Bali1A, a Possible LINE Partner for the SINE S1 in <I>Brassica napus</I>

Abstract

SINEs (short interspersed elements) are nonautonomous retroposons that may use the enzymatic machinery of autonomous LINEs (long interspersed elements) for retroposition. We have iso- lated a potentially active LINE element in Brassica napus. This 5.4-kb LINE, named Bali1A, is the only full-length member of a small LINE family composed of three copies per haploid genome. Bali1A ends with a poly(A) region, is flanked by direct repeats, and possesses two uninterrupted open reading frames (ORFs) characteristic of LINEs: an ORF1 presenting the cysteine-rich motifs and an ORF2 showing strong similarities to reverse transcriptase and endonuclease. A phylogenetic comparison between the endonu- clease and reverse transcriptase domain of Bali1A and other LINEs allowed its classification in the L1 clade. Bali1A transcripts were detected in Brassica napus, but its 5 � -UTR is not able to drive the expres- sion of a reporter gene in Arabidopsis thaliana. Although no primary sequence homology exists between Bali1A and S1, the perfect association in the Cruciferae family (46 species tested) of the LINE Bali1 family with the SINE S1 family suggests that Bali1A may be the retroposition partner of S1. In that case, the Bali1A/S1 association could depend on a shared poly(A) 3 � region as proposed for the L1/Alu association in humans.