CMT3 and SUVH4/KYP silence the exonic Evelknievel retroelement to allow for reconstitution of CMT1 mRNA 06 Biological Sciences 0604 Genetics

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

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

Background: 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). Results: We 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. Conclusions: Our 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.

Original languageEnglish
Article number69
JournalEpigenetics and Chromatin
Volume11
Issue number1
DOIs
StatePublished - 16 Nov 2018

Keywords

  • Arabidopsis
  • CMT3
  • Chromomethylase 1 (CMT1)
  • DDM1
  • Evelknievel
  • Intragenic retroelements
  • RdDM
  • SUVH4/KYP
  • Splicing

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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