The Genetic Control of Morphogenesis 
Thomas C. Kaufman, Ph.D. — Investigator 
Dr. Kaufman is also Professor of Genetics in the Department of Biology at Indiana University, 
Bloomington, and Adjunct Professor of Medical Genetics in the Department of Medical Genetics at Indiana 
University Medical Center. He received his M.A. and Ph.D. degrees from the University of Texas, Austin, 
and did his postdoctoral research at the University of British Columbia in Vancouver. 
THE long-term goal of our laboratory is to con- 
tribute to an understanding of the genetic 
basis of the developmental program of higher or- 
ganisms. The organism chosen for our studies is 
the fruit fly Drosophila melanogaster, and our 
principal focus is a set of genes called homeotic, 
which play a crucial role in development. 
The homeotic genes were first identified by 
virtue of the striking phenotypes observed when 
flies carried mutations at these loci. Specifically 
these homeotic lesions cause one portion of the 
animal to be transformed into an identity nor- 
mally found in another region. Thus mutations at 
the Antennapedia locus cause a transformation 
of the antennae of the adult fly into a leg, and 
lesions in the proboscipedia gene result in the 
development of legs in place of the adult mouth- 
parts. Both genes are members of a cluster of five 
homeotic genes called the Antennapedia com- 
plex (ANT-C), which is found in a restricted 
domain at the base of the right arm of chromo- 
some 3. 
The aggregate results of genetic, developmen- 
tal, and molecular analyses of the ANT-C have re- 
vealed that the role of the resident loci is best 
viewed as a series of developmental switches for 
either/or decisions of cellular fate in the embry- 
onic and larval stages of the organism. Further- 
more, DNA sequence analysis of the homeotic 
loci reveals that they encode proteins containing 
a motif, dubbed the homeodomain, that endows 
the proteins with DNA-binding ability. Indeed, 
the homeotic proteins are found complexed with 
the nuclear DNA of the cells in which they are 
expressed. Thus it appears that the switch activity 
of the loci is reflected in their functioning as regu- 
lators of specific target genes. Not entirely clear 
at this point is how each homeotic locus is re- 
stricted to its own unique pattern of expression 
and which sets of genes are the targets of the 
switches. 
In order to investigate these two unknowns, we 
have concentrated our efforts on three of the resi- 
dent members of the ANT-C: Sex combs reduced 
(5cr), proboscipedia (pb), and labial (lab). 
Each gene was chosen for the unique properties it 
displayed during initial characterization. For ex- 
ample, Scr is the only homeotic gene expressed 
at the juncture between the head and trunk of the 
developing animal, and there were indications 
that the regulatory hierarchy of genes expressed 
in these two domains is different. Additionally, a 
genetic analysis revealed pb and lab to be small 
by homeotic standards. This meant that for the 
two genes, a complete dissection of the regula- 
tory elements of each locus was feasible. 
The Sex combs reduced Gene 
Our prior genetic and molecular analyses of 
the Scr locus had shown that DNA sequences 50 
kilobases (kb) distal to the point at which the 
RNA product is initiated were necessary for nor- 
mal gene expression. Using "enhancer sniffers" — 
constructs capable of detecting DNA fragments 
that have the ability to regulate gene expression 
— we surveyed the entire Scr locus for such ele- 
ments. To date we have found at least five frag- 
ments that specify the accumulation of gene 
product in the posterior head and anterior 
thorax. These are scattered over a 30-kb interval; 
consistent with our earlier genetic results, the re- 
gions of DNA that control head and trunk expres- 
sion appear to be physically separate. 
Genetic analysis has also shown that Scr is sub- 
ject to the regulatory effects of "transvection." 
Normally the gene is only expressed in the first, 
or most anterior, thoracic segment; however, cer- 
tain mutants in the gene allow its product to ac- 
cumulate more posteriorly, in the second and 
third thoracic segments. We have shown that the 
normal restriction of pattern results from nega- 
tive regulation and requires that the two copies of 
the gene in the cells of the posterior thorax be 
paired with each other. If this pairing is 
disrupted, the negative effect is removed and ab- 
normal ectopic expression occurs. 
Using sniffer constructs similar to those above, 
we have identified three DNA fragments that ap- 
pear to be associated with the transvection effects 
at the Scr locus. Two of these three elements are 
located approximately 40 and 10 kb upstream of 
the gene, while the third is located within an in- 
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