Worm Breeder's Gazette 8(3): 80

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.

Progress Toward the Cloning of lin-14

G.B. Ruvkun, V. Ambros, R. Horvitz

Figure 1

We have previously described a protocol by which we mapped Bergerac 
Tc1 elements near lin-14 X (Newsletter Vol.  8 No.  1).  We reported 
then that three Tc1 elements mapped to within 0.2 map units of lin-14.  
However, by higher resolution gel electrophoresis and Southern blot 
analysis we have now found that in fact seven Bergerac Tc1 elements 
map within this genetic interval.  We cloned the EcoRI restriction 
fragments that contain five of these Tc1 elements into phage lambda-
gt7 and used unique flanking DNA segments from each of these clones to 
identify overlapping cosmids in two independent genomic C.  elegans 
strain N2 Bristol libraries, one constructed by Guy Benian (in Bob 
Waterston's laboratory) and the other by John Sulston.  Contiguous 
stretches of DNA ('contigs') as defined by overlapping cosmids were 
established either by traditional chromosomal walking (a total of 
about 200 Kb) or by telephoning to John Sulston and Alan Coulson the 
microtitre well addresses in the library of cosmids of interest.  John 
and Alan then kindly fingerprinted these cosmid clones (see Newsletter 
Vol.  8 No.  2) and in many cases found overlaps with extant contigs 
in their collection of cosmid fingerprints and contigs.  By this 
combination of approaches we established contigs around each of the 
five Tc1 elements ranging in length from approximately 50 to 180 Kb 
and totalling about 400 Kb.
Because the contigs isolated begin with restriction fragments 
genetically mapping very close to each other, we expected that the 
expanding contigs would overlap as new cosmids were added in the 
chromosomal walk.  By calculation, 0.1 map unit represents about 30 Kb 
of DNA, so that the seven Tc1 elements within 0.2 map units should 
have been within 60 Kb of each other.  In fact, no two of the five 
contigs have yet overlapped, so that the simple assumption of 300 Kb 
of DNA per genetic map unit is incorrect in this genetic interval.
It was clear from these data that the resolution achieved using 
recombinants within a 1 map unit interval was not sufficient to limit 
or orient our chromosomal walk around lin-14.  We therefore designed 
an experiment in which a much rarer recombination event between a 
Bristol chromosome containing two lin-14 mutations and the Bergerac 
lin-14 region could be detected.  This experiment allowed the Bergerac 
Tc1 dimorphisms near lin-14 to be ordered relative to a recombination 
point that by definition occurred within lin-14.  The double mutant 
lin-14 allele used was n536 n540; n536 is a semidominant allele, and 
n540 is a recessive intragenic suppressor of n536.  The lin-14 allele 
was placed in trans to an X chromosome containing the Bristol 
chromosome from near dpy-6 to the left, a region of the Bergerac 
chromosome flanking lin-14(Bergerac) and containing all of the Tc1 
elements near lin-14(Bergerac), and the Bristol chromosome from near 
unc-9 to the right.  A total of 10+E4 to 10+E5 animals of the genotype 
lin-14(n536 n540)/dpy-6 lin-14(Bergerac) 
eened for the n5367+ or n536/n536 n540 
heterozygote phenotype of Lon, Egl, and Vul.  One such animal was 
found.  Subsequent progeny tests showed this animal to be of the 
genotype dpy-6 36)/lin-14(n536 n540), showing that 
n540 maps to the left of n536 on the genetic map.  DNA was prepared 
from homozygous dpy-6 36) recombinant animals and 
by Southern blot analysis with a Tc1 probe shown to be missing just 
one of the Tc1 elements ('b,' see map below) near lin-14(Bergerac), 
mapping this element to the right of lin-14.About 50 Kb on one side 
and 130 Kb on the other side of Tc1 element b had already been cloned 
by chromosome walking; therefore it was possible that even though Tc1 
element b maps to the right of the lin-14 intragenic recombination 
point, a cosmid at either extreme of this 180 Kb contig could map to 
the left of this recombination point.  Cosmids from both ends of the 
contig were used as probes in Southern blot analyses of DNAs isolated 
from the Bristol, the Bergerac, and the lin-14 intragenic recombinant 
strains to search for Bristol/Bergerac restriction fragment length 
dimorphisms that could be mapped relative to lin-14.  One cosmid, KKH9,
at one end of contig b about 40 Kb from Tc1 element b, was found to 
identify a Bristol/Bergerac XhoI site dimorphism that mapped to the 
left of Tc1 element b, based upon the presence of the Bergerac XhoI 
fragment length dimorphism in the lin-14 intragenic recombinant strain.
Therefore, the lin-14 recombination point and presumably at least 
part of the lin-14 gene is located between Tc1 element b on the right 
and the KKH9 defined XhoI site on the left.  Cosmid KKH9 was then used 
to screen DNA from 20 other lin-14 mutants for restriction fragment 
length polymorphisms using a variety of restriction enzymes.  
Polymorphisms were detected in DNAs isolated from mutants carrying 
three lin-14 alleles, including one allele isolated after EMS 
mutagenesis and two after gamma ray mutagenesis.  In fact n536 (as 
well as n536 n540) has an associated BglII restriction fragment length 
polymorphism, which has also been detected in the dpy-6 
36) intragenic recombinant strain, thus defining 
the recombination point in this strain and at least part of lin-14 to 
be located to the left of this BglII restriction fragment.
These data strongly suggest -- but do not prove -- that we have 
cloned at least part of lin-14.  We are now preparing to attempt to 
definitively establish that we have cloned lin-14 by microinjecting 
the clone into lin-14 mutant strains to rescue the mutant phenotype.  
Unfortunately this protocol can prove but not disprove our conjecture.
[See Figure 1]

Figure 1