Isolation of a gene enhancer within an amplified inverted duplication after "expression selection"

We have attempted to isolate and identify cellular expression sequences from F9 teratocarcinoma DNA by utilizing their ability to reactivate a selectable gene devoid of its own expression sequences (expression selection). Restriction nuclease-digested F9 cellular DNA was ligated to a polyoma virus (Py) DNA fragment which contains an intact transforming region but is incapable of inducing transformation because it lacks the viral 5' enhancer sequence. The ligation mixture was used to transfect Rat-1 cells and a transformed cell line, 3B, was isolated. The 3B cell line contained a single type of Py DNA insert, which was molecularly cloned as an 18-kilobase BglII fragment. A weak cellular enhancer was identified in a 4.7-kilobase BamHI fragment upstream from the Py sequences. Both the Py DNA and the enhancer sequences were found to be present in an inverted duplication in the 3B clone. The presence of this structure in 3B genomic DNA was confirmed by the analysis of selectively isolated inverted duplicated sequences, and the structure was found to be at least 22 kilobases long. In the 3B cell line, the inverted duplicated sequences containing the Py and enhancer sequences are quite stable and are amplified 20- to 40-fold. The strongly transformed phenotype of the 3B cells may be a result of this amplification. The formation of inverted duplications as a part of the amplification mechanism as well as a general strategy for the cloning of inverted duplicated (amplified) sequences is discussed.