the maintenance of genome stability. Eukaryotic genomes are usually littered with transposable elements (TEs) and repeats, which pose threats to genome stability due to their tendency to move or recombine. Mechanisms are in place to silence these elements, such as RNA-directed DNA methylation (RdDM) and histone H3 lysine 9 dimethylation (H3K9me2) in plants. Two plant-specific RNA polymerases, Pol IV and Pol V, generate small and long noncoding RNAs, respectively, from TEs and repeats. These RNAs then recruit protein factors to deposit DNA methylation or H3K9me2 to silence the loci. In this study, we found that treatment of plants with camptothecin, a TOP1α inhibitor, or loss of function in TOP1α, led to the de-repression of RdDM target loci, which was accompanied by loss of H3K9me2 or DNA methylation. The role of TOP1α in RdDM could be attributed to its promotion of Pol V, but not Pol IV, transcription to generate long noncoding RNAs.
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Affiliation(s)
- Thanh Theresa Dinh
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- ChemGen IGERT program, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Lei Gao
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Xigang Liu
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Dongming Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shengben Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Yuanyuan Zhao
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Michael O'Leary
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Brandon Le
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Robert J. Schmitz
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Pablo Manavella
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Shaofang Li
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Olga Pontes
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Joseph R. Ecker
- Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America
- Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Xuemei Chen
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California Riverside, Riverside, California, United States of America
- Howard Hughes Medical Institute, University of California Riverside, Riverside, California, United States of America
- * E-mail:
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Sheth BP, Thaker VS. Plant systems biology: insights, advances and challenges. PLANTA 2014; 240:33-54. [PMID: 24671625 DOI: 10.1007/s00425-014-2059-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/06/2014] [Indexed: 05/20/2023]
Abstract
Plants dwelling at the base of biological food chain are of fundamental significance in providing solutions to some of the most daunting ecological and environmental problems faced by our planet. The reductionist views of molecular biology provide only a partial understanding to the phenotypic knowledge of plants. Systems biology offers a comprehensive view of plant systems, by employing a holistic approach integrating the molecular data at various hierarchical levels. In this review, we discuss the basics of systems biology including the various 'omics' approaches and their integration, the modeling aspects and the tools needed for the plant systems research. A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends.
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Affiliation(s)
- Bhavisha P Sheth
- Department of Biosciences, Centre for Advanced Studies in Plant Biotechnology and Genetic Engineering, Saurashtra University, Rajkot, 360005, Gujarat, India,
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Nonogaki H. Seed dormancy and germination-emerging mechanisms and new hypotheses. FRONTIERS IN PLANT SCIENCE 2014; 5:233. [PMID: 24904627 PMCID: PMC4036127 DOI: 10.3389/fpls.2014.00233] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 05/10/2014] [Indexed: 05/18/2023]
Abstract
Seed dormancy has played a significant role in adaptation and evolution of seed plants. While its biological significance is clear, molecular mechanisms underlying seed dormancy induction, maintenance and alleviation still remain elusive. Intensive efforts have been made to investigate gibberellin and abscisic acid metabolism in seeds, which greatly contributed to the current understanding of seed dormancy mechanisms. Other mechanisms, which might be independent of hormones, or specific to the seed dormancy pathway, are also emerging from genetic analysis of "seed dormancy mutants." These studies suggest that chromatin remodeling through histone ubiquitination, methylation and acetylation, which could lead to transcription elongation or gene silencing, may play a significant role in seed dormancy regulation. Small interfering RNA and/or long non-coding RNA might be a trigger of epigenetic changes at the seed dormancy or germination loci, such as DELAY OF GERMINATION1. While new mechanisms are emerging from genetic studies of seed dormancy, novel hypotheses are also generated from seed germination studies with high throughput gene expression analysis. Recent studies on tissue-specific gene expression in tomato and Arabidopsis seeds, which suggested possible "mechanosensing" in the regulatory mechanisms, advanced our understanding of embryo-endosperm interaction and have potential to re-draw the traditional hypotheses or integrate them into a comprehensive scheme. The progress in basic seed science will enable knowledge translation, another frontier of research to be expanded for food and fuel production.
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Affiliation(s)
- Hiroyuki Nonogaki
- *Correspondence: Hiroyuki Nonogaki, Department of Horticulture, Oregon State University, 4017 ALS Bldg., Corvallis OR 97331, USA e-mail:
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Schiffer PH, Kroiher M, Kraus C, Koutsovoulos GD, Kumar S, R Camps JI, Nsah NA, Stappert D, Morris K, Heger P, Altmüller J, Frommolt P, Nürnberg P, Thomas WK, Blaxter ML, Schierenberg E. The genome of Romanomermis culicivorax: revealing fundamental changes in the core developmental genetic toolkit in Nematoda. BMC Genomics 2013; 14:923. [PMID: 24373391 PMCID: PMC3890508 DOI: 10.1186/1471-2164-14-923] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Accepted: 12/17/2013] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The genetics of development in the nematode Caenorhabditis elegans has been described in exquisite detail. The phylum Nematoda has two classes: Chromadorea (which includes C. elegans) and the Enoplea. While the development of many chromadorean species resembles closely that of C. elegans, enoplean nematodes show markedly different patterns of early cell division and cell fate assignment. Embryogenesis of the enoplean Romanomermis culicivorax has been studied in detail, but the genetic circuitry underpinning development in this species has not been explored. RESULTS We generated a draft genome for R. culicivorax and compared its gene content with that of C. elegans, a second enoplean, the vertebrate parasite Trichinella spiralis, and a representative arthropod, Tribolium castaneum. This comparison revealed that R. culicivorax has retained components of the conserved ecdysozoan developmental gene toolkit lost in C. elegans. T. spiralis has independently lost even more of this toolkit than has C. elegans. However, the C. elegans toolkit is not simply depauperate, as many novel genes essential for embryogenesis in C. elegans are not found in, or have only extremely divergent homologues in R. culicivorax and T. spiralis. Our data imply fundamental differences in the genetic programmes not only for early cell specification but also others such as vulva formation and sex determination. CONCLUSIONS Despite the apparent morphological conservatism, major differences in the molecular logic of development have evolved within the phylum Nematoda. R. culicivorax serves as a tractable system to contrast C. elegans and understand how divergent genomic and thus regulatory backgrounds nevertheless generate a conserved phenotype. The R. culicivorax draft genome will promote use of this species as a research model.
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Affiliation(s)
| | - Michael Kroiher
- Zoologisches Institut, Universität zu Köln, Cologne, NRW, Germany
| | | | - Georgios D Koutsovoulos
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Sujai Kumar
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Julia I R Camps
- Zoologisches Institut, Universität zu Köln, Cologne, NRW, Germany
| | - Ndifon A Nsah
- Zoologisches Institut, Universität zu Köln, Cologne, NRW, Germany
| | - Dominik Stappert
- Institute für Entwicklungsbiologie, Universität zu Köln, Cologne, NRW, Germany
| | - Krystalynne Morris
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Peter Heger
- Zoologisches Institut, Universität zu Köln, Cologne, NRW, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, Universität zu Köln, Cologne, NRW, Germany
| | - Peter Frommolt
- Cologne Center for Genomics, Universität zu Köln, Cologne, NRW, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, Universität zu Köln, Cologne, NRW, Germany
| | - W Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Mark L Blaxter
- Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland, UK
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31
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McCue AD, Nuthikattu S, Slotkin RK. Genome-wide identification of genes regulated in trans by transposable element small interfering RNAs. RNA Biol 2013; 10:1379-95. [PMID: 23863322 PMCID: PMC3817159 DOI: 10.4161/rna.25555] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Transposable elements (TEs) are known to influence the regulation of neighboring genes through a variety of mechanisms. Additionally, it was recently discovered that TEs can regulate non-neighboring genes through the trans-acting nature of small interfering RNAs (siRNAs). When the epigenetic repression of TEs is lost, TEs become transcriptionally active, and the host cell acts to repress mutagenic transposition by degrading TE mRNAs into siRNAs. In this study, we have performed a genome-wide analysis in the model plant Arabidopsis thaliana and found that TE siRNA-based regulation of genic mRNAs is more pervasive than the two formerly characterized proof-of-principle examples. We identified 27 candidate genic mRNAs that do not contain a TE fragment but are regulated through partial complementarity by the accumulation of TE siRNAs and are therefore influenced by TE epigenetic activation. We have experimentally confirmed several gene targets and demonstrated that they respond to the accumulation of specific 21 nucleotide TE siRNAs that are incorporated into the Arabidopsis Argonaute1 protein. Additionally, we found that one TE siRNA specifically targets and inhibits the formation of a host protein that acts to repress TE activity, suggesting that TEs harbor and potentially evolutionarily select short sequences to act as suppressors of host TE repression.
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Affiliation(s)
- Andrea D McCue
- Department of Molecular Genetics & Center for RNA Biology; The Ohio State University; Columbus, OH, USA
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32
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33
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Stroud H, Greenberg MVC, Feng S, Bernatavichute YV, Jacobsen SE. Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 2013. [PMID: 23313553 DOI: 10.1016/j.cell.2012.10.054.comprehensive] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in different sequence contexts, but the factors that regulate DNA methylation at a given site in the genome largely remain unknown. Here we have surveyed the methylomes of a comprehensive list of 86 Arabidopsis gene silencing mutants by generating single-nucleotide resolution maps of DNA methylation. We find that DNA methylation is site specifically regulated by different factors. Furthermore, we have identified additional regulators of DNA methylation. These data and analyses will serve as a comprehensive community resource for further understanding the control of DNA methylation patterning.
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Affiliation(s)
- Hume Stroud
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
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34
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Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 2013; 152:352-64. [PMID: 23313553 DOI: 10.1016/j.cell.2012.10.054] [Citation(s) in RCA: 612] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Revised: 09/05/2012] [Accepted: 10/26/2012] [Indexed: 11/23/2022]
Abstract
Cytosine methylation is involved in various biological processes such as silencing of transposable elements (TEs) and imprinting. Multiple pathways regulate DNA methylation in different sequence contexts, but the factors that regulate DNA methylation at a given site in the genome largely remain unknown. Here we have surveyed the methylomes of a comprehensive list of 86 Arabidopsis gene silencing mutants by generating single-nucleotide resolution maps of DNA methylation. We find that DNA methylation is site specifically regulated by different factors. Furthermore, we have identified additional regulators of DNA methylation. These data and analyses will serve as a comprehensive community resource for further understanding the control of DNA methylation patterning.
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35
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Claycomb JM. Caenorhabditis elegans small RNA pathways make their mark on chromatin. DNA Cell Biol 2013; 31 Suppl 1:S17-33. [PMID: 23046453 DOI: 10.1089/dna.2012.1611] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Endogenous small-RNA-mediated gene silencing pathways are generally recognized for their functions in halting gene expression by the degradation of a transcript or by translational inhibition. However, another important mode of gene regulation by small RNAs is mediated at the level of chromatin modulation. Over the past decade a great deal of progress on understanding the molecular mechanisms by which small RNAs can influence chromatin has been made for fungi, ciliated protozoans, and plants, while less is known about the functions and consequences of such chromatin-directed small RNA pathways in animals. Several recent studies in the nematode Caenorhabditis elegans have provided mechanistic insights into small RNA pathways that impact chromatin throughout development. The "worm" has been instrumental in uncovering the mechanisms of RNA interference and remains a powerful system for dissecting the molecular means by which small RNA pathways impact chromatin in animals. This review summarizes our current knowledge of the various chromatin-directed small RNA pathways in C. elegans and provides insights for future study.
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Affiliation(s)
- Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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36
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Biogenesis and mechanism of action of small non-coding RNAs: insights from the point of view of structural biology. Int J Mol Sci 2012; 13:10268-10295. [PMID: 22949860 PMCID: PMC3431858 DOI: 10.3390/ijms130810268] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/17/2012] [Accepted: 08/02/2012] [Indexed: 01/17/2023] Open
Abstract
Non-coding RNAs are dominant in the genomic output of the higher organisms being not simply occasional transcripts with idiosyncratic functions, but constituting an extensive regulatory network. Among all the species of non-coding RNAs, small non-coding RNAs (miRNAs, siRNAs and piRNAs) have been shown to be in the core of the regulatory machinery of all the genomic output in eukaryotic cells. Small non-coding RNAs are produced by several pathways containing specialized enzymes that process RNA transcripts. The mechanism of action of these molecules is also ensured by a group of effector proteins that are commonly engaged within high molecular weight protein-RNA complexes. In the last decade, the contribution of structural biology has been essential to the dissection of the molecular mechanisms involved in the biosynthesis and function of small non-coding RNAs.
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Lee TF, Gurazada SGR, Zhai J, Li S, Simon SA, Matzke MA, Chen X, Meyers BC. RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics 2012; 7:781-95. [PMID: 22647529 PMCID: PMC3679228 DOI: 10.4161/epi.20290] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In plants, heterochromatin is maintained by a small RNA-based gene silencing mechanism known as RNA-directed DNA methylation (RdDM). RdDM requires the non-redundant functions of two plant-specific DNA-dependent RNA polymerases (RNAP), RNAP IV and RNAP V. RNAP IV plays a major role in siRNA biogenesis, while RNAP V may recruit DNA methylation machinery to target endogenous loci for silencing. Although small RNA-generating regions that are dependent on both RNAP IV and RNAP V have been identified previously, the genomic loci targeted by RNAP V for siRNA accumulation and silencing have not been described extensively. To characterize the RNAP V-dependent, heterochromatic siRNA-generating regions in the Arabidopsis genome, we deeply sequenced the small RNA populations of wild-type and RNAP V null mutant (nrpe1) plants. Our results showed that RNAP V-dependent siRNA-generating loci are associated predominately with short repetitive sequences in intergenic regions. Suppression of small RNA production from short repetitive sequences was also prominent in RdDM mutants including dms4, drd1, dms3 and rdm1, reflecting the known association of these RdDM effectors with RNAP V. The genomic regions targeted by RNAP V were small, with an estimated average length of 238 bp. Our results suggest that RNAP V affects siRNA production from genomic loci with features dissimilar to known RNAP IV-dependent loci. RNAP V, along with RNAP IV and DRM1/2, may target and silence a set of small, intergenic transposable elements located in dispersed genomic regions for silencing. Silencing at these loci may be actively reinforced by RdDM.
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Affiliation(s)
- Tzuu-fen Lee
- Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
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38
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Matsunaga W, Kobayashi A, Kato A, Ito H. The effects of heat induction and the siRNA biogenesis pathway on the transgenerational transposition of ONSEN, a copia-like retrotransposon in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2012; 53:824-33. [PMID: 22173101 DOI: 10.1093/pcp/pcr179] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Environmental stress influences genetic and epigenetic regulation in plant genomes. We previously reported that heat stress activated a copia-like retrotransposon named ONSEN. To investigate the heat sensitivity and transgenerational activation of ONSEN, we analyzed the stress response by temperature shift and multiple heat stress treatments. ONSEN was activated at 37°C, and the newly inserted ONSEN was transcriptionally active and mobile to the next generation subjected to heat stress, indicating that the regulation of ONSEN is independent of positional effects on the chromosome. Reciprocal crosses with activated ONSEN revealed that the transgenerational transposition was inherited from both sexes, indicating that the transposition is suppressed independently of gametophytic regulation. We showed previously that ONSEN was transposed in mutants deficient in small interfering RNA (siRNA) biogenesis, including nrpd2 and rdr2, but not dcl3. To define the functional redundancy of Dicer-like (DCL) proteins in Arabidopsis, we analyzed ONSEN activation in mutants deficient in DCL proteins, including dcl2, dcl3 and dcl4. ONSEN was nearly immobile in a single Dicer mutant; however, some transgenerational transpositions were observed in dcl2/dcl3/dcl4 triple mutants subjected to heat stress. This indicated that the Dicer family is redundant for ONSEN transposition. To examine the activation of ONSEN in undifferentiated cells, ONSEN transcripts and synthesized DNA were analyzed in heat-stressed callus tissue. In contrast to vegetative tissue, high accumulation of the transcripts and amplified DNA copies of ONSEN were detected in callus. This result indicated that ONSEN activation is controlled by cell-specific regulatory mechanisms.
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Affiliation(s)
- Wataru Matsunaga
- Faculty of Science, Hokkaido University, Kita10 Nishi 8, Kitaku, Sapporo, Hokkaido 060-0810, Japan
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39
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Greco M, Chiappetta A, Bruno L, Bitonti MB. In Posidonia oceanica cadmium induces changes in DNA methylation and chromatin patterning. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:695-709. [PMID: 22058406 PMCID: PMC3254685 DOI: 10.1093/jxb/err313] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Revised: 07/08/2011] [Accepted: 08/18/2011] [Indexed: 05/17/2023]
Abstract
In mammals, cadmium is widely considered as a non-genotoxic carcinogen acting through a methylation-dependent epigenetic mechanism. Here, the effects of Cd treatment on the DNA methylation patten are examined together with its effect on chromatin reconfiguration in Posidonia oceanica. DNA methylation level and pattern were analysed in actively growing organs, under short- (6 h) and long- (2 d or 4 d) term and low (10 μM) and high (50 μM) doses of Cd, through a Methylation-Sensitive Amplification Polymorphism technique and an immunocytological approach, respectively. The expression of one member of the CHROMOMETHYLASE (CMT) family, a DNA methyltransferase, was also assessed by qRT-PCR. Nuclear chromatin ultrastructure was investigated by transmission electron microscopy. Cd treatment induced a DNA hypermethylation, as well as an up-regulation of CMT, indicating that de novo methylation did indeed occur. Moreover, a high dose of Cd led to a progressive heterochromatinization of interphase nuclei and apoptotic figures were also observed after long-term treatment. The data demonstrate that Cd perturbs the DNA methylation status through the involvement of a specific methyltransferase. Such changes are linked to nuclear chromatin reconfiguration likely to establish a new balance of expressed/repressed chromatin. Overall, the data show an epigenetic basis to the mechanism underlying Cd toxicity in plants.
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Affiliation(s)
| | | | | | - Maria Beatrice Bitonti
- Department of Ecology, University of Calabria, Laboratory of Plant Cyto-physiology, Ponte Pietro Bucci, I-87036 Arcavacata di Rende, Cosenza, Italy
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40
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Kim ED, Sung S. Long noncoding RNA: unveiling hidden layer of gene regulatory networks. TRENDS IN PLANT SCIENCE 2012; 17:16-21. [PMID: 22104407 DOI: 10.1016/j.tplants.2011.10.008] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Revised: 10/24/2011] [Accepted: 10/25/2011] [Indexed: 05/19/2023]
Abstract
Long noncoding RNAs (lncRNAs) are increasingly recognized as functional regulatory components in eukaryotic gene regulation. Distinct classes of lncRNAs have been identified in eukaryotes and they play roles in various regulatory networks. Previously characterized lncRNAs include primary transcripts for small regulatory RNAs. In the era of deep sequencing, new classes of lncRNAs have emerged as potent regulatory components in gene regulation. Recent studies showed that many lncRNAs are potent cis- and trans-regulators of gene activity and they can function as scaffolds for chromatin-modifying complexes. Furthermore, differential expressions of lncRNAs suggest that transcription of lncRNAs can modulate gene activity during development and in response to external stimuli. Here, we summarize our current understanding on potential roles of lncRNAs in plants.
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Affiliation(s)
- Eun-Deok Kim
- Section of Molecular Cell and Developmental Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
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41
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Yang X, Xie Y, Raja P, Li S, Wolf JN, Shen Q, Bisaro DM, Zhou X. Suppression of methylation-mediated transcriptional gene silencing by βC1-SAHH protein interaction during geminivirus-betasatellite infection. PLoS Pathog 2011; 7:e1002329. [PMID: 22028660 PMCID: PMC3197609 DOI: 10.1371/journal.ppat.1002329] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 09/06/2011] [Indexed: 12/23/2022] Open
Abstract
DNA methylation is a fundamental epigenetic modification that regulates gene expression and represses endogenous transposons and invading DNA viruses. As a counter-defense, the geminiviruses encode proteins that inhibit methylation and transcriptional gene silencing (TGS). Some geminiviruses have acquired a betasatellite called DNA β. This study presents evidence that suppression of methylation-mediated TGS by the sole betasatellite-encoded protein, βC1, is crucial to the association of Tomato yellow leaf curl China virus (TYLCCNV) with its betasatellite (TYLCCNB). We show that TYLCCNB complements Beet curly top virus (BCTV) L2- mutants deficient for methylation inhibition and TGS suppression, and that cytosine methylation levels in BCTV and TYLCCNV genomes, as well as the host genome, are substantially reduced by TYLCCNB or βC1 expression. We also demonstrate that while TYLCCNB or βC1 expression can reverse TGS, TYLCCNV by itself is ineffective. Thus its AC2/AL2 protein, known to have suppression activity in other geminiviruses, is likely a natural mutant in this respect. A yeast two-hybrid screen of candidate proteins, followed by bimolecular fluorescence complementation analysis, revealed that βC1 interacts with S-adenosyl homocysteine hydrolase (SAHH), a methyl cycle enzyme required for TGS. We further demonstrate that βC1 protein inhibits SAHH activity in vitro. That βC1 and other geminivirus proteins target the methyl cycle suggests that limiting its product, S-adenosyl methionine, may be a common viral strategy for methylation interference. We propose that inhibition of methylation and TGS by βC1 stabilizes geminivirus/betasatellite complexes. Plants employ repressive viral genome methylation as an epigenetic defense against geminiviruses, and geminiviruses respond by elaborating proteins that inhibit methylation and transcriptional gene silencing (TGS). Some geminiviruses have acquired a satellite called DNA β (betasatellite), which depends on the helper virus for replication and spread within and between hosts. In return, the sole betasatellite encoded protein, βC1, encodes a pathogenicity factor that enhances viral replication and is responsible for inducing disease symptoms. Geminivirus/betasatellite complexes are common and cause significant losses of food and fiber crops. Here, we explore the molecular basis of the association between Tomato yellow leaf curl China virus (TYLCCNV) and its betasatellite (TYLCCNB). We show that TYLCCNV by itself is unable to reverse TGS. However, co-inoculation of TYLCCNB, or expression of βC1 protein, results in reduced methylation of both the helper virus and host genome, and reversal of TGS directed against a transgene and an endogenous locus. We also present evidence that βC1 accomplishes this by interacting with and inhibiting the activity of S-adenosyl homocysteine hydrolase (SAHH), an enzyme needed to maintain the methyl cycle that generates the methyltransferase co-factor S-adenosyl methionine. Thus, we propose that inhibition of methylation-mediated TGS by βC1 drives geminivirus/betasatellite association.
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Affiliation(s)
- Xiuling Yang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Yan Xie
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - Priya Raja
- Department of Molecular Genetics, Plant Biotechnology Center, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Sizhun Li
- Department of Molecular Genetics, Plant Biotechnology Center, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Jamie N. Wolf
- Department of Molecular Genetics, Plant Biotechnology Center, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
| | - Qingtang Shen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
| | - David M. Bisaro
- Department of Molecular Genetics, Plant Biotechnology Center, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail: (XZ);
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, People's Republic of China
- * E-mail: (XZ);
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Simon SA, Meyers BC. Small RNA-mediated epigenetic modifications in plants. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:148-55. [PMID: 21159545 DOI: 10.1016/j.pbi.2010.11.007] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 11/16/2010] [Accepted: 11/17/2010] [Indexed: 05/21/2023]
Abstract
Epigenetic modifications in plants can be directed and mediated by small RNAs (sRNAs). This regulation is composed of a highly interactive network of sRNA-directed DNA methylation, histone, and chromatin modifications, all of which control transcription. Identification and functional characterization of components of the siRNA-directed DNA methylation pathway have provided insights into epigenetic pathways that form heterochromatin and into chromatin-based pathways for gene silencing, paramutation, genetic imprinting, and epigenetic reprogramming. Next-generation sequencing technologies have facilitated new discoveries and have helped create a basic blueprint of the plant epigenome. As the multiple layers of epigenetic regulation in plants are dissected, a more comprehensive understanding of the biological importance of epigenetic marks and states has been developed.
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Affiliation(s)
- Stacey A Simon
- Department of Plant and Soil Sciences & Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
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43
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Schmitz RJ, Zhang X. High-throughput approaches for plant epigenomic studies. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:130-6. [PMID: 21470901 PMCID: PMC3112054 DOI: 10.1016/j.pbi.2011.03.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Revised: 03/07/2011] [Accepted: 03/09/2011] [Indexed: 05/05/2023]
Abstract
In plant cells, DNA is packaged into chromatin by wrapping around histone octamers. Pathways that lead to cytosine DNA methylation, posttranslational histone modifications and certain components of the RNA interfering (RNAi) pathway are critically important in modulating chromatin structure, thereby affecting many molecular processes that take place in a cell. Recent advances in microarray and high-throughput sequencing technologies have made it possible to study these pathways on a genome-wide scale. Results from such epigenomic studies are broadening our understanding of plant genomes and are also providing important clues regarding the mechanisms and functions of these pathways that can be further tested using genetic and biochemical approaches. This review focuses on the high-throughput approaches that have been successfully applied in plant epigenomic studies.
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Affiliation(s)
- Robert J Schmitz
- Plant Biology and Genomic Analysis Laboratories, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
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44
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Yang H, Lu P, Wang Y, Ma H. The transcriptome landscape of Arabidopsis male meiocytes from high-throughput sequencing: the complexity and evolution of the meiotic process. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:503-16. [PMID: 21208307 DOI: 10.1111/j.1365-313x.2010.04439.x] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Meiosis is essential for eukaryotic sexual reproduction, with two consecutive rounds of nuclear divisions, allowing production of haploid gametes. Information regarding the meiotic transcriptome should provide valuable clues about global expression patterns and detailed gene activities. Here we used RNA sequencing to explore the transcriptome of a single plant cell type, the Arabidopsis male meiocyte, detecting the expression of approximately 20 000 genes. Transcription of introns of >400 genes was observed, suggesting previously unannotated exons. More than 800 genes may be preferentially expressed in meiocytes, including known meiotic genes. Of the 3378 Pfam gene families in the Arabidopsis genome, 3265 matched meiocyte-expressed genes, and 18 gene families were over-represented in male meiocytes, including transcription factor and other regulatory gene families. Expression was detected for many genes thought to encode meiosis-related proteins, including MutS homologs (MSHs), kinesins and ATPases. We identified more than 1000 orthologous gene clusters that are also expressed in meiotic cells of mouse and fission yeast, including 503 single-copy genes across the three organisms, with a greater number of gene clusters shared between Arabidopsis and mouse than either share with yeast. Interestingly, approximately 5% transposable element genes were apparently transcribed in male meiocytes, with a positive correlation to the transcription of neighboring genes. In summary, our RNA-Seq transcriptome data provide an overview of gene expression in male meiocytes and invaluable information for future functional studies.
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Affiliation(s)
- Hongxing Yang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, Center for Evolutionary Biology, School of Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China
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Abstract
The epigenomic regulation of chromatin structure and genome stability is essential for the interpretation of genetic information and ultimately the determination of phenotype. High-resolution maps of plant epigenomes have been obtained through a combination of chromatin technologies and genomic tiling microarrays and through high-throughput sequencing-based approaches. The transcriptomic activity of a plant at a certain stage of development is controlled by genome-wide combinatorial interactions of epigenetic modifications. Tissue- or environment-specific epigenomes are established during plant development. Epigenomic reprogramming triggered by the activation and movement of small RNAs is important for plant gametogenesis. Genome-wide loss of DNA methylation in the endosperm and the accompanying endosperm-specific gene expression during seed development provide a genomic insight into epigenetic regulation of gene imprinting in plants. Global changes of histone modifications during plant responses to different light environments play an important regulatory role in a sophisticated light-regulated transcriptional network. Epigenomic natural variation that developed during evolution is important for phenotypic diversity and can potentially contribute to the molecular mechanisms of complex biological phenomena such as heterosis in plants.
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Affiliation(s)
- Guangming He
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.
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46
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Knowledge and technologies for sustainable intensification of food production. N Biotechnol 2010; 27:505-16. [DOI: 10.1016/j.nbt.2010.05.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Accepted: 05/29/2010] [Indexed: 11/17/2022]
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47
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Abstract
Cytosine methylation silences transposable elements in plants, vertebrates, and fungi but also regulates gene expression. Plant methylation is catalyzed by three families of enzymes, each with a preferred sequence context: CG, CHG (H = A, C, or T), and CHH, with CHH methylation targeted by the RNAi pathway. Arabidopsis thaliana endosperm, a placenta-like tissue that nourishes the embryo, is globally hypomethylated in the CG context while retaining high non-CG methylation. Global methylation dynamics in seeds of cereal crops that provide the bulk of human nutrition remain unknown. Here, we show that rice endosperm DNA is hypomethylated in all sequence contexts. Non-CG methylation is reduced evenly across the genome, whereas CG hypomethylation is localized. CHH methylation of small transposable elements is increased in embryos, suggesting that endosperm demethylation enhances transposon silencing. Genes preferentially expressed in endosperm, including those coding for major storage proteins and starch synthesizing enzymes, are frequently hypomethylated in endosperm, indicating that DNA methylation is a crucial regulator of rice endosperm biogenesis. Our data show that genome-wide reshaping of seed DNA methylation is conserved among angiosperms and has a profound effect on gene expression in cereal crops.
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48
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van Wolfswinkel JC, Ketting RF. The role of small non-coding RNAs in genome stability and chromatin organization. J Cell Sci 2010; 123:1825-39. [PMID: 20484663 DOI: 10.1242/jcs.061713] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small non-coding RNAs make up much of the RNA content of a cell and have the potential to regulate gene expression on many different levels. Initial discoveries in the 1990s and early 21st century focused on determining mechanisms of post-transcriptional regulation mediated by small-interfering RNAs (siRNAs) and microRNAs (miRNAs). More recent research, however, has identified new classes of RNAs and new regulatory mechanisms, expanding the known regulatory potential of small non-coding RNAs to encompass chromatin regulation. In this Commentary, we provide an overview of these chromatin-related mechanisms and speculate on the extent to which they are conserved among eukaryotes.
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Affiliation(s)
- Josien C van Wolfswinkel
- Hubrecht Institute-KNAW and University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
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Qin FJ, Sun QW, Huang LM, Chen XS, Zhou DX. Rice SUVH histone methyltransferase genes display specific functions in chromatin modification and retrotransposon repression. MOLECULAR PLANT 2010; 3:773-82. [PMID: 20566579 DOI: 10.1093/mp/ssq030] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Histone lysine methylation plays an important role in heterochromatin formation and reprogramming of gene expression. SET-domain-containing proteins are shown to have histone lysine methyltransferase activities. A large number of SET-domain genes are identified in plant genomes. The function of most SET-domain genes is not known. In this work, we studied the 12 rice (Oryza sativa) homologs of Su(var)3-9, the histone H3 lysine 9 (H3K9) methyltransferase identified in Drosophila. Several rice SUVHs (i.e. SDG714, SDG727, and SDG710) were found to have an antagonistic function to the histone H3K9 demethylase JMJ706, as down-regulation of these genes could partially complement the jmj706 phenotype and reduced histone H3K9 methylation. Down-regulation of a rice Su(var)3-9 homolog (SUVH), namely SDG728, decreased H3K9 methylation and altered seed morphology. Overexpression of the gene increased H3K9 methylation. SDG728 and other SUVH genes were found to be involved in the repression of retrotransposons such as Tos17 and a Ty1-copia element. Analysis of histone methylation suggested that SDG728-mediated H3K9 methylation may play an important role in retrotransposon repression.
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Affiliation(s)
- Fu-Jun Qin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China
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50
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Abstract
DNA methylation is an epigenetic mark that has key roles in the control of genome activity in plants and mammals. It is critical for the stable silencing of repeat elements and is also involved in the epigenetic regulation of some genes. Despite similarities in the controlling functions of DNA methylation, its dynamics and deposition patterns differ in several respects between plants and mammals. One of the most striking differences is that plants tend to propagate pre-existing DNA methylation states across generations, whereas mammals re-establish them genome wide at every generation. Here, we review our current understanding of DNA methylation in the flowering plant Arabidopsis. We discuss in particular the role of RNAi in the incremental methylation and silencing of repeat elements over successive generations. We argue that paramutation, an epigenetic phenomenon first described in maize, is an extreme manifestation of this RNAi-dependent pathway.
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