Isolation and characterization of copia-type retrotransposons in Arabidopsis thaliana

We isolated two copia-type retrotransposons from Arabidopsis thaliana. We named these elements AtRE1 (Arabidopsis thaliana Retro Element 1) and AtRE2. Nucleotide sequence analysis revealed that both elements have long terminal repeats (LTRs), and that their internal sequences include one large open reading frame that could encode Gag protein, protease, integrase, reverse transcriptase, and RNaseH. The deduced amino acids sequences contain several domains that are conserved among a large family of retrotransposons. The primer binding site for first-strand DNA synthesis and the polypurine tract for second-strand DNA synthesis existed at corresponding positions. A 5bp target site duplication (TSD) sequence was also found in the flanking region of LTRs. Southern hybridization and sequence determination of the flanking region demonstrated that AtREs exist at different loci in the two A. thaliana ecotypes Columbia and Landsberg erecta. Moreover, AtRE2 exists at two loci in Landsberg erecta, in contrast to the existence of only one copy in Columbia. These findings suggest that AtREs were recently transfected via some mediators or that AtREs were transposed after differentiation of the two ecotypes. One cDNA clone derived from the transcripts of AtRE1 was isolated, and the nucleotide sequence showed that this RNA was transcribed in the antisense direction. RT-PCR analysis revealed that AtRE1 was transcribed in both directions. This result suggests that the antisense RNA controls the expression of AtRE1 at the post-transcriptional level.