Embryo CHH hypermethylation is mediated by RdDM and is autonomously directed inBrassica rapa

Abstract

Background: RNA directed DNA methylation (RdDM) initiates cytosine methylation in all contexts, and maintains asymmetric CHH methylation (where H is any base other than G). Mature plant embryos show one of the highest levels of CHH methylation, and it has been suggested that RdDM is responsible for this hypermethylation. Because loss of RdDM in Brassica rapa causes seed abortion, embryo methylation might play a role in seed development. RdDM is required in the maternal sporophyte, suggesting that small RNAs from the maternal sporophyte might translocate to the developing embryo, triggering DNA methylation that prevents seed abortion. This raises the question whether embryo hypermethylation is autonomously regulated by the embryo itself or influenced by the maternal sporophyte. Results: Here, we demonstrate that B. rapa embryos are hypermethylated in both euchromatin and heterochromatin and that this process requires RdDM. Contrary to current models, B. rapa embryo hypermethylation is not correlated with demethylation of the endosperm. We also show that maternal somatic RdDM is not sufficient for global embryo hypermethylation, and we find no compelling evidence for maternal somatic influence over embryo methylation at any locus. Decoupling of maternal and zygotic RdDM leads to successful seed development despite loss of embryo CHH hypermethylation. Conclusions: We conclude that embryo CHH hypermethylation is conserved, autonomously controlled, and not required for embryo development. Furthermore, maternal somatic RdDM, while required for seed development, does not directly influence embryo methylation patterns.

Resetting of the 24-nt siRNA landscape in rice zygotes

“…Newly detected zygote siRNAs mark future CHH hypermethylation sites in mature embryos Hypermethylation of embryo has been reported in a number of angiosperm species, including Arabidopsis, soybean, chickpea, Brassica rapa, and rice (Bouyer et al, 2017;Chakraborty et al, 2020;Kawakatsu et al, 2017;Li et al, 2020b;Lin et al, 2017;Rajkumar et al, 2020;Zhou et al, 2021). We found that newly detected siRNA loci have abundant CHH methylation in embryos that is dependent on the RdDM methyltransferase DRM2 (Fig 5C).…”

Embryo-specific epigenetic mechanisms reconstitute the CHH methylation landscape during Arabidopsis embryogenesis

“…Whether embryonic siRNAs were generated in situ by the embryo, or transported from endosperm or the surrounding seed coat has not been resolved, nor has their function fully elucidated (Bouyer et al 2017;Grover et al 2020;Kirkbride et al 2019;Chakraborty et al 2021). Of note, in Brassica rapa, maternal sporophytic RdDM, but not zygotic RdDM, is required for seed viability, showing that at least in this species, parental siRNA contributions are important for seed development, though maternal sporophyte RdDM was not sufficient to drive embryo hypermethylation (Chakraborty et al 2021;Grover et al 2020). The overlap between embRdDM loci and DME targets may reflect communication between embryo, endosperm and/or the seed coat, due to their intimate development within the seed.…”

Plant Epigenetics: Propelling DNA Methylation Variation across the Cell Cycle

“…In contrast, CHH methylation is dramatically increased upon cell-cycle arrest in vegetative nuclei, mature embryos and columella root caps 5,14,17 . Progressive CHH hypermethylation correlates with reduced cell cycle activity during embryogenesis 14 , but loss of embryonic CHH hypermethylation did not cause observable developmental defects 18,19 . Upon seed germination, cell-cycle activities increase while CHH methylation decreases 20 .…”