An alternative polyadenylation mechanism coopted to the Arabidopsis RPP7 gene through intronic retrotransposon domestication

Abstract

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...

The effect of transposable elements on phenotypic variation: insights from plants to humans

“…These findings from G. raimondii transcriptome further reveal that TE insertions can induce alternative splicing by genetic mechanisms. The retrotransposon COPIA-R7 controls expression of the disease resistance gene RPP7 (Resistance to Peronospora parasitica 7) by alternative polyadenylation in Arabidopsis (Tsuchiya and Eulgem, 2013). The COPIA-R7 element, which inserted in the first intron of RPP7, introduces an alternative polyadenylation site from the TE LTRs to regulate pathogen responsiveness mediated by the critical balance between the functional and nonfunctional RPP7 transcripts (Tsuchiya and Eulgem, 2013).…”

The Hairless Stem Phenotype of Cotton (Gossypium barbadense) Is Linked to a Copia-Like Retrotransposon Insertion in a Homeodomain-Leucine Zipper Gene (HD1)

“…The activation of retrotransposons, particularly the Gypsy-like retrotransposons, is suggested to be one of the major forces driving genome size variation of diploid cotton species (Hawkins et al 2009). Also, it is thought that the activity of retrotransposons could drive cotton speciation by inserting into important genes that would result in dramatic changes in important evolutionary or agronomic traits Tsuchiya and Eulgem 2013). Until now, direct evidence of cotton retrotransposons affecting phenotypic evolution had not been reported.…”

Role of alternative polyadenylation in epigenetic silencing and antisilencing

“…This binding of EDM2 somehow blocks the poly(A) site choice of the transcript in the vicinity of the binding location. This is deduced from the fact that in the edm2 mutant, use of intronic poly(A) sites [so called proximal poly(A) sites, in contrast to the full-length distal poly(A) sites] results in the generation of shortened transcripts that encode no or nonfunctional proteins (4,5). In other words, the normal function of EDM2 is to reduce the production of nonfunctional transcripts and to promote the generation of full-length mRNA ending at the distal poly(A) site.…”

“…Moreover, genomewide epigenetic modification profiles of all three mutants (asi1, edm2, and ibm1) largely overlap, which indicates that they work together through a similar antisilencing pathway. In fact, it was suggested that both ASI1 and EDM2 function mostly through IBM1 by modulating APA of IBM1 transcripts (4,5).…”

“…Clearly this is a posttranscriptional regulation event. Particularly in RPP7, the degree of disease resistance conferred is tightly associated with its transcript level (5 The significance of the work on EDM2 and ASI1 is that they provide direct genetic evidence demonstrating an involvement of epigenetic marks in the selection of APA sites.…”