Chromatin insulators and boundaries: effects on transcription and nuclear organization

Chromatin boundaries and insulators are transcriptional regulatory elements that modulate interactions between enhancers and promoters and protect genes from silencing effects by the adjacent chromatin. Originally discovered in Drosophila, insulators have now been found in a variety of organisms, ranging from yeast to humans. They have been found interspersed with regulatory sequences in complex genes and at the boundaries between active and inactive chromatin. Insulators might modulate transcription by organizing the chromatin fiber within the nucleus through the establishment of higher-order domains of chromatin structure.

A chromatin insulator determines the nuclear localization of DNA

Chromatin insulators might regulate gene expression by controlling the subnuclear organization of DNA. We found that a DNA sequence normally located inside of the nucleus moved to the periphery when the gypsy insulator was placed within the sequence. The presence of the gypsy insulator also caused two sequences, normally found in different regions of the nucleus, to come together at a single location. Alterations in this subnuclear organization imposed by the gypsy insulator correlated with changes in gene expression that took place during the heat-shock response. These global changes in transcription were accompanied by dramatic alterations in the distribution of insulator proteins and DNA. The results suggest that the nuclear organization imposed by the gypsy insulator on the chromatin fiber is important for gene expression.

The lawc gene is a new member of the trithorax-group that affects the function of the gypsy insulator of Drosophila

Mutations in the lawc gene result in a pleiotropic phenotype that includes homeotic transformation of the arista into leg. lawc mutations enhance the phenotype of trx-G mutations and suppress the phenotype of Pc mutations. Mutations in lawc affect homeotic gene transcription, causing ectopic expression of Antennapedia in the eye-antenna imaginal disc. These results suggest that lawc is a new member of the trithorax family. The lawc gene behaves as an enhancer of position-effect variegation and interacts genetically with mod(mdg4), which is a component of the gypsy insulator. In addition, mutations in the lawc gene cause alterations in the punctated distribution of mod(mdg4) protein within the nucleus. These results suggest that the lawc protein is involved in regulating the higher-order organization of chromatin.

Polycomb and trithorax group proteins mediate the function of a chromatin insulator

Chromatin boundaries or insulator elements affect the interaction between enhancers and promoters. The gypsy insulator contains two proteins, Su(Hw) and Mod(mdg4). Both proteins colocalize on several hundred sites on polytene chromosomes and are distributed in a punctated pattern in the nuclear matrix. Mutations in mod(mdg4) have properties characteristic of a trxG gene. In addition, mutations in trxG genes enhance insulator effects on adjacent enhancers, whereas mutations in Pc have the opposite result. These alterations correlate with changes in the pattern of nuclear localization of insulator components. The results suggest a model in which PcG and TrxG proteins regulate insulator function by establishing higher order domains of chromatin organization required for the assembly of functional insulators at the nuclear matrix.

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.

Boundary and insulator elements in chromosomes

Recent progress in understanding boundary and insulator elements has concentrated on the identification of their protein components. BEAF-32 is a protein present in the scs' element of Drosophila that is also localized to most interband regions and puffs of polytene chromosomes, suggesting a role in the organization of structural chromosomal domains. The suppressor of Hairy-wing and modifier of mdg4 proteins have been characterized as components of the gypsy insulator. The latter seems to play a crucial role in conferring on the insulator its ability to unidirectionally affect enhancer function.

[Determination of a temperature-sensitive period of the new mutation lawc(P1) in Drosophila melanogaster]

Determination of the period of temperature sensitivity in the temperature-sensitive allele of the regulatory lawc(P1) mutation was performed. Homeotic transformation of arista into tarsus, frequency of leg deformation, and bristle superexpression were examined. The sensitive periods were detected using reciprocal changes of cultivation temperature from 28 to 17 degrees C and from 17 to 28 degrees C. The temperature-sensitive period (TSP) for arista transformation was shown to manifest polyphasic expression and sexual dimorphism. In females, it occurred in late third instar larvae (the first phase) and prepupae (the second stage); in males, it includes the whole period from the late third instar larva upto and including prepupa. TSP for the frequency of deformed legs was polyphasic and took place during the third larval instar (the first phase) and prepupa stage (the second one). TSP for bristle superexpression occurred during a single interval from the late third larval instar until the early prepupa stage. The products of the lawc gene are assumed to play a role both in the cell proliferation in the legs of antennal and imaginal discs and in the control of bristle expression at the final stages of Drosophila ontogeny.

A Drosophila protein that imparts directionality on a chromatin insulator is an enhancer of position-effect variegation

The suppressor of Hairy wing (su(Hw)) protein inhibits the function of transcriptional enhancers located distally from the promoter with respect to the location of su(Hw)-binding sites. This polarity is due to the ability of the su(Hw)-binding region to form a chromatin insulator. Mutations in modifier of mdg4 (mod(mdg4)) enhance the effect of su(Hw) by inhibiting the function of enhancers located on both sides of the su(Hw)-binding region. This inhibition results in a variegated expression pattern, and mutations in mod(mdg4) act as classical enhancers of position-effect variegation. The mod(mdg4) and su(Hw) proteins interact with each other. The mod(mdg4) protein controls the nature of the repressive effect of su(Hw): in the absence of mod(mdg4) protein, su(Hw) exerts a bidirectional silencing effect, whereas in the presence of mod(mdg4), the silencing effect is transformed into unidirectional repression.

[Complex instability in the system of hobo and stalker mobile element interaction in Drosophila melanogaster]

A number of mutations in different Drosophila loci resulted from the relationship between hobo and stalker mobile elements. In this investigation an insertion from the parential white mutation-waG-was cloned. And the Doc element, that is the reason of the mutation, is not moving in the observed instability system. But transpositions of the copia-like elements (e.g. mdg1, 2, 3 and copia) were shown in this system. A cases of chromosomal rearrangements and abnormal recombination in compound with transpositions of different mobile elements were found. Thus, the system of instability could be explained in terms of universal mechanism which involved both transpositions and recombinations phenomena.

Dominant effects of suppressor of Hairy-wing mutations on gypsy-induced alleles of forked and cut in Drosophila melanogaster

Mutations induced by the gypsy retrotransposon in the forked (f) and cut (ct) loci render their expression under the control of the suppressor of Hairy-wing [su(Hw)] gene. This action is usually recessive, but su(Hw) acts as a dominant on the alleles fk, ctk and ctMRpN30. Molecular analysis of the gypsy element present in fk indicates that this allele is caused by the insertion of a modified gypsy in which the region normally containing twelve copies of the octamer-like repeat that interacts with the su(Hw) product is altered. Analysis of the gypsy element responsible for the ctk and ctMRpN30 mutations also reveals a correlation between the dominant action of su(Hw) and disruption of the octamer region. We propose that these disruptions alter the affinity and interaction of su(Hw) protein with gypsy DNA, thereby sensitizing the mutant phenotype to fluctuations in su(Hw) product.

Intragenic suppression: Stalker, a retrovirus-like transposable element, can compensate for a deficiency at the cut locus of Drosophila melanogaster

A number of mutations at the cut locus were induced by non-precise excision of a silent P-element insertion which resulted in deletions at the regulatory region of the locus. Unexpectedly, a reversion of one of these mutations was found, which appears as a result of insertion of Stalker (a retrovirus-like mobile element) near the 1.3 kb deletion. Thus an insertion of a retrovirus-like mobile element can suppress the deficiency at the regulatory region of a gene.

[A new allele variant of ssa and its participation in regulating the proliferation of the stem elements of the leg and antenna imaginal disks in Drosophila melanogaster]

Using a highly mutable FM/w oc system, we have established a new allele of ssa40aSc mutation whose phenotype is identical to ssa40aNs compound described in the literature. The following features are characteristic of the ssa40aSc flies phenotype: (1) the increased number of sex comb teeth, (2) complete fusion of tarsal segments, and (3) the decreased bristle size corresponding to that of ss flies. The first two features are evidence for the impaired stem cell proliferation in the antennal and leg imaginal discs which are determined to form distal structures. This assumption was experimentally confirmed when we transplanted leg imaginal discs from III instar larvae of different age into prepupae. The observed phenomenon is probably due to the defects of the Antp and Pc translation products binding site in the ss locus.

INDUCTION OF UNSTABLE MUTATIONS IN DROSOPHILA MELANOGASTER BY THE MICROINJECTION OF ONCOGENIC VIRAL DNA INTO THE POLAR PLASM OF EMBRYOS: THE INSERTIONAL NATURE OF THE MUTATIONS

MUTATIONS INDUCED BY THE MICROINJECTION OF ADENOVIRUS SA7 DNA INTO THE POLAR PLASM OF DROSOPHILA MELANOGASTER EMBRYOS WERE SHOWN TO BE OF THE INSERTIONAL TYPE. THE INSERTED ELEMENTS RESPONSIBLE FOR THESE MUTATIONS WERE ENDOGENOUS TRANSPOSONS RATHER THAN VIRAL SEQUENCES. THUS, GENETIC INSTABILITY ACTIVATED BY ONCOVIRAL DNA RESULTED FROM THE ABILITY OF THESE DNA SEQUENCES TO INDUCE TRANSPOSITION OF MOBILE ELEMENTS IN THE RECIPIENT GENOMES.

A novel transposition system in Drosophila melanogaster depending on the Stalker mobile genetic element

Crosses between the Drosophila melanogaster y2sc1waG strain or some of its derivatives and the FM4 strain yielded insertional mutagenesis with a frequency of 10(-3)-10(-4). The system differs in several respects from the known cases of hybrid dysgenesis: (i) it does not depend on the direction of a cross; (ii) destabilization continues for a long time after initial crosses; (iii) mutations may occur at different stages of development. The mutation in the yellow locus has been cloned and found to depend on insertion into the coding region of the gene of a novel mobile genetic element designated as Stalker. The sequencing of Stalker termini reveals 405 bp direct repeats (LTRs) and a target 3 bp duplication, as well as some other sequences typical of retrovirus-like retrotransposons. The number of Stalker copies per genome and chromosomal localization vary among D. melanogaster strains. Before crosses, the location of Stalker on chromosomes is fairly stable in a particular strain but thereafter numerous changes in Stalker distribution take place. Most novel substrains are internally heterogenous which is indicative of the continuing Stalker transposition. Other mobile elements tested do not move. Possibly, only Stalker is mobilized in the system. Many known and novel mutations have been obtained. Comparison of their genetic localization with Stalker distribution suggests that the majority of them have been induced by the Stalker insertion.

Mitomycin C induces genomic rearrangements involving transposable elements in Drosophila melanogaster

Mitomycin C was injected into the abdomen of male flies of the y2 sc1 waG strain of Drosophila melanogaster. They were mated with females bearing attached-X chromosomes, and the male offspring (F1) were analysed for the appearance of mutations in the X chromosome. We observed y+ and sc+ reversions induced either by excision of mdg4 (gypsy) with retention of one long terminal repeat (LTR) or by insertion of a foreign sequence into mdg4, partial reversion of the waG mutation, waG----waGd, and unstable f mutations. The overall mutation frequency was considerably higher than in control flies of the y2 sc1 waG strain. Possible mechanisms of genomic rearrangements induced by Mitomycin C, in particular the role of homologous recombination, are discussed.

Novel genes influencing the expression of the yellow locus and mdg4 (gypsy) in Drosophila melanogaster

We used a system with a mobilized Stalker transposable element, sometimes in combination with P-M hybrid dysgenesis, in the search for new mutations interfering with the y2 mutation induced by mdg4 (gypsy) insertion into the yellow locus. A novel gene, modifier of mdg4, was detected in chromosome 3. The mutation mod(mdg4) either enhanced or suppressed phenotypic changes in different mutations induced by mdg4 insertions. Thus, mod(mdg4) seems to be involved in the control of mdg4 expression. Six other loci designated as enhancers of yellow were also detected. The e(y)n (with n from 1-6) mutations enhanced the expression of several y mutations induced by different insertions into the yellow locus. The major change is a damage of bristle and hair pigmentation which is not suppressed by su(Hw) mutations. On the other hand, e(y)n alleles do not interact with mdg4 induced mutations in other loci. All e(y)n genes are located in different regions of the X chromosome. One may speculate that e(y)n genes are involved in trans-regulation of the yellow locus and possibly of some other loci.

Mobile elements and transposition events in the cut locus of Drosophila melanogaster

We have cloned from the Oregon R strain of Drosophila melanogaster a 240 kb segment of DNA that contains the cut (ct) locus, and characterized the region for the presence of repetitive elements. Within this region at least five copies of the suffix element were detected, as well as several putatively novel mobile elements. A number of mutations obtained from the unstable ctMR2 strain and its derivatives were mapped within the cut locus. Comparison between parental and daughter strains indicates that frequently two or more independent transposition events involving the cut locus occur simultaneously within a single germ cell, thus providing a molecular basis for the transposition explosion phenomenon.

Instability in the ctMR2 strain of Drosophila melanogaster: role of P element functions and structure of revertants

Simultaneous multiple transpositions and long-term genetic instability have been described in the ctMR2 strain of Drosophila melanogaster and its derivatives. This strain originated from a cross that was dysgenic in the P-M system. While spontaneous instability declined over 2 years, instability has been reactivated by backcross to the progenitor P element bearing strain MRh12/Cy. We show here using germline transformation that active P factor alone cannot mimic the effect of this cross, suggesting that MRh12/Cy contains some other activator. In addition, we have observed that ct+ exceptional progeny arise in the F1 as well as the F2 generations. Molecular analysis of X chromosomes from some ct+ progeny indicates that phenotypic reversion of the ct mutation can arise through two unrelated mechanisms.

Mobile genetic elements in Drosophila melanogaster (recent experiments)

Recent data obtained in the authors' laboratories concerning the behaviour of mobile genetic elements of Drosophila melanogaster are reviewed. It was found that the mobile element jockey represents the typical LINE element. It is efficiently transcribed in D. melanogaster cells in flies and in culture. Transcription is initiated from the +1 nucleotide of jockey and depends on an internal promoter. This is the first case of an internal promoter being used by RNA polymerase II. Several events which take place during the transposition bursts in ctMR2 family of strains were described. Among them are the removal of mobile dispersed genetics (mdg) elements (with solo long terminal repeat (LTR) remaining at the site of excision), complete removal of an mdg element, and reinsertion of the same mdg to the same place either in the presence or in absence of solo LTR sequence. Finally, the formation of deletions was observed. A 462-bp deletion destroying the white locus can be further repaired (w+ reversion). Thus, transposition bursts include many different genetic events. A novel system of prolonged genome destabilization was described. It depends on mobilization of a new mobile element called Stalker. After certain crosses Stalker actively moves for dozens of generations giving rise to large numbers of insertion mutations. Several novel genes were detected using mobilized Stalker. They include a modifier of mdg4 and six enhancers of yellow mutations.

The nature of unstable insertion mutations and reversions in the locus cut of Drosophila melanogaster : molecular mechanism of transposition memory

The segment of the locus cut containing the mobile genetic element mdg4 (gypsy) insertions which induce unstable ct and ct mutations has been cloned. Both mutations depend on the insertion of mdg4 into the same sequence, which coincides with that in ct allele. The ct mutation differs from ct by additional insertion of a novel mobile element jockey into mdg4. Jockey is 2.8 kb long, represented by 2-100 copies per genome, very homogeneous and lacks long terminal repeats (LTRs). The excision of mdg4 takes place in stable ct reversions. On the other hand, a complete single LTR is retained in the case of unstable ct reversions characterized by a high level of reverse directed transpositions of mdg4 into the locus cut. The LTR serves as a guide for reinsertion of mdg4 itself or mdg4 with jockey into the same site of the genome. A possible mechanism of transposition memory (homologous recombination with extrachromosomal circular DNA) is discussed.

Successive transposition explosions in Drosophila melanogaster and reverse transpositions of mobile dispersed genetic elements

Transposition outbursts occur in the destabilized Drosophila melanogaster strain ct carrying a mutation in the locus cut induced by an insertion of mdg4. While the distribution of mobile genetic elements remained unchanged in the great majority of germ cells, in a few cells numerous transpositions had occurred involving mdg (copia-like), fold-back and P-elements. We used in situ hybridization to analyze the distribution of five families of mdg elements in the X-chromosome during several consequent mutational changes in D. melanogaster. Each of them was accompanied by many changes in mdg localization, all of which occurred in one and the same cell. Thus, we could observe the series consisting of up to five successive transposition explosions leading to an almost complete change in the distribution of the mdg elements tested. We also found that in the course of successive transposition explosions, mdg elements often inserted into those sub-sections of the X-chromosome where they had previously been located. This phenomenon, designated as reverse directed transposition, was studied in more detail on insertion into the locus yellow. The rate of reverse transposition of the same mdg element to the corresponding locus was 10-100 times as high as that of primary insertion. In some cases, ;the transposon shuttle' into and out of the locus was observed. The existence of ;transposition memory' partially explains the specificity of mdg localization in closely related strains as well as the co-ordinated behaviour of different mdg elements in independent transposition explosions. The evolutionary significance of transposition explosions and directed reverse transposition (transposon shuttle) is discussed.

Superunstable alleles at the cut locus in Drosophila melanogaster

This is a detailed study of the reversions of the ctMR2 allele putatively carrying á mobile element (MR-transposon) in the cut locus. Stable, unstable and superunstable revertants have been identified. Besides, a series of multiple unstable visible and lethal ct mutations derived from the ctMR2 allele have been obtained. They are shown to include supermutable alleles. The results suggest that the MR-transposon is connected with at least three functions: excision; change of orientation; and change of position within the cut locus, these functions being disturbed in different ways in different unstable ct+ and ct alleles. In some cases the mutant transitions are somehow strongly stimulated leading to superinstability, reaching the rate of 0.5.

Genetic instability at the cut locus of Drosophila melanogaster induced by the MR-h12 chromosome

Unstable mutations were generated at the cut locus by the MR-h12 factor which induces male recombination. The unstable allele ctMR2, containing the MR-transposon in the cut locus is a very powerful mutator producing a number of different viable and lethal mutations both in the cut locus and outside it. I describe several types of mutations: stable reversion to wild type, which were sometimes associated with the appearance of unstable mutations in other loci; of stable deficiencies at the cut locus (lethals); new unstable mutations at different loci with the ctMR2 allele conserved; new unstable cut alleles with a phenotype other than that of ctMR2. The possible mechanisms of these mutational events are discussed. The genetic system constructed in the present work affords an opportunity for molecular studies of the cut locus and the MR-transposon, as a sequence from the cut locus has recently been cloned (Tchurikov et al. 1981).

[Study of the maternal effect on genes coding 6-phosphogluconate dehydrogenase and glucose-6-phosphate dehydrogenase in Drosophila melanogaster]

The maternal effect of two pentose cycle enzymes, 6-phosphogluconate dehydrogenase (6PGD) and glucose-6-phosphate dehydrogenase (G6PD) was investigated using a genetical system based on the interaction of Pgd- and Zw- alleles, inactivating 6PGD and G6PD respectively. The presence of enzymes and their formation in individuals free of maternal encoding genes was studied. Maternal forms of enzymes, which can be revealed under the pupa stage, were detected. The activity of maternal 6PGD and G6PD, calculated per one individual, grows 20--30-fold since the egg stage to the III larval age even in the absence of normal Pgd and Zw genes. The immunological studies have shown that the growth of 6PGD activity is defined by an increase in the number of molecules of maternal type enzyme. A hybrid isozyme arising from integration of isozyme subunits, controlled by the maternal genes and those of embryo itself, was found. All this is evidence to the fact that the maternal effect in the 6PGD case is due to a long-life stable in mRNa, transfered along with the egg cytoplasm and translated in the course of Drosophila melanogaster development.

[Nature of mutations disrupting the formation of 6-phosphogluconate dehydrogenase in Drosophila melanogaster, and their suppression]

Molecular nature of lethal and semilethal mutations in the Pgd locus of D. melanogaster coding for 6-phosphogluconate dehydrogenase (6tpgd) was studied. All these mutations affect the structural gene of the Pgd locus: 3 semilethal mutations resulted in altered 6PGD molecules with the decreased catalytic activity; the remaining 8 lethals were "zero" alleles possessing mutant polypeptides inactive but capable to react with antisera against highly purified 6PGD. "Zero" or low activity alleles for glucose-6-phosphate dehydrogenase induced by ethyl methansulfonate were shown to be supressors for the lethal mutations in the Pgd locus. A monocistronic type of organization of the Pgd locus is suggested taking into account the biochemical mechanism of supression of the Pgd-lethals and their location in the structural gene coding for 6GPD.

Investigations on the organization of genetic loci in Drosophila melanogaster: lethal mutations affecting 6-phosphogluconate dehydrogenase and their suppression

The molecular nature of lethal and semilethal mutations in the Pgd locus of D. melanogaster coding for 6-phosphogluconate dehydrogenase (6PGD) was studied. All the 11 mutations affect the structural gene of the Pgd locus: 3 semilethal mutations resulted in altered 6PGD molecules with decreased catalytic activities; the rest 8 lethals were "null" alleles characterized by mutant polypeptides capable of reacting with antisera against highly purified 6PGD. "Null" or low activity alleles for glucose-6-phosphate dehydrogenase induced by ethyl methanesulfonate were shown to be suppressores for the lethal mutations in the Pgd locus. A monocistronic type of organization of the Pgd locus is suggested taking into account the biochemical mechanism of suppression of the Pgd-lethals and their location in the structural gene coding for 6PGD.

Fine genetic structure of the 2D3-2F5 region of the X-chromosome of Drosophila melanogaster

97 lethal and semilethal mutations were induced by ethyl methanesulfonate, nitrosomethyl urea and gamma-irradiation in the 2D3-F5 region of the X-chromosome of D. melanogaster. Approximately 1 per cent of the tested X-chromosomes carried a lethal in the 2D3-2F5 region. The mutation frequencies per band or DNA content in the region and the whole X-chromosome are equal. Complementation analysis revealed at least 10 functionally independent essential loci in this region including about 10 bands. The data presented in this study support the one band--one gene hypothesis. The Pgd locus coding for 6-phosphogluconate dehydrogenase (6PGD) is mapped in the 2D3 (OR 2D4) band. Isolation of 11 lethal or semilethal point mutations with null or reduced 6PGD activity shows that the Pgd locus is a vital one.