Worm Breeder's Gazette 9(3): 88

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Estimating the Number of Maternally Expressed Genes in C. elegans

K. Kemphues, M. Kusch and N. Wolf

Figure 1

C. velopment is dependent on maternally 
expressed genes which can be identified by maternal-effect lethal 
mutations (mels). Homozygous progeny of heterozygotes for mels are 
viable and fertile, but produce self-fertilized eggs which fail to 
hatch. Strict mels are those for which progeny of homozygous mothers 
die even when a wild-type allele has been provided by mating to males. 
Partial mels are rescued by the wild-type allele. We know there must 
be two classes of maternally expressed genes required for embryonic 
development: those that are expressed at many or at all stages of the 
life cycle, and those that are expressed exclusively by the maternal 
genome (pure maternal-effect genes). We wished to know how these two 
classes of genes would be represented in collections of mels, and 
whether we could establish critera for identifying pure maternal-
effect genes, so that we could estimate the number of such genes in C. 
lts suggest that there are between 25 and 60 
such genes. The data base for our analysis is a set of mels on 
chromosome 11 (WBG 8 (2), 5). We have now screened 13,900 chromosomes 
to identify 54 chromosome 11 mels which fall into 29 complementation 
groups, uniformly distributed on the chromosome. Of the 26 loci for 
which tests are completed, 15 mutated only to strict mels. The 
frequency distribution of these mutations is shown below. Typically, 
estimating the size of the gene pool being sampled by mutation is done 
using calculations based upon the Poisson distribution. However, in 
order for these calculations to be valid it is necessary that the 
events being sampled occur at equal frequency, in this case that the 
genes be equally mutable to maternal-effect lethality. Chi square 
analysis to test our data for a fit with the Poisson reveals a 
significant deviation from expected frequencies for genes with higher 
than three mutations. The basis for the deviation from expected could 
be either that the loci with high numbers of mutations are mutational 
hot spots or that the other mutations are mutational cold spots. 
{Figure 1}
The average mutation rate for loci in our frequent class is 3.6 x 10-
4, reasonably close to knockout rate. Because we would expect null 
mutations in pure maternal effect genes to cause strict maternal-
effect lethality, it seems likely that the loci in which we isolated 
multiple alleles are pure maternal-effect genes. In fact, two of the 
loci in the high frequency class, zyg-11 and zyg-9, had previously 
been identified as pure maternal-effect genes (Kemphues et al. Dev. 
Biol. 113: 449). We hypothesized that the low frequency mutations 
resulted from rare mutations in essential genes. Null mutations in 
these genes should result in phenotypes other than maternal-effect 
lethality (for example, larval lethality or defective gonadogenesis) 
and would not be isolated in our screens. However, rare mutations that 
reduce the activity, alter the function, or affect an embryo-specific 
domain of the gene product could result in maternal-effect lethality 
and appear in our screens. To test this hypothesis, we have carried 
out complementation tests of nine loci that map under chromosome 11 
deletions with lethal mutations mapping within the same deletions. Two 
of the nine mel loci tested were identical with lethal loci (lethal 
mutations failed to compliment the maternal-effect lethal phenotype). 
These results support our hypothesis that there are two classes of 
genes that can mutate to maternal-effect lethality: rare mutations in 
essential genes, and pure maternal-effect genes. Results of rescue 
tests are consistent with this interpretation. Alleles at 26 of the 29 
loci have been tested for male rescue. All loci with mutations in the 
high frequency class mutate only to strict mel while high proportions 
of the loci in the low frequency class mutate to partial mel. If all 
genes in the high frequency class are pure maternal-effect genes, then 
we have reached saturation for such genes on chromosome 11 with a 
total of four. If we then make allowances for statistical fluctuation 
and the possibility that some pure maternal-effect genes are 
hypomutable, we can estimate that there are probably fewer than ten 
pure maternal-effect genes on chromosome 11. Extrapolating to the 
whole genome, there are as few as 24, and probably no more than 60, 
pure maternal effect genes in the entire C. 
We are currently studying mutations in the 
two uncharacterized genes in the high frequency class to determine if 
any of the mutations are amber suppressible and hence likely null 
alleles, and also to determine their embryonic phenotypes. Our 
preliminary observations are: 1) mutations in one of these genes (mel-
5) results in severe defects in cellular organization in the one-cell 
embryo leading to abnormal early cleavage, 2) all mutations in the 
other gene (mel-4) are incompletely expressed and 1/4 to 1/2 of the 
surviving progeny are males. This latter phenotype suggests that the 
gene plays a role either in chromosome segregation or in sex 

Figure 1