GENETIC CONTROL OF PATTERN FORMATION 
Matthew R Scott, Ph.D., Associate Investigator 
The pattern of structures formed by a developing 
embryo is controlled by a set of regulatory genes 
that specify how cells are to divide, move, interact, 
produce, and localize particular molecules. Many of 
the relevant regulatory genes have been identified 
in Drosophila, including the segmentation genes 
that govern subdivision of the embryo into the 
proper number of correctly patterned segments 
and the homeotic genes that direct the formation of 
the structures that make the different segments 
unique. It is now crucial to learn how the regula- 
tory genes interact and how the products of the 
genes control cellular differentiation and pattern 
formation. There is precise temporal and spatial 
control of the transcription of many of the regula- 
tory genes, and it is often found that the places 
where a gene is expressed correspond well with 
the parts of the embryo that are affected by the loss 
of the gene's functions. Dr. Scott's laboratory is ad- 
dressing two key questions: How is the spatial and 
temporal regulation of segmentation and homeotic 
gene expression attained? How do the spatially re- 
stricted proteins carry out their functions? 
I. Gene Structure and Control Elements of Segmen- 
tation and Homeotic Genes. 
Segmentation genes are expressed in striking pat- 
terns of transverse stripes in blastoderm stage em- 
bryos and in more complex patterns in the devel- 
oping nervous system. At the blastoderm stage, 
homeotic genes are expressed in simple patterns, 
such as in all the cells of one or two segment 
primordia, but the patterns of homeotic gene 
transcription become extremely complex later in 
development. Sandra Sonoda has used regulatory 
sequences from the fushi tarazu (ftz) segmentation 
gene in experiments in which a lacZ gene is fused 
to the control sequences and introduced into Dro- 
sophila. She has demonstrated that the binding site 
in the ftz gene for a protein that has been purified 
by a collaborator, Dr. Carl Wu (National Institutes 
of Health), is important for activation of the expres- 
sion of ftz in stripes. The properties of the binding 
site are being further explored. 
John Bermingham and Matthew Petitt have ana- 
lyzed the expression of the two Antennapedia 
(Antp) homeotic gene promoters. They have used 
in situ hybridization of promoter-specific probes to 
whole-mount embryos and sectioned embryos to 
reveal the different patterns of expression of the 
two promoters and to examine the changes in tran- 
scription from both promoters in embryos that are 
mutant for certain regulators of Antp or (or Antp it- 
self Thus the two promoters are regulated differ- 
ently. Dr. Anne Boulet has found that 10 kb up- 
stream of the second Antp promoter is sufficient for 
a partially normal pattern of expression of a lacZ 
construct and has begun to identify cis-acting ele- 
ments responsible for different aspects of the ex- 
pression pattern. Dr. Deborah Andrew has studied 
the structure of the homeotic gene, Sex combs re- 
duced (5cr), that is adjacent to Antp on the chro- 
mosome and has done an evolutionary comparison 
of some of the promoter sequences. She has found 
that Scr also has two promoters, but both promot- 
ers are expressed in the same pattern. Possible reg- 
ulatory elements in the Antp gene have been identi- 
fied by Dr. Joan Hooper, who has compared the 
103 kb gene from Drosophila melanogaster with 
the even larger gene from D. virilis. Highly con- 
served sequences are present in many regions 
within and upstream of the transcription units; 
these conserved regions will serve to guide the con- 
struction and deletion analyses of the lacZ fusions. 
John Bermingham has analyzed the alternative RNA 
splicing patterns of Antp and has found that four 
somewhat different proteins are encoded by the 
gene's transcripts. 
II. Homeodomain Proteins Are Transcription 
Factors. 
Mutations in homeotic genes cause dramatic 
transformations, such as the development of legs 
where the antennae should be or of antennae 
where the mouthparts should be. These erroneous 
choices of developmental pathway can be due to a 
single protein expressed in the wrong place or to 
the absence of a single protein from the cells where 
it normally functions. A single protein must there- 
fore be capable of affecting many cellular processes. 
Dr. Rolf Reuter has been examining the functions of 
homeotic proteins in internal tissues and has dis- 
covered cases where a relatively simple morpholog- 
ical event results from the presence of a homeotic 
protein in certain cells. The goal is to understand 
the cell biology of the transformations and obtain 
clues as to what sorts of genes might be coordi- 
nately regulated by homeotic proteins. Another ap- 
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