OKADA
Laboratory

This question was addressed by demonstrating that SINEs are present in both squid (Ohshima et al. PNAS 1993) and plants (Yoshioka et al. PNAS 1993). By our discovery, it is now established that, in general, multicellular eukaryotes harbor SINEs that originated from tRNA.

This is a very exciting question that is not yet answered. Although we have proposed a model for the mechanism by which SINEs are generated (Ohshima et al.1993, PNAS), this model is not verified yet and we continue to refine this mechanism through our research. We are also pursuing the question of why the majority of SINEs are generated from tRNA.

This question constitutes a very active area of research in our lab (see our HP for details). Our first clue came with the discovery that several pairs of SINEs and LINEs have similar 3' tails. We then proposed that a LINE-encoded reverse-transcriptase (RTase) recognizes the 3' tail of a SINE in the same way that it recognizes the 3' tail of a LINE (Ohshima et al., 1996, Mol. Cell. Biol.; For review, see Okada et al., 1997, GENE). 　Recently, we provided convincing evidence for this intriguing model (Kajikawa & Okada, 2002, Cell). Our research continues toward the goal of elucidating the precise mechanism of SINE and LINE amplification. Our work may also reveal why there are so many retroposons in mammalian genomes.

This question led to the following two perspectives during the course of our study:

・Molecular mechanisms of speciation.
・Phylogenetic analysis using SINE insertions.

Three different SINE families derived from different tRNAs were dispersed throughout the salmon genome during evolution. This finding led to a new method of phylogenetic analysis using retroposon insertions as molecular markers. Indeed, in 1993 we determined the phylogeny among salmonids using this SINE method (Murata et al., PNAS). Subsequently, Takasaki et al. (1994, PNAS) reported that SINE amplification obeyed the multiple source genes model. SINE insertion analysis was also used to determine whale phylogeny (Shimamura et al., 1997, Nature; Nikaido et al., 1999, PNAS; Nikaido et al., 2001, PNAS). We extended the use of the SINE method to elucidate phylogenetic relationships among cichlid fishes from the Great Lakes of East Africa. In the course of this work, Takahashi asserted that rigorous phylogenetic analyses should accommodate ancestral polymorphisms and incomplete linage sorting (Takahashi et al., 2001, Mol. Biol. Evol.). These problems and the ascertainment of bias represent future challenges toward enhancing the determination of phylogenetic relationships using the SINE method. Moreover, there is also the problem of how older lineages may be determined using the SINE method. Still, our work over the past 20 years shows that significant progress has been made regarding the processes involved in the amplification of SINEs.

SINEs have become inserted and amplified in genomes throughout evolution. Indeed, ~30% of mammalian genomes were generated by retroposition, and therefore it is clear that SINEs have made a significant impact on mammalian genome evolution. However, at present it is difficult to clearly define their evolutionary consequences, and at best we can vaguely conjecture that SINE amplification diversifies the genome. SINE amplification is assumed to have played an important role in speciation, but current molecular evidence is lacking. To address this deficiency, we are intensively investigating the molecular mechanisms of speciation using cichlid fishes (Terai et al., 2002, PNAS).