Distinct regulatory pathways contribute to dynamic CHH methylation patterns in transposable elements throughout Arabidopsis embryogenesis

Abstract

CHH methylation (mCHH) increases gradually during embryogenesis across dicotyledonous plants, indicating conserved mechanisms of targeting and conferral. Although it is suggested that methylation increase during embryogenesis enhances transposable element silencing, the detailed epigenetic pathways underlying this process remain unclear. In Arabidopsis, mCHH is regulated by both small RNA-dependent DNA methylation (RdDM) and RNA-independent Chromomethylase 2 (CMT2) pathways. Here, we conducted DNA methylome profiling at five stages of Arabidopsis embryogenesis, and classified mCHH regions into groups based on their dependency on different methylation pathways. Our analysis revealed that the gradual increase in mCHH in embryos coincided with the expansion of small RNA expression and regional mCHH spreading to nearby sites at numerous loci. We identified distinct methylation dynamics in different groups of mCHH targets, which vary according to transposon length, location, and cytosine frequency. Finally, we highlight the characteristics of transposable element loci that are targeted by different mCHH machinery, showing that short, heterochromatic TEs with lower mCHG levels are enriched in loci that switch from CMT2 regulation in leaves, to RdDM regulation during embryogenesis. Our findings highlight the interplay between the length, location, and cytosine frequency of transposons and the mCHH machinery in modulating mCHH dynamics during embryogenesis.

Involvement of Abscisic Acid in Transition of <em>Pisum sativum</em> L. from Germination to Post-germination Stage

“…DNA methylation (mC) occurs in three sequence contexts (CG, CHG, and CHH) and refers as addition a methyl group to the C5 position of cytosine to form 5-methylcytosine [96]. Methylation of CHH sites notably increases from early to late stages of seed development, then decreases during germination [8,47,48]. Two DNA methylases, RdDM (RNA directed DNA methylation) and CMT2 (DOMAINS REARRANGED METHYLTRANSFERASE 2), responsible for methylating CHH sites in developing seeds, are inactivated during germination [51,52].…”

Involvement of Abscisic Acid in Transition of Pea (Pisum sativum L.) Seeds from Germination to Post-Germination Stages

“…Germination-related repression of the LAFL transcriptional network is due to epigenetic regulation of gene expression through DNA methylation and post-translational modifications of histones [ 5 , 8 , 32 , 42 , 43 , 44 ]. DNA methylation patterns change throughout seed development, germination, and seedling establishment [ 8 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 ]. DNA methylation occurs in three sequence contexts (CG, CHG, and CHH) and refers to the addition of a methyl group to the C5 position of cytosine to form 5-methylcytosine [ 56 ].…”

“…DNA methylation occurs in three sequence contexts (CG, CHG, and CHH) and refers to the addition of a methyl group to the C5 position of cytosine to form 5-methylcytosine [ 56 ]. Methylation of CHH sites notably increases from early to late stages of seed development, then decreases during germination [ 8 , 49 , 50 ]. Two DNA methylases, RdDM (RNA directed DNA methylation) and CMT2 (DOMAINS REARRANGED METHYLTRANSFERASE 2), responsible for methylating CHH sites in developing seeds, are inactivated during germination [ 53 , 54 ].…”