Male fertility in Arabidopsis requires active DNA demethylation of genes that control pollen tube function

Abstract

Active DNA demethylation is required for sexual reproduction in plants but the molecular determinants underlying this epigenetic control are not known. Here, we show in Arabidopsis thaliana that the DNA glycosylases DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1) act semi-redundantly in the vegetative cell of pollen to demethylate DNA and ensure proper pollen tube progression. Moreover, we identify six pollen-specific genes with increased DNA methylation as well as reduced expression in dme and dme;ros1. We further show that for four of these genes, reinstalling their expression individually in mutant pollen is sufficient to improve male fertility. Our findings demonstrate an essential role of active DNA demethylation in regulating genes involved in pollen function.

The epigenetic origin of life history transitions in plants and algae

“…The sporophyte and gametophyte often exhibit substantial differences in physical size, cell types and duration spent in either phase (Bell 1989 ). A striking evolutionary trend observed in the plant and brown algal lineages, both of which evolved complex multicellularity, is a tendency for a dominant diploid phase and a concomitant reduction in the number of mitotic divisions and cell types of the haploid phase (Rudall 2006a ; Rudall and Bateman 2007a ). The life cycle of angiosperms serves as an apt example, where the diploid sporophyte represents the bulk of the vegetative plant body while the inconspicuous pollen grain and ovule represent the male and female gametophytes, respectively.…”

“…In plants, VIM proteins represent the orthologs of mammalian UHRF1 that probably also act to recruit MET1, the plant ortholog of mammalian DNMT1 that restores CG methylation (Woo et al 2008 ), while symmetric CHG methylation is restored by Chromomethylase 3 (CMT3) (Lindroth et al 2001 ). In contrast, asymmetric CHH methylation is deposited by Domains Rearranged Methyltransferase 2 (DRM2) through RNA-directed DNA methylation (RdDM) and by CMT2 (Matzke et al 2009 ; Zemach et al 2013 ). A feedback loop mechanism is required where CMT2 and CMT3 recognize H3K9me2 to methylate neighboring CHH and CHG sites while the H3K9 methyltransferase KRYPTONITE (KYP) recognizes methylated cytosines, further reinforcing the transcriptional silencing of heterochromatin (Wilkins and Holliday 2009 ; Du et al 2014 ; Niklas et al 2014 ; Lenormand et al 2016 ).…”

“…In contrast, asymmetric CHH methylation is deposited by Domains Rearranged Methyltransferase 2 (DRM2) through RNA-directed DNA methylation (RdDM) and by CMT2 (Matzke et al 2009 ; Zemach et al 2013 ). A feedback loop mechanism is required where CMT2 and CMT3 recognize H3K9me2 to methylate neighboring CHH and CHG sites while the H3K9 methyltransferase KRYPTONITE (KYP) recognizes methylated cytosines, further reinforcing the transcriptional silencing of heterochromatin (Wilkins and Holliday 2009 ; Du et al 2014 ; Niklas et al 2014 ; Lenormand et al 2016 ). In the yeast Cryptococcus neoformans , CG methylation is propagated by the maintenance methyltransferase DNMT5 in the absence of a de novo methyltransferase and also involves an H3K9 methylation loop (Catania et al 2020 ).…”

“…PRC2-mediated silencing of developmental genes is highly conserved across animals and plants and is essential for maintaining cellular identity during growth and development (Margueron and Reinberg 2011 ). In animals, PRC2 localizes to replication foci throughout S-phase where it propagates H3K27me3 domains across the cell cycle using pre-existing H3K27me3-marked nucleosomes as a template (Hansen et al 2008 ; Margueron et al 2009 ; Coleman and Struhl 2017 ; Laprell et al 2017 ).…”

“…H3K27me3 maintenance involves the initial K27 mono-methylation of replicative histone H3.1 by the plant-specific SET domain methyltransferases ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 and 6 (ATXR5/6) (Jacob et al 2014 ; Jiang and Berger 2017 ). The coupling of read–write activity in H3K27me3 inheritance also involves LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), which binds H3K27me3 and interacts with the PRC2 subunit MULTICOPY SUPRESSOR OF IRA 1 (MSI1) (Derkacheva et al 2013 ), and potentially also FERTILIZATION INDEPENDENT ENDOSPERM (FIE) (Ohad et al 1999 ), the plant ortholog of the EED subunit that tethers PRC2 to H3K27me3 in animals (Margueron et al 2009 ). This leads to a model where ATXR5/6 and multiple Polycomb group proteins cooperate with the replication fork to faithfully restore H3K27me3 domains during DNA replication, which is discussed in-depth in a recent review on the subject (Borg et al 2021a ).…”