An AP endonuclease functions in active DNA demethylation and gene imprinting in Arabidopsis [corrected

Yan Li,Huiming Zhang,Dolores Córdoba-Cañero,Jian-Kang Zhu,Xiaohong Zhu,Teresa Roldán-Arjona,Weiqiang Qian,Rafael R. Ariza,Kai Tang,Craig S. Pikaard

doi:10.1371/journal.pgen.1004905

Abstract

Active DNA demethylation in plants occurs through base excision repair, beginning with removal of methylated cytosine by the ROS1/DME subfamily of 5-methylcytosine DNA glycosylases. Active DNA demethylation in animals requires the DNA glycosylase TDG or MBD4, which functions after oxidation or deamination of 5-methylcytosine, respectively. However, little is known about the steps following DNA glycosylase action in the active DNA demethylation pathways in plants and animals. We show here that the Arabidopsis APE1L protein has apurinic/apyrimidinic endonuclease activities and functions downstream of ROS1 and DME. APE1L and ROS1 interact in vitro and co-localize in vivo. Whole genome bisulfite sequencing of ape1l mutant plants revealed widespread alterations in DNA methylation. We show that the ape1l/zdp double mutant displays embryonic lethality. Notably, the ape1l+/−zdp−/− mutant shows a maternal-effect lethality phenotype. APE1L and the DNA phosphatase ZDP are required for FWA and MEA gene imprinting in the endosperm and are important for seed development. Thus, APE1L is a new component of the active DNA demethylation pathway and, together with ZDP, regulates gene imprinting in Arabidopsis.

Highlights

DNA methylation is a stable epigenetic mark that regulates numerous aspects of the genome, including transposon silencing and gene expression [1,2,3,4,5,6,7]
DNA cytosine methylation (5-methylcytosine, 5-meC) is an important epigenetic mark, and methylation patterns are coordinately controlled by methylation and demethylation reactions during development and reproduction
Our previous work showed that a 39-DNA phosphatase, ZDP, functions downstream of REPRESSOR OF SILENCING1 (ROS1) during active DNA demethylation in Arabidopsis

Summary

Introduction

DNA methylation is a stable epigenetic mark that regulates numerous aspects of the genome, including transposon silencing and gene expression [1,2,3,4,5,6,7]. DNA methylation can occur within CG, CHG, and CHH motifs (H represents A, T, or C). Genome-wide mapping of DNA methylation in Arabidopsis has revealed that methylation in gene bodies is predominantly at CG context whereas methylation in transposon- and other repeatenriched heterochromatin regions can be within all three motifs [8]. In Arabidopsis, symmetric CG and CHG methylation can be maintained by DNA METHYLTRANSFERASE 1 (MET1) and CHROMOMETHYLASE 3 (CMT3), respectively, during DNA replication. Asymmetric CHH methylation cannot be maintained and is established de novo by DOMAINS REAR-

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