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These sequence structures may indicate internal priming of the L1 RT at A-rich tracts of a transcript during the process of TPRT.
A full-length L1 insertion in the genome is approximately 6,000 nucleotides long and consists of a 5' untranslated region (UTR), two open reading frames (ORFs), and a 3' UTR terminating in a poly(A) tail [ 11 ] . The second ORF of L1 encodes three domains critical for L1 propagation: endonuclease (EN) [ 12 ] , reverse transcriptase (RT) [ 13 14 ] , and a 3' terminal zinc-finger-like domain [ 15 ] . The EN and RT nick a target site in DNA and reverse transcribe L1 RNA, respectively, to integrate into a new genomic locus [ 12 16 17 18 ] ; this process is known as target-site-primed reverse transcription (TPRT).
They propagate by being transcribed from an internal RNA polymerase II promoter [ 15, 16], and then use their endonuclease and reverse transcriptase respectively to nick a target site and reverse transcribe L1 RNA, integrating the L1 into a new genomic locus [ 12, 17, 18]; this process is known as target-site-primed reverse transcription (TPRT).
During the process of TPRT, whereby a copy of an L1 is inserted into the genome, reverse transcription is believed to be primed on the poly(A) tail of the L1 transcript [ 12, 14, 17, 27].