Staggered Break in a chromosome
A common property of virtually all transposable elements is that they move by inserting into a staggered break in a chromosome, i.e. one strand is slightly longer than the other at the break (Figure 9.9). The first indication of this was the observation that the same short DNA sequence is found on each side of a transposable element. The sequence within these flanking direct repeats (FDRs) is distinctive for each copy of the transposable element, but the size of the FDR is characteristic of a particular family of transposable elements. Some families of transposable elements have FDRs as short as 4 bp and other families have FDRs as long as 12 bp. However, within a particular family, the sequence of the FDR will differ between individual copies. These FDRs are hallmarks of transposable elements.
Since the FDRs are distinctive for each copy, they are not part of the transposable element themselves. Some families of transposable elements do have repeated sequences at their flanks that are identical for all members of the family, but these are integral parts of the transposable element. The variation in sequence of the FDRs indicates that they are generated from the target sites for the transposition events. If the transposable element inserted into a break in the chromosome that left a short overhang (one strand longer than the other), and this overhang were filled in by DNA polymerase as part of the transposition, then the sequence of that overhang would be duplicated on each side of the new copy. Such a break with an overhang is called a staggered break. The size of the staggered break would determine the size of the FDR.
Mechanistic studies of the enzymes used for transposition have shown that such staggered breaks are made at the target site prior to integration and are repaired as part of the process of transposition (see below). The staggered breaks are used in transposition both by DNA intermediates and by RNA intermediates.