This paper describes molecular and cytogenetic evidence for the instab
ility of a transgene locus that is present on the triplicated chromoso
me in an aneuploid tobacco line. This instability was manifested in se
veral ways in trisomics including a major chromosome rearrangement tha
t was detectable cytogenetically, smaller scale DNA rearrangements tha
t occurred both germinally and somatically, and methylation/epigenetic
silencing. In a deletion derivative of the locus, DNA breakpoints wer
e found in AT-rich regions. One of these regions binds to nuclear scaf
folds in vitro, suggesting a possible role for aberrant topoisomerase
II cleavage in destabilization of the locus. The implications of incre
ased chromosome instability in aneuploids for plant karyotype evolutio
n and human carcinogenesis are discussed.