CMT3 and SUVH4/KYP silence the exonic Evelknievel retroelement to allow for reconstitution of CMT1 mRNA

Narendra Singh Yadav,Janardan Khadka,Assaf Zemach,Katherine Domb,Gideon Grafi

doi:10.1186/s13072-018-0240-y

Narendra Singh Yadav, Janardan Khadka + Show 3 more

Open Access

https://doi.org/10.1186/s13072-018-0240-y

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Abstract

BackgroundThe Chromomethylase 1 (CMT1) has long been considered a nonessential gene because, in certain Arabidopsis ecotypes, the CMT1 gene is disrupted by the Evelknievel (EK) retroelement, inserted within exon 13, or contains frameshift mutations, resulting in a truncated, non-functional protein. In contrast to other transposable elements, no transcriptional activation of EK was observed under stress conditions (e.g., protoplasting).ResultsWe wanted to explore the regulatory pathway responsible for EK silencing in the Ler ecotype and its effect on CMT1 transcription. Methylome databases confirmed that EK retroelement is heavily methylated and methylation is extended toward CMT1 downstream region. Strong transcriptional activation of EK accompanied by significant reduction in non-CG methylation was found in cmt3 and kyp2, but not in ddm1 or RdDM mutants. EK activation in cmt3 and kyp2 did not interfere with upstream CMT1 expression but abolish transcription through the EK. We identified, in wild-type Ler, three spliced variants in which the entire EK is spliced out; one variant (25% of splicing incidents) facilitates proper reconstitution of an intact CMT1 mRNA. We could recover very low amount of the full-length CMT1 mRNA from WT Ler and Col, but not from cmt3 mutant.ConclusionsOur findings highlight CMT3-SUVH4/KYP as the major pathway silencing the intragenic EK via inducing non-CG methylation. Furthermore, retroelement insertion within exons (e.g., CMT1) may not lead to a complete abolishment of the gene product when the element is kept silent. Rather the element can be spliced out to bring about reconstruction of an intact, functional mRNA and possibly retrieval of an active protein.

Highlights

The Chromomethylase 1 (CMT1) has long been considered a nonessential gene because, in certain Arabidopsis ecotypes, the CMT1 gene is disrupted by the Evelknievel (EK) retroelement, inserted within exon 13, or contains frameshift mutations, resulting in a truncated, non-functional protein
Evelknievel (EK) is heavily methylated in the Ler genome We investigated the regulation of the intragene class I, copia-like Evelknievel (EK) retroelement, which is inserted in exon 13 of the CMT1 gene in the Ler, but not in the Col genome
EK is expressed in cmt3 and kyp2, but not in ddm1 or RNAs (siRNAs)-directed DNA methylation (RdDM) mutants Commonly, retrotransposons are activated following exposure of plants to stress or in meristematic tissues [29]

Summary

Introduction

The Chromomethylase 1 (CMT1) has long been considered a nonessential gene because, in certain Arabidopsis ecotypes, the CMT1 gene is disrupted by the Evelknievel (EK) retroelement, inserted within exon 13, or contains frameshift mutations, resulting in a truncated, non-functional protein. In contrast to other transposable elements, no transcriptional activation of EK was observed under stress conditions (e.g., protoplasting) Because of their abundance and the potential to modify/ mutate the genome [1, 2], transposable elements (TEs) are subjected to multiple layers of epigenetic control to ensure their silencing. Single mutants of met or cmt displayed significant accumulation of CACTA transcript [14], the most abundant class II superfamily of plant transposons [15]. The chromatin remodeling factor DDM1 appears to play a major role in maintaining cytosine methylation in CpG and non-CG contexts and silencing of genes and transposable elements. DDM1 appears to provide DNA methyltransferases such as CMT2 access to H1-containing heterochromatin to maintain silencing of TEs in cooperation with the RdDM pathway [12]

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