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The P-Ph Protein-Mediated Repression of yellow Expression Depends on Different cis- and trans-Factors in Drosophila melanogaster
Inna Biryukovaa, Tatyana Belenkayaa, Haik Hovannisiana, Elena Kochievab, and Pavel Georgievaa Department of the Control of Genetic Processes, Institute of Gene Biology, Russian Academy of Sciences, Moscow 117334, Russia
b Department of Biotechnology, Moscow Agriculture Academy, Moscow, 550400, Russia
Corresponding author: Pavel Georgiev, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St. Moscow 117334, Russia., georg{at}biogen.msk.su (E-mail)
Communicating editor: J. A. BIRCHLER
| ABSTRACT |
|---|
The phP1 allele of Drosophila melanogaster encodes a chimeric P-Ph protein that contains the DNA-binding domain of the P-element transposase and the Ph protein lacking 12 amino-terminal amino acids. It has been shown that the P-Ph protein is responsible for the formation of a repressive complex on P elements inserted at the yellow locus. Here we demonstrate that an enhancer element can suppress the P-Ph-mediated inhibition of yellow transcription. However, an increase of P-element copy number at the yellow locus overcomes the enhancer effect. The mobilization of P-element transposition induced the appearance with a high frequency of Su(y) mutations that partially or completely suppressed the inhibitory effect of phP1 on yellow expression. The Su(y) mutations were localized at different sites on chromosomes. One strong Su(y) mutation, sneP1, was found to be induced by a 1.2-kb P-element insertion into the transcribed noncoding region of the singed locus. The Su(y) mutations resulted in a high level of transcription of the 1.2-kb P element that contained the sequences encoding one DNA-binding and two protein-protein interaction domains of the transposase. The effect of Su(y) mutations can be explained by the competition between the truncated transposase encoded by a 1.2-kb P element and the P-Ph protein for binding sites on P-element insertions.
THE polyhomeotic (ph) gene is a member of the group consisting of at least 20 genes with similar functions that are required for normal segmental specification in Drosophila and referred to as the Polycomb group (Pc-G) genes(![]()
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We have discovered a new P-element-induced mutation in the polyhomeotic (ph) gene, phP1, which represses yellow expression in the yellow alleles containing P-element insertions (![]()
Previously we described a family of highly unstable y mutations induced by chimeric mobile elements located 69 bp upstream to the yellow transcription start site (![]()
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In this article, we have characterized the interactions of the phP1 mutation with the y+s1 allele and its derivatives. The inhibiting effect of phP1 on yellow expression can be suppressed either by the enhancer element located in the chimeric y+s1 insertion or by the yellow wing and body enhancers. However, an increase of P-element copy number either in cis or in trans strongly elevates the phP1-mediated repression that overcomes the effect of the enhancers. We have also studied the effect of phP1 on P-element-induced mutations in the singed locus, which is expressed at the same middle pupal stage as yellow during the formation of adult bristles and hairs, and in the female germline during oogenesis (![]()
During this work, we discovered a number of P-element-induced mutations designated as Su(y) that partially or completely suppress the inhibitory effect of phP1 on the y+s1 allele and its derivatives. The effect of Su(y) mutations results in a high level of P-element expression. The truncated transposase competes with the chimeric P-Ph protein for the same binding sites on P elements.
| MATERIALS AND METHODS |
|---|
Drosophila strains:
All flies were maintained at 25° in a standard yeast medium. Genetic symbols of the y alleles and the origin of the y+s1 allele and some of its derivatives were described in other articles (![]()
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2-3] (99B) e/TM6,e stock, providing a stable source of transposase (![]()
2-3](99B) is referred to as
2-3. The rest of the Drosophila melanogaster strains and mutations are described in ![]()
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Genetic crosses:
To induce mutagenesis, y+s1 phP1 females were crossed to w; Sb
2-3 e/TM6,e males to produce dysgenic males of the y+s1phP1/Y; Sb
2-3 e/TM6,e/+ genotype. In each vial,
2-3 males were mated to 1012 C(1)RM,yf females. The F2 progeny was analyzed for mutagenesis. All males with a new y phenotype were individually mated to virgin C(1)RM,yf females and their phenotype was examined in the next generation. Determination of the yellow phenotype was performed as previously described (![]()
Combinations of phP1 with different y alleles were obtained according to the following scheme:
- F0:
y1scD1phP1wa/y1scD1phP1wa x
y*/Y, where y* is any y allele used; - F1:
y1scD1phP1wa/y* x
y1scD1phP1wa/Y; - F2: Selection of y*phP1wa males (sc+ phenotype and orange eyes).
The introduction of phP1 was confirmed by Southern blot hybridization with labeled probes from the ph gene. The wa (1-1.5) mutation was used as the closest marker for the ph gene (1-0.5).
The removal of phP1 from a X chromosome with a y* allele was performed according to the following scheme:
- F0:
y1scD1wa/y1scD1wa x
y*phP1/Y; - F1:
y1scD1wa/y*phP1 x
y1scD1wa/Y; - F2: Selection of y*wa males (sc+ phenotype and orange eyes).
The removal of phP1 was confirmed by Southern blot hybridization.
Combinations of autosome Su(y) mutations with y*phP1 were obtained and analyzed according to the following scheme: F0:
y*phP1/FM4 x
y+s1phP1; Su(y)/CyO or Su(y)/TM3,Sb; analysis of the y phenotype in y*phP1/Y; Su(y)/+ males.
To study the eye phenotype on the phP1 background we constructed the yphP1w line. The su(Hw)2/su(Hw)v mutations in the su(Hw) gene were combined with the y*phP1 mutations as described previously (![]()
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DNA manipulations:
DNA from adult flies was isolated using the protocol described in ![]()
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The genomic DNAs were subjected to PCR to amplify sequences from the derivative alleles (![]()
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The PCR products were directly sequenced using a Sequenase II DNA sequencing kit for PCR product (Amersham, Arlington Heights, IL) according to manufacturer's instructions.
Northern blot hybridization:
Total RNA was isolated by homogenization in 4 M guanidine isothiocyanate, 0.2% N-lauryl sarcosine, 150 mM mercaptoethanol, 12.5 mM EDTA, and 50 mM tris-hydrochloride, pH 7.5, with subsequent phenol extraction and ethanol precipitation (![]()
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Construction of P{w+,
P-yellow} and P-element transformation:
The structure and expression of the yellow gene were described earlier (![]()
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P-yellow}, where w+ indicates a miniwhite gene included into the vector and
P-yellow indicates a complete yellow gene with an insertion of a small part of the P element. The control construct P{w+, yellow+} has an unchanged structure of yellow sequences. This construct was obtained by direct cloning of the 10-kb fragment including the yellow gene in the CaSpeR3 plasmid.
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DNAs of the P{w+,
P-yellow} and P{w+, yellow+} constructs and of a P element with a defective inverted repeat used as a transposase source, P25.7wc (![]()
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P-yellow} and P{w+, yellow+} were made homozygous and their copy number was determined by Southern blot analysis using the yellow and white sequences as probes.
| RESULTS |
|---|
Cis-elements influencing the repression effect of the phP1 mutation on yellow expression:
In a previous article (![]()
In this article, we studied the y+s1 allele (![]()
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The phP1 mutation only partially repressed yellow transcription in the y+s1 allele: the pigmentation of the body, wings, thoracic, and leg bristles was decreased (Figure 1). Thus, the presence of the genomic insertion possessing the 1A enhancer reduces the effect of the P-Ph protein.
To further analyze the role of different cis-regulatory elements in formation of repressive complex, we studied the y+s1 derivatives obtained after P-element mobilization in the y+s1 phP1 and y+s1 strains. The structure of insertions in some of these derivatives was described in a previous article (![]()
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The y2s10-2 allele was obtained as a result of 1A enhancer deletion (![]()
The y+s27 allele was generated by excision of P1 element. PCR cloning and sequencing showed that only 1517 bp from each terminus were retained (Figure 1). The phP1 mutation failed to influence the phenotype of y+s27 flies, suggesting that the 1A enhancer completely overcomes phP1-mediated repression, if only one P element is present at the yellow locus.
The y+s alleles associated with duplication of any P element were characterized by an almost complete inactivation of yellow expression by the phP1 mutation (Figure 1). The y+sA11 allele was associated with duplication of the P1 element in the head-to-head orientation (Figure 1). Another y allele, y+sA12, had P2-element duplication also in the head-to-head orientation. Both y+s alleles had the same strong mutant phenotype in combination with the phP1 mutation. Thus, only the number of P-element copies at the yellow locus was important for the enhancement of the effect of the phP1 mutation, but not their localization in the chimeric element.
The y+s22 allele was induced by an inversion of the central 2.9-kb region without P-element deletion (![]()
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To further study the dependence of phP1 repression on the orientation of the chimeric element, we mobilized P elements in the y+s22phP1 strain. As a result, we obtained a y+s32 derivative characterized by a variegated pigmentation of bristles in combination with phP1 (Figure 1). The y+s32 allele was generated by an excision of P2 element, leaving only 14 and 18 bp of the terminal repeats. Thus, the phP1 mutation can inhibit yellow expression in the presence of just a single distal P element located at a 3-kb distance from the yellow promoter if an inversion of the 2.9-kb sequence takes place.
The upstream region of the yellow gene contains the yellow wing and body enhancers, which are blocked due to the presence of the su(Hw) insulator (Figure 2). To study the role of yellow enhancers in the phP1-mediated repression, we inactivated the su(Hw) insulator, crossing the combination of y and phP1 mutations into su(Hw)- background. The su(Hw)v/su(Hw)2 transheterozygote completely suppressed the mutant y phenotype of flies carrying the combination of the phP1 mutation with either y+s1 or y+s32 mutation (Figure 1). Thus, the yellow body and wing enhancers are also able to suppress a weak phP1-mediated repression.
The su(Hw)v/su(Hw)2 transheterozygote partially suppressed the phP1-mediated repression in the y+sA11, y+sA11, and y+s22 alleles. This result shows that 1A and yellow enhancers cooperatively protect yellow expression from the phP1 repression. However, the yellow enhancers fail to influence strong repression in the y2s10-2phP1; su(Hw)v/su(Hw)2 flies (Figure 1). Thus, the yellow enhancers have weaker effect on the phP1-mediated inhibition of transcription than the 1A enhancer in the y+s1 allele.
The P-element sequences responsible for phP1-mediated repression:
In an earlier article (![]()
As was shown previously, the phP1 mutation mildly repressed yellow expression in the y2s14 allele containing a single P-element copy (![]()
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Another derivative, y2s42 allele, which had only 41 bp of the 3' end and 852 bp of the 5' end, was affected by phP1: the notum and leg bristles acquired a variegated mutant phenotype (Figure 3). The P element in the y2s42 allele had a deletion of 3' transposase-binding sites, but it differed from the y2s34 allele by the presence of a part of the central region of the defective P element between 767 and 852 bp. The latter included the breakpoint of the deletion and the filler sequence TAGCTACAAA, suggesting the presence of additional binding sites for the chimeric P-Ph protein in this region.
To identify the role of the central region of the P element in the phP1 repression, we prepared the P{w+,
P-yellow} construct containing two 179-bp XhoI-ScaI restriction fragments of the 1.2-kb P element (the fragment between 730 and 909 bp of the latter) at the position of -340 bp from the yellow transcription start site (Figure 2). Seven independent transformants were obtained, possessing a single insertion as confirmed by Southern blot analysis. All of them displayed wild-type levels of yellow expression. The combination of the phP1 mutation with the P{w+,
P-yellow} construct in five cases led to mosaic pigmentation of bristles, while the pigmentation of the body and wings was not changed (data not shown). The level of repression was the same for heterozygous and homozygous states of the P{w+,
P-yellow} construct. As a control, we used P{w+, yellow+} transposon, which contained the unmodified yellow gene. Nine transgenic lines carrying P{w+, yellow+} transposon were obtained. The y phenotype of flies from these lines was not changed on a phP1 background. This result confirms the role of the central XhoI-ScaI region of the 1.2-kb P element in the phP1-mediated repression of the yellow expression.
We also compared eye pigmentation in either the presence or absence of the phP1 mutation. The miniwhite gene is very sensitive to repression by Pc-G complex. For example, a 661-bp PRE core fragment from the Ubx gene, inserted in a CaSpeR3 vector, generally causes variegated miniwhite gene expression in 5060% of the lines (![]()
P-yellow} transposon in heterozygous state displayed a weak decrease of eye pigmentation after cross to a phP1w background. In the homozygous state of the P{w+,
P-yellow} transposon, flies from four of six lines showed decrease of eye pigmentation and a weak variegation characteristic for Pc-G repression of white expression (data not shown). Thus, the ends of P elements in the presence of phP1 have only a weak repression potential compared to natural PREs.
As shown previously (![]()
To make the difference between strong and weak phP1-mediated repression more clear, we introduced the combinations of phP1 with the y mutations into a su(Hw)- background (Figure 3). The su(Hw)2/su(Hw)v transheterozygote completely suppressed the mutant yellow phenotype of flies carrying the combination of the phP1 mutation with either y2s14 or y2s16 mutation induced by single P-element insertion. Thus, the yellow body and wing enhancers are able to suppress a weak phP1-mediated repression. On the contrary, the su(Hw)2/su(Hw)v transheterozygote only weakly influences the phenotype of flies carrying the phP1 mutation with either y2s11, y2s26, or y2s25 alleles. Thus, the 3' sequences of the P element can strongly enhance the phP1-mediated repression.
Pairing-dependent repression of yellow expression mediated by phP1:
The repressive effect of the phP1 mutation was stronger in homozygous y+s1 females than in y+s1 males or heterozygous y1/y+s1 females (Table 1), where the y1 allele was generated by a point mutation in the coding region of the yellow gene (![]()
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To further study the role of P-element sequences in the formation of a phP1-dependent repression complex, we studied the phenotype of heterozygotes for the above mentioned y+s1, y+s32, or y+s27 alleles with the y alleles possessing one, one and one-half, or two P-element copies in combination with phP1. For a y allele with a single P-element copy, we used the y1s8 mutation (![]()
The combination of y1s8 with either y+s1, y+s32, or y+s27 did not significantly increase the effect of phP1 as compared to its effect in heterozygous females (Table 1). Thus, a single P-element copy failed to induce a strong pairing-dependent repression by the phP1 mutation. In contrast, the y2s7, y2s11, and y2s25 alleles induced a strong pairing-dependent repression (Table 1). These y2s alleles were induced either by two P elements or by the P2 element and the 3' terminus of the P1 element (Figure 2 and Figure 3). However, the effect of phP1 was weaker in heterozygous females with the y2s26 allele. The y2s26 allele differed from the y2s25 allele only by a deletion of the central region of the P1 element, further confirming the role of this part of the 1.2-kb P element in the phP1-mediated repression of yellow transcription.
Su(y) mutations:
In the progeny obtained after P-element mobilization in y+s1 phP1 flies, we could frequently observe the appearance of autosomal suppressors of phP1-mediated repression. These mutations, designated as Su(y), were widely spread on the X, second, and third chromosomes and displayed different levels of the suppression effect. Eleven Su(y) mutations were lethal in the homozygous state, 9 possessed normal or decreased viability, and 2 were associated with female sterility. One of the Su(y) mutations appeared simultaneously with a mutation in the ebony (e) locus, and the recombination analysis showed them to be one and the same mutation. Another strong Su(y) mutation was obtained in the singed locus (sneP1).
For further study, we selected three Su(y) alleles, Su(y)P31 (third chromosome), Su(y)P22 (second chromosome), and sneP1. To compare the levels of suppression, we studied the phenotype of females with the y phP1/y* phP1; Su(y)/+ genotype, where y* was one of the y alleles described above (Figure 4). All three Su(y) mutations completely suppressed the effect of phP1 on the y2s14 and y+s1 alleles. The Su(y)P31 mutation also almost completely suppressed the effect of phP1 on the y alleles induced by a chimeric element containing even three P elements (y+sA8 and y+sA22) or an inversion of the chimeric element (y+s12). Su(y)P22 and sneP1 had only a weak suppressive effect in these combinations. However, the Su(y) mutations did not have any visible effect on the combination of phP1 with y2s7, y2s11, y2s25, and y2s26 alleles, in which yellow expression is completely repressed (data not shown).
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The most plausible explanation was that Su(y) mutations were induced by P-element insertions into regulatory or transcribed regions of different genes that led to a high level of transcription of the defective P elements and to the accumulation of truncated transposase that might suppress the mutant phenotype of the y alleles competing with the P-Ph protein for binding sites. To test this hypothesis, we performed a Northern blot analysis of mRNA from the Su(y) and control strains using as a probe the P-element HindIII-XhoI fragment that included the sequences encoding the DNA-binding domain of transposase (![]()
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Molecular study of the sneP1 allele:
To gain a better insight into the mechanism of Su(y) action, we used for molecular analysis the sneP1 mutation in the well-characterized singed locus (![]()
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To prove the responsibility of sneP1 for the Su(y) effect, we studied revertants induced by crossing with
2-3. Five sn+P revertants were obtained and shown by Southern blot hybridization to lack the P element. As expected, the sn+P revertants, sn+P11 and sn+P12, simultaneously lost the ability to suppress the mutant phenotype of the y2s14phP1 combination (Figure 5).
We also studied two snwP mutations, snwP13 and snwP14, obtained from sneP1 as a result of P-element duplication in the head-to-head orientation, as in the case of the well-known snw mutation (![]()
The P elements in the previously described snw mutation (![]()
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The phP1 mutation does not affect singed expression in P-element-induced sn mutations:
The singed gene of D. melanogaster plays a role in both somatic and germ cells (![]()
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The P element in the above described sn mutations was inserted at a distance of <50 bp from the core region of the downstream promoter element (DPE) of the singed gene (![]()
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P-element-induced sn mutations did not significantly influence the singed function in gonads: females homozygous for a sn mutation were fertile. Only the sneP1 mutation reduced female fertility. The phP1 mutation did not significantly increase the sterility of females with homozygous sn mutations.
| DISCUSSION |
|---|
The properties of P-element-mediated repression of the yellow gene by the phP1 mutation:
The chimeric P-Ph protein encoded by the phP1 locus consists of the P-element transposase DNA-binding domain and an almost full-length Ph protein (![]()
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The y alleles used in this study have been generated by an insertion of the 2.9-kb genomic DNA sequence from the 1A region of X chromosome located more distally with respect to the yellow gene. The genomic duplication is flanked by two identical copies of a deleted 1.2-kb P element (![]()
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The level of repression induced by phP1 depends directly on the number of P elements but not on their localization. The phP1-mediated repression may act at a distance from the yellow promoter. In the y+s32 allele the P element is located ~3 kb from the yellow promoter and is separated from the latter by the 1A enhancer. Still in this case, the phP1 mutation inhibits yellow transcription. In this respect, the P elements act like PREs that are responsible for the repressive state in the adjacent genome region in a cooperative manner (![]()
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The phP1 mutation induces only a weak repression in y alleles containing a single P-element copy upstream of the yellow gene. Thus, one copy of P element is not sufficient for the formation of a strong repression complex. Addition to a single copy of the 1.2-kb P element of 153-bp 3'-terminal P-element sequences strongly enhances phP1-mediated repression, leading to a complete inactivation of yellow expression. As expected, the deletion of transposase-binding sites or 11-bp inverted repeats reduces the phP1-mediated repression. Unexpectedly, the internal region of the 1.2-kb P element is also important for the phP1-mediated repression that suggests the presence of a potential site(s) for binding of the chimeric P-Ph protein.
PRE-containing transposons often show a dramatic enhancement of silencing when a fly is homozygous for a transposon insertion, indicating that the homologously paired PREs interact to produce a more stable and more repressive Pc-G complex (![]()
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Truncated P-element transposase similar in structure to the KP protein suppresses the inhibitory effect of the chimeric P-Ph protein on the expression of P-element-induced y alleles:
The inhibitory effect of the phP1 mutation can be partially suppressed by Su(y) mutations induced by a P-element insertion into regulatory or coding regions of different genes. The inserted 1.2-kb P element is transcribed at a high level and gives rise to a truncated transposase. For example, in the sneP1 mutation, the 1.2-kb P element is inserted into the 5' transcribed noncoding region leading to an enhanced P-element transcription. As shown before, mRNA encoding truncated transposase was also formed as a result of the phP1 mutation (![]()
The 1.2-kb P element has a deletion between 830 and 2560 bp and resembles the previously described KP element (![]()
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The KP protein binds to multiple sites on the P-element termini with a higher affinity than the full-length transposase (![]()
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2-3 construct generating a full length transposase has a very weak suppression effect on the phP1 mutation (T. BELENKAYA, unpublished results). This may also be explained by its lower affinity to the P-element DNA.
The defective transposase with the DNA-binding domain and two protein-protein interaction domains is most efficient for realization of the suppression effect. Thus, the suppression of phP1-induced inhibition is a result of the competition for binding sites on the P elements between the KP-like protein and the P-Ph protein.
The presence of a strong enhancer in the chimeric element helps the KP-like protein in blocking the assembly of a P-Ph-mediated Pc-G complex on the P element. However, the Su(y) mutations, even expressing the truncated P-element transposase at high levels at all stages of Drosophila development, fail to affect the phP1-mediated inhibition of y2s alleles induced by a double P element in the absence of the 1A enhancer. The formation of a strong repression complex prevents binding of the KP protein to transposase-binding sites on the P elements. Thus, the general low level of transcription activity facilitates P-Ph protein binding to DNA and the formation of a repressive complex.
singed expression is insensitive to the phP1 mutation in the P-element-induced mutations:
The singed gene plays a role in somatic cells during the formation of adult bristles and hairs, and in the female germline during oogenesis (![]()
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As we have found here, the miniwhite expression in transposons is weakly sensitive to the phP1 mutation that may be explained by a large distance between the white promoter and P-element sequences in the transposon. However the effect of the phP1 mutation is not restricted to the yellow gene. In another article (![]()
A relatively weak effect of the phP1 mutation in several cases may be explained by the low level of the P-Ph protein produced by the phP1 allele. To examine this possibility, we are constructing the transgenic lines producing a large amount of P-Ph protein.
| ACKNOWLEDGMENTS |
|---|
The authors are greatly indebted to M. Gause for her help in some experiments and to K. O'Hare and P. Geyer for plasmids of the singed and yellow genes, respectively. This work was supported by the Russian Foundation for Basic Research, N 96-15-97032 and N 97-04-48742, by an International Research Scholar's award from the Howard Hughes Medical Institute, and by a Human Frontier Science Program Organization grant to P.G.
Manuscript received September 14, 1998; Accepted for publication April 21, 1999.
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