Worm Breeder's Gazette 10(2): 77
These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.
Sequencing of dpy-13 (a collagen gene) has been completed. Including two introns, 50 and 56 bp long (not three introns as mentioned in the last WBG), the distance from the initiator methionine codon to the stop codon is 1017 bp, with exons totaling 909 bp. The TATA box is 46 bp upstream of the initiator codon and the deduced poly- A addition site, AATAAA, is located only 43 bp downstream of the stop codon. When comparing dpy-13 with col-1 and col-2 (Kramer et al., 1982, Cell 30: 599-606) at the protein level, a distinct similarity between these three collagens can be observed, in particular between dpy-13 and col-1 (Figure). In order to obtain the best alignment among the three proteins (helical regions are shown as boxes), six amino acids in dpy-13 and five amino acids in col-2 were looped out in the area of least homology. Shaded areas indicate regions of more than 57% amino acid identity. Each point in the graph represents the number of identical amino acids within a window of seven amino acids. The dpy- 13 collagen has two extra cysteines in addition to the highly conserved positions of 9 cysteines (dotted lines) in col-1 and col-2. These might provide dpy-13 with a specific role in collagen linkage. Only 6 positions of the 16 Iysines (solid lines) in dpy-13 are identical with both col-1 and col-2; seven are specific to dpy-13. The divergent sequence upstream of the first helical (gly-x-y) region in dpy-13 was chosen as potential region for a gene specific probe (GSP). When subcloned and hybridized to wildtype genomic DNA digested with EcoRI, this 100 bp probe detects only the single 7.1 kb band that carries dpy-13, whereas the 1.25 kb probe containing the entire dpy-13 gene detects a large number of bands, which presumably represent other collagen genes. On a northern blot with wildtype RNA, the GSP detects a 1kb transcript, and in two of the Tc1 insertion mutants a larger transcript of about 1.2 kb. We tentatively conclude that the 1.2 kb RNA is a product of mis-splicing, resulting from Tc1 insertion near the 5' splice site of the first intron.