Figure 5

Estimated ranges for four potential APE mechanisms for FAPs. This semi-log chart illustrates the activity of the one previously identified [25] and three new APE mechanisms. The APE Type 1 mechanism can also be termed 'hairpin APEs' and has been previously identified as related to Alu-Alu hairpin formation with subsequent deletion. The range of this mechanism has been demonstrated to extend up to 100 bp in a yeast model [25]. The APE Type 2 mechanism can be described as 'TSDs APEs' and refers to a potential orientational insertion preference for Alu element insertions within the TSD of existing Alu elements. This mechanism would preferentially form direct-oriented FAPs. As with TSD APEs (Type 2), the Type 3 APE mechanism appears to reflect an insertional preference for the formation of head-to-head (inverted) FAPs. Type 3 APEs occur approximately within the range of 21 to 50 bp (Figure 1). The proposed mechanism for formation of Type 4 APEs is described in Figures 6 and S7 and is hypothesized to arise through a DNA conformation termed a 'doomsday junction'. APE: Alu pair exclusion; bp: base pair; FAP: full-length Alu pair.