MBE Advance Access published online on April 2, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg075
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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1 Genetic Information Research Institute, 2081 Landings Drive, Mountain View, CA 940043
* To whom correspondence should be addressed. E-mail: vladimir{at}ulam.girinst.org.
Eukaryotic genomes are colonized by different retroposons, including short interspersed repetitive elements (SINEs). All currently known SINEs are derived from tRNA and 7SL RNA genes, and exploit their type 2 internal pol III promoters. We report here a novel class of SINE elements, called SINE3, derived from 5S rRNA. SINE3s are transcribed from the type 1 internal pol III promoter. Approximately 10,000 copies of SINE3 elements are present in the zebrafish genome, they constitute Key Words:
SINE, non-LTR retrotransposon, CR1 clade, LINE, 5S rRNA, pol III, transposable element
© 2003 Society for Molecular Biology and Evolution
Original Articles
A Novel Class of SINE Elements Derived from 5S rRNA
Abstract 
0.4% of the genomic DNA. Some elements are as little as 1% diverged from each other, indicating that the retrotransposition of SINE3 in zebrafish is an ongoing process. The 3'-tail of SINE3 is significantly similar to that of CR1-like non-LTR retrotransposons, represented by numerous subfamilies in the zebrafish genome. Analogously to CR1-like elements, SINE3 copies are not flanked by target site duplications, and their 3' termini are composed of (ACATT)n and (ATT)n microsatellites, specific for different subfamilies of SINE3. Given the common structural features, it is highly likely that the enzymatic machinery encoded by CR1-like elements powers proliferation of SINE3.
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