Enhancer-promoter communication at the yellow gene of Drosophila melanogaster: diverse promoters participate in and regulate trans interactions

The many reports of trans interactions between homologous as well as nonhomologous loci in a wide variety of organisms argue that such interactions play an important role in gene regulation. The yellow locus of Drosophila is especially useful for investigating the mechanisms of trans interactions due to its ability to support transvection and the relative ease with which it can be altered by targeted gene replacement. In this study, we exploit these aspects of yellow to further our understanding of cis as well as trans forms of enhancer-promoter communication. Through the analysis of yellow alleles whose promoters have been replaced with wild-type or altered promoters from other genes, we show that mutation of single core promoter elements of two of the three heterologous promoters tested can influence whether yellow enhancers act in cis or in trans. This finding parallels observations of the yellow promoter, suggesting that the manner in which trans interactions are controlled by core promoter elements describes a general mechanism. We further demonstrate that heterologous promoters themselves can be activated in trans as well as participate in pairing-mediated insulator bypass. These results highlight the potential of diverse promoters to partake in many forms of trans interactions.     

应用果蝇yellow基因的分子模式分析基因转应作用(英文)

基因转应作用（ｔｒａｎｓｖｅｃｔｉｏｎ）是基因表达的一种方式,这种方式是由等位基因配对及其相互作用所介导的。基因转应作用的现象已在果蝇的多种基因中发现。这种作用可产生正负两种效应。而且,在其它物种中,也逐渐发现了类似的现象。例如,在植物中的基因沉默现象（ｇｅｎｅｓｉｌｅｎｃｉｎｇ）以及在小鼠中的基因转激活作用（ｔｒａｎｓａｃｔｉｖａｔｉｏｎ）等。因此,阐明基因转应作用的机理,将有助于了解基因表达调节及增强子调控活动的分子基础。本文应用果蝇ｙｅｌｏｗ基因为模式来探讨基因转应作用的分子机制。前期研究表明,ｙｅｌｏｗ基因转应作用发生于ｇｙｐｓｙ诱导的ｙ２突变种和ｙｅｌｏｗ亚等位基因（ｙｈ）之间。为了证实是否ｇｙｐｓｙ是基因转应作用所必需的ＤＮＡ元件,我们鉴定了一种新的ｙｅｌｏｗ突变种,称为ｙ２３７４。ｙ２３７４突变是一种基因表达的组织特异性改变,这一改变使ｙ２３７４果蝇在翅和身体部位表皮着色呈突变型。通过遗传分析表明,ｙ２３７４也可与ｙｈ（如ｙ１＃８）产生基因转应作用。ｙ１＃８是一种无效的ｙｅｌｏｗ等位基因,它包含一个启动子和部分编码区序列的缺失。然而,当ｙ２３７４与ｙ１＃８杂交后,其杂交后代的表现型可由ｙ２３７     

Enhancer choice in cis and in trans in Drosophila melanogaster: role of the promoter

Eukaryotic enhancers act over very long distances, yet still show remarkable specificity for their own promoter. To better understand mechanisms underlying this enhancer-promoter specificity, we used transvection to analyze enhancer choice between two promoters, one located in cis to the enhancer and the other in trans to the enhancer, at the yellow gene of Drosophila melanogaster. Previously, we demonstrated that enhancers at yellow prefer to act on the cis-linked promoter, but that mutation of core promoter elements in the cis-linked promoter releases enhancers to act in trans. Here, we address the mechanism by which these elements affect enhancer choice. We consider and explicitly test three models that are based on promoter competency, promoter pairing, and promoter identity. Through targeted gene replacement of the endogenous yellow gene, we show that competency of the cis-linked promoter is a key parameter in the cis-trans choice of an enhancer. In fact, complete replacement of the yellow promoter with both TATA-containing and TATA-less heterologous promoters maintains enhancer action in cis.     

Interactions between su(Hw)-binding regions in neighboring y2 and scD1 alleles hinder trans-activation of the y2 promoter by yellow enhancers located on a homologous chromosome

The phenomenon of transvection has been well characterized for the yellow locus in Drosophila. Enhancers of a promoterless yellow locus in one homologous chromosome can activate the yellow promoter in the other when its own enhancers are blocked by the su(Hw) insulator introduced by the gypsy retrotransposon. Insertion of another gypsy into the neighboring scute locus hinders transvection presumably owing to disruption of chromosomal synapsis between the yellow alleles. We determined the sequences of gypsy required for inhibition of transvection. Two partial revertants of the scD1 mutation were obtained in which transvection between the yellow alleles was restored. Both sc revertants were generated by deletion of nine of the twelve su(Hw)-binding sites of gypsy inserted into the scute locus. This result suggests that the su(Hw) region is required for an interaction between two gypsy elements that disrupts trans activation of the yellow promoter by enhancers located on the homologous chromosome.     

Detection of new genes participating in the trans-regulation of locus yellow of MDG-4 in Drosophila melanogaster

The aim of the present work was to obtain mutations in the genes involved in regulation of the yellow locus and mdg4. For this purpose, we searched for mutations changing phenotypic expression of the y(2) mutation induced by mdg4 insertion into the regulatory region of the yellow locus. Mutations have been obtained in the earlier described system of prolonged genome instability, sometimes combined with P-M hybrid dysgenesis. The mutation mod(mdg4) in a novel gene, modifier of mdg4, was detected which either enhanced or suppressed a phenotypic expression of several mutations induced by mdg4 insertion. We suggest that mod(mdg4) controls the expression of mdg4. In addition, the mutations in five loci located on the X chromosome have been found which enhanced the mutation phenotype of several y alleles induced by insertions of different mobile elements in the regulatory region of the latter. Possibly, the protein products of these genes designated as enhancers of yellow-1, 2, 3, 4 and 5 are directly or indirectly involved in control of the yellow locus expression.     

Effect of mutations in the genes su(Hw) and mod(mdg4) on transvection between alleles of the Yellow locus in Drosophila melanogaster]

A typical example of transvection is a complementation between alleles in the yellow locus: y2 (mdg4 insertion inactivating certain y-enhancers) and y1 (deletion of the y-promoter but not of the enhancer). Transvection was explained by trans-activation of promoter in y2-allele by enhancer of y1-allele. Here we found that the mutation mod(mdg4)1u1 in the modifier of mdg4 locus (a regulatory gene controlling, together with suppressor of Hairy wing) expression of (mdg4) completely suppress the complementation. Removal of an acidic domain from su(Hw) protein product in su(Hw)j mutation partially suppress the complementation. We also have found that mod(mdg4)1u1 mutation trans-inactivates the yellow allele with a wild type phenotype (y+2MC) in heterozygote with the y2 allele, i.e. the negative transvection takes place. In this case, deletion removing an acidic domain even in one copy of su(Hw) suppresses the effect of mod(mdg4)1u1 mutation.     

Pairing between gypsy insulators facilitates the enhancer action in trans throughout the Drosophila genome

The Suppressor of the Hairy wing [Su(Hw)] binding region within the gypsy retrotransposon is the best known chromatin insulator in Drosophila melanogaster. According to previous data, two copies of the gypsy insulator inserted between an enhancer and a promoter neutralize each other's actions, which is indicative of an interaction between the protein complexes bound to the insulators. We have investigated the role of pairing between the gypsy insulators located on homologous chromosomes in trans interaction between yellow enhancers and a promoter. It has been shown that trans activation of the yellow promoter strongly depends on the site of the transposon insertion, which is evidence for a role of surrounding chromatin in homologous pairing. The presence of the gypsy insulators in both homologous chromosomes even at a distance of 9 kb downstream from the promoter dramatically improves the trans activation of yellow. Moreover, the gypsy insulators have proved to stabilize trans activation between distantly located enhancers and a promoter. These data suggest that gypsy insulator pairing is involved in communication between loci in the Drosophila genome.     

Mutations in the Bli-4 (I) Locus of Caenorhabditis Elegans Disrupt Both Adult Cuticle and Early Larval Development

The bli-4 (I) gene of Caenorhabditis elegans had been previously defined by a single recessive mutation, e937, which disrupts the structure of adult-stage cuticle causing the formation of fluid-filled separations of the cuticle layers, or blisters. We report the identification of 11 new alleles of bli-4, all early larval lethals, including an allele induced by transposon mutagenesis. Nine of the lethal alleles failed to complement the blistered phenotype of e937; two alleles, s90 and h754, complement e937. The complementing alleles arrested development somewhat later than the noncomplementing alleles, which blocked just prior to hatching. We conclude that bli-4 is a complex locus with an essential function late in embryogenesis. We investigated the blistered phenotype of e937 through interactions with other mutations that alter worm morphology or cuticle structure. Recessive and dominant epistasis of several dumpy mutations over the blistered phenotype was observed. Using two heterochronic mutations that alter the developmental stage at which adult cuticle is expressed, we observed that adult worms that lack an adult-stage cuticle could not express blisters. However, late larval worms that expressed the adult cuticle did not express blisters either. It seems likely that the presence of the adult cuticle is necessary, but not sufficient, for blister expression. Blistering resulting from e937 is more severe in trans to null alleles, indicating that e937 is hypomorphic. We postulate that the adult-specific blistering is due to an altered or reduced function of bli-4 gene product in the adult cuticle.(ABSTRACT TRUNCATED AT 250 WORDS)     

Effects of mutations at thestambh A locus ofDrosophila melanogaster

We report novel findings on the cytogenetic location, functional complexity and maternal and germline roles of thestambh A locus ofDrosophila melanogaster. stmA is localized to polytene bands 44D1.2 on 2R.stmA mutations are of two types: temperature-sensitive (ts) adult and larval paralytic or unconditional embryonic or larval lethal. Twelve alleles reported in this study fall into two intragenic complementing groups suggesting thatstmA is a complex locus with more than one functional domain. Some unconditional embryonic lethal alleles show a ‘neurogenic’ phenotype of cuticle loss accompanied by neural hypertrophy. It is shown that embryos of ts paralytic alleles also show mild neural hypertrophy at permissive temperatures while short exposure to heat induces severe cuticle loss in these embryos.stmA exerts a maternal influence over heat-induced cuticle loss. Unconditional embryonic lethal alleles ofstmA are also germline lethal.     

The effect of heterologous insertions on gene conversion in mitotically dividing cells in Drosophila melanogaster

We examined the influence that heterologous sequences of different sizes have on the frequency of double-strand-break repair by gene conversion in Drosophila melanogaster. We induced a double-strand break on one X chromosome in female flies by P-element excision. These flies contained heterologous insertions of various sizes located 238 bp from the break site in cis or in trans to the break, or both. We observed a significant decrease in double-strand-break repair with large heterologous insertions located either in cis or in trans to the break. Reestablishing the homology by including the same heterologous sequence in cis and in trans to the double-strand break restored the frequency of gene conversion to wild-type levels. In one instance, an allelic nonhomologous insertion completely abolished repair by homologous recombination. The results show that the repair of a double-strand break by gene conversion requires chromosome pairing in the local region of the double-strand break.