Transgenic Petunia plants with a chsA coding sequence under the contro
l of a 35S promoter sometimes lose endogene and transgene chalcone syn
thase activity and purple flower pigment through posttranscriptional c
hsA RNA degradation. In these plants, shorter poly(A)(+) and poly(A)(-
) chsA RNAs are found, and a 3' end-specific RNA fragment from the end
ogene is more resistant to degradation. The termini of this RNA fragme
nt are located in a region of complementarity between the chsA 3' codi
ng region and its 3' untranslated region. Equivalent chsA RNA fragment
s remain in the white flower tissue of a nontransgenic Petunia variety
. We present a model involving cycles of RNA-RNA pairing between compl
ementary sequences followed by endonucleolytic RNA cleavages to descri
be how RNA degradation is likely to be promoted.