Genome-Wide Demethylation of Arabidopsis Endosperm

Abstract

Parent-of-origin-specific (imprinted) gene expression is regulated in Arabidopsis thaliana endosperm by cytosine demethylation of the maternal genome mediated by the DNA glycosylase DEMETER, but the extent of the methylation changes is not known. Here, we show that virtually the entire endosperm genome is demethylated, coupled with extensive local non-CG hypermethylation of small interfering RNA–targeted sequences. Mutation of DEMETER partially restores endosperm CG methylation to levels found in other tissues, indicating that CG demethylation is specific to maternal sequences. Endosperm demethylation is accompanied by CHH hypermethylation of embryo transposable elements. Our findings demonstrate extensive reconfiguration of the endosperm methylation landscape that likely reinforces transposon silencing in the embryo.

Extensive, clustered parental imprinting of protein-coding and noncoding RNAs in developing maize endosperm

“…Previous studies suggested a potential role of transposable elements (TEs) in imprinting (15,22,25). In maize overall, there is no statistical difference in the appearance of TEs between the imprinted genes and nonimprinted genes, whereas a specific group of TEs (CACTA superfamily) is enriched around MEGs (P = 3.46e −5 ) (SI Appendix, Table S9).…”

“…Screening of differentially methylated regions (DMRs) between embryo and endosperm resulted in the identification of five imprinted genes in Arabidopsis (22). Mutation of genes responsible for methylation maintenance (MET1) or demethylation (DME) had effects on a subset of imprinted genes in Arabidopsis (14,25).…”

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

“…3A), although the biological roles of endosperm hypomethylation remain unknown. Interestingly, the global CHH methylation of endosperms was not reduced substantially compared with the embryo in castor bean, distinct from that in Arabidopsis (Hsieh et al, 2009) and rice (Zemach et al, 2010a). In contrast to other plants tested, in which CG methylation is most abundant, castor bean showed rich CHH methylation (68%) in both endosperm and embryo (Fig.…”

“…3A). Compared with the genomic DNA methylation levels in Arabidopsis (Hsieh et al, 2009), rice (Zemach et al, 2010a), and maize (Zhang et al, 2014;Lu et al, 2015), we found that the genomic DNA hypomethylation of endosperm tissues relative to embryo tissues was extensive in angiosperms, particularly for dicotyledons ( Fig. 3A), although the biological roles of endosperm hypomethylation remain unknown.…”

“…In particular, DNA methylation was considered as a major regulator of gene imprinting that mainly manifests itself in the endosperm of angiosperm plants, closely associated with endosperm and seed development, such as the imprinted genes MEA (Grossniklaus et al, 1998;Köhler et al, 2003), FWA (Kinoshita et al, 2004), and FIS2 (Jullien et al, 2006). Investigations of genomic DNA methylation in the seeds of Arabidopsis (Gehring et al, 2009;Hsieh et al, 2009), rice (Oryza sativa; Zemach et al, 2010a), and maize (Zea mays; Zhang et al, 2014;Lu et al, 2015) revealed extensive hypomethylation in the endosperm genome. However, the mechanism of how the extent and pattern of DNA methylation are established and whether the extent and pattern of DNA methylation are conserved in plant seeds is largely unclear.…”