Identification and structural analysis of SINE elements in the Arabidopsisthaliana genome

An insertion sequence was found in a Mu homologue in the genome of Arabidop sis thaliana. The insertion sequence had poly(A) at the 3' end, and promote r motifs (A- and B-boxes) recognized by RNA polymerase III. The sequence wa s flanked by direct repeats of a 15-bp sequence of the Mu homologue, which appears to be a target-site sequence duplicated upon insertion. These findi ngs indicate that the insertion sequence is a retroposon SINE, and it was t herefore named AtSN (A. thaliana SINE). Many members of the AtSN family wer e identified through a computer-aided homology search of databases and clas sified into two subfamilies, AtSN1 and AtSN2, having consensus sequences 15 9 and 149 bp in length, respectively. These had no homology to SINEs in oth er organisms. About half of AtSN members were truncated through loss of a r egion at either end of the element. Most of them were truncated at the 5' e nd, and had a duplication of the target-site sequence. This suggests that t he ones with 5' truncation retroposed by the same mechanism as those withou t truncation. Members of the AtSN1 or AtSN2 subfamilies had many base subst itutions when compared with the consensus sequence. All of the members exam ined were present in three different ecotypes of A. thaliana (Columbia, Lan dsberg erecta, and Wassilewskija). These findings suggest that AtSN members had proliferated before the A. thaliana ecotype strains diverged.