A model for the mechanism of initial generation of short interspersed elements (SINEs)

Abstract

Most animal genomes contain a large number of short interspersed elements (SINEs) that have a composite structure and contain a region that is homologous to a tRNA. The majority of SINEs have been found to be derived from a tRNA(Lys), being categorized as members of a superfamily of tRNA(Lys)-related SINEs. The consensus sequences of five SINEs that belong to this superfamily were aligned. It was found that, in the tRNA-unrelated region, there are two sequence motifs that are almost identical among these five SINEs and are at a distance of 10-11 nucleotides from each other. This observation suggests a common evolutionary origin of these SINEs and/or some function(s) for these motifs. Similar sequences were unexpectedly found to be present in the sequences complementary to the U5 regions of several mammalian retroviruses whose primer is a tRNA(Lys). On the basis of these findings, we propose a possible model for the generation of SINEs whereby they are derived from a "strong stop DNA" with a primer tRNA that is an intermediate in the process of reverse transcription of certain retroviruses.

Evolution and recombination of bovine DNA repeats

“…Other mammalian SINE sequences are specific for the orders of the primates, rodents (Weiner et al 1986), carnivores (Coltman and Wright 1994;Van der Vlugt and Lenstra 1995), or Equidae (Sakagami et al 1994). The evolution of SINE elements may be explained by amplification of pseudogenes of a tRNA (Sakamoto and Okada 1985;Okada and Ohshima 1993) or other small RNAs, during which sequence variants with the highest frequency of retroposition accumulate and established copies acquire random mutations. Apparently, the time scale of these changes in relation to the mammalian speciation is such that SINE elements are specific for zoological orders or suborders.…”

CanSINEs: a family of tRNA-derived retroposons specific to the superfamily Canoidea

“…SINEs were first isolated from mammals, with distinct SINE families present in different lineages (11). More recently, SINE families have been found in other eukaryotes such as fishes (12), higher plants (13) and cephalopods (14). Many SINE families have a composite structure that includes a tRNA-like region at the 5' end which tends to be conserved between families, a central family-specific or tRNA-unrelated region, and an AT rich region at the 3' end (12-14).…”

Several short interspersed repetitive elements (SINEs) in distant species may have originated from a common ancestral retrovirus: characterization of a squid SINE and a possible mechanism for generation of tRNA-derived retroposons.

“…5), the 3'-terminal sequence of a tRNALYS (15)(16)(17)(18) (36), and Okada and coworkers (13,17) discussed such a mechanism subsequently. The model presented here has been briefly described elsewhere (37). When Saigo's model was proposed in 1986, it appeared to be very difficult to detect any similarities between SINEs and U5 regions of retroviruses, since the evolutionary rate of mutation ofgenes in retroviruses is 106 times higher than that of nuclear genes (38).…”