Transposable elements (TEs) can drive evolution by creating genetic and epigenetic variation. Although examples of adaptive TE insertions are accumulating, proof that epigenetic information carried by such "domesticated" TEs has been coopted to control host gene function is still limited. We show that COPIA-R7, a TE inserted into the Arabidopsis thaliana disease resistance gene RPP7 recruited the histone mark H3K9me2 to this locus. H3K9me2 levels at COPIA-R7 affect the choice between two alternative RPP7 polyadenylation sites in the pre-mRNA and, thereby, influence the critical balance between RPP7-coding and non-RPP7-coding transcript isoforms. Function of RPP7 is fully dependent on high levels of H3K9me2 at COPIA-R7. We present a direct in vivo demonstration for cooption of a TE-associated histone mark to the epigenetic control of premRNA processing and establish a unique mechanism for regulation of plant immune surveillance gene expression. Our results functionally link a histone mark to alternative polyadenylation and the balance between distinct transcript isoforms from a single gene.post translational histone modification | EDM2 | Hyaloperonospora arabidopsidis | PHD finger A s transposition of transposable elements (TEs) can cause detrimental mutations, TE expression must be tightly suppressed by host silencing mechanisms. In plants, besides methylation of the DNA base cytosine, the posttranslational histone modifications (PHMs) H3K9me2 (dimethylated lysine 9 of histone H3) and H3K27me1 (monomethylated lysine 27 of H3) are closely associated with transcriptional silencing of TEs (1). In Arabidopsis thaliana (Arabidopsis), H3K9me2 is mainly catalyzed by the partially functionally redundant Su(var)3-9 family histone methyltransferases SUVH4/KRYPTONITE, SUVH5, and SUVH6 (2-5). ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 and 6 (ATXR5 and ATXR6) have overlapping roles in mediating H3K27me1 (6).Despite their detrimental potenial, TEs can also be beneficial for adaptive evolution of host genome structure and expression control (7-10). For example, TEs have been shown to influence expression of nearby genes by altering local epigenetic states or providing cis-regulatory promoter elements. In eukaryotes, the expression of protein-encoding genes is typically regulated at multiple levels including RNA polymerase II (RNAPII)-mediated transcription, pre-mRNA processing, translation, and transcript or protein turnover (11). Alternative polyadenylation (APA) has recently emerged as an important contributor to global gene regulation (12). Differential choice of APA sites (APAS) can affect the protein-coding potential of a given mRNA and/or its stability, localization, or translation efficiency (13).APA has been thought to be predominantly regulated by polyadenylation factors binding to cis elements within pre-mRNAs (14). However, such interactions seem not sufficient to explain all APA-related events observed in vivo. Importantly, RNA processing factors are recruited to pre-mRNA cotranscriptionally when the nascent transcrip...

SummarySpecific disease resistance of Arabidopsis thaliana against the Hyaloperonospora parasitica isolate Hiks1 (HpHiks1) is mediated by RPP7. Although this disease resistance gene encodes a typical nucleotide binding site leucine-rich repeat (NB-LRR) disease resistance protein, its function is independent of the defense hormone salicylic acid and most known genes required for plant immune responses. We identified EDM2 (enhanced downy mildew 2) in a genetic screen for RPP7 suppressors. Mutations of EDM2 phenocopy RPP7 mutations, but do not affect other tested disease resistance genes. We isolated EDM2 by map-based cloning. The predicted EDM2 protein is structurally unrelated to previously identified components of the plant immune system, bears typical features of transcriptional regulators, including plant homeodomain (PHD)-finger-like domains, and defines a plant-specific protein family. In edm2 mutants both constitutive and HpHiks1-induced RPP7 transcript levels are reduced, suggesting that EDM2 is either a direct or an indirect regulator of RPP7 expression. Microarray analyses defined a set of defense-associated genes, the expression of which is suppressed during successful HpHiks1 colonization of either rpp7 or edm2 plants. This transcriptional phenotype is counteracted by an EDM2/RPP7-dependent mechanism.

SUMMARYArabidopsis thaliana EDM2 was previously shown to be specifically required for disease resistance mediated by the R protein RPP7. Here we provide additional data showing that the role of EDM2 in plant immunity is limited and does not include a function in basal defense. In addition, we found that EDM2 has a promoting effect on the floral transition. We further found that the protein kinase WNK8 physically interacts with EDM2 in the nucleus. Unlike EDM2, which serves as a substrate of this kinase, WNK8 appears not to be required for RPP7-mediated defense. As reported previously, however, WNK8 does affect flowering time. Epistasis analyses suggested that EDM2 acts upstream of the floral repressor FLC (AT5G10140) and downstream of WNK8 (AT5G41990) in a regulatory module that resembles the autonomous floral promotion pathway, comprising a set of mechanisms that are known to affect the floral transition by regulating FLC transcript levels.

Plant NLR-type receptors serve as sensitive triggers of host immunity. Their expression has to be well-balanced, due to their interference with various cellular processes and dosedependency of their defense-inducing activity. A genetic "arms race" with fast-evolving pathogenic microbes requires plants to constantly innovate their NLR repertoires. We previously showed that insertion of the COPIA-R7 retrotransposon into RPP7 co-opted the epigenetic transposon silencing signal H3K9me2 to a new function promoting expression of this Arabidopsis thaliana NLR gene. Recruitment of the histone binding protein EDM2 to COPIA-R7associated H3K9me2 is required for optimal expression of RPP7. By profiling of genomewide effects of EDM2, we now uncovered additional examples illustrating effects of transposons on NLR gene expression, strongly suggesting that these mobile elements can play critical roles in the rapid evolution of plant NLR genes by providing the "raw material" for gene expression mechanisms. We further found EDM2 to have a global role in NLR expression control. Besides serving as a positive regulator of RPP7 and a small number of other NLR genes, EDM2 acts as a suppressor of a multitude of additional NLR genes. We speculate that the dual functionality of EDM2 in NLR expression control arose from the need to compensate for fitness penalties caused by high expression of some NLR genes by suppression of others. Moreover, we are providing new insights into functional relationships of EDM2 with its interaction partner, the RNA binding protein EDM3/AIPP1, and its target gene IBM1, encoding an H3K9-demethylase.