Effects of genomic position on the expression of transduced copies of the white gene of Drosophila

Structure, function, and replication of Saccharomyces cerevisiae telomeres

A combination of classical genetic, biochemical, and molecular biological approaches have generated a rather detailed understanding of the structure and function of Saccharomyces telomeres. Yeast telomeres are essential to allow the cell to distinguish intact from broken chromosomes, to protect the end of the chromosome from degradation, and to facilitate the replication of the very end of the chromosome. In addition, yeast telomeres are a specialized site for gene expression in that the transcription of genes placed near them is reversibly repressed. A surprisingly large number of genes have been identified that influence either telomere structure or telomere function (or both), although in many cases the mechanism of action of these genes is poorly understood. This article reviews the recent literature on telomere biology and highlights areas for future research.

Genetic and molecular analysis of a set of unstable white mutants in Drosophila melanogaster

Two related unstable mutants at the white locus of Drosophila melanogaster show different interactions with the zeste1 mutant: one mutated white gene becomes repressed in males, whereas the other is unaffected by z1. By use of Southern blot techniques and by constructing genomic lambda-libraries, molecular analyses of the white regions of these two strains were performed. The results showed a single difference at a site 2.5 kb (kilobases) downstream of the white transcription unit. In both strains, FB (foldback) elements were integrated at this site, but the repressed strain also harboured a 4 kb NOF (Nofretete) element. No other restriction site polymorphisms between the two strains were observed within a 120 kb region surrounding the white gene. The extent of twelve white deletions and twelve white transpositions deriving from these unstable strains was analysed by in situ hybridisation and Southern blot techniques. The results revealed that the distal breakpoint of all aberrations coincided with the insertion site of the mobile elements, but that the centromere proximal breakpoints varied. The mechanisms for the instability and the interaction with the zeste1 mutant are discussed.

Genetic and molecular analysis of the gypsy chromatin insulator of Drosophila

Boundary or insulator elements set up independent territories of gene activity by establishing higher order domains of chromatin structure. The gypsy retrotransposon of Drosophila contains an insulator element that represses enhancer-promoter interactions and is responsible for the mutant phenotypes caused by insertion of this element. The gypsy insulator inhibits the interaction of promoter-distal enhancers with the transcription complex without affecting the functionality of promoter-proximal enhancers; in addition, these sequences can buffer a transgene from chromosomal position effects. Two proteins have been identified that bind gypsy insulator sequences and are responsible for their effects on transcription. The suppressor of Hairy-wing [su(Hw)] protein affects enhancer function both upstream and downstream of its binding site by causing a silencing effect similar to that of heterochromatin. The modifier of mdg4 [mod(mdg4)] protein interacts with su(Hw) to transform this bi-directional repression into the polar effect characteristic of insulators. These effects seem to be modulated by changes in chromatin structure.

TEL2, an essential gene required for telomere length regulation and telomere position effect in Saccharomyces cerevisiae

The DNA-protein complexes at the ends of linear eukaryotic chromosomes are called the telomeres. In Saccharomyces cerevisiae, telomeric DNA consists of a variable length of the short repeated sequence C1-3A. The length of yeast telomeres can be altered by mutation, by changing the levels of telomere binding proteins, or by increasing the amount of C1-3A DNA sequences. Cells bearing the tel1-1 or tel2-1 mutations, known previously to have short telomeres, did not respond to perturbations that caused telomere lengthening in wild-type cells. The transcription of genes placed near yeast telomeres is reversibly repressed, a phenomenon called the telomere position effect. The tel2-1 mutation reduced the position effect but did not affect transcriptional repression at the silent mating type cassettes, HMRa and HML alpha. The TEL2 gene was cloned, sequenced, and disrupted. Cells lacking TEL2 function died, with some cells arresting as large cells with three or four small protrusions or "blebs."

Tethered Sir3p nucleates silencing at telomeres and internal loci in Saccharomyces cerevisiae

Rap1p binds to sites embedded within the Saccharomyces cerevisiae telomeric TG1-3 tract. Previous studies have led to the hypothesis that Rap1p may recruit Sir3p and Sir3p-associating factors to the telomere. To test this, we tethered Sir3p adjacent to the telomere via LexA binding sites in the rap1-17 mutant that truncates the Rap1p C-terminal 165 amino acids thought to contain sites for Sir3p association. Tethering of LexA-Sir3p adjacent to the telomere is sufficient to restore telomeric silencing, indicating that Sir3p can nucleate silencing at the telomere. Tethering of LexA-Sir3p or the LexA-Sir3p(N2O5) gain-of-function protein to a telomeric LexA site hyperrepresses an adjacent ADE2 gene in wild-type cells. Hence, Sir3p recruitment to the telomere is limiting in telomeric silencing. In addition, LexA-Sir3p(N2O5) hyperrepresses telomeric silencing when tethered to a subtelomeric site 3.6 kb from the telomeric tract. This hyperrepression is dependent on the C terminus of Rap1p, suggesting that subtelomeric LexA-Sir3p(N205) can interact with Rap1p-associated factors at the telomere. We also demonstrate that LexA-Sir3p or LexA-Sir3p(N205) tethered in cis with a short tract of telomeric TG1-3 sequences is sufficient to confer silencing at an internal chromosomal position. Internal silencing is enhanced in rap1-17 strains. We propose that sequestration of silencing factors at the telomere limits the efficiency of internal silencing.

Molecular characterization of the Anopheles gambiae 2L telomeric region via an integrated transgene

A Drosophila P-element derivative (pUChsneo) integrated into the telomeric region of the left arm of the second chromosome of Anopheles gambiae was used to clone the proximally flanking An. gambiae sequences. Molecular analyses revealed that the pUChsneo construct was partially duplicated and had integrated into a subterminal minisatellite. This satellite has a repeat unit of 820 bp and is located exclusively at the tip of 2L. No sequence similarity to subterminal minisatellites from other dipterans was detected, but some structural features such as tandem subrepeats are shared. The end of the chromosome was mapped with respect to restriction sites in pUChsneo at approximately generation 100 after the integration event. Considering inevitable terminal nucleotide loss due to incomplete DNA replication, we conclude that the chromosome end must have undergone a dramatic elongation process since it was mapped in generation 23.

Telomeres: beginning to understand the end

Telomeres are the protein-DNA structures at the ends of eukaryotic chromosomes. In yeast, and probably most other eukaryotes, telomeres are essential. They allow the cell to distinguish intact from broken chromosomes, protect chromosomes from degradation, and are substrates for novel replication mechanisms. Telomeres are usually replicated by telomerase, a telomere-specific reverse transcriptase, although telomerase-independent mechanisms of telomere maintenance exist. Telomere replication is both cell cycle- and developmentally regulated, and its control is likely to be complex. Because telomere loss causes the kinds of chromosomal changes associated with cancer and aging, an understanding of telomere biology has medical relevance.

DNA organization and polymorphism of a wild-type Drosophila telomere region

Telomeres at the ends of linear chromosomes of eukaryotes protect the chromosome termini from degradation and fusion. While telomeric replication/elongation mechanisms have been studied extensively, the functions of subterminal sequences are less well understood. In general, subterminal regions can be quite polymorphic, varying in size from organism to organism, and differing among chromosomes within an organism. The subterminal regions of Drosophila melanogaster are not well characterized today, and it is not known which and how many different components they contain. Here we present the molecular characterization of DNA components and their organization in the subterminal region of the left arm of chromosome 2 of the Oregon RC wild-type strain of D. melanogaster, including a minisatellite with a 457bp repeat length. Two distinct polymorphic arrangements at 2L were found and analyzed, supporting the Drosophila telomere elongation model by retrotransposition. The high incidence of terminal chromosome deficiencies occurring in natural Drosophila populations is discussed in view of the telomere structure at 2L.

A Drosophila insulator protein facilitates dosage compensation of the X chromosome min-white gene located at autosomal insertion sites

The suppressor of Hairy-wing [su(Hw)] gene encodes a zinc finger protein that binds to a repeated motif in the gypsy retrotransposon. These DNA sequences, called the su(Hw)-binding region, have properties of an insulator region because they (1) disrupt enhancer/silencer function in a position-dependent manner and (2) protect the mini-white gene from both euchromatic and heterochromatic position effects. To gain further insights into the types of position effects that can be insulated, we determined the effects of the su(Hw)-binding region on dosage compensation of the X-linked mini-white gene. Dosage compensation is the process that equalizes the unequal content of X-linked genes in males and females by increasing the X-linked transcription level twofold in males. Transposition of X-linked genes to the autosomes commonly results in incomplete dosage compensation, indicating that the distinct male X chromatin environment is important for this process. We found that dosage compensation of autosomally integrated mini-white genes flanked by su(Hw)-binding regions was greatly improved, such that complete or nearly complete compensation was observed at the majority of insertion sites. The su(Hw) protein was essential for this enhanced dosage compensation because in a su(Hw) mutant background compensation was incomplete. These experiments provide evidence that the su(Hw)-binding region facilitates dosage compensation of the mini-white gene on the autosomes. This may result from protection of the mini-white gene from a negative autosomal chromatin environment.

Mei-S332, a Drosophila protein required for sister-chromatid cohesion, can localize to meiotic centromere regions

Mutations in the Drosophila mei-S332 gene cause premature separation of the sister chromatids in late anaphase of meiosis I. Therefore, the mei-S332 protein was postulated to hold the centromere regions of sister chromatids together until anaphase II. The mei-S332 gene encodes a novel 44 kDa protein. Mutations in mei-S332 that differentially affect function in males or females map to distinct domains of the protein. A fusion of mei-S332 to the green fluorescent protein (GFP) is fully functional and localizes specifically to the centromere region of meiotic chromosomes. When sister chromatids separate at anaphase II, mei-S332-GFP disappears from the chromosomes, suggesting that the destruction or release of this protein is required for sister-chromatid separation.

A functional analysis of 5′, intronic and promoter regions of the homeotic gene proboscipedia in Drosophila melanogaster

In Drosophila, the homeotic gene proboscipedia (pb) is required for the formation of the adult mouthparts. To determine the functional significance of putative pb regulatory DNA, we have performed an in vivo analysis of sequences upstream of and within pb using a series of minigenes. Additionally, we have initiated a dissection of pb's promoter and enhancer elements using lacZ reporter gene constructs. Our results establish that a conserved region located in the second intron is essential for proper formation of the adult mouthparts. A 0.5 kb fragment from this region was shown to direct lacZ expression in a pb pattern in both embryos and third instar labial discs when combined with a 600 bp pb basal promoter sequence. A 32 bp element contained within the 0.5 kb region functions as a labial disc enhancers for pb. Surprisingly, the conserved second intron pb enhancers do not function properly with a heterologous hsp70 promoter, suggesting that promoter-specific interactions occur at the pb locus. We also found redundant and cryptic enhancers in the large introns of pb that are not required for pb function. Finally, we demonstrate that the pb transcription unit does not require sequences upstream of −98 bp to provide pb function in the labial discs. Rather, pb's upstream DNA appears to contain negative regulatory DNA required for silencing PB accumulation in inappropriate domains of third instar imaginal discs. Thus, we have defined many of pb's cis-controlling sequences to an experimentally manageable size, thereby making this an attractive system for the discovery of transacting proteins and, consequently, for elucidating the mechanisms of homeotic gene regulation.

The unusual telomeres of Drosophila

The telomeres of most eukaryotes contain short, simple repeats that are highly conserved. Drosophila, on the other hand, does not have such sequences, but carries at the ends of its chromosomes one or more LINE-like retrotransposable elements. Instead of elongation by telomerase, incomplete DNA replication at the termini of Drosophila chromosomes is counterbalanced by transposition of these elements at high frequency specifically to the termini. These transposable elements are not responsible for distinguishing telomeric ends in Drosophila from broken chromosome ends; the structure performing this function is not yet known. Proximal to the terminal array of transposable elements are regions of tandem repeats that are structurally, and probably functionally, analogous to the subterminal regions in other eukaryotes.

Transposition of the LINE-like retrotransposon TART to Drosophila chromosome termini

TART, a telomere-associated DNA element from Drosophila, is shown in this paper to have structural homology to LINE (long interspersed element)-like retrotransposons and to transpose to broken chromosome ends. TART DNA was detected by in situ hybridization in 7 of 10 independent additions of DNA to a chromosome end. We found evidence that a TART element had transposed to the chromosome end in each of two additions that were examined in detail. From the DNA sequence of a TART element that recently transposed, we infer that TART encodes two proteins having significant sequence similarity to the putative proteins of many LINEs. These results support the hypothesis that TART elements preferentially retrotranspose to the termini of chromosomes as part of the essential process by which Drosophila telomeres are maintained.

DPhK-gamma, a putative Drosophila kinase with homology to vertebrate phosphorylase kinase gamma subunits: molecular characterisation of the gene and phenotypic analysis of loss of function mutants

Partial and total loss of function mutant alleles of a putative Drosophila homologue (DPhK-gamma) of the vertebrate phosphorylase kinase gamma-subunit gene have been isolated. DPhK-gamma is required in early embryonic processes, such as gastrulation and mesoderm formation; however, defects in these processes are seen only when both the maternal and zygotic components of DPhK-gamma expression are eliminated. Loss of zygotic expression alone does not appear to affect normal embryonic and larval development; some pupal lethality is observed but the majority of mutant animals eclose as adults. Many of these adults show defects in their leg musculature (e.g. missing and degenerating muscles), in addition to exhibiting melanised "tumours" on their leg joints. Loss of only the maternal component has no obvious phenotypic consequences. The DPhK-gamma gene has been cloned and sequenced. It has an open reading frame (ORF) of 1680 bp encoding a 560 amino acid protein. The predicted amino acid sequence of DPhK-gamma has two conserved domains, the catalytic kinase and calmodulin-binding domains, separated by a linker sequence. The amino acid sequence of DPhK-gamma is homologous to that of mammalian PhK-gamma proteins but differs in the length and amino acid composition of its linker sequence. The expression of DPhK-gamma mRNA is developmentally regulated. We discuss the implications of these observations.

White gene expression, repressive chromatin domains and homeotic gene regulation in Drosophila

The use of Drosophila chromosomal rearrangements and transposon constructs involving the white gene reveals the existence of repressive chromatin domains that can spread over considerable genomic distances. One such type of domain is found in heterochromatin and is responsible for classical position-effect variegation. Another type of repressive domain is established, beginning at specific sequences, by complexes of Polycomb Group proteins. Such complexes, which normally regulate the expression of many genes, including the homeotic loci, are responsible for silencing, white gene variegation, pairing-dependent effects and insertional targeting.

Internal tracts of telomeric DNA act as silencers in Saccharomyces cerevisiae

Telomeric position effect (TPE) refers to the ability of telomeres to repress the transcription of genes in their vicinity. Internal stretches of C1-3A DNA, the sequence found at Saccharomyces telomeres, also repressed transcription of nearby genes. This repression, hereafter called C1-3A-based silencing, was observed at several chromosomal loci, including on a circular chromosome. The magnitude of C1-3A-based silencing was increased by both proximity to a telomere and increased length of the C1-3A tracts. C1-3A-based silencing was affected by many of the same genes and conditions that influence TPE and acted in an orientation-independent manner. Thus, in yeast, an expanded array of a simple repetitive DNA, C1-3A, is sufficient to promote the assembly of a transcriptionally silent chromosomal domain.

A rosy future for heterochromatin

The demonstration by Zhang and Spradling (1) of efficient P element transposition into heterochromatic regions will aid ongoing studies of heterochromatin structure and function. P element insertions will provide entry points for further molecular analysis of heterochromatin and will allow the isolation of small and large heterochromatic deficiencies. The generation of heterochromatic P insertions also will aid the study of heterochromatic genes. Of the heterochromatic insertions isolated by Zhang and Spradling, five were homozygous lethal, and one of these defined a lethal locus not previously uncovered by heterochromatic deficiencies. P elements have previously been used to mutagenize and clone specific heterochromatic genes (14, 19, 26). New methods, like those described here (1, 32), should allow the efficient identification and molecular isolation of other single-copy heterochromatic genes. Furthermore, since position-effect suppression allowed the recovery of heterochromatic P insertions, it may also allow the recovery of insertions in euchromatic regions previously refractory to P mutagenesis. Studies of position-effect variegation show that genes normally found in heterochromatin require a heterochromatic context for normal expression and that heterochromatin is inhibitory to euchromatic gene expression (16). The physical basis of these related phenomena--chromatin assembly, nuclear positioning, and/or heterochromatin elimination--can be resolved only with a more thorough understanding of heterochromatin structure and functions. Analyzing heterochromatin also will help define the chromosomal components responsible for inheritance processes such as chromosome pairing, sister chromatid adhesion, and centromere function. These efforts will be facilitated by the effective use of P elements combined with other current molecular-genetic approaches.

Differential regulation of P and hobo mobile elements by two laboratory strains of Drosophila melanogaster

Analysis of the transposition behaviour of the P and hobo elements borne by the 31.1/CyL4 MRF (P), 23.5 delta/CyL4 MRF (hobo) and 23.5*/Cy MRF (hobo) strains in the progeny of dysgenic crosses with two ME laboratory strains (Berlin-k and dp b cn bw) at 25 degrees C revealed that: (a) the two ME laboratory strains affect differently the transposition rates of P and hobo elements. More precisely, P element transposition is higher in heterozygotes with dp b cn bw than in those with Berlin-k. In contrast, the transposition rate of hobo elements is higher in Berlin-k than in dp b cn bw heterozygotes. (b) Like P, hobo has the potential to transpose at high frequencies and to nonhomologous chromosomes. (c) The dysgenically inactive hobo elements of the 31.1 MRF strain transpose more frequently than the dysgenically active hobo elements of the 23.5 MRF strains in certain crosses. (d) There are insertion hot spots for P and hobo elements. For the P elements there are enough data to suggest that the insertion hot spots are different in the two EM strains. The data are discussed on the basis of the involvement of putative host factors in transposition regulation of the P and hobo elements.

Position effect variegation at fission yeast centromeres

Chromatin structure at Schizosaccharomyces pombe centromeres is unusual. The insertion of the ura4 gene within these centromeres resulted in genetically identical cells mosaic for its expression. Placement of the ade6 gene within cen1 or cen3 resulted in red-white sectored colonies, demonstrating the instability of gene expression. The occurrence of pink colonies implied that intermediate levels of repression were established. Repression of both genes within centromeres was temperature sensitive. The chromatin structure of the ura4 gene at centromeres was altered, suggesting that the unusual chromatin encroaches into the gene and inhibits normal expression. These repressive effects at S. pombe centromeres resemble the classical phenomenon of position effect variegation imposed by Drosophila heterochromatin on nearby genes. However, since the epigenetic states can be set at intermediate levels of expression, a purely euchromatin-heterochromatin dichotomy does not apply. A model for the epigenetic regulation of genes placed within S. pombe centromeres is presented.

The basic-helix-loop-helix domain of Drosophila lethal of scute protein is sufficient for proneural function and activates neurogenic genes

The development of most epidermal sensory organs in Drosophila is controlled by achaete and scute, two of the genes of the achaete-scute complex (AS-C). The genes of the AS-C encode members of the basic-helix-loop-helix (bHLH) class of transcriptional regulators, and their activity defines proneural cell clusters in the imaginal discs from which sensory organ mother cells are singled out by a process of lateral inhibition. Ectopic expression of lethal of scute, another member of the AS-C, normally dispensable for sensory organ development in the adult, promotes this process independently of the activity of the other AS-C genes. This demonstrates a high degree of functional redundancy of the products of the AS-C. Furthermore, neurogenic genes are activated in ectopic proneural clusters, allowing development of epidermal progenitor cells. Finally, the bHLH domain is necessary and sufficient to mediate the proneural function, to activate neurogenic genes, and to allow lateral inhibition.

Isolation of silencer-containing sequences causing a tissue-specific position effect on alcohol dehydrogenase expression in Drosophila melanogaster

A transient expression assay has been used to investigate the cause of a tissue-specific position effect on Adh expression from a transgene insertion in Drosophila. A 15.4-kb genomic clone containing the 3.2-kb Adh insert along with flanking regions of genomic DNA is expressed in this assay in a tissue-specific pattern resembling the abnormal expression pattern of the position effect. The 3.2-kb Adh insert is expressed normally without the flanking sequences. A silencer element is located upstream of the Adh gene within a 2-kb fragment that acts in both orientations and at a distance of at least 6.5 kb from the larval Adh promoter to suppress ADH expression in a nontissue specific fashion. The DNA sequence of the 2-kb fragment indicates that it is a noncoding region. A 17-bp sequence is repeated within this region and may be associated with the silencer activity, since subclones from the 2-kb fragment, each containing one of the repeated regions, both retain full silencer activity. This silencer fails to suppress expression from an alpha 1-tubulin promoter-LacZ fusion construct or an hsp70 promoter-Adh fusion construct. In addition to the silencer, another element is located downstream of the Adh gene that produces a higher level of anterior than posterior midgut expression. These results suggest that the 5' silencer and the 3' element act together to create the tissue specific position effect characteristic of the GC-1 line.

A 5' element of the chicken beta-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila

We have characterized an element near the 5' boundary of the chicken beta-globin domain that insulates a reporter gene from the activating effects of a nearby beta-globin locus control region (5'HS2) when assayed in the human erythroid cell line K562. We show that the insulation mechanism is directional, that it operates at the level of transcription, and that it involves the alteration of chromatin structure over the promoter of the gene. The insulator has no significant stimulatory or inhibitory effects of its own. In transgenic Drosophila, the insulator protects the white minigene from position effects. The action of the insulator thus is not restricted to erythroid or mammalian cells, suggesting that such elements may serve an important and widely distributed function in the organization of chromatin structure.

The Drosophila bendless gene encodes a neural protein related to ubiquitin-conjugating enzymes

The bendless (ben) mutation of Drosophila alters synaptic connectivity between a subset of CNS neurons. Here, we show that ben also causes morphological abnormalities within the visual system, suggesting that ben functions in a number of different developmental processes. We show that the ben gene encodes a protein which is closely related to ubiquitin-conjugating enzymes and that a missense mutation in the highly conserved active site region is associated with the ben mutation. High levels of ben expression are restricted to the nervous system during development. These results suggest a role for ubiquitin-mediated protein modification in nervous system development, including, but not exclusive to, the regulation of synaptic connectivity.

polyhomeotic regulatory sequences induce developmental regulator-dependent variegation and targeted P-element insertions in Drosophila

Variegation of the miniwhite gene is observed in a euchromatic context in transformant lines that contain a P transposon including regulatory sequences of the polyhomeotic (ph) gene upstream of the resident miniwhite gene (P[ph]). This variegated phenotype is not affected by most of the genetic modifiers of heterochromatic position-effect variegation (PEV) nor by removal of the Y chromosome. Interestingly, it is sensitive to ph and Polycomb (Pc) mutations, which are known to affect homeotic gene regulation. Regulatory DNA of ph can also mediate transvection of the miniwhite gene. This transvection is abolished in a ph but not in a zeste mutant background. In addition, P[ph] inserts preferentially in sites corresponding to PH/PC protein-binding sites as defined at the polytene chromosome level. These insertions induce an unusually high proportion of mutations in genes affecting homeotic gene regulation. In particular, one insertion is located within the tramtrack locus, which is thought to regulate fushi tarazu, an Ultrabithorax activator. We suggest that a multimeric complex containing PH and PC proteins, at a minimum, causes a local and clonally inherited heterochromatinization, which maintains the repressed state of transcription of the homeotic genes.

A non-flight muscle isoform of Drosophila tropomyosin rescues an indirect flight muscle tropomyosin mutant

The tropomyosin I(TmI) gene of Drosophila melanogaster encodes two isoforms of tropomyosin. The Ifm-TmI isoform is expressed only in indirect flight and jump muscles; the Scm-TmI isoform is found in other muscles of the larva and adult. The level of Ifm-TmI is severely reduced in the flightless mutant Ifm(3)3, which also is unable to jump. To explore the functional significance of tropomyosin isoform diversity in Drosophila, we have used P element-mediated transformation to express Scm-TmI in the indirect flight and jump muscles of Ifm(3)3 flies. Transformants gained the ability to jump and fly. The mechanical properties of isolated indirect flight muscle myofibres, and the ultrastructure of indirect flight and jump muscles from the transformants were comparable to wildtype. Thus, the Scm-TmI isoform can successfully substitute for Ifm-TmI in the indirect flight and jump muscles of the Ifm(3)3 strain.

Molecular organization and embryonic expression of the hedgehog gene involved in cell-cell communication in segmental patterning of Drosophila

hedgehog is a segment polarity gene necessary to maintain the proper organization of each segment of the Drosophila embryo. We have identified the physical location of a number of rearrangement breakpoints associated with hedgehog mutations. The corresponding hh RNA is expressed in a series of segmental stripes starting at cellular blastoderm in the posterior portion of each segment. This RNA is localized predominantly within nuclei until stage 10, when the localization becomes primarily cytoplasmic. Expression of hh RNA in the posterior compartment is independent of most other segment polarity genes, including en, until the late extended germ-band stage (stage 11). Sequence analysis of the hedgehog locus suggests the protein product is a transmembrane protein, which may, therefore, be directly involved in cell-cell communication.

Tissue-specific position effects on alcohol dehydrogenase expression in Drosophila melanogaster

Twenty transformed lines have been isolated as a result of the germ line insertion of a 3.2 kb alcohol dehydrogenase (Adh) gene fragment into an Adh negative strain of Drosophila melanogaster by P element-mediated transformation. More than half of these lines exhibited abnormal ADH expression. The level of ADH expression ranges from zero in some lines to near normal levels in others, and the pattern of ADH expression in the larval gut is also abnormal in many of these lines. Each of the abnormal tissue-specific patterns is stable and characterized by the absence or reduction of ADH expression in certain tissues. High levels of ectopic expression were not observed. In two of these lines, the pattern of ADH staining is highly restricted: it is limited to the medial midgut in line MM-50, and to the gastric caecae and the proventriculus in line GC-1. In heterozygotes between these two lines ADH is expressed in both of these tissues. To test the hypothesis that this abnormal expression is due to position effects, inserts were mobilized to new locations. The mobilized inserts exhibited new patterns of tissue-specific expression associated with new cytological insert locations, showing that the abnormal expression in lines MM-50 and GC-1 is due to tissue-specific position effects and not to mutations. The results are discussed in the context of chromatin structure as a possible cause of these position effects.

Transposable DNA elements and life history traits. I. Transposition of P DNA elements in somatic cells reduces the lifespan of Drosophila melanogaster

As an initial study of the influence of transposable DNA elements on life history traits, and as a model system for estimating the impact of somatic genetic damage on longevity, the effect of P DNA element movement in somatic cells on adult lifespan was measured in Drosophila melanogaster males. Lifespan was significantly reduced in males that contained the somatically active P[ry+ delta 2-3](99B) element and 17, 4, 3, but not just a single P element. Furthermore, there appears to be a direct correlation between the number of transposing P elements and the amount of lifespan reduction. This reduction in lifespan observed in males with somatically active P elements is probably due to genetic damage in embryos, larvae and pupae from P-element excisions and insertions, leading to changes in gene structure and regulation, chromosome breakage, and subsequent cell death in adults. This hypothesis is supported in this study by a significant increase in recessive sex-linked lethal mutations in the same males that had reduced lifespans and by the previous observation of chromosome breakage in somatic cells of similar males. The evolutionary implications of these results are discussed, including the possible influence of somatic DNA transpositions on fitness and other life history traits.

Telomeric position effect in yeast

Telomeres are the physical ends of chromosomes. In yeast, when a gene is placed near a telomere, its transcription is repressed. Genes under the influence of this telomeric position effects switch between a repressed state and a transcriptionally active state, each of which is stable for many cell generations. Telomeric position effect may provide a model system for the study of heritable gene regulation in other, more complex organisms.

Modifiers of position effect are shared between telomeric and silent mating-type loci in S. cerevisiae

Genes placed near telomeres in S. cerevisiae succumb to position-effect variegation. SIR2, SIR3, SIR4, NAT1, ARD1, and HHF2 (histone H4) were identified as modifiers of the position effect at telomeres, since transcriptional repression near telomeres was no longer observed when any of the modifier genes were mutated. These genes, in addition to SIR1, have previously been shown to repress transcription at the silent mating loci, HML and HMR. However, there were differences between transcriptional silencing at telomeres and the HM loci, as demonstrated by suppressor analysis and the lack of involvement of SIR1 in telomeric silencing. These findings provide insights into telomeric structure and function that are likely to apply to many eukaryotes. In addition, the distinctions between telomeres and the HM loci suggest a hierarchy of chromosomal silencing in S. cerevisiae.

A position-effect assay for boundaries of higher order chromosomal domains

Eukaryotic chromosomes are thought to be organized into a series of discrete higher order chromatin domains. This organization is believed to be important not only in the compaction of the chromatin fiber, but also in the utilization of genetic information. Each domain would define an independent unit of gene activity, insulated from the regulatory influences of adjacent domains. Critical to this model of chromosome organization and function are the domain boundaries: the special nucleoprotein structures that delimit each higher order domain and segregate the chromosome into units of independent gene activity. In the work reported here we have tested whether two putative domain boundaries, scs and scs', from the Drosophila 87A7 heat shock locus can establish a domain of independent gene activity in vivo and insulate against chromosomal position effects.

Segmentally restricted, cephalic expression of a leucine zipper gene during Drosophila embryogenesis

The expression pattern and DNA sequence of a newly identified gene, CNC (cap'n'collar), suggest a role for this gene in cephalic patterning during Drosophila embryogenesis. In situ hybridization reveals transcripts localized to the mandibular segment and the hypopharyngeal and labral primordia first detectable in late blastoderm stages. Sequence analysis of cDNA clones from the CNC locus shows the CNC gene product to be related to transcription factors of the leucine zipper (bZIP) class. Based on its protein sequence, we propose that CNC is a subunit of a heterodimeric regulatory protein involved in the control of head morphogenesis.

Position effect at S. cerevisiae telomeres: reversible repression of Pol II transcription

S. cerevisiae chromosomes end with the telomeric repeat (TG1-3)n. When any of four Pol II genes was placed immediately adjacent to the telomeric repeats, expression of the gene was reversibly repressed as demonstrated by phenotype and mRNA analyses. For example, cells bearing a telomere-linked copy of ADE2 produced predominantly red colonies (a phenotype characteristic of ade2- cells) containing white sectors (characteristic of ADE2+ cells). Repression was due to proximity to the telomere itself since an 81 bp tract of (TG1-3)n positioned downstream of URA3 when URA3 was approximately 20 kb from the end of chromosome VII did not alter expression of the gene. However, this internal tract of (TG1-3)n could spontaneously become telomeric, in which case expression of the URA3 gene was repressed. These data demonstrate that yeast telomeres exert a position effect on the transcription of nearby genes, an effect that is under epigenetic control.

Genetic analysis of the enhancer of zeste locus and its role in gene regulation in Drosophila melanogaster

The Enhancer of zeste [E(z)] locus of Drosophila melanogaster is implicated in multiple examples of gene regulation during development. First identified as dominant gain-of-function modifiers of the zeste1-white (z-w) interaction, mutant E(z) alleles also produce homeotic transformations. Reduction of E(z)+ activity leads to both suppression of the z-w interaction and ectopic expression of segment identity genes of the Antennapedia and bithorax gene complexes. This latter effect defines E(z) as a member of the Polycomb-group of genes. Analysis of E(z)S2, a temperature-sensitive E(z) allele, reveals that both maternally and zygotically produced E(z)+ activity is required to correctly regulate the segment identity genes during embryonic and imaginal development. As has been shown for other Polycomb-group genes, E(z)+ is required not to initiate the pattern of these genes, but rather to maintain their repressed state. We propose that the E(z) loss-of-function eye color and homeotic phenotypes may both be due to gene derepression, and that the E(z)+ product may be a general repressing factor required for both examples of negative gene regulation.

Proposed genetic basis of Huntington's disease

I propose that Huntington's disease (HD) is caused by dominant position-effect variegation, a phenomenon for which new information is available in Drosophila melanogaster. The essential features of this proposal are that (1) the HD mutation is the result of a chromosome alteration that inactivates transcription of a nearby structural gene or genes (cis-inactivation); the combination of this proposed chromosome alteration and the structural gene(s) is termed the HD allele; (2) there is pairing in some somatic cells between the HD and HD+ alleles on homologous chromosomes; (3) as a result of this somatic pairing, the HD mutation also inactivates transcription of the HD+ structural gene on the normal homologue (trans-inactivation), resulting in complete dominance of the mutation; (4) polymorphism for an X-linked recessive modifier of position-effect variegation means that the age of onset of symptoms of HD will depend on which parent the HD mutation was inherited from. The fully dominant nature of HD and the parental-source effect on the age of onset are thus both understandable within the genetic and epigenetic paradigm of position-effect variegation.

Cytotype control of Drosophila P element transposition: the 66 kd protein is a repressor of transposase activity

Drosophila P transposable elements encode two proteins, an 87 kd transposase protein and a 66 kd protein that has been hypothesized to repress transposition. We have made germline transformants carrying modified P element derivatives that encode only the 66 kd protein and shown that these elements repress transposase activity in both the germline and the soma. The position of these elements in the genome quantitatively affected their ability to negatively regulate transposase and to express the 66 kd protein. Single 66 kd element-containing strains did not exhibit the maternal inheritance of P cytotype characteristic of P strains. However, we demonstrated that a true P strain produced higher levels of the 66 kd protein during oogenesis than single 66 kd P elements. Thus, the expression of the 66 kd repressor during oogenesis may be a major determinant of the maternal effect of P cytotype.

Overproduction and translational regulation of rp49 ribosomal protein mRNA in transgenic Drosophila carrying extra copies of the gene

During Drosophila early development the translation of ribosomal protein mRNAs is regulated specifically and coordinately. In this study we assayed for changes of ribosomal protein rp49 gene expression in flies transformed with extra copies of the gene. RNA blot analysis revealed that the rp49 transcript was overrepresented in most of the transformed fly lines: flies carrying three times more genes than the wild type contained up to seven times more mRNA. The abundance of other ribosomal protein mRNAs was not affected. Despite the large differences in rp49 mRNA content, the proportion of the rp49 mRNA which was associated with polysomes during oogenesis and early embryogenesis did not differ significantly from the wild type, implying that rp49 protein is overproduced in the transgenic flies. The results indicate that the basis for coordinate r-protein gene expression lies in the intrinsic properties of r-protein genes, rather than in a dynamic system that separately modulates the expression of individual genes.

Analysis of cis-acting requirements of the Rh3 and Rh4 genes reveals a bipartite organization to rhodopsin promoters in Drosophila melanogaster

The rhodopsin genes of Drosophila melanogaster are expressed in nonoverlapping subsets of photoreceptor cells within the insect visual system. Two of these genes, Rh3 and Rh4, are known to display complementary expression patterns in the UV-sensitive R7 photoreceptor cell population of the compound eye. In addition, we find that Rh3 is expressed in a small group of paired R7 and R8 photoreceptor cells at the dorsal eye margin that are apparently specialized for the detection of polarized light. In this paper we present a detailed characterization of the cis-acting requirements of both Rh3 and Rh4. Promoter deletion series demonstrate that small regulatory regions (less than 300 bp) of both R7 opsin genes contain DNA sequences sufficient to generate their respective expression patterns. Individual cis-acting elements were further identified by oligonucleotide-directed mutagenesis guided by interspecific sequence comparisons. Our results suggest that the Drosophila rhodopsin genes share a simple bipartite promoter structure, whereby the proximal region constitutes a functionally equivalent promoter "core" and the distal region determines cell-type specificity. The expression patterns of several hybrid rhodopsin promoters, in which all or part of the putative core regions have been replaced with the analogous regions of different rhodopsin promoters, provide additional evidence in support of this model.

cis-regulatory elements of the Drosophila blastoderm-specific serendipity alpha gene: ectopic activation in the embryonic PNS promoted by the deletion of an upstream region

The Drosophila serendipity alpha gene (sry alpha) is specifically expressed at the blastoderm stage in all somatic cells. By deletion analysis of sry alpha-lacZ fusion genes, the sry alpha cis-acting regulatory elements have been restricted to the [-311, +130] 5'-region of the gene and separated in two domains. The [-118, +130] domain is sufficient for transcriptional activation at the blastoderm stage. The [-311, -118] domain is required for a full level of expression. Deletion of this upstream domain leads to a secondary pattern of lacZ expression in precursor cells of the peripheral nervous system (PNS). The sry alpha gene is not itself secondarily expressed in the PNS, as shown by in situ hybridization. The patterns of expression of the different sry alpha-lacZ fusion genes suggest a combinatorial mode of regulation of sry alpha expression at blastoderm.

Viable deletions of a telomere from a Drosophila chromosome

Destabilization of a P element transposon inserted in the subtelomeric region induced a set of similar chromosomal rearrangements. These rearrangements appear to be terminal deletions with endpoints clustered at the centromere-distal end of the transposon. The terminally deleted chromosome progressively loses sequences from the broken end at a rate of approximately 50-100 bp per fly generation, suggesting that the replication of this end may be incomplete. In most cases, capping of the broken end by readdition of new sequences was not observed. Past failures to recover terminal deletions of Drosophila chromosomes following X-ray mutagenesis may have been due to a cell cycle arrest in response to unrepaired DNA damage rather than to an absolute requirement for the telomere.

The glass gene encodes a zinc-finger protein required by Drosophila photoreceptor cells

Null mutations of glass specifically remove photoreceptor cells, leaving other cell types intact. We have isolated the glass gene and have shown that its transcript encodes a putative protein of 604 amino acids with five zinc-fingers. The glass product may be a transcription factor required for the development of a single neuronal cell type.

Analysis of the cis-acting requirements for germ-line-specific splicing of the P-element ORF2-ORF3 intron

P-element transposition is limited to the germ line because the element's third intron is only spliced in germ line cells. We show that a 240-bp fragment containing this 190-bp intron can confer germ line specificity when placed in the context of another gene. We find that the cis-acting regulatory sequences required for germ line regulation map near to, but not at, the 5' or 3' splice junctions.

Molecular hypotheses for position-effect variegation: anti-sense transcription and promoter occlusion

There is currently no comprehensive molecular hypothesis to account for position-effect variegation, the mosaic expression of a gene lying near a breakpoint of a chromosomal rearrangement. Here it is proposed that position-effect variegation arises from either anti-sense transcription or from promoter occlusion (transcription readthrough), the former mechanism operating for breakpoints on the 3' side of the affected gene and the latter for breakpoints on the 5' side. Anti-sense transcription will occur in rearrangements that place the anti-sense strand of genes next to a promoter. This anti-sense RNA hybridizes to, and thereby inactivates, sense mRNA transcripts (as anti-sense RNA is known to do). Promoter occlusion may occur in rearrangements that place the affected gene near an open upstream promoter. This promoter drives readthrough transcription that inhibits most normal transcripts. Occasional normal transcripts lead to phenotypic variegation. These hypotheses have three strengths: (i) they predict the major observed features of position-effect variegation including variegated phenotype, stable inheritance, the involvement of rearrangements, only some rearrangements causing variegation, the occurrence of both dominant and recessive variegation, the spreading effect of variegation to several loci, and the conditions required for expression of variegation; (ii) they can plausibly account for features of position-effect variegation that they do not specifically predict; (iii) they lead to a series of novel and testable predictions, including the presence of altered transcripts in rearrangements including position-effect variegation, the location of breakpoints required to cause variegation, and a correlation between the extent of the spreading effect and the length of the novel transcript. These mechanisms can account for several other cases of variegation in addition to classic position-effect variegation. Actual or putative examples of phenotypic variegation due to these mechanisms are known.

The proboscipedia locus of the Antennapedia complex: a molecular and genetic analysis

The homeotic proboscipedia (pb) locus of the Antennapedia Complex (ANT-C) directs the differentiation of adult labial and maxillary structures. Loss-of-function pb alleles show a transformation of adult mouth parts to legs and affect maxillary palp morphology. We have identified the pb transcription unit by inducing and analyzing a series of pb null chromosomal breakpoints. In addition, we describe a variegating pb phenotype associated with two rearrangement breakpoints. Having identified the pb locus, we describe the expression of its RNA and protein products. Unlike the other homeotic genes of the ANT-C, pb has no obvious role in embryonic development. Nevertheless, pb protein is detected during embryogenesis in nuclei of the labial and maxillary lobes and in part of the mandibular segment. In this respect, pb expression parallels the early segment-specific expression of neighboring, embryonically essential homeotic genes. Accumulation of pb protein is also detected in mesodermal cells and in a unique subset of nuclei throughout the central nervous system. We also describe a transcription unit very close to pb, which is expressed dorsally during embryogenesis in a pattern resembling that of the nearby zygotic lethal zerknüllt (zen) locus. This transcription unit has been shown to contain a homeo box and has been designated z2. Surprisingly, we find that individuals deleted for both the pb and z2 transcription units survive to adulthood and produce normal larval cuticular structures. Thus, pb and z2 show similarities to neighboring ANT-C genes in their expression patterns, yet these similarities are not manifested in comparable loss-of-function embryonic phenotypes.