![]() ![]() Very little is known about the sequences required at the 3′ ends of non-LTR retrotransposons that are not sequence specific to allow initiation of reverse transcription. The additional nucleotides at the 3′ end of the RNA presumably facilitate alignment of the RNA with the site of insertion during reverse transcription. Reverse transcription of R2Bm initiates precisely at the 3′ end of the element provided that the RNA template contains additional nucleotides corresponding to DNA downstream of the site of insertion ( 12, 13). R2Bm is a non-LTR retrotransposon of Bombyx mori with a single ORF which encodes both reverse transcriptase and endonuclease activities. Some steps of this process have been demonstrated in vitro using the site-specific R2Bm element ( 9– 12). According to current models, the endonuclease encoded by the element makes staggered single strand breaks at the target site and the reverse transcriptase uses the 3′ hydroxyl at one of the nicks to prime synthesis of the first DNA strand using the RNA transposition intermediate as template. Reverse transcription of the RNA transposition intermediate of non-LTR retrotransposons is thought to occur at the site of integration (reviewed in 8). The latter include R1 and R2 which insert at specific sites in rRNA genes of insects ( 5), and HeT-A and TART in Drosophila melanogaster ( 6, 7) which insert at chromosome ends and compensate for the absence of standard telomeric repeats. Most non-LTR retrotransposons are dispersed in the genome but some insert at specific sites. They usually have two open reading frames (ORFs), the second of which encodes nuclease ( 1, 2) and reverse transcriptase ( 3, 4) activities. Non-LTR retrotransposons contain dA-rich sequences at the 3′ end of their coding strand which, in many cases, is poly(dA). The mechanism by which the RNA transposition intermediates of non-long terminal repeat (LTR) retrotransposons or LINEs are reverse transcribed is still poorly understood. Reverse transcriptases of other non-LTR retrotransposons may function in a similar way. Our results suggest that during integration the 3′ end of the I factor RNA template can pair with nucleotides at the target site and that tandem duplications are generated by the reverse transcriptase of the I factor in a manner that is reminiscent of the activity of the reverse transcriptases of telomerases. We also show that the TAA repeats are not required for transposition and that I elements containing mutations affecting the TAA sequences generate transposed copies ending with tandem repeats of various types. We report results showing that I factor transcripts end a few nucleotides downstream of the TAA repeats and that these extra nucleotides are not integrated into chromosomal DNA during retrotransposition. Many of them terminate in a poly(dA) sequence at the 3′ end of the coding strand although some, like the I factor of Drosophila melanogaster, have 3′ ends formed by repeats of the trinucleotide TAA. ![]() Non-long terminal repeat (LTR) retrotransposons or LINEs transpose by reverse transcription of an RNA intermediate and are thought to use the 3′ hydroxyl of a chromosomal cleavage to initiate synthesis of the first strand of the cDNA.
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