ANU Open Research Repository has been upgraded. We are still working on a few minor issues, which may result in short outages throughout the day. Please get in touch with repository.admin@anu.edu.au if you experience any issues.
 

DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis

Date

2014

Authors

Le, Tuan-Ngoc
Schumann, Ulrike
Smith, Neil A
Tiwari, Sameer
Chi Khang Au, Phil
Zhu, Qian-Hao
Taylor, Jennifer
Kazan, Kemal
Llewellyn, Danny
Zhang, Ren

Journal Title

Journal ISSN

Volume Title

Publisher

BioMed Central

Abstract

Background: DNA demethylases regulate DNA methylation levels in eukaryotes. Arabidopsis encodes four DNA demethylases, DEMETER (DME), REPRESSOR OF SILENCING 1 (ROS1), DEMETER-LIKE 2 (DML2), and DML3. While DME is involved in maternal specific gene expression during seed development, the biological function of the remaining DNA demethylases remains unclear. Results: We show that ROS1, DML2, and DML3 play a role in fungal disease resistance in Arabidopsis. A triple DNA demethylase mutant, rdd (ros1 dml2 dml3), shows increased susceptibility to the fungal pathogen Fusarium oxysporum. We identify 348 genes differentially expressed in rdd relative to wild type, and a significant proportion of these genes are downregulated in rdd and have functions in stress response, suggesting that DNA demethylases maintain or positively regulate the expression of stress response genes required for F. oxysporum resistance. The rdd-downregulated stress response genes are enriched for short transposable element sequences in their promoters. Many of these transposable elements and their surrounding sequences show localized DNA methylation changes in rdd, and a general reduction in CHH methylation, suggesting that RNA-directed DNA methylation (RdDM), responsible for CHH methylation, may participate in DNA demethylase-mediated regulation of stress response genes. Many of the rdd-downregulated stress response genes are downregulated in the RdDM mutants nrpd1 and nrpe1, and the RdDM mutants nrpe1 and ago4 show enhanced susceptibility to F. oxysporum infection. Conclusions: Our results suggest that a primary function of DNA demethylases in plants is to regulate the expression of stress response genes by targeting promoter transposable element sequences

Description

Keywords

Citation

Source

Genome Biology

Type

Journal article

Book Title

Entity type

Access Statement

Open Access

License Rights

DOI

10.1186/s13059-014-0458-3

Restricted until