Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis

Abstract

DNA methylation occurs in CG and non-CG sequence contexts. Non-CG methylation is abundant in plants, and is mediated by CHROMOMETHYLASE (CMT) and DOMAINS REARRANGED METHYLTRANSFERASE (DRM) proteins; however its roles remain poorly understood. Here we characterize the roles of non-CG methylation in Arabidopsis thaliana. We show that a poorly characterized methyltransferase, CMT2, is a functional methyltransferase in vitro and in vivo. CMT2 preferentially binds histone H3 lysine 9 (H3K9) dimethylation and methylates non-CG cytosines that are regulated by H3K9 methylation. We revealed the contributions and redundancies between each non-CG methyltransferase in DNA methylation patterning and in regulating transcription. We also demonstrate extensive dependencies of small RNA accumulation and H3K9 methylation patterning on non-CG methylation, suggesting self-reinforcing mechanisms between these epigenetic factors. The results suggest that non-CG methylation patterns are critical in shaping the histone modification and small non-coding RNA landscapes.

High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns inArabidopsisand rice

“…[46][47][48][49][50] Interestingly, our results showed a significant positive correlation between H4K16ac and H3K23ac (Pearson's correlation coefficient D 0.73, P < 2.2 £ 10 ¡16 ), previously shown to be associated with transcriptional activation. 18 It is to be noted that the published H3K23ac ChIP-seq was performed using 3-week-old leaves, 18 whereas, in our study, H4K16ac was profiled from 2-week-old seedlings. To rule out the possibility that H3K23ac may have distinct distribution patterns in different developmental stages, we determined the genomewide profile of H3K23ac in parallel with that of H4K16ac from 2-weekold seedlings and found a significant correlation (Pearson's correlation coefficient D 0.52, P < 2.2 £ 10 ¡16 ).…”

“…[8][9][10][11][12][13] In plants, recent advances in high throughput sequencing technology have enabled the large-scale profiling of histone acetylation marks and have greatly improved our understanding of the function of histone acetylation and its relationship with transcription. [14][15][16][17][18] Besides its role in gene expression, plant histone acetylation plays crucial roles in the crosstalk between genomes and the environment during plant responses to diverse stresses at the cellular and organismal levels. [19][20][21][22][23][24] Acetylation occurs at many histone lysine residues and regulates chromatin activity by at least 2 different mechanisms.…”

Genomic DNA methylation analyses reveal the distinct profiles in castor bean seeds with persistent endosperms

“…Generally, CG methylation is generated by the conserved DNA methyltransferase METHYLTRANSFERASE1 (MET1; Vongs et al, 1993;Genger et al, 1999;Kankel et al, 2003;Law and Jacobsen, 2010) and CHG methylation is produced by the plant-specific DNA methyltransferase CHROMO-METHYLASE3 (CMT3; Cao and Jacobsen, 2002a;Law and Jacobsen, 2010;Zemach et al, 2010b), whereas CHH de novo methylation is established by a 24-nucleotide small interfering RNA (siRNA) directed DNA methylation (RdDM) pathway to guide the DNA methyltransferases DOMAINS REARRANGED METHYLTRANSFERASE1 (DRM1) and DRM2 in plants (Cao and Jacobsen, 2002b;Law and Jacobsen, 2010;Mosher and Melnyk, 2010). Also, several studies have demonstrated that de novo CHH methylation could be established by the plant-specific DNA methyltransferase CMT2 in an independent RdDM pathway (Zemach et al, 2013;Stroud et al, 2014). In addition, the DNA methyltransferase-like Dnmt2, first identified from bacteria, also was detected in plants, although its function in regulating DNA methylation remained largely unknown (Hermann et al, 2003;Mund et al, 2004;Ponger and Li, 2005).…”

Azacitidine (5-AzaC)-treatment and mutations in DNA methylase genes affect embryogenic response and expression of the genes that are involved in somatic embryogenesis in Arabidopsis

“…However, it recently became evident that DNA methylation appears to control the expression of only a small number of genes (Seymour and Becker 2017) and that the impact of DNA methylation on gene expression is distinctly influenced by other epigenetic modifications including histone modification and gene silencing by small noncoding RNA (Stroud et al 2014;Du et al 2015;Niederhuth and Schmidt 2017). Thus, to fully understand the function of DNA methylation in the embryogenic transition the functional outcome of DNA methylation in the context of other epigenetic changes remains to be uncovered.…”

“…By trapping the DNA methyltransferase in the replication fork, 5-AzaC causes passive DNA demethylation that results in a global and stochastic reduction of the 5metC content in the genome (Chang and Pikaard 2005;Szyf 2009). In contrast to 5-AzaC, the mutations in CMT3 and DRM methylases only cause a mild decrease in the overall DNA methylation level Table S4) and the demethylation is specific to the DNA sequences (Cokus et al 2008;Stroud et al 2013Stroud et al , 2014.…”