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Transposable elements of about 300 bp, termed "short interspersed nucleotide elements or SINEs are common in eukaryotes. However, Alu elements, SINEs containing restriction sites for the AluI enzyme, have been known only from primates. Here I report the first SINE found in the genome of the cephalochordate, amphioxus. It is an Alu element of 375 bp that does not share substantial identity with any genomic sequences in vertebrates. It was identified because it was located in the FoxD regulatory region in a cosmid derived from one individual, but absent from the two FoxD alleles of BACs from a second individual. However, searches of sequences of BACs and genomic traces from this second individual gave an estimate of 50-100 copies in the amphioxus genome. The finding of an Alu element in amphioxus raises the question of whether Alu elements in amphioxus and primates arose by convergent evolution or by inheritance from a common ancestor. Genome-wide analyses of transposable elements in amphioxus and other chordates such as tunicates, agnathans and cartilaginous fishes could well provide the answer.
Figure 1. The Amphi-Alu SINE from the FoxD gene in an individual of Branchiostoma floridae. A. Schematic diagram of the upstream regulatory region showing the FoxD repeat region in cosmid MPMGc117O0129, which we have shown is essential for directing expression of FoxD to the notochord just upstream of the Amphi-Alu element, which is inserted into the FoxD gene at base –1168 upstream of the ATG start codon. This element contains two binding sites for FoxA2 which is also expressed in the notochord, but as it is not present in two other FoxD alleles, it cannot be essential for notochord expression. B. Representative sequence variations of the Amphi-Alu SINE from the FoxD gene in cosmid MPMGc117O0129 and from six BAC clones and two genomic traces from the trace archive database (http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?). All eight sequences are from the same individual. The Amphi-Alu SINE in BAC CH302 63L21 is located in the presumed upstream regulatory region of the Tbx15/18/21 gene and that from CH302 119J21 within an intron of a hypothetical gene coding for a cyclic nucleotide gated cation channel. Since the other sequences are either from BAC end sequencing or shot-gun sequencing, it is not possible as yet to determine if they are within regulatory regions of genes. The Amphi-Alu sequence is shown in the reverse orientation of its insertion into the FoxD locus to orient the polyA stretches as polyA tails (double-underlining). The 5' end of the Alu element is shown as 1, the Alu sites are shaded in grey, two regions corresponding to the binding sites for RNA polymerase on the tRNA-like region are underlined and the binding sites for FoxA2 are shown by thick lines over the sequence
Figure 2. The AmphiFoxD genomic region lacking the Amphi-Alu SINE from a sequence in the Trace Archives of GenBank (gnl|ti|545126576 name:AFSA504495.g2). The site corresponding to the insertion site of the Amphi-Alu SINE in the FoxD gene in cosmid MPMGc117O0129 is shown by the arrowhead. Repeated sequenced flanking the insertion site are underlined.
Figure 3. Alignment of the sea urchin (Strongylocentrotus purpuratus) tRNA for asparagine and the corresponding region of the Amphi-Alu element. The regions with high identity to the A and B binding sites for RNA polymerase III are boxed.
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