Chromosome Organization and Gene Function 
in Drosophila 
Steven Henikoff, Ph.D. — Investigator 
Dr. Henikoff is also a member of the Basic Sciences Division of the Fred Hutchinson Cancer Research 
Center, Seattle. He received a B.S. degree in chemistry at the University of Chicago and a Ph.D. degree in 
biochemistry and molecular biology at Harvard University, working in the laboratory of Matthew Mesel- 
son. He did postdoctoral work with Charles Laird at the University of Washington. 
EACH individual gene occupies a fixed posi- 
tion on a chromosome. By and large, moving 
a gene has only a minor effect on its expression. 
Thus most studies of gene expression are able to 
focus on the gene as an independent unit, with- 
out taking into account larger organizational fea- 
tures. There are exceptional cases, however, in 
which the relationship between a gene and its 
environment plays a role in expression of the 
gene. Our work has concentrated on two of these 
exceptions in the fruit fly. 
Several years ago, we found a surprising associa- 
tion between two apparently unrelated genes. A 
gene encoding a secreted component of the Dro- 
sophila cuticle lay entirely within an intron of 
another gene, called Gart, which encodes enzy- 
matic activities necessary for biosynthesis of pur- 
ine bases. These oppositely oriented nested genes 
are regulated quite differently from each other 
during development. The cuticle gene belongs to 
a family of genes that is expressed at high levels 
in certain epidermal cells during two phases of 
the life cycle of the fly, late larval and prepupal. 
The Gart purine gene is apparently expressed at 
low levels in all cells throughout development, 
consistent with its housekeeping role. We won- 
dered whether the expression of either gene was 
influenced by its neighbor — the cuticle gene by 
its surrounding neighbor, and the purine gene by 
its neighbor within. 
Examination of the structure of the Gart locus 
in other insects revealed that the nested gene ar- 
rangement is nearly identical in a distantly re- 
lated species of fruit fly (although the cuticle 
gene is absent from the intron of an even more 
distant now- Drosophila relative). The nested 
genes derived from one species are able to func- 
tion correctly when introduced into the other 
species. By introducing segments of the locus 
from one species into the other, we are attempt- 
ing to evaluate what components are necessary 
for expression of each of the nested genes, using 
the fully functional resident locus as a control. 
Somewhat to our surprise, we found that regu- 
lation of either gene depends in part upon compo- 
nents closely associated with the other. These re- 
lationships between seemingly unrelated genes 
that occupy the same segments of DNA may have 
relevance to recently discovered examples of 
nested genes involved in human disease, includ- 
ing those for factor VIII and neurofibromatosis. 
The relationship between a gene and its chro- 
mosomal environment is especially apparent in 
examples of "position effects" associated with 
chromosomal rearrangements. In flies a well- 
known class of position effects involves inactiva- 
tion of genes in the vicinity of rearrangement 
breakpoints. Gene inactivation is extremely vari- 
able from cell to cell, such that the affected tissue 
shows a variegated pattern of expression. In each 
case, it is found that the gene has been juxtaposed 
to heterochromatin, the deeply staining regions 
of chromosomes that flank the centromere. Al- 
though heterochromatin contains a substantial 
fraction of DNA in all higher eukaryotes, the re- 
petitive sequence structure characteristic of het- 
erochromatin and the near absence of genes have 
hampered attempts to understand its role in 
the genome. Genes that show variegated expres- 
sion when placed next to heterochromatin pro- 
vide a reporter function, allowing us to inves- 
tigate these poorly understood regions of 
chromosomes. 
Variegated position effects caused by juxtapo- 
sition to heterochromatin are seen for a large 
number of genes in Drosophila. One well-stud- 
ied example is the brown gene, required for full 
pigmentation of the eye. Unlike nearly all other 
genes, however, such position effects on the 
brown gene are dominant over wild type — that 
is, placing one copy of brown next to heterochro- 
matin can lead to inactivation of the other copy. 
We have investigated the genetic basis for this 
gene inactivation in trans and have found that a 
necessary component is the pairing of homo- 
logues in the immediate vicinity of the brown 
gene. These findings have led to an explanation 
for "trans-inactivation" whereby protein compo- 
nents of heterochromatin make direct contact 
with the trans copy of the brown gene across 
paired homologues. In suppon of this hypothe- 
sis, we have been able to reproduce trans-inacti- 
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