A variant C.elegans Tc4 transposable element, TcA-rh1030, has been sequenced and Is 3483 bp long. The Tc4 element that had been analyzed previously is 1605 bp long, consists of two 774-bp nearly perfect Inverted terminal repeats connected by a 57-bp loop, and lacks significant open reading frames. In Tc4-rh1030, by comparison, a 2343-bp novel sequence is present in place of a 477-bp segment in one of the Inverted repeats. The novel sequence of Tc4-rh1030 is present about five times per haplold genome and is invariably associated with Tc4 elements; we have used the designation Tc4v to denote this variant subfamily of Tc4 elements. Sequence analysis of three cDNA clones suggests that a Tc4v element contains at least five exons that could encode a novel basic protein of 537 amlno acid residues. On northern blots, a 1.6-kb Tc4v-specific transcript was detected In the mutator strain TR679 but not In the wild-type strain N2; Tc4 elements are known to transpose in TR679 but appear to be quiescent in N2. We have analyzed transcripts produced by an unc-33 gene that has the Tc4-rh1030 insertlonal mutation in its transcribed region; all or almost all of the Tc4v sequence is frequently spliced out of the mutant unc-33 transcripts, sometimes by means of non-consensus splice acceptor sites.
Bibliographical noteFunding Information:
We thank E.Hedgecock for unc-33(rhl030), J.Yuan and R.Horvitz for Tc4-nl416, J.Ahringer, J.Kimble, R.Barstead, and R.Waterston for cDNA libraries, and M.Krause for pT7/T3-18-103. We thank J.Collins for sharing unpublished data with us and we thank S.Gantt for help with the manuscript. W.L. was supported by NIH grant GM22387 to R.K.Herman. This research was supported by NIH grant HD22163 to J.E.S.