||Do SINEs exist universally in the genomes of all animals and plants?
If so, then did all SINEs originate from tRNAs?
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.
||How are tRNA-derived SINEs generated?
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.
||Since SINEs do not encode proteins, how do they become amplified?
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.
||What processes for SINE amplification were taken in one individual or from an
individual to a population during evolution?
This question led to the following two perspectives during the
course of our study:
EMolecular mechanisms of speciation.
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.
EPhylogenetic analysis using
||What are the consequences and significance of SINE retroposition in
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,