A Reconsideration of the Mechanism of Position Effect

Chromatin structure and the regulation of gene expression: the lessons of PEV in Drosophila

Position-effect variegation (PEV) was discovered in 1930 in a study of X-ray-induced chromosomal rearrangements. Rearrangements that place euchromatic genes adjacent to a region of centromeric heterochromatin give a variegated phenotype that results from the inactivation of genes by heterochromatin spreading from the breakpoint. PEV can also result from P element insertions that place euchromatic genes into heterochromatic regions and rearrangements that position euchromatic chromosomal regions into heterochromatic nuclear compartments. More than 75 years of studies of PEV have revealed that PEV is a complex phenomenon that results from fundamental differences in the structure and function of heterochromatin and euchromatin with respect to gene expression. Molecular analysis of PEV began with the discovery that PEV phenotypes are altered by suppressor and enhancer mutations of a large number of modifier genes whose products are structural components of heterochromatin, enzymes that modify heterochromatic proteins, or are nuclear structural components. Analysis of these gene products has led to our current understanding that formation of heterochromatin involves specific modifications of histones leading to the binding of particular sets of heterochromatic proteins, and that this process may be the mechanism for repressing gene expression in PEV. Other modifier genes produce products whose function is part of an active mechanism of generation of euchromatin that resists heterochromatization. Current studies of PEV are focusing on defining the complex patterns of modifier gene activity and the sequence of events that leads to the dynamic interplay between heterochromatin and euchromatin.

Engrailed gene dosage determines whether certain recessive cubitus interruptus alleles exhibit dominance of the adult wing phenotype in Drosophila

The cubitus interruptus (ci) locus of Drosophila melanogaster is needed for normal development. Some mutants of this gene result in embryonic lethality, while others just disrupt adult wing veins. While undertaking a genetic screen for additional ci mutations that affect the wing veins, we recovered a modifier mutation on chromosome two that produced a ci phenotype in recessive ci heterozygotes (ci(recessive)/+). We identified the modifier mutation as an allele of engrailed and have called it engrailed-enhancer of cubitus interruptus (enEnci). As a double heterozygote (en-/+; ci-/+) this new en allele dominantly generates a ci wing vein phenotype. As a double heterozygote, it also enhances the ci wing vein phenotype of the dominant alleles ciW and ciCe2, but not ciD. Other loss-of-function en alleles also enhance the ci phenotype, with the en lethal alleles (and deletions) showing the strongest effect, while the homozygous viable en alleles show weaker enhancement. Strong en- alleles failed to induce a ci phenotype with heterozygotes of ci recessive lethal alleles l(4)13, l(4)17, or ciDrev, which are loss-of-function mutations. This supports a previous proposal that the ci wing vein phenotype is not due to loss of ci+ function, as would be expected for most recessive alleles. Instead, the adult wing vein abnormality is due to ectopic expression (or de-repression) of the ci transcript in the posterior compartment of the wing disc. We also observed that en-/+ heterozygotes could induce a ci phenotype in situations where the ci+ locus is either unpaired or hemizygous. Since loss of one en+ gene dose enhanced the ci phenotype, three doses of en+ were tested and found to suppress expression of the ci phenotype in ci1 homozygotes and ciW heterozygotes. These observations show that correct regulation of the ci gene involves more than the simple interaction of upstream regulatory elements. some pairing, pairing dependent gene repression, position effects.

An analysis of transvection at the yellow locus of Drosophila melanogaster

Studies of a wide variety of organisms have shown that homologous sequences can exert a significant 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 first 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 transcriptional mechanism, whereby the ability of an allele to support transvection is influenced by its transcriptional competency, and (2) a structural mechanism, whereby the pairing of structurally dissimilar homologues results in conformational changes that affect gene expression.

Two modes of transvection: enhancer action in trans and bypass of a chromatin insulator in cis

Ed Lewis introduced the term "transvection" in 1954 to describe mechanisms that can cause the expression of a gene to be sensitive to the proximity of its homologue. Transvection since has been reported at an increasing number of loci in Drosophila, where homologous chromosomes are paired in somatic tissues, as well as at loci in other organisms. At the Drosophila yellow gene, transvection can explain intragenic complementation involving the yellow2 allele (y2). Here, transvection was proposed to occur by enhancers of one allele acting in trans on the promoter of a paired homologue. In this report, we describe two yellow alleles that strengthen this model and reveal an unexpected, second mechanism for transvection. Data suggest that, in addition to enhancer action in trans, transvection can occur by enhancer bypass of a chromatin insulator in cis. We propose that bypass results from the topology of paired genes. Finally, transvection at yellow can occur in genotypes not involving y2, implying that it is a feature of yellow itself and not an attribute of one particular allele.

Copy number and orientation determine the susceptibility of a gene to silencing by nearby heterochromatin in Drosophila

The classical phenomenon of position-effect variegation (PEV) is the mosaic expression that occurs when a chromosomal rearrangement moves a euchromatic gene near heterochromatin. A striking feature of this phenomenon is that genes far away from the junction with heterochromatin can be affected, as if the heterochromatic state "spreads." We have investigated classical PEV of a Drosophila brown transgene affected by a heterochromatic junction approximately 60 kb away. PEV was enhanced when the transgene was locally duplicated using P transposase. Successive rounds of P transposase mutagenesis and phenotypic selection produced a series of PEV alleles with differences in phenotype that depended on transgene copy number and orientation. As for other examples of classical PEV, nearby heterochromatin was required for gene silencing. Modifications of classical PEV by alterations at a single site are unexpected, and these observations contradict models for spreading that invoke propagation of heterochromatin along the chromosome. Rather, our results support a model in which local alterations affect the affinity of a gene region for nearby heterochromatin via homology-based pairing, suggesting an alternative explanation for this 65-year-old phenomenon.

Distance and pairing effects on the brownDominant heterochromatic element in Drosophila

We examined the behavior of the brownDominant (bwD) heterochromatic insertion moved to different locations relative to centric heterochromatin. Effects were measured as the degree of silencing of a wild-type brown eye pigment gene by bwD across a tandem duplication. A series of X-ray-induced effects were recovered at high frequency. Cis-acting enhancers were obtained by relocation of the duplication closer to autosomal heterochromatin. Enhancers were also recovered on the homologous chromosome when it was similarly rearranged, revealing a novel interhomologue effect whereby interactions occur between genetic elements near opposite ends of a chromosome arm rather than between paired alleles. Cis-acting suppressors were obtained as secondary rearrangements in which the duplication was moved farther away from heterochromatin. Suppression was correlated with loss of cytological association between bwD and the polytene chromocenter. Surprisingly, the distance from bwD to the chromocenter was not correlated with the strength of enhancement or suppression. We propose that bwD fails to coalesce with the chromocenter when its position along the chromosome places it beyond a threshold distance from heterochromatin, and this threshold depends upon the configuration of both the chromosome carrying bwD and its paired homologue.

A genetic analysis of the Suppressor 2 of zeste complex of Drosophila melanogaster

The zeste1 (z1) mutation of Drosophila melanogaster produces a mutant yellow eye color instead of the wild-type red. Genetic and molecular data suggest that z1 achieves this change by altering expression of the wild-type white gene in a manner that exhibits transvection effects. There exist suppressor and enhancer mutations that modify the z1 eye color, and this paper summarizes our studies of those belonging to the Suppressor 2 of zeste complex [Su(z)2-C]. The Su(z)2-C consists of at least three subregions called Psc (Posterior sex combs), Su(z)2 and Su(z)2D (Distal). The products of these subregions are proposed to act at the level of chromatin. Complementation analyses predict that the products are functionally similar and interacting. The alleles of Psc define two overlapping phenotypic classes, the hopeful and hapless. The distinctions between these two classes and the intragenic complementation seen among some of the Psc alleles are consistent with a multidomain structure for the product of Psc. Psc is a member of the homeotic Polycomb group of genes. A general discussion of the Polycomb and trithorax group of genes, position-effect variegation, transvection, chromosome pairing and chromatin structure is presented.

Molecular analysis of cubitus interruptus (ci) mutations suggests an explanation for the unusual ci position effects

The cubitus interruptus (ci) locus of Drosophila melanogaster is located proximally on chromosome 4. In ci mutants cubital wing veins are interrupted or absent. We have cloned this locus using a gypsy element associated with the ci1 mutation. Analysis of all extant ci mutations reveals that they contain conspicuous molecular alterations within a 13.7 kb region. Of the four homozygous viable mutations, three (ci1, ci361, ciw) have single insertions, while one (ci57g) has a small deletion, all located within a more restricted 1 kb region. The dominant mutations, ciD and Ce2 each contain two insertions within the 13.7 kb region. All these molecular alterations are located upstream of a transcript previously associated with the ciD mutation and thought to derive from a segment polarity gene. We induced revertants of the dominant ci phenotype (wing vein interruption) in ciD and found molecular alterations in this transcript (the ci+ transcript) in two revertant alleles, thereby demonstrating this transcript's involvement in the ci phenotype. The locations of the molecular alterations, together with the results of the ciD reversion experiment, provide a connection between the dominant and recessive ci mutations and argue that all are likely to be alleles of the same complex locus, ci, not two separate loci as previously proposed. The ci phenotype of dominant and recessive mutations can be explained by inappropriate expression of the ci+ transcript in the posterior wing compartment where the cubital vein is affected, while loss of ci+ function generates recessive lethality. Lack of repression of ci+ transcription, through a pairing-dependent, trans-acting silencer element, can explain the unusual position effects associated with ci (the Dubinin effect).

Modification of the Drosophila heterochromatic mutation brownDominant by linkage alterations

The variegating mutation brownDominant (bwD) of Drosophila melanogaster is associated with an insertion of heterochromatin into chromosome arm 2R at 59E, the site of the bw gene. Mutagenesis produced 150 dominant suppressors of bwD variegation. These fall into two classes: unlinked suppressors, which also suppress other variegating mutations; and linked chromosome rearrangements, which suppress only bwD. Some rearrangements are broken at 59E, and so might directly interfere with variegation caused by the heterochromatic insertion at that site. However, most rearrangements are translocations broken proximal to bw within the 52D-57D region of 2R. Translocation breakpoints on the X chromosome are scattered throughout the X euchromatin, while those on chromosome 3 are confined to the tips. This suggests that a special property of the X chromosome suppresses bwD variegation, as does a distal autosomal location. Conversely, two enhancers of bwD are caused by translocations from the same part of 2R to proximal heterochromatin, bringing the bwD heterochromatic insertion close to the chromocenter with which it strongly associates. These results support the notion that heterochromatin formation at a genetic locus depends on its location within the nucleus.

Analysis of Drosophila chromosome 4 using pulsed field gel electrophoresis

Previous estimates of the size of Drosophila melanogaster chromosome 4 have indicated that it is 1% to 4% of the genome or approximately 6 Mb. We have used pulsed field gel electrophoresis (PFGE) to separate megabase-sized molecules of D. melanogaster chromosomal DNA. Southern blots of these gels were probed with DNA fragments from the cubitus interruptus and zfh-2 genes, which are located on chromosome 4. They each identify the same-sized distinct band that migrates at approximately 5.2 Mb in DNA preparations from the Kc cell line. We interpret this band to be intact chromosome 4. In DNA obtained from embryos of various D. melanogaster wild-type strains, this chromosome band showed strain-specific size variation that ranged from 4.5 to 5.2 Mb. The D. melanogaster chromosome 4 probes also identified a single, 2.4 Mb band in embryonic DNA from Drosophila simulans. We conclude that D. simulans chromosome 4 is substantially smaller than that of D. melanogaster, presumably owing to differences in the amount of heterochromatic DNA sequences. Our simple DNA preparation from embryos and PFGE conditions should permit preparative isolation of chromosome 4 DNA and will facilitate the molecular mapping of this chromosome.

A pairing-sensitive element that mediates trans-inactivation is associated with the Drosophila brown gene

Position-effect variegation in Drosophila is the mosaic expression of a gene juxtaposed to heterochromatin by chromosome rearrangement. The brown (bw+) gene is unusual in that variegating mutations are dominant, causing "trans-inactivation" of the homologous allele. We show that copies of bw+ transposed to ectopic sites are not trans-inactivated by rearrangements affecting the endogenous gene. However, when position-effect variegation is induced on an ectopic copy by chromosome rearrangement, the allele on its paired homolog is trans-inactivated, whereas other copies of bw+ are not. This confirms that trans-inactivation is "chromosome local" and maps the responsive element to the immediate vicinity of brown. Subsequent P-transposase-induced deletions within the ectopic copy in cis to the rearrangement breakpoint caused partial suppression of trans-inactivation. Surprisingly, the amount of suppression was correlated with deletion size, with some degree of trans-inactivation persisting even when the P[bw+] transposon was completely excised. The chromosome-local nature of the phenomenon and its extreme sensitivity to small disruptions of somatic pairing leads to a model in which a regulator of the brown gene is inactivated by direct contact with heterochromatic proteins.

The effects of chromosome rearrangements on the expression of heterochromatic genes in chromosome 2L of Drosophila melanogaster

The light (lt) gene of Drosophila melanogaster is located at the base of the left arm of chromosome 2, within or very near centromeric heterochromatin (2Lh). Chromosome rearrangements that move the lt+ gene from its normal proximal position and place the gene in distal euchromatin result in mosaic or variegated expression of the gene. The cytogenetic and genetic properties of 17 lt-variegated rearrangements are described in this report. We show that five of the heterochromatic genes adjacent to lt are subject to inactivation by these rearrangements and that the euchromatic loci in proximal 2L are not detectably affected. The properties of the rearrangements suggest that proximity to heterochromatin is an important regulatory requirement for at least six 2Lh genes. We discuss how the properties of the position effects on heterochromatic genes relate to other proximity-dependent phenomena such as transvection.

Trans-inactivation of the Drosophila brown gene: evidence for transcriptional repression and somatic pairing dependence

Position-effect variegation in Drosophila is the variable inactivation of a gene that occurs when it is juxtaposed to heterochromatic regions of chromosomes. The brown gene, required for pteridine pigment in the eye, is unusual in that expression of the unrearranged homolog also is affected. This dominant effect can be very strong, as inactivation is detectable when as many as three trans copies of the gene are present. We show that pteridine reductions coincide with similar reductions in the accumulation of brown mRNA. The dominant effect is suppressed by certain altered structural configurations of the brown region, suggesting that somatic pairing is involved in the phenomenon. We propose that direct transmission of the altered chromatin structure characteristic of position-effect variegation (heterochromatinization) occurs between paired homologs in the region of the brown locus.

Trans-inactivation of the Drosophila brown gene: evidence for transcriptional repression and somatic pairing dependence

Position-effect variegation in Drosophila is the variable inactivation of a gene that occurs when it is juxtaposed to heterochromatic regions of chromosomes. The brown gene, required for pteridine pigment in the eye, is unusual in that expression of the unrearranged homolog also is affected. This dominant effect can be very strong, as inactivation is detectable when as many as three trans copies of the gene are present. We show that pteridine reductions coincide with similar reductions in the accumulation of brown mRNA. The dominant effect is suppressed by certain altered structural configurations of the brown region, suggesting that somatic pairing is involved in the phenomenon. We propose that direct transmission of the altered chromatin structure characteristic of position-effect variegation (heterochromatinization) occurs between paired homologs in the region of the brown locus.

The gene

The gene has sometimes been described as a purely idealistic concept, divorced from real things, and again it has been denounced as wishful thinking on the part of those too mechanically minded. And some critics go so far as to assert that there is not even such a thing as genetic material at all, as distinct from other constituents of living matter.