Maintenance of genomic methylation requires a SW12/SNF2-like protein

Altering cytosine methylation by genetic means leads to a variety of develo pmental defects in mice(1), plants(2-5) and fungi(6,7) Deregulation of cyto sine methylation also has a role in human carcinogenesis(8). In some cases, these defects have been tied to the inheritance of epigenetic alterations (such as chromatin imprints and DNA methylation patterns) that do not invol ve changes in DNA sequence(3,8-10). Using a forward genetic screen, we iden tified a gene (DDM1, decrease in DNA methylation) from the flowering plant Arabidopsis thaliana required to maintain normal cytosine methylation patte rns(11). Additional ddm1 alleles (som4, 5, 6, 7, 8) were isolated in a sele ction for mutations that relieved transgene silencing(12) (E.J.R., unpublis hed data). Loss of DDM1 function causes a 70% reduction of genomic cytosine methylation, with most of the immediate hypomethylation occurring in repea ted sequences(11). In contrast, many low-copy sequences initially retain th eir methylation in ddm1 homozygotes, but lose methylation over time as the mutants are propagated through multiple generations by self-pollination(3,1 3). The progressive effect of ddm1 mutations on low-copy sequence methylati on suggests that ddm1 mutations compromise the efficiency of methylation of newly incorporated cytosines after DNA replication. In parallel with the s low decay of methylation during inbreeding, ddm1 mutants accumulate heritab le alterations (mutations or stable epialleles) at dispersed sites in the g enome that lead to morphological abnormalities(3,5,14). Here we report that DDM1 encodes a SWI2/SNF2-like protein, implicating chromatin remodelling a s an important process for maintenance of DNA methylation and genome integr ity.