Exploring the epigenetic dynamics of early plant development

Three new articles published in Genome Biology explain the various epigenetic dynamics occurring in the earliest stages of plant development.

Because plants are able to pause their life cycle as dormant seeds, germination requires going from complete metabolic dormancy to a metabolically active, growing seedling. Regulation of gene expression at this stage is dependent on major changes in the epigenome – including DNA methylation reprogramming, transposon silencing, and expression of small RNAs.

Although we know plenty about the epigenetic processes involved in post-germination plant development, what we know about the epigenetics of seed germination is a bit murkier. But now, three articles published in Genome Biology’s special issue on Plant Epigenomics are shedding light on this process.

DNA methylation – how it happens

DNA methylation is a modification that affects gene expression, transposon activity, and the formation of heterochromatin. In plants, DNA methylation occurs at cytosines in three distinct contexts: CG, CHG, and CHH (where H = C, A, or T).

These three methylation contexts are maintained by four DNA methylation pathways. CG methylation is maintained by DNA METHYLTRANSFERASE 1 (MET1), CHG methylation is maintained by CHROMOMETHYLASE 3 (CMT3), and CHH methylation is maintained by RNA-directed DNA methylation (RdDM), which relies on RNA polymerases, small RNAs, and a protein called DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2). CHH methylation is often found around transposable elements, silencing them and keeping them from moving around the genome. CHG and CHH methylation can also be maintained by CMT2 in a pathway that is associated with heterochromatin formation.

In the model plant Arabidopsis thaliana, four DNA demethylation enzymes have also been studied: DME, ROS1/DML1, DML2, and DML3. DME is required for genomic imprinting in the endosperm, while the other demethylases are active in vegetative tissues.

The processes of DNA methylation and demethylation are constant in cells, and generally balance each other out.

DNA methylation dynamics in developing embryos

By comparing early and mature embryos (4-day-old vs 10-day-old, respectively), Daniel Bouyer and co-authors observed increased overall DNA methylation in mature embryos, mainly caused by elevated CHH methylation. The differences in CHH methylation seen in early vs mature embryos is most pronounced in the transposable element-rich, gene-poor pericentromeric regions, suggesting distinct methylation dynamics along the chromosome as the embryo develops.

Those loci with increased CHH methylation in mature embryos were also seen to be affected by decreased CHH methylation earlier in seed development, particularly in the endosperm. Embryo development is also marked by a change in CHH methylation at transposable elements, moving from full methylation at all of the CHH sites on within the transposable element in the early embryo, to full CHH methylation only in transposable element boundaries in the mature embryos, a pattern seen throughout the rest of the plant’s lifespan.

Epigenetic reprogramming during germination

In their article, Joseph Ecker and colleagues tease apart the dynamics of global methylation reprogramming during seed development (4-18 days after pollination) and germination in Arabidopsis plants. They look at single-base resolution methylomes of seeds at the seed/embryo development and germination stages, as well as in the growing plant.

They also find an increase in CHH methylation in the developing embryo, peaking in dry seeds compared to other stages in the germination and developmental processes. Most of the methylated CHH sites in both embryo development and in germination overlapped with transposable elements.

Using plants lacking functional components of the methylation/demethylation pathways, the authors show that both the RdDM and CMT2 pathways are active and required for DNA methylation during seed development. The components of the other DNA methylation pathways are active before desiccation, and only DRM2 is active throughout the whole process, including when seeds are drying.

During germination, global demethylation occurs independently of the DNA demethylation enzymes, since these are weakly (or not at all) expressed at this stage. The observed demethylation likely happens passively during cell division.

Effects on gene expression

Taking this information a step further, Reena Narsai and colleagues looked at genome-wide DNA methylation, gene expression, and small RNA expression over embryo/seed development and germination.

The authors found over 24 000 genes that were differentially expressed during germination compared to dry seeds, many of which have light-related or root-related functions. Meanwhile, genes with RNA splicing and histone functions were highly expressed in dry seeds. In fact, widespread alternative splicing of transcripts was observed, and likely has a large contribution to transcriptome reprogramming during germination.

Modeling the RNA expression data over a time course facilitated the reconstruction of a complex network of 287 transcription factors that regulate gene expression in the germination process. Mutant lines that were inactive for 7 of these identified transcription factors were late to germinate and had varying amounts of mis-expressed genes.

Over the germination time course, there are also over 10 000 sRNA loci that are differentially regulated. Most of these were found overlapping with transposable elements and differentially methylated regions in the genome, particularly those that were depleted in CHH methylation. This all suggests that the methylation and expression patterns seen at these loci in germination are due to changes in the activity of the RdDM pathway.

Summary and moving forward

These three studies have revealed the DNA methylation dynamics that occur during embryo/seed development, germination, and early seedling development. Daniel Bouyer and colleagues have shown that DNA methylation changes occur along the chromosome as embryos mature, with inverse methylation changes occurring at the same loci in the embryo and endosperm. Joseph Ecker and co-authors have shown the mechanisms underlying DNA methylation reprogramming in the transition from dry seed to germinating seedling. And finally, Reena Narsai and coworkers have shown the transcriptome changes that occur during this process, regulated both by DNA methylation and a complex network of transcription factors.

Integrating new information about histone dynamics and the role of other epigenetic enzymes with this information will give us an even more complete picture of the epigenetic dynamics involved in seed development and germination.

These three articles were published as part of Genome Biology’s special issue on Plant Epigenomics. Read the rest of the collection here.

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