Fluorescent chromatin tagging by the lacO operator/lac repressor system in 
Arabidopsis thaliana is useful to trace distinct chromatin domains in living 
cells. Nevertheless, the tandem repeats of the tagging system may alter the 
spatial organisation of chromatin within nuclei by increasing homologous pairing 
as well as association with heterochromatin. Efficient homologous pairing occurs 
if lacO repeat arrays of ∼10 kb are present at two loci, either on the same 
chromosome or on different chromosomes. DNA hypomethylation of lacO repeats 
results in reduced homologous pairing. Because, in plants, DNA methylation can 
serve as a signal for H3-lysine9-dimethylation (H3K9me2), and subsequently for 
non-CG-context DNA methylation, SET-domain histone methyltransferase and 
chromodomain dna methyltransferase 3 (cmt3) mutations were introgressed. In 
suvh4 suvh5 suvh6 and cmt3 mutants, H3K9me2 associated with lacO repeats is 
diminished, but homologous pairing persists. Thus, neither H3K9me2 nor 
CMT3-mediated non-CG methylation are required at wild-type level for homologous 
pairing of lacO repeat loci.