Demethylation of ERECTA receptor genes by IBM1 histone demethylase affects stomatal development

Abstract

DNA methylation and histone modifications interact to modulate gene expression in biological organisms. The histone demethylase IBM1 suppresses DNA methylation and gene silencing, primarily by targeting genic regions in the Arabidopsis genome. The chromatin regulator EDM2 is also required for prevention of genic DNA methylation because it maintains IBM1 expression by promoting IBM1 mRNA distal polyadenylation. Loss-of-function ibm1 and edm2 mutant plants display a wide range of developmental defects, but little is known about which developmentally important genes are regulated by IBM1 and EDM2. Here, we show that both ibm1 and edm2 mutants display defects in production of stomatal lineage cells, which is linked to DNA hypermethylation of the ERECTA family genes, including ER, ERL1 and ERL2. Stomatal phenotypes and DNA methylation levels of ER genes in ibm1 and edm2 mutants are restored by mutations in the genes encoding the histone methyltransferase KYP and DNA methyltransferase CMT3. Our data demonstrate that a specific plant developmental context is influenced by IBM1-regulated histone modification and DNA methylation on the gene body region of the ERECTA receptors.

SPEECHLESS Speaks Loudly in Stomatal Development

“…Epigenetic modifications on EPF2 and ERf genes have been found to regulate stomatal development. The expression of EPF2 is regulated by RNA-directed DNA methylation (RdDM), and the expression of ERf genes is regulated by histone modification and DNA methylation (Yamamuro et al, 2014;Wang et al, 2016). In addition, the subtilisin STOMATAL DENSITY AND DISTRIBUTION (SDD1), which is predicted to process peptide precursors that remain elusive, also acts upstream of TMM and YODA to repress stomatal formation (Berger and Altmann, 2000;von Groll, 2002;Lampard et al, 2008).…”

UTR-Dependent Control of Gene Expression in Plants

“…IBM1 (Increase in Bonsai Methylation 1) is a histone demethylase that regulates the expression of many genes by removing the repressive H3K9me2 mark from gene bodies [16]. Arabidopsis ibm1 mutant plants display a wide range of developmental defects including a decreased production of stomatal lineage cells, which is associated with reduced expression of ERECTA-family genes [17]. IBM1 has a large intron that harbors a heterochromatic repeat element [20].…”

Genome-wide investigation and transcriptional analysis of cytosine-5 DNA methyltransferase and DNA demethylase gene families in tea plant (Camellia sinensis) under abiotic stress and withering processing

“…On the basis of the base excision repair mechanism, these dMTases recognize and excise the 5mC base and replace it with an unmethylated cytosine. In the ros1 mutant of A. thaliana, both CHH and CHG methylation increased in the transposon region, and many genes were found to be highly methylated and silenced at the transcriptional level (Wang et al, 2016a;Yamamuro et al, 2014). Moreover, the expression level of some genes in the triple mutant (ros1-dml2-dml3) of A. thaliana was suppressed due to hypermethylation of the upstream promoter regions (Zhang, Lang & Zhu, 2018).…”