1
|
Zhao L, Zhou Q, He L, Deng L, Lozano-Duran R, Li G, Zhu JK. DNA methylation underpins the epigenomic landscape regulating genome transcription in Arabidopsis. Genome Biol 2022; 23:197. [PMID: 36127735 PMCID: PMC9487137 DOI: 10.1186/s13059-022-02768-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 09/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It is challenging to determine the effect of DNA methylation on the epigenetic landscape and the function in higher organisms due to the lack of DNA methylation-free mutants. RESULTS Here, the analysis of a recently generated Arabidopsis mutant completely devoid of DNA methylation reveals that DNA methylation underpins the genome-wide landscape of histone modifications. Complete loss of DNA methylation causes an upheaval of the histone modification landscape, including complete loss of H3K9me2 and widespread redistribution of active and H3K27me3 histone marks, mostly owing to the role of DNA methylation in initiating H3K9me2 deposition and excluding active marks and repressive mark H3K27me3; CG and non-CG methylation can act independently at some genomic regions while they act cooperatively at many other regions. The transcriptional reprogramming upon loss of all DNA methylation correlates with the extensive redistribution or switches of the examined histone modifications. Histone modifications retained or gained in the DNA methylation-free mutant serve as DNA methylation-independent transcriptional regulatory signals: active marks promote genome transcription, whereas the repressive mark H3K27me3 compensates for the lack of DNA hypermethylation/H3K9me2 at multiple transposon families. CONCLUSIONS Our results show that an intact DNA methylome constitutes the scaffolding of the epigenomic landscape in Arabidopsis and is critical for controlled genome transcription and ultimately for proper growth and development.
Collapse
Affiliation(s)
- Lun Zhao
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.,Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Qiangwei Zhou
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li He
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Li Deng
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rosa Lozano-Duran
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.,Department of Plant Biochemistry, Centre for Plant Molecular Biology (ZMBP), Eberhard Karls University, D-72076, Tübingen, Germany
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, National Engineering Research Center of Rapeseed, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China. .,Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China. .,Center for Advanced Bioindustry Technologies, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
2
|
Vigneau J, Borg M. The epigenetic origin of life history transitions in plants and algae. PLANT REPRODUCTION 2021; 34:267-285. [PMID: 34236522 PMCID: PMC8566409 DOI: 10.1007/s00497-021-00422-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 05/17/2023]
Abstract
Plants and algae have a complex life history that transitions between distinct life forms called the sporophyte and the gametophyte. This phenomenon-called the alternation of generations-has fascinated botanists and phycologists for over 170 years. Despite the mesmerizing array of life histories described in plants and algae, we are only now beginning to learn about the molecular mechanisms controlling them and how they evolved. Epigenetic silencing plays an essential role in regulating gene expression during multicellular development in eukaryotes, raising questions about its impact on the life history strategy of plants and algae. Here, we trace the origin and function of epigenetic mechanisms across the plant kingdom, from unicellular green algae through to angiosperms, and attempt to reconstruct the evolutionary steps that influenced life history transitions during plant evolution. Central to this evolutionary scenario is the adaption of epigenetic silencing from a mechanism of genome defense to the repression and control of alternating generations. We extend our discussion beyond the green lineage and highlight the peculiar case of the brown algae. Unlike their unicellular diatom relatives, brown algae lack epigenetic silencing pathways common to animals and plants yet display complex life histories, hinting at the emergence of novel life history controls during stramenopile evolution.
Collapse
Affiliation(s)
- Jérômine Vigneau
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
| |
Collapse
|