The maize transposable element Activator (Ac) transposes after replica
tion from only one of the two daughter chromatids. It has been suggest
ed that DNA methylation in conjunction with methylation-sensitive tran
sposase binding to DNA may control the association of Ac transposition
and replication. We present hem a detailed genomic sequencing analysi
s of the cytosine methylation patterns of the transposase binding site
s within both Ac ends in the wx-m9::Ac allele, where Ac is inserted in
to the tenth exon of the Waxy gene. The Ac elements in wx-m9::Ac kerne
ls exhibit intriguing methylation patterns and fall into two distinct
groups. Approximately 50% of the elements are fully unmethylated at cy
tosine residues through the 256 nucleotides at the 5' end (the promote
r end). The other half is partially methylated between Ac residues 27
and 92. In contrast, at the 3' end, all Ac molecules are heavily methy
lated between residues 4372 and 4554. The more internally located Ac s
equences and the flanking Waxy DNA are unmethylated. Although most met
hylated cytosines in Ac are in the symmetrical CpG and CpNpG arrangeme
nts, nonsymmetrical cytosine methylation is also common in the hyperme
thylated regions of Ac. These results suggest a model in which differe
ntial activation of transposon ends by hemimethylation controls the ch
romatid selectivity of transposition and the association with replicat
ion.