Plant intra-individual and inter-individual variation can be determined by the epigenome, a set of covalent modifications of DNA and chromatin that can alter genome structure and activity without changes to the genome sequence. The epigenome of plant cells is plastic, that is, it can change in response to internal or external cues, such as during development or due to environmental changes, to create a memory of such events. Ongoing advances in technologies to read and write epigenomic patterns with increasing resolution, scale and precision are enabling the extent of plant epigenome variation to be more extensively characterized and functionally interrogated. In this Review, we discuss epigenome dynamics and variation within plants during development and in response to environmental changes, including stress, as well as between plants. We review known or potential functions of such plasticity and emphasize the importance of investigating the causality of epigenomic changes. Finally, we discuss emerging technologies that may underpin future research into plant epigenome plasticity.
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The authors thank B. Kidd and A. de Mendoza for critical feedback on this manuscript, and M. Oliva and D. Lam for insightful discussions.
The authors declare no competing interests.
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A recording of past events or actions that is ‘stored’ at the epigenetic level.
The process of generating a heritable phenotypic change without change in the genome sequence, which creates an epiallele.
- DNA methylation
Covalent addition of a methyl group to the fifth carbon of cytosine bases in DNA.
- Histone post-translational modifications
(Histone PTMs). Covalent modification of the tails of histone proteins, around which DNA is wrapped, that can affect gene expression and DNA accessibility.
- Transposable elements
Selfish genetic elements that can expand in copy number within a genome, often at a fitness cost to the host.
Heritable phenotypic changes that are not the result of a change in the genome sequence, often encoded by stable changes in DNA methylation or histone post-translational modifications (PTMs).
The map of epigenetic marks decorating the genome, which can be informative about how epigenetic information can produce a particular phenotype.
- RNA-directed DNA methylation
(RdDM). A molecular pathway in plants, in which small RNAs target de novo DNA methylation and silence the locus.
The process of a differentiated cell adopting the cell type identity of another cell type without going through a dedifferentiation process.
A term to denote a living factor that can influence plant growth, such as a bacterial pathogen.
A term to denote a non-living factor that can have an impact on plant growth, such as salt or heat.
- Epigenetic recombinant inbred lines
(epiRILs). Plants derived from a cross of genetically identical plants, except for one parent harbouring a mutation that disrupts a certain epigenetic mark. Over subsequent generations, the lines become homozygous for the normal or disrupted epigenetic states at particular genomic regions, with each line harbouring normal or altered modification states at different regions in the genome.
- Epigenome-wide association study
A study design that aims to link the presence or absence of an epigenetic mark, such as DNA methylation, at different genomic positions, with a phenotypic trait.
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Lloyd, J.P.B., Lister, R. Epigenome plasticity in plants. Nat Rev Genet 23, 55–68 (2022). https://doi.org/10.1038/s41576-021-00407-y
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