Worm Breeder's Gazette 10(2): 158
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.
The sequence of a genomic clone of the cell lineage gene unc-86 is nearly complete. Its cloning was described at the 1987 meeting; in brief, the gene was found by walking from linked Tc1 polymorphisms and the exact location determined using eight alleles that had associated DNA rearrangements. Although a 1.8 Kb message has been seen on Northerns, the message is too rare to appear in any cDNA library tested. A 6 Kb EcoRI fragment was chosen for sequencing because it contains all allele-associated rearrangements and all sequences in the area that hybridize strongly with C. briggsae. About 5.5 Kb have been sequenced so far. Worm consensus splice sites, from the Hirsh and Emmons Worm Book article, were used to find the most likely splicing pattern of the sequences in hand. On one strand, this resulted in several large open reading frames being joined into one. The resulting assemblage was translated and compared to the NBRF/Dayhoff protein data bank using the Lipman and Pearson fastp program. All of the best matches were with homeobox-containing proteins. Further examination and consultation with our resident homeobox expert, Thomas B rglin, showed that unc-86 indeed encodes a homeobox ( see figure). All residues that are identical in all known homeoboxes are present, as well as many of the residues that are highly but not absolutely conserved. Many of the substitutions are conservative. The unc-86 homeobox spans two splice sites (see figure). Since the second one is only two residues from the end, it is uncertain whether the last two residues listed are actually part of the protein. The C. elegans gene mec-3 also has a splice site in its homeobox (J. Way, personal communication), but it is positioned differently. Although the sequence is clearly a homeobox, it does not belong to any of the four classes of Drosophila homeoboxes (defined by Antennapedia, paired, engrailed and even-skipped), nor is it similar to the yeast genes Mat a1, Mat alpha2, and PHO 2 or mec-3. Thus, unc- 86 defines a new class of homeobox. This class may have other members in C. elegans or in other species. [See Figure 1]