The DNA Glycosylase/Lyase ROS1 Functions in Pruning DNA Methylation Patterns in Arabidopsis

Abstract

The Arabidopsis DNA glycosylase/lyase ROS1 participates in active DNA demethylation by a base-excision pathway [ 1 Gong Z. Morales-Ruiz T. Ariza R.R. Roldan-Arjona T. David L. Zhu J.K. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase.Cell. 2002; 111 : 803-814 Abstract Full Text Full Text PDF PubMed Scopus (355) Google Scholar , 2 Agius F. Kapoor A. Zhu J.K. Role of the Arabidopsis DNA glycosylase/lyase ROS1 in active DNA demethylation.Proc. Natl. Acad. Sci. USA. 2006; 103 : 11796-11801 Crossref PubMed Scopus (163) Google Scholar ]. ROS1 has been shown to be required for demethylating a transgene promoter [ 1 Gong Z. Morales-Ruiz T. Ariza R.R. Roldan-Arjona T. David L. Zhu J.K. ROS1, a repressor of transcriptional gene silencing in Arabidopsis, encodes a DNA glycosylase/lyase.Cell. 2002; 111 : 803-814 Abstract Full Text Full Text PDF PubMed Scopus (355) Google Scholar ]. To determine the function of ROS1 in demethylating endogenous loci, we carried out bisulfite-sequencing analysis of several transposons and other genes in the ros1 mutant. In the wild-type, although CpG sites at the majority of these loci are heavily methylated, many of the CpXpG and CpXpX sites have low levels of methylation or are not at all methylated. However, these CpXpG and CpXpX sites become heavily methylated in the ros1 mutant. Associated with this increased DNA methylation, these loci show decreased expression in the ros1 mutant. Our results suggest that active DNA demethylation is important in pruning the methylation patterns of the genome, and even the normally “silent” transposons are under dynamic control by both methylation and demethylation. This dynamic control may be important in keeping the plant epigenome plastic so that it can efficiently respond to developmental and environmental cues.