In several plant systems expression of structurally intact genes may b
e silenced epigenetically when a transgenic construct increases the co
py number of DNA sequences. Here we report epigenetic silencing in Ara
bidopsis lines containing transgenic inserts of defined genetic struct
ure, all at the same genomic locus. These comprise an allelic series t
hat includes a single copy of the primary insert, which carries repeat
ed drug resistance transgenes, and a set of its derivatives, which as
a result of recombination within the insert carry different numbers an
d alleles of resistance genes. Although the drug resistance genes rema
ined intact, both the primary and some recombinant lines nevertheless
segregated many progeny that were partly or fully drug-sensitive becau
se of silencing. As in other systems silencing was reversible, and cor
related with decreased steady-state mRNA and increased DNA methylation
. Each different number and combination of genes, on the same or diffe
rent (i.e., homologous) chromosomes, conditioned its own idiosyncratic
segregation pattern. Strikingly, lines with a single gene segregated
only a few slightly drug-sensitive progeny whereas multi-gene lines se
gregated many highly sensitive progeny, indicating dependence of silen
cing at this locus on repeated sequences. This argues strongly against
explanations based on antisense RNA, but is consistent with explanati
ons based on ectopic DNA pairing. One possibility is that silencing re
flects the interaction of paired homologous DNA with flanking heterolo
gous DNA, which induces condensation of chromatin into a non-transcrib
able state.