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Into the lair of the gene.

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Archives of insect Biochemistry and Physiology 143-155 (1986)
Into The Lair of the Gene
Geoff Richards
Laboratoire de G6n6tique Moliculaire des Eucaryotes du CNRS, et Unit6 184 de Biologie
Molkculaire et de G6nie Ginetique de I’INSERM, Institut de Chimie Biologique, Faculty of
Medecine, Strasbourg
A new picture of gene and chromosome structure is emerging in Drosophila
that differs considerably from that largely derived from polytene chromosome
banding patterns and saturation mutagenesis. In particular, gene transfer has
enabled us to more clearly limit the functional unit of a number of genes.
Gene regulation may be studied at the molecular level with such techniques.
The possible complexity of regulatory elements that may pose problems in
their analysis is discussed.
Key words: Drosophila, P elements, regulatory sequences, polytene chromosomes
INTRODUCTION
”With these ... discoveries before us ... it was clear that we had within our
grasp the material of which every one had been dreaming. We found ourselves
out of the woods and upon a plainly marked highway with by-paths stretching
in every direction. It was clear that the highway led to the lair of the gene.”T.S. Painter, Salivary chromosomes and the attack on the gene. J Hered 25:465
(1934).
In his early review of Drosophila melanogaster polytene chromosome studies, Painter [l] summarized the evidence that the giant banded salivary gland
chromosomes provided a physical counterpart to the genetic maps derived
from meiotic recombination distances obtained in breeding experiments.
Although the nature of the genetic material was unknown at that time, and
was to remain so for ten more years, it was a clear vindication of the working
model of ”beads on a string” in which genes were considered as discrete
units joined together in a linear array by linker material to form chromosomes. Although Painter was careful to conclude that genes might correspond to a band or part of a band, the combined results of Alikhanian [2],
who calculated that the Drosophila X chromosome contained 968 genes capable of mutating to a lethal state, and Bridges [3], who showed that the same
chromosome contained 1,024 polytene bands, were largely responsible for
the adoption of the one band-one gene hypothesis. For nearly 40 years the
Address reprint requests to Dr. C. Richards, LCME du CNRS, 11 rue Hurnann, 67085 Strasbourg Cedex, France.
0 1986 Alan R. Liss, Inc.
144
Richards
majority of experimental evidence was interpreted in the light of this hypothesis, which was extended by polytene chromosome puffing studies that
showed at least in some cases, either in development or following experimental treatments, that individual bands decondensed to form puffs that were
sites of intense RNA synthesis. This led to a simple model of one gene-one
band-one puff in which an active gene gives rise to a puff. In cases in which
large puffs involving several bands were formed, it was considered likely
either that adjacent bands contained genes with similar developmental regulation or that a single band decondensed actively and that its decondensation spread passively into neighboring bands. Later, following estimations of
the potential informational content of the average chromosome band (with
20-30 kb* of DNA), a modification of this concept was proposed in which
the band or chromomere remained the functional unit but might contain
related genes in an arrangement similar to the prokaryotic cistron [4].
In this review I will consider the genetic and molecular studies, including
gene transfer, of the past few years that demand a complete reappraisal of
our views of Drosophila gene organization and discuss some features of
regulation that may complicate our final analysis of the lair of the gene.
PUFFS, BANDS, AND GENES; THE CYTOGENETIC APPROACH
If the alternating dark and light bands of the polytene chromosomes were
really genes and their spacers and these genes were the same in all cell types
of an organism, then it followed that banding patterns should remain constant. The essential constancy of banding patterns in different Dipteran
tissues was demonstrated by Beermann, Pavan and Breuer, and Mechelke
(see Richards [5] for references), and the notion that their genetic content
remained constant in development derived support from the totipotency
experiments of Gurdon using nuclear transplants in Xenopus [6]. While there
was thus compelling circumstantial evidence supporting the hypothesis, a
number of heretical views had already been expressed in recent years from a
purely cytogenetic approach. The most critical reappraisal of the significance
of the chromosomal banding patterns was that of Zhimulev and Belyaeva
and their colleagues in Novosibirsk [7,8]. The original alternative to the
constancy of the banding pattern was the ”Istanbul hypothesis” of Sengun
191, who proposed that banding patterns reflected the condensation of inac-
*Abbreviations: Adh = alcohol dehydrogenase; B helix = B-form of DNA having a righthanded double helix with about 10 bp per complete turn; bp = base pairs of DNA; HSE =
heat shock regulatory sequence elements; hsp-lacZ = heat shock puff 70-linked to the @galactosidase structural gene; kb = kilobase; kd = kilodalton; P element = a type of
transposable element of Drosophila melanogaster characterized by frequent insertion and
deletion in flies with cytotype M; ry = rosy eye color of Drosophila melanogaster; sgs3 =
salivary gland secretion protein 3; TATA box = an adeninekhymine-rich sequence located
about 25 base pairs before the first nucleotide of a transcriptional unit; YP1,2,3 = yolk
proteins; Z DNA = form of DNA with the left-handed helix with 12 bp per turn; -100 bp =
negative sign indicates the 5’ direction , upstream, from the first nucleotide transcribed; + I 6
bp = positive sign indicates the 3’ or downstream direction from the site of initiation of
transcription.
Into the Lair of the Gene
145
tive chromatin and that tissue-specific gene activity, or potential gene activity, would lead to tissue differences in banding pattern. The Novosibirsk
group have reformulated this hypothesis, adding their considerable experimental results, by suggesting that interbands contain "housekeeping" genes
that are active in most tissues. This gives a basic banding pattern common to
all tissues that is modified by decondensations related to tissue-specific gene
activity. These modifications may occur before the gene is active (puffed) and
will reflect a tissue-specific chromatin structure determined during differentiation of the cell type. Regions containing genes that will not be expressed
in this cell type may form bands containing one or many inactive genes.
Technical limitations preclude a wholly satisfactory conclusion that all
interbands are sites of active mRNA synthesis; however, there are small but
consistent differences in banding patterns in Drosophilu tissues [10,11] and
even more dramatic differences in banding patterns were found by Ribbert
[12], studying secondary polytene chromosomes of ovarian nurse cells and
normal polytene chromosomes of trichogen cells of Culliphora erythrocephalu.
That bands can contain more than one gene is best illustrated by the genetic
and electron microscope studies of chromosome band 10A1.2, which contains
at least three distinct genes that can be physically separated by chromosomal
rearrangements and yet function independently in their new positions [13].
A different experimental approach, also important for the problem of gene
content in bands, is that undertaken by Keppy and Welshons [14], who
synthesized new compound (multifunctional) bands in Drosophilu by X-ray
deletions of interband material.
Combining their genetic analysis with early biochemical analyses of transcription in Drosophila, Zhimulev and Belyaeva [7l suggested in 1975 that
20,000-30,000 was a more realistic minimum number of genes in Drosophila
than the 5,000 derived from band counts. They have since reviewed many of
the saturation mutation studies whose results did not differ appreciably from
the one band-one gene hypothesis [8]. In agreement with Young and Judd
[15] they suggest that problems derive both from inadequate cytology of the
region studied and from the failure of the majority of screens to detect
mutations other than lethals or clear visibles. That many characterized genes
have viable null alleles suggests that this class escaped detection and that
previous results should be reconsidered as showing an approximate correlation of one essential gene per band. This, however, differs significantly from
the original hypothesis of a strict one-to-one correspondence of bands to
genes.
Using the electron microscope, the Novosibirsk group have made important advances in studies of puffing [16,17l. They have recently reported
examples both of the decondensation of part of a band and the simultaneous
decondensation of adjacent bands to form a large puff, in addition to many
more traditional cases where either a single band undergoes uniform decondensation or adjacent bands appear to be drawn passively into a puff as the
principal band decondenses. The former exceptions clearly support their
notion that the chromosome band is not a genetic unit whose expression is
simply dependent upon its decondensation in puff formation. One refinement of the basic model that we should bear in mind in later analyses is the
146
Richards
two-step model of puffing, suggested by the large number of ecdysoneinducible puffs found in more than one tissue [18-201. In this model it is
envisaged that the hormone acts first to cause the decondensation of a
chromosome region into a puff and that a second level of regulation, perhaps
also hormonally dependent, is necessary to select the particular sequence to
be transcribed in a given tissue [20,21].
BANDS AND GENES: THE MOLECULAR APPROACH
The one band-one gene hypothesis was born in a period when the genome
was considered highly stable. Indeed the fact that polytene chromosome
banding patterns could be used in phylogeny studies of Drosophilu groups
was itself strong evidence for such a stability. The earliest molecular cloning
studies in Drosophila were to upset this view as the middle repeat sequences,
such as copiu, not only proved to be present at multiple chromosome sites,
but also were highly polymorphic in their sites both within and between
populations. Other genes coding for abundant products such as the histones
or tRNAs were also immediate exceptions to the one band-one gene hypothesis, the former being present in tandem repeats covering several chromosome bands, whereas the latter were in multiple mixed clusters in extremely
short lengths of DNA (see Richards [5] and Spradling and Rubin, [22] for
reviews).
As to unique genes, studies of Dmsophiln gene structure have so far
revealed two general classes of transcription units: 1)small, compact genes
with short introns (e.g., those for alcohol dehydrogenase [23], larval serum
proteins [24], dopa decarboxylase 1251, yolk proteins [26], larval cuticle proteins [ 2 7 , and salivary gland glue proteins [28,29]) and 2) complex transcription units with short coding sequences and large introns that may extend
over 50-100 kb of genomic sequence (e.g., ultrubithorax [30] and untennupediu
[31]).The genes of the first class are typical protein-coding genes where the
coding sequence and introns span no more than 2-3 kb of DNA. Much larger
introns have been found in many vertebrates, and initially we might have
expected that Dvosophilu genes with large introns would account for the 2030 kb of a chromosome band. This is not the case for these genes, although
some of them are found in clusters that might suggest coordinate regulation.
However one such cluster, that of the four heat shock genes at 67 B, was
shown to be interspersed by three other transcription units that are not
induced by heat shock. In this case, there are seven transcription units in
about 14 kb of DNA, all of which are taken into the 67 B heat shock puff,
which forms at most from two bands and their neighboring interbands [16].
Similar high densities of transcripts have been detected following chromosomal walks in Drosophilu (e.g., Bossy et al. [32]). If there are also regions
where lower densities of transcripts have been detected, we cannot exclude
that this is a technical problem of detecting low-abundance transcripts, including transcripts restricted to a few highly specialized cells. The evidence
so far is that the figure of 20,000-30,000 genes proposed from the combination of genetic and message complexity studies will be justified by transcript
analyses. There are two further points to be made regarding such analyses:
Into the Lair of the Gene
147
One is the detection of alternative splicing to produce different messengers
from a single region (e.g., Adh, [23]), and the other is evidence from a
number of studies in progress that there may be genes within genes in
DrosophiZu, i.e., the exons of one gene may be contained within an intron of
another. Such results are contrary to the "beads on a string" model. In some
respects this model needed modification once it was proposed that bands
contained coordinately regulated genes as that implied that each gene was
not self-contained but could depend on more distal sequences regulating the
coordinated cluster. As we shall see in the next section, the coordinated
cluster model is not necessary to explain results from gene transfer experiments. We should not, however, eliminate the possibility that elements
regulating a gene may be found beyond, or within, neighboring transcription
units.
GENES: THE GENE TRANSFER APPROACH
To test gene function, it is important to be able to reintroduce cloned genes
into cells. Two systems are currently available: permanent cell lines or transgenic animals. Cell line transformation has certain disadvantages for the
study of developmentally specific gene regulation. One of the most difficult
aspects is controlling the number of sequences entering a cell, which may be
as many as several thousand. Another is that we do not always have cell
lines equivalent to those cells in which the gene is normally expressed. Even
when these are available we cannot be sure that the incoming DNA will be
packaged in a conformation identical to the resident gene, or indeed, if there
are specific regulatory molecules being produced in a cell type, that these
will be sufficient to regulate the multiple copies of the introduced gene. All
these points are avoided in whole-animal transformation with I' elements in
Drosophilu [XI, where it is possible to rapidly isolate lines containing a single
nonrearranged copy of the gene per haploid genome.
The major problem that exists in following the activity of a transformed
gene is that of the activity of the homologous gene in its normal chromosomal
site in the recipient strain, the resident gene. If the introduced gene and the
resident gene are identical, then we are unable to distinguish the RNA
transcripts or the protein products of the former from those of the latter,
unless the introduced gene displays an abnormal stage or tissue distribution.
A number of different strategies to overcome this problem have been used in
Drosophilu studies, all of which have used small genes of the first class
discussed in the previous section. The strategies include: 1)the introduction
of a wild-type gene into a mutant strain where the resident gene is inactive
(e.g., rosy (ry) [34,35] or alcohol dehydrogenase [36]) and where, under
permissive conditions, the homozygous recessive strain is viable; 2) the
rescue of an otherwise sterile genotype by the insertion of a wild-type gene
(e.g., K10 [37J);3) the insertion of a modified gene, in which the transcribed
region has been altered by the introduction of homologous or heterologous
DNA so as to produce either an altered RNA or indeed a fusion protein that
has an enzymatic activity not normally found in DrosophiZu (e.g., the hsp-lucZ
fusion of Lis et al. [38]); and 4)the insertion of a wild-type gene where there
148
Richards
exists a series of alleles producing recognizable variants either at the RNA or
protein level. This last approach is the most useful if one wishes to study the
regulation of transcription, as the resident gene serves as an internal control
in all assays. It is the approach we have chosen with sgs3, a choice that
derives essentially from the studies of Korge [39], which showed the existence of extensive size polymorphisms in the salivary gland secretion proteins in a number of strains of D. melunoguster.
The first successful gene transfers in the P system were those with the ry
gene coding for xanthine dehydrogenase [34,35] using genomic segments of
7.2 or 8.1 kb. While all inserts showed correct developmental expression,
there was a fivefold range in levels of expression. These differences are
considered a consequence of position effects. In particular, genes inserted on
the X chromosome showed at least partial dosage compensation in males,
that is, they acquired a regulation of the level of expression at their site of
insertion. A number of other genes have been transformed using similarsized segments, dopa decarboxylase (7.5 kb, [40]), Adh (11.8 kb, [36]), and
sgs3, (6.7 kb, [41]). All showed correct developmental regulation but overall
levels ranged from wild-type to 10% of wild-type as judged in the various
RNA or protein assays. This raises the question of the nature of the position
effects on expression. Apparently, these genomic segments have the elements necessary for stage- and tissue-specific responses in the sequences
flanking the gene but cannot always ensure normal levels of expression. This
may result either from a property of the chromosomal region in which they
are inserted or from a lack of sufficient flanking sequences. Using the imagery
of the "beads on a string" model, we must ask whether we have transferred
the whole bead or not. If so, will it be expressed equally in all chromosomal
sites? If not, can elements flanking the insertion sometimes substitute for its
normal sequences?
This first round of experiments showed that genes transferred with P
elements, using pieces of DNA much smaller than those previously involved
in classic chromosomal rearrangements, could be regulated in new chromosomal sites. In addition, the ry constructs are unlikely to contain all the DNA
of band 87Dll or its adjacent interbands (see Bossy et al. [32]), while the sgs3
construct g l has only two of the three glue genes clustered at 68C (see Fig.
1).This suggests that for ry the band is not a functional unit and that for sgs3
the cluster is not contained within a functional domain. Other members of
clusters have also been successfully expressed in isolation following transforH Xb H X b E Xb H
I
l
l
CI
sgs8
g1'
lkb
,
I
I
Xb
S
Xh
S
S
E
I
I
I
I
I
I
111,
Iu17;
sgs7
sgs3
1
Fig. 1. The glue gene cluster at 68C in Drosophila mehogaster. The 6.7 kb EcoRl fragment
of the Formosa strain, gl, used in transformation experiments [41] i s indicated by a bar. The
transcribed regions of sgs3, sgs7, and sgs8 are shown by arrows 5'+3'; introns are denoted
by an open space. The central region of sgs3, which contains an array of 15 bp repeats whose
length differs between strains [29,33] i s shown as a hatched region. E = EcoRI, H = Hindlll,
S = Sall, X h = Xhol, Xb = Xbal.
Into the Lair of the Gene
149
mation, e.g., chorion genes [42] and heat shock genes [38,43]. In the case of
sgs3 the 6.7-kb construct resulted in normal levels of expression in the two
sites of insertion studied. A second series of experiments showed that while
most of the 3’ flanking sequences could be removed, there were elements
between 1.4 and 2.7 kb 5’ to the gene necessary for normal levels of expression [44]. With 1kb of 5‘ sequence, low but developmentally specific levels
of sgs3 RNA were detected, suggesting as with other systems that this
specificity is determined close to the gene. In a related set of sgs3 constructs,
using a different P-element vector, Meyerowitz and his co-workers find that
as little as 127-bp of 5’ sequence will confer developmental specificity of
transcription (see Cherbas et a1 [45]). Our own experiments have shown that
upstream elements in the region -127 bp to -2.7 kb will act bidirectionally
on this minimum construct to restore normal levels of transcription [44].
Evidence for rather remote sequences determining tissue specificity has been
obtained by Garabedian et al. [46] with the yolk protein genes ypl and yp2,
which share two distinct cis-acting elements in the 1.2 kb region between
their 5‘ ends, one responsible for ovarian transcription and the other for fat
body transcription. One element is at least 880 bp 5’ to ypl.
These and other experiments have shown that DNA sequences more than
1 kb away from the capsite may have important roles to play in gene
regulation and this is rather more than was previously expected. In contrast
to these results, the regulation of transcription and puffing of heat shock
genes has been shown by gene transfer to be relatively simple, in that for
hsp70 the necessary elements lie between -89 and +65 from the transcription
start site [54]. This is in accord with the functional and evolutionary argument
that heat shock genes must maintain a simple and rapid response to environmental stress and have not evolved a differential regulation such as that
required for genes showing stage- and tissue-specific activity. In the next
section I shall speculate on the elements that contribute to the regulation of
such genes in a eukaryotic chromosome.
WHAT LIES IN THE LAIR OF THE GENE?
Initially it was assumed that the regulatory elements of eukaryotic genes
would be found in the first 1-200 bp 5’ to the capsite and that elements such
as hormone-receptor complex binding sites would be revealed by sequence
comparisons between genes subjected to the same developmental regulation.
Indeed sequence comparisons of a number of cloned genes led to important
discoveries regarding elements such as the TATA box. We can attempt to
extend this kind of analysis further upstream, either for members of closely
related gene families, such as cuticle genes [47] or chorion genes [48], where
the members are clustered and appear to derive from recent duplication
events, or dispersed functionally related families, such as the glue genes.
While such sequence comparisons have revealed conserved sequences in the
upstream regions, not all of the members of the family have necessarily
retained these sequences, and their positions relative to the transcribed
regions and each other can be highly variable [47,48]. To date this approach
has not delineated functional elements and results suggesting that elements
150
Richards
may extend over a number of kilobases have not simplified the analysis. The
lengths of DNA sequence that may regulate transcription in even these
relatively simple genes also imposes limitations on the use of experimental
approaches. Thus the fine analysis of promoters by base-by-base mutation as
applied in viral systems for regions of 100-200 bp is clearly not practical with
P-element analysis.
The following questions may be helpful in arriving at a new view of the
gene: 1)How many types of regulatory elements are there? 2) Are these
elements independent? 3) Can there be more than one element of a given
type? 4) Is the order of the elements fixed? 5) How important are the
interactions or the spacings between different elements? 6) How is the ultimate level of gene transcription determined? It is not clear whether the
elements that we are searching for are unique, both in the sense of being
limited to a single copy of a given type of element for each gene and in the
sense that a gene may be regulated correctly in development only by its own
flanking sequence. There is already preliminary evidence on both these
points that suggest that the elements may not be unique in either sense.
Murine mammary tumor virus DNA sequences have been shown to contain many regions that bind the receptor for glucocorticoids in vitro [49-511.
These regions are found both upstream of the transcription start site and
within the transcribed regions and are all of sufficiently high affinity to be
mapped by nuclease footprinting. While it has been shown by Chandler et
al. [52] that a single region will confer glucocorticoid regulation in a gene
fusion, this does not exclude the possibility that the other sites may have a
functional role in normal regulation. If there are many functional sites, it is
clear that deletion analysis alone may be misleading, as the deletion of one
of a number of sites may either result in minor alterations in transcript level
or lead to the substitution of another sequence as the major regulatory
element. A similar multiplicity of sites has been observed in the heat shock
regulatory sequence elements (HSE) (see Bienz [53] for review), and there is
evidence that this also leads to difficulties of interpretation under noncritical
conditions. In transfected cells, where there are multiple copies of the introduced gene, a single HSE will give rise to a clear temperature-dependent
induction of transcription, whereas in transformed flies, further upstream
sequences, containing a second HSE, are necessary for normal levels of
transcription [54]. It would not be surprising if similar complications exist in
ecdysteroid regulatory sequences. In particular the two-step model of puffing
would predict two kinds of binding site, one responsible for the opening of
the puff and the second, close to the gene, for the induction of transcription.
With regard to the substitution of regulatory elements there are two classes
to be considered, the first consisting of developmentally specific elements
and the second of a more general nature. We suspect that in the case of one
sgs3 construct [44] sgs3 is benefiting from specific regulatory elements normally associated with sgs7 and sgs8, and experiments are in progress to test
this hypothesis. In the case of regulatory elements of a more general nature,
chromosome puffing may still be a source of ideas. It seems reasonable that
a major problem in eukaryotic gene expression is decondensing chromatin
so that the transcription complex can recognize a 1- or 2-kb sequence nor-
Into the Lair of the Gene
151
mally contained in a 30,000-kb DNA molecule. A number of possible elements important for this process can already be suggested: a) attachment
sites to the nuclear matrix; b)topoisomerase sites for nicking or cutting the
helix, thereby facilitating the rotations necessary for unwinding chromatin
from its condensed form, and c) alternating purine-pyrimidine tracts, which
appear to stimulate transcription; also perhaps by facilitating conformational
changes.
In Dvosophila, studies of the role of topoisomerases in transcription are
preliminary but encouraging. Using an indirect immunoflourescence approach, Fleischmann et al. [55] have shown that there are high concentrations
of topoisomerase I, which makes single-strand nicks in DNA,in the region
of salivary gland puffs, and in a related study Steiner et al. [56] showed that
in a larva heterozygous for an sgs4 wild-type and a mutant allele, only the
former was brightly stained. Using a different approach, Udvardy et al. [57]
have shown that, in vitro, topoisomerase 11, which makes transient doublestrand breaks, shows major binding and cleavage sites close to the 5’ and 3’
boundaries of hsp70 gene sequences. These authors note that this distribution
is similar to the attachment sites to the nuclear scaffold described for this
gene by Mirkovitch et al. [58]. The loop model of chromosome organization
of Laemmli et al. [59] predicts that there are specific attachment sites in DNA
that result in the formation of loops or domains and enable active genes to
be positioned close to the nuclear matrix. The possible role of alternating
purine-pyrimidine tracts is more complicated. Some of these sequences appear to have the potential to form Z DNA and this suggests that even short
sequences may disrupt the normal B helix. Certain of these sequences appear
to stimulate transcription (e.g., Karin et al. [60]) and have been found in a
number of viral enhancer sequences. Whether they do in fact form Z DNA
in vivo is not known, nor is it known if their primary role is to disrupt
chromatin structure perhaps thereby facilitating the entry of transcription
complexes, or if they act as recognition sites for specific regulatory proteins.
The fine tuning of the level of transcription of a gene may depend on the
number and placing of such tracts.
I have summarized these ideas schematically in Figure 2 to try to give an
idea of the complexity that may be present. We do not know how the
regulation of a gene evolves but we may speculate that logically it is a
progressive refinement of an initial differential regulation. The specific regulation afforded by a hormone-receptor complex is at least initially close to the
transcription unit that it regulates. This does not prevent later duplications
- -- -
n
.....
n
n
0
.....
TAA-
lkb
I
Fig. 2. A general scheme indicating some of the regulatory sequences that may be associated
with ecdysteroid-regulated genes. A model gene is denoted as in Figure 1, with i t s TATA box.
Symbols are as follows: open circles, hormone-receptor binding sequences; open boxes, sites
of topoisomerase I or II activity; solid boxes, enhancer-like sequences; hatched boxes,
nuclear matrix attachment sites. Lines connecting elements imply interactions that may
require strict spacing in the DNA sequence- see text.
152
Richards
of hormone-binding sites or refinements in the regulation such as a hormonedependent enhancer or indeed a repressor sequence. It is not clear whether
the more general elements will be intimately associated with the specific
regulatory elements or whether they are distributed in a random fashion in
chromosomes. In the latter case, we can expect that in different chromosomal
insertions transferred genes will benefit from such adjacent sequences although their effects on transcription may be highly variable. There may be at
least three factors involved in the ability of these sequences to modulate gene
activity, their sequence, their length, and their distance from the gene. As
the first is not necessarily the most important factor, they may prove difficult
to detect simply by sequence analysis, as a short sequence at -100 bp may
have an effect equivalent to a much longer sequence at -1.5 kb. We must
also break away from a tendency to see gene regulation as a linear problem.
That is, regulation may require interactions between sequences that are
separated by considerable linear distances in the primary sequence but in the
folded chromatin may be in close association. I have indicated such associations in Figure 2 by joining elements by line sections. Even with these
considerations we have not resolved the basis of tissue specificity, as the
same DNA sequence is inactive in some tissues and not in others. This must
be a consequence of differences in proteins in different cell types, which, by
binding in the regulatory region of the gene, dictate the chromatin structure
of the gene. Indeed, perhaps all the DNA sequences indicated should be
seen as binding sites for regulatory proteins either of a specific or a general
nature.
If regulation evolves in the manner I have suggested, then it is possible
that the order in the DNA sequence of the various elements is not the same
for all genes. There is already evidence for this from the study of Garabedian
et al. [46] (see above), where ypl has the fat body-specific element proximal,
whereas yp2 has the ovary-specific element proximal, both genes presumably
sharing both of these elements. Such a possibility will lead to problems in
gene constructs where upstream sequences are exchanged between genes,
as there may not be an equivalent site that will allow an exchange of regulatory elements. We have recently discussed other aspects of such gene fusions
in the context of our attempts to establish whether units of regulation may
be exchanged between genes [61]. While there is every hope that hormonereceptor binding sites will be rapidly determined for a number of ecdysteroidregulated genes, if there is a fraction of the complexity I have suggested for
other elements, our future analyses will reveal a number of surprises.
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Drosophilu rnelunoguster. Zoo1 Zhur (Moscow) 16, 247 (1937).
3. Bridges CB: A revised map of the salivary gland X-chromosome of Drosophilu rnelunoguster.
J Hered 29, 11(1938).
4. Judd BH, Young Mw: An examination of the one cistron: one chromomere concept. Cold
Spring Harbor Symp Quant Biol38, 573 (1974).
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5. Richards G: Polytene chromosomes. In: Comprehensive Insect Physiology, Biochemistry
and Pharmacology. Kerkut GA, Gilbert LI, eds. Pergamon, Oxford, Vol. 2, pp 255-300
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(1973).
7. Zhimulev IF, Belyaeva ES: Proposals to the problem of structural and functional organization of polytene chromosomes. Theor Appl Genet 45, 335 (1975).
8. Zhimulev, IF, Belyaeva ES, Semeshin VF: Informational content of polytene chromosome
bands and puffs. CRC Crit Rev Biochem 11, 303 (1981).
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(1954).
10. Zhimulev IF, Belyaeva ES: Variation of banding pattern in polytene chromosomes of
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