Figure 7.

Revised model for Alu integration explaining the resulting variable TSD size. The L1 endonuclease first nicks the consensus site TTTT|AA in the antisense strand and then 15–16 bp downstream in the sense strand in a TNTN|AA site. The 5′ portion of the 15–16 bp spacer is often A-rich. The antisense polyT stretch serves as a template for the polyA tail of the Alu RNA during the subsequent TPRT. The size of polyT stretch dictates the size of the resulting variable TSD, which is equal to the distance between the two nicks (15–16 bp) minus the length of the polyT stretch. Finally, the DNA is ligated and the single-stranded parts are replicated using the DNA template to create a dsDNA flanked by an upstream polyA stretch and TSD and a downstream TSD.