DEMETER DNA Glycosylase Establishes MEDEA Polycomb Gene Self-Imprinting by Allele-Specific Demethylation

Abstract

MEDEA (MEA) is an Arabidopsis Polycomb group gene that is imprinted in the endosperm. The maternal allele is expressed and the paternal allele is silent. MEA is controlled by DEMETER (DME), a DNA glycosylase required to activate MEA expression, and METHYLTRANSFERASE I (MET1), which maintains CG methylation at the MEA locus. Here we show that DME is responsible for endosperm maternal-allele-specific hypomethylation at the MEA gene. DME can excise 5-methylcytosine in vitro and when expressed in E. coli. Abasic sites opposite 5-methylcytosine inhibit DME activity and might prevent DME from generating double-stranded DNA breaks. Unexpectedly, paternal-allele silencing is not controlled by DNA methylation. Rather, Polycomb group proteins that are expressed from the maternal genome, including MEA, control paternal MEA silencing. Thus, DME establishes MEA imprinting by removing 5-methylcytosine to activate the maternal allele. MEA imprinting is subsequently maintained in the endosperm by maternal MEA silencing the paternal allele.

Parental epigenetic control of embryogenesis: a balance between inheritance and reprogramming?

“…The mechanism behind this demethylation has been the subject of many years of research. It was hypothesized that, following a paradigm established in plants [21], deamination and subsequent DNA repair might be involved in DNA demethylation. Deletion of the cytidine deaminase Aid in the mouse provided some support for this model as PGCs in these animals display modest DNA hypermethylation [20].…”

Endosperm: an integrator of seed growth and development

“…Real-time quantitative PCR has shown that MEA expression in the central cell is inhibited by MEA itself [39]. DME is required for MEA activation [40] and is able to remove methylated cytosine from domains linked to the MEA locus [38 ]. However, the degree of DNA methylation of MEA varies depending on natural Arabidopsis accessions Endosperm in seed growth and development Berger, Grini and Schnittger 667 ) that is reduced in size and whose seed integuments (int) do not elongate, whereas embryo growth is not altered.…”

“…[38 ,41]. Moreover, DNA methylation does not play a major role in silencing MEA in vegetative tissues or in pollen [37 ], and loss of DNA methylation on MEA paternal allele does not alter their silenced state in endosperm [36,38 ]. Hence, DNA methylation probably plays a limited regulatory role in MEA imprinting.…”

“…What mechanism is responsible for the removal of H3K27 methylation that is essential for MEA imprinting is unclear. DME DNA glycosylase activity causes singlestrand breaks in DNA [38 ]. It is possible, therefore, that DNA repair mechanisms that follow DME action involve the deposition of new chromatin and that methylated H3K27 are removed, causing loss of repression of MEA transcriptional activity (Figure 4).…”

Targeted DNA demethylation in human cells by fusion of a plant 5-methylcytosine DNA glycosylase to a sequence-specific DNA binding domain

“…Convincing biochemical and genetic evidence indicates that proteins belonging to a plant-specific family of DNA glycosylases directly excise 5mC from DNA and initiate active DNA demethylation through a base excision repair (BER) pathway. [7][8][9] Arabidopsis thaliana REPRESSOR OF SILENCING 1 (ROS1) is a representative member of this 5mC DNA glycosylase family, whose members are uniquely characterized by a discontinuous DNA glycosylase domain, 10 a conserved C-terminal domain that is essential for the catalytic activity, 11,12 and a basic amino-terminal domain that mediates nonspecific binding to DNA but it is not required for catalysis. 13 The understanding of active DNA demethylation mechanisms may have broad implications for epigenetic editing, a new discipline aimed to develop molecular tools to modulate gene expression.…”