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An Analysis of Transvection at the Yellow Locus of Drosophila Melanogaster

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An Analysis of Transvection at the Yellow Locus of Drosophila Melanogaster Copyright 1999 by the Genetics Society of America An Analysis of Transvection at the yellow Locus of Drosophila melanogaster James R. Morris,* Ji-long Chen,² Stephen T. Filandrinos,* Rebecca C. Dunn,² Ridgely Fisk,* Pamela K. Geyer² and Chao-ting Wu* *Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115 and ²Department of Biochemistry, University of Iowa, Iowa City, Iowa 52242 Manuscript received June 8, 1998 Accepted for publication October 5, 1998 ABSTRACT Studies of a wide variety of organisms have shown that homologous sequences can exert a signi®cant impact on each other, resulting in changes in gene sequence, gene expression, chromatin structure, and global chromosome architecture. Our work has focused on transvection, a process that can cause genes to be sensitive to the proximity of a homologue. Transvection is seen at the yellow gene of Drosophila, where it mediates numerous cases of intragenic complementation. In this article, we describe two approaches that have characterized the process of transvection at yellow. The ®rst entailed a screen for mutations that support intragenic complementation at yellow. The second involved the analysis of 53 yellow alleles, obtained from a variety of sources, with respect to complementation, molecular structure, and transcriptional competence. Our data suggest two ways in which transvection may be regulated at yellow: (1) a transcrip- tional mechanism, whereby the ability of an allele to support transvection is in¯uenced by its transcrip- tional competency, and (2) a structural mechanism, whereby the pairing of structurally dissimilar homo- logues results in conformational changes that affect gene expression. HE structure and function of a segment of DNA whose evolution may have been in response to the ap- Tcan be profoundly affected by the presence of ho- pearance of homologous sequences, such as must have mologous sequences (reviewed by Bestor et al. 1994; happened during transitions from haploidy to higher Henikoff and Comai 1998). In some cases, the impact ploidies (for related interpretations, see Bestor 1990; of homologous sequences is revealed through the intro- Flavell 1994; Bestor and Tycko 1996; Matzke et al. duction of transgenes bearing sequence homology to 1996; Mittelsten Scheid et al. 1996; Bingham 1997; endogenous genes. Such transgenes can induce se- Henikoff and Matzke 1997; Yoder et al. 1997; Jorgen- quence alterations and de novo methylation in fungi sen et al. 1998; Kumpatla et al. 1998; Matzke and (reviewed by Selker 1997) and gene silencing in plants Matzke 1998; references therein). In this article, we (reviewed by Meyer and Saedler 1996; Depicker and explore the manner in which homologous sequences Van Montagu 1997; Jorgensen et al. 1998; Matzke can interact by examining the phenomenon of transvec- and Matzke 1998), insects (Dorer and Henikoff 1994; tion. Pal-Bhadra et al. 1997), and mammals (Garrick et al. In Drosophila, the state of diploidy is accompanied 1998). Diploidy and polyploidy provide more natural by the feature of somatic homologue pairing (Metz states where genes are present in multiple copies, and 1916; Fung et al. 1998 and references therein). The in these contexts, homologous sequences can also in- expression of some genes can be modulated by proxim- ¯uence gene expression. Here, examples are provided ity to a homologue, and these genes are said to exhibit by paramutation in plants (reviewed by Hollick et al. transvection effects (Lewis 1954). While transvection 1997), imprinting in mammals (reviewed by Lalande was de®ned in Drosophila, there is evidence for its oc- 1996; Bartolomei and Tilghman 1997; Reik and Wal- currence, and the occurrence of related phenomena, ter 1998), and sex chromosome and autosomal dosage elsewhere (Judd 1988; Tartof and Henikoff 1991; compensation (reviewed by Cline and Meyer 1996; Wu 1993; Henikoff 1997; Henikoff and Comai 1998; Heard et al. 1997; Lucchesi 1998; also Hiebert and references therein). Recent studies in a wide variety of Birchler 1994; Birchler 1996). In fact, ploidy itself systems further suggest that the impact of homologue can alter gene expression (Mittelsten Scheid et al. pairing may be quite broad. For example, homologue 1996 and references therein). Taken together, these pairing may in¯uence DNA accessibility in yeast ªhomology effectsº attest to a diverse set of mechanisms (Keeney and Kleckner 1996), may be associated with the process of parental imprinting in mammals (LaSalle and Lalande 1996), may allow nonintegrated plasmids to transinduce a chromosomal gene in mam- Corresponding author: Chao-ting Wu, Department of Genetics, Har- vard Medical School, 200 Longwood Ave., Boston, MA 02115. malian cell lines (Ashe et al. 1997), and may play a E-mail: [email protected] general role in methylation transfer (for example, Bes- Genetics 151: 633±651 (February 1999) 634 J. R. Morris et al. tor and Tycko 1996; Colot et al. 1996; Forne et al. the action of the wing and body enhancers of y1#8 in 1997). The mechanisms by which homologous se- trans on the y2 promoter when the two alleles are in quences in¯uence each other are not well understood, close proximity (Figure 1A). and many models have been proposed (reviewed by Transvection is a regulated process at the yellow gene. Henikoff 1997; Henikoff and Comai 1998; references Some alleles with intact wing and body enhancers, such therein; also see Peterson et al. 1994; Judd 1995; as y1#8, complement y2, while others that carry these en- Goldsborough and Kornberg 1996; Donaldson and hancers do not. For example, the y1 allele, which has Karpen 1997; Morris et al. 1998; Sipos et al. 1998). intact wing and body enhancers, does not complement Some of the underlying mechanisms may be common y2 (Figure 1B; Geyer et al. 1990). This allele is an A to among different processes, while others may be process, C transversion in the ATG translation initiation codon locus, or allele speci®c. (Geyer et al. 1990). As the y2 promoter is the only pro- We have asked how the proximity of homologous moter in the y2/y1#8 and y2/y1 genotypes that can give rise genes can in¯uence gene expression and have focused to functional transcripts, issues regarding the control of our attention on the Drosophila X-linked yellow gene (y, transvection can be reduced in these cases to asking 1±0.0), which shows transvection effects (Geyer et al. why the y2 promoter is activated to complementing levels 1990). The yellow gene is required for pigmentation of in the former, but not the latter, genotype. Differences larval and adult cuticular structures and its pattern of in the number of wing and body enhancers present expression is under the control of tissue-speci®c en- cannot account for the differences in complementation hancers located in the upstream 59 regulatory region because both genotypes are identical in this respect. and in the single intron (Geyer and Corces 1987; Mar- This article is concerned with the manner in which tin et al. 1989). Interestingly, there exist several re- transvection is regulated at yellow. It has been proposed cessive mutant alleles which, on their own, reduce pig- that a prerequisite for the trans action of an enhancer mentation in wings and body, but which, in certain at yellow is the disruption of its own promoter in cis combinations, complement each other to give ¯ies with (Geyer et al. 1990). For example, the release of the nearly wild-type pigmentation in these structures (Stone enhancers of y1#8 to act upon the y2 promoter may result 1935; Frye 1960; Green 1961; Nash 1976; Geyer et al. from deletion of the promoter of y1#8. By contrast, the 1990). These cases of intragenic complementation can intact promoter of y1 may preclude such trans interac- be explained by transvection (Geyer et al. 1990). tions. Cis-preference of regulatory elements for their One model for transvection at yellow suggests that en- own promoter may be a general modulator of transvec- hancers of one allele act in trans on the promoter of the tion because correlations between changes in the pro- other allele when the two alleles are in close proximity moter region and the ability of a gene to support trans- (Geyer et al. 1990; Morris et al. 1998). This model can vection have also been noted at Ultrabithorax (Ubx, be illustrated by the complementation seen between the MartõÂnez-Laborda et al. 1992; Casares et al. 1997) y2 and y1#8 alleles (Figure 1A; Geyer et al. 1990). The y2 and Abdominal-B (Abd-B, Sipos et al. 1998). allele produces ¯ies with mutant pigmentation of the Our studies have extended the promoter-based wings and body, but wild-type pigmentation of other model. We began by asking whether there are regions structures. The mutant phenotype is caused by the inser- outside the promoter that control transvection. Evi- tion of a gypsy retrotransposon between the promoter dence for such regions exists at Abd-B (Hendrickson and the two upstream enhancers responsible for pig- and Sakonju 1995; Hopmann et al. 1995; Sipos et al. mentation of the wings and body (reviewed by Corces 1998). We took two experimental approaches. Impor- and Geyer 1991). The gypsy element inhibits communi- tantly, neither was biased toward the promoter. First, cation between these enhancers and the promoter be- we carried out mutageneses to identify elements that cause it has binding sites for the suppressor of Hairy- control transvection. Second, we characterized 53 yellow wing [su(Hw)] protein, which, when bound, establishes alleles, obtained from a variety of sources, according to a chromatin insulator that prevents the enhancers on their complementation patterns, molecular structures, one side from communicating productively with the and transcriptional competence. The data emphasize promoter on the other side (reviewed by Dorsett 1996; that the promoter region is important in the regulation Gdula et al.
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