Steps of the LINE-1 integration process. The L1 endonuclease domain encoded by the ORF2 protein loosely recognizes a consensus 5′-TTTTAA-3′ sequence (shown in green) in the genomic DNA and introduces a first-strand nick between the T and A nucleotides of the minus strand. The resulting free 3′ end of the host DNA is proposed to base-pair with the poly(A) tail of the L1 mRNA (shown in red) and serves as a primer for the first-strand cDNA synthesis (shown in blue) by the L1 reverse transcriptase that uses L1 mRNA as the template. This process is known as a target-primed reverse transcription (TPRT). Mechanistic details of the rest of the L1 integration process are not well defined yet. At some point during L1 integration, either L1 ORF2 or a cellular activity introduces a nick into the plus strand and the structure is resolved to utilize the 3′ end as a primer for the second-strand DNA synthesis (shown in light blue) by an unknown polymerase activity. Finally, the two nicks in the cellular DNA are repaired to complete the L1 integration event.
