Distinctive families of both short and long interspersed DNA elements, SINEs, and Lines, respectively, are repeated within genomes, in addition to the abundant primate family of short repeats called Alu sequences. SINEs are typically shorter than 500 bp and occur on the order of hundreds to thousands of times within each genome. Each family of SINEs comprises a set of segments that are nonidentical but closely similar in length and sequence. The members of any given family are dispersed throughout the genome. SINEs are detected by probe hybridization using radiolabeled probes. They are found between genes, inside introns and within satellite DNA, but never in regions coding for protein. SINEs are the major component of dispersed repetitive DNA in all mammalian genomes. Most SINEs contain an intragenic RNA polymerase III promoter that initiates transcription at the 5′ end of the repeated DNA sequence and which, it has been proposed, facilitates the transposition and amplification of these sequences by an RNA-intermediate mechanism.
The term SINEs is restricted to short retroposons, which have internal RNA polymerase III promoter sites in a region derived from a structural RNA (usually a transfer RNA), that are amplified via cDNA intermediates and then enter the host genome. There is considerable evidence that these DNA transposable elements result from self-primed reverse transcription of their RNA transcripts with subsequent DNA integration. In contrast to retroviruses and retrotransposons, SINEs do not encode the enzymes, such as reverse transcriptases, required for their amplification. Thus it is presumed that they borrow these enzymes from other sources. In the human genome, however, two families of mobile elements have been identified which have the sequence characteristics of transposons that move directly from DNA to DNA, rather than requiring the reverse transcription of an RNA intermediate. One type of element comprises a coding region for a transposase flanked by short terminal repeats of 31 or 32 bp (1).
Alu sequences are a type of SINE but, in contrast to Alu sequences, the other SINEs are not confined to primates. SINEs have been characterized in the genomes of many organisms, including mammals and other vertebrates (Xenopus borealis), salmonid fishes, in many plants, in the nematode Caenorhabditis elegans, in several filamentous fungi of the genus Podospora, and in Dictyosteliumdiscoideum. A SINE of 470 bp, occurring in 100 copies per haploid genome, isolated and characterized in Magnaporthe grisea, the rice blast fungus, as an insertion element within an inverted repeat transposon, shows the typical features of a mammalian SINE. At its 5′ end, a secondary structural analysis reveals a tRNA-related region that could fold into a tRNA-like cloverleaf structure (2). DANA, the first SINE isolated from Danio rerio, the zebrafish, is unique in its substructure of distinct cassettes. In contrast to classical SINE elements, it appears to have been assembled by insertions of short sequences into a progenitor tRNA-derived element. Once associated with each other, these subunits are amplified as a new transposable element with such success that DANA-related sequences form 10% of the modern zebrafish genome (3). Three different kinds of SINEs were isolated and characterized in Octopus vulgaris. Two of them seem to have been derived from tRNAArg, and the third is from a tRNA that could not be identified because of sequence divergence from the original tRNA sequence (4).
A family of SINEs described in the hamster genome constitutes approximately 0.3 to 0.5% of the genome. The repeats are about 300 bp long and are highly divergent (differing by up to 30% from the consensus sequence ). In contrast to the usual SINEs, the repeats are not flanked by short direct repeats and lack sequences corresponding to the RNA polymerase III promoter (5). Other SINEs had already been found highly homologous to tRNA genes, which suggested that many SINE mammalian families are amplified tRNA pseudogenes (6).