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.

unc-86 Encodes a Homeobox of a New Class

Michael Finney and Gary Ruvkun

Figure 1

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]

Figure 1