Variegated Position Effects 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 
Meselson. 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 expression of 
the gene. Thus most studies of gene expression 
are able to focus on the gene as an independent 
unit, without taking into account larger organiza- 
tional features. However, there are exceptional 
cases in which the relationship between a gene 
and its environment plays a role in expression of 
the gene. 
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. Although 
heterochromatin contains a substantial fraction of 
DNA in all higher eukaryotes, the repetitive se- 
quence structure characteristic of heterochromatin 
and the near absence of genes have hampered at- 
tempts to understand its role in the genome. Genes 
that show variegated expression when placed next 
to heterochromatin provide a reporter function, 
allowing us to investigate 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 ho- 
mologues. In support of this hypothesis, we have 
been able to reproduce trans-inactivation at sites of 
transposons carrying tht brown gene, but only for 
paired copies of the gene. In addition, we have 
found that even very small lesions that disrupt pair- 
ing in the immediate vicinity of the gene also re- 
duce trans-inactivation. 
Mapping of the sequence-specific component 
necessary for trans-inactivation to occur has local- 
ized it to the brown gene itself, probably to the 
region immediately upstream. This supports the 
notion that the contact between homologues is 
between a DNA-binding protein necessary for 
normal brown gene activity and a protein compo- 
nent of heterochromatin. 
Our current efforts are aimed at identification 
of the protein components involved in trans- 
inactivation. One approach is to focus on the se- 
quences in the immediate upstream region of the 
brown gene, where we expect that the sequence- 
specific component should bind. Another is to 
identify genes that encode proteins involved in 
the process by screening for mutations that specif- 
ically reduce the degree of trans-inactivation. We 
have now isolated several such mutations and are 
in the process of precisely mapping them to 
clone the corresponding genes. 
A new research direction for us came from a 
serendipitous finding (during a screen for posi- 
tion-effect variegation mutations) of an unstable 
chromosome that causes gene markers carried on 
it to appear variegated. This chromosome derives 
from a fusion between a chromosome arm carry- 
ing the markers and a centromere from another 
chromosome. The unstable chromosome is inter- 
mediate in size among wild-type and rearranged 
linear Drosophila chromosomes, all of which are 
quite stable in somatic cells. The instability re- 
sults from failure of the two products of replica- 
tion — called sister chromatids — to come apart 
reliably at mitosis, leading to clones and single 
cells that have either gained an extra copy of the 
chromosome or have lost it entirely. 
The appearance of the unstable chromosome 
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