Mechanism for full-length RNA processing of Arabidopsis genes containing intragenic heterochromatin

Abstract

Genomes of higher eukaryotes contain many transposable elements, which often localize within the transcribed regions of active genes. Although intragenic transposable elements can be silenced to form heterochromatin, the impact of intragenic heterochromatin on transcription and RNA processing remains largely unexplored. Here we show using a flowering plant, Arabidopsis, that full-length transcript formation over intragenic heterochromatin depends on a protein named IBM2 (Increase in Bonsai Methylation 2), which has a Bromo-Adjacent Homology domain and an RNA recognition motif. Mutation of ibm2 triggers premature termination of transcripts with 3 0 RNA processing around intragenic heterochromatin at loci including the H3K9 demethylase gene IBM1. The need for IBM2 is circumvented in variant alleles that lack the heterochromatic domain. Our results reveal a mechanism that masks deleterious effects of intragenic heterochromatin, providing evolutionary sources for genetic and epigenetic variations.

DNA Methylation within Transcribed Regions

“…Indeed, the IBM1 transgene without the sequence of heterochromatic domain in the intron can rescue these ibm1-like phenotypes of ibm2. In edm2 and ibm2 mutants, in addition to the IBM1 gene, the full-length transcript of genes containing heterochromatic TE was reduced, and instead transcripts were prematurely terminated and polyadenylated within the associated TE sequences (Saze et al, 2013;Tsuchiya and Eulgem, 2013). Interestingly, RNA polymerase II elongation over the heterochromatic domains within introns is not affected in ibm2, suggesting that IBM2 is not required for passage of PolII; it more likely affects posttranscriptional processes, such as efficient splicing of heterochromatic introns and/or suppression of cryptic poly(A) signal sequences in the intronic repeats.…”

“…An interesting question is what mechanisms allow plants to mask the deleterious effects of intronic TE sequences associated with repressive epigenetic marks. Indeed, recent studies identified factors in plants required for proper transcription of genes containing repressive epigenetic marks in intronic regions (Saze et al, 2013;Wang et al, 2013a;Coustham et al, 2014;Lei et al, 2014). One of the factors, ENHANCED DOWNY MILDEW2 (EDM2), was initially identified as a factor required for plant resistance to pathogen and was subsequently found to be required for proper transcription of a disease resistance gene, Resistance to Peronospora parasitica7 (RPP7), that contains a number of intronic TEs forming heterochromatic domains (Tsuchiya and Eulgem, 2013).…”

“…EDM2 has Plant Homeodomain domains that recognize H3K9me and a putative RNA methyltransferase domain in its C-terminal part (Lei et al, 2014;Tsuchiya and Eulgem, 2014). Another factor, INCREASE IN BONSAI MATHYLATION2 (IBM2)/ANTI-SILENCING1 (ASI1)/ SHOOT GROWTH1 (SG1), was identified as a gene responsible for DNA hypermethylation of gene bodies (Saze et al, 2013), an antisilencing effect for a transgene (Wang et al, 2013a), and pleiotropic developmental abnormalities (Coustham et al, 2014) in these Arabidopsis mutants. IBM2 contains the bromoadjacent homology domain that likely binds to chromatin and an RNA recognition motif, although the direct target of IBM2 is still unclear.…”

“…That is the case for intronic TEs in both maize and A. lyrata. Even in the exceptionally compact genome Arabidopsis, long introns often contain non-CpG methylation, mainly associated with TE insertions there (Saze et al, 2013;Le et al, 2015;Fig. 1).…”

Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing inArabidopsis thalianaF1 epihybrids

“…sites. Lack of either type of methylation in this region disrupts the heterochromatin structure and is associated with impaired production of the long IBM1 transcript IBM1-L, which encodes the functional form of IBM1 (23,25). In addition to the ROS1-and IBM1-mediated defects in met1 mutants, genes premarked with H3K27me3 tend to gain ectopic H3K9me2 and to be depleted in H3K27me3 in met1 whereas heterochromatic loci show depletion in H3K9me2 and ectopic H3K27me3 upon CG methylation loss (26,27).…”