The Arabidopsis RRM domain protein EDM3 mediates race‐specific disease resistance by controlling H3K9me2‐dependent alternative polyadenylation of RPP7 immune receptor transcripts

Abstract

The NLR-receptor RPP7 mediates race-specific immunity in Arabidopsis. Previous screens for enhanced downy mildew (edm) mutants identified the co-chaperone SGT1b (EDM1) and the PHD-finger protein EDM2 as critical regulators of RPP7. Here, we describe a third edm mutant compromised in RPP7 immunity, edm3. EDM3 encodes a nuclear-localized protein featuring an RNA-recognition motif. Like EDM2, EDM3 promotes histone H3 lysine 9 dimethylation (H3K9me2) at RPP7. Global profiling of H3K9me2 showed EDM3 to affect this silencing mark at a large set of loci. Importantly, both EDM3 and EDM2 co-associate in vivo with H3K9me2-marked chromatin and transcripts at a critical proximal polyadenylation site of RPP7, where they suppress proximal transcript polyadeylation/termination. Our results highlight the complexity of plant NLR gene regulation, and establish a functional and physical link between a histone mark and NLR-transcript processing.An RRM protein controls plant immunity 649 Figure 3. Subcellular localization of EDM3 isoforms. Confocal microscopy images of tissues from transgenic Col-0 plants expressing a CaMV35S-promoter::GFP construct (GFP) or transgenic edm3-1 plants expressing the p2X35S::GFP-E3cds-1 (GFP-E3cds-1) or p2X35S::GFP-E3cds-2 (GFP-E3cds-2) constructs (see also Figure 2d). White arrowheads point to nuclear regions. Scale bar: 10 lM. Selected GFP-fluorescing nuclei are shown enlarged in white-framed squares in the lower left corners of some panels. Overlay: merged GFP, DAPI and bright-field images. An RRM protein controls plant immunity 653H3K9me2 ChIP-seq and data analysis Chromatin immunoprecipitation-seq libraries were prepared using NEBNext Ultra TM II DNA library prep kit for Illumina (E7645; New England Biolabs) according to the manufacturer's instruction.

The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression

“…Only at a small number of loci, such as RPP7 and IBM1 , such mechanistic details have been uncovered. In each of these cases, EDM2 serves as a chromatin binding protein, recruiting the RNA binding proteins ASI1/IBM2 and EDM3/AIPP1 to intronic heterochromatic regions [ 16 , 18 – 20 , 67 , 68 ]. Together with additional factors, such as AIPP2, AIPP3 and AIPP4 [ 19 ] the EDM2-containing complex controls alternative polyadenylation.…”

“…We also reported the identification of EDM2-interacting proteins, which include EMSY-like nucleosome remodeling factors and the WNK8 protein kinase [ 15 , 17 ]. Besides this EDM2 has been shown to interact with the RNA binding proteins ASI1/IBM2 and EDM3/AIPP1 [ 19 , 20 ]. We further found that EDM2 controls silencing of some transposable elements (TEs) by modulating levels of di-methylated lysine 9 of histone H3 (H3K9me2), a ubiquitous TE silencing signal in plants [ 21 ].…”

Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by Fusarium fujikuroi

“…One of the four amino acid changes between ‘Junam’ and ‘Samgwang’ exists in the second RRM domain. Interestingly, an Arabidopsis RRM domain protein, ENHANCED DOWNY MILDEW 3 (EDM3), reportedly mediates resistance to the downy mildew disease pathogen, Hyaloperonospora arabidopsis [25]. EDM3 controls the alternative polyadenylation of RPP7 resistance gene transcripts by suppressing proximal polyadenylation at a transposon insertion site in the first RPP7 intron.…”

The Crosstalk Between Epigenetic Mechanisms and Alternative RNA Processing Regulation

“…Thus, the AAE complex is indispensable for the generation of full-length transcripts of genic heterochromatin-containing genes. Regarding the underlying mechanism, recent report indicates that EDM2 and AIPP1 mutations can slow down Pol II elongation rate at proximal polyadenylation site, leading to a promotion of proximal polyadenylation site usage ( Lai et al, 2019 ). AAE complex-mediated polyadenylation regulation plays an important role in multiple biological processes, including modulating plant immunity by targeting innate immunity receptor gene RPP7 ( Tsuchiya and Eulgem, 2013 ), epigenome regulation by targeting histone H3K9me2 demethylase gene IBM1 , and T-DNA suppression ( Saze et al, 2013 ; Wang et al, 2013 ).…”