B2 elements present in the human genome

The B2 element is a typical tRNA super(lys)-derived SINE, specific for three rodent families: Muridae, Cricetidae, and Spalacidae. These elements are composed of three regions: a 5' RNA-related region (RNA-polymerase III promoter), a tRNA-unrelated region, and a 3' AT-rich region (polyadenylation signals); the total length of a B2 element is approximately 200 bp (Deininger 1989; Weiner et al. 1986; Rogers 1985; Krayev et al. 1982). Previously, Kass et al. (1997) and Serdobova and Kramerov (1998) concluded B2 elements do not exist in the human genome. Our computer analysis of sequences from nucleotide databases (Altschul et al. 1990; Benson et al. 1999) revealed several human sequences with significant homology to the rodent B2 consensus sequence (Bains and Temple-Smith 1989; Jurka et al. 1992; Okada and Oshima 1995). However, some of these sequences were obtained from human-rodent hybrid cells and may represent contamination or transposition within the cells of the hybrids. To verify the presence of B2 SINEs in the human genome, we designed oligonucleotide primers from the mouse B2 element consensus sequence. The 5' primer identified the tRNA-related region, and the 3' primer identified the 3' region immediately upstream from the AT-rich sequences of the B2 consensus sequence (Fig. 1).