DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases

doi:10.1073/pnas.0601109103

DEMETER and REPRESSOR OF SILENCING 1 encode 5-methylcytosine DNA glycosylases

Departamento de Genética, Universidad de Córdoba, 14071 Córdoba, Spain

Edited by Philip C. Hanawalt, Stanford University, Stanford, CA, and approved March 15, 2006 (received for review February 9, 2006)

Abstract

Cytosine methylation is an epigenetic mark that promotes gene silencing and plays important roles in development and genome defense against transposons. Methylation patterns are established and maintained by DNA methyltransferases that catalyze transfer of a methyl group from S-adenosyl-l-methionine to cytosine bases in DNA. Erasure of cytosine methylation occurs during development, but the enzymatic basis of active demethylation remains controversial. In Arabidopsis thaliana, DEMETER (DME) activates the maternal expression of two imprinted genes silenced by methylation, and REPRESSOR OF SILENCING 1 (ROS1) is required for release of transcriptional silencing of a hypermethylated transgene. DME and ROS1 encode two closely related DNA glycosylase domain proteins, but it is unknown whether they participate directly in a DNA demethylation process or counteract silencing through an indirect effect on chromatin structure. Here we show that DME and ROS1 catalyze the release of 5-methylcytosine (5-meC) from DNA by a glycosylase/lyase mechanism. Both enzymes also remove thymine, but not uracil, mismatched to guanine. DME and ROS1 show a preference for 5-meC over thymine in the symmetric dinucleotide CpG context, where most plant DNA methylation occurs. Nevertheless, they also have significant activity on both substrates at CpApG and asymmetric sequences, which are additional methylation targets in plant genomes. These findings suggest that a function of ROS1 and DME is to initiate erasure of 5-meC through a base excision repair process and provide strong biochemical evidence for the existence of an active DNA demethylation pathway in plants.

Footnotes

*To whom correspondence should be addressed at:
Departamento de Genética, Edificio Gregor Mendel, Campus de Rabanales s/n, Universidad de Córdoba, 14071 Córdoba, Spain.
E-mail: ge2roarm{at}uco.es
Author contributions: T.M.-R., R.R.A., and T.R.-A. designed research; T.M.-R., A.P.O.-G., M.I.P.-M., and M.I.M.-M. performed research; R.R.A. and T.R.-A. analyzed data; and R.R.A. and T.R.-A. wrote the paper.
Conflict of interest statement: No conflicts declared.
This paper was submitted directly (Track II) to the PNAS office.
Data deposition: The sequence reported in this paper for DME cDNA has been deposited in the GenBank database (accession no. DQ335243).
Abbreviations:

Abbreviations:

5-meC,

5-methylcytosine;

8-OG,

7,8-dihydro-8-oxoguanine;

TDG,

thymine DNA glycosylase;

MBD,

methyl-CpG binding protein;

AtOGG1,

Arabidopsis thaliana 8-OG-DNA glycosylase.