Worm Breeder's Gazette 16(2): 30

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Insertional polymorphism of rte-1 retrotransposon in wild-type C. elegans strains

Eugene Berezikov1, Svetlana Scherbik1, Ronald H.A. Plasterk2

1 Institute of Cytology and Genetics, prospect Lavrentjeva 10, Novosibirsk 630090, Russia
2 The Netherlands Cancer Institute, Division of Molecular Biology, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands

We are interested to use C. elegans for studies of retrotransposition processes and particularly regulation of non-LTR elements. The rte-1 retrotransposon is the most abundant element in C. elegans genome and has all structural features of an active non-LTR element. We have studied polymorphism of rte-1 in wild-type strains to estimate levels of its activity.

Southern blot analysis of 20 natural C. elegans isolates revealed some differences in rte-1 banding patterns between strains. All strains contain approximately the same number of rte-1 copies. Observed differences in banding patterns are due to insertional polymorphism of rte-1 but could also be explained by other RFLPs unrelated to rte-1.

Next we have checked the presence of individual rte-1 elements in different strains by PCR with elements-specific and site-specific primers. Among 17 loci analysed for 15 strains 4 loci appeared to be variable for insertion of an rte-1 (Fig. 1). "Empty" sites have been PCR amplified and sequenced. Analysis of variable sites allowed to determine precisely changes in target sequences which take place upon insertion of rte-1 elements. Briefly, insertion of rte-1 element may cause a) deletion of several nucleotides in target sequence; b) formation of target site duplications of variable length; c) addition of tandem repeats derived from upstream target site region to the 5' end of the element; d) addition of non-templated nucleotides to the 5' end of the element. All of the above kinds of structural changes have been previously reported for other non-LTR retrotransposons and may be explained by a template switch model of retrotransposition.

Insertional polymorphism of rte-1 element observed in wild-type strains indicates that rte-1 at present is an active, capable of retrotransposition element. However the rate of retrotransposition seems to be quite low. Currently we make attempts to mobilize rte-1 in laboratory strains to detectable levels of transposition.