Heterochromatization as a change of chromosome cycle

Cellular mechanism for targeting heterochromatin formation in Drosophila

Near the end of their 1990 historical perspective article "60 Years of Mystery," Spradling and Karpen (1990) observe: "Recent progress in understanding variegation at the molecular level has encouraged some workers to conclude that the heterochromatization model is essentially correct and that position-effect variegation can now join the mainstream of molecular biology." In the 18 years since those words were written, heterochromatin and its associated position effects have indeed joined the mainstream of molecular biology. Here, we review the findings that led to our current understanding of heterochromatin formation in Drosophila and the mechanistic insights into heterochromatin structural and functional properties gained through molecular genetics and cytology.

Intercalary heterochromatin in polytene chromosomes of Drosophila melanogaster

Intercalary heterochromatin consists of extended chromosomal domains which are interspersed throughout the euchromatin and contain silent genetic material. These domains comprise either clusters of functionally unrelated genes or tandem gene duplications and possibly stretches of noncoding sequences. Strong repression of genetic activity means that intercalary heterochromatin displays properties that are normally attributable to classic pericentric heterochromatin: high compaction, late replication and underreplication in polytene chromosomes, and the presence of heterochromatin-specific proteins. Late replication and underreplication occurs when the suppressor of underreplication protein is present in intercalary heterochromatic regions. Intercalary heterochromatin underreplication in polytene chromosomes results in free double-stranded ends of DNA molecules; ligation of these free ends is the most likely mechanism for ectopic pairing between intercalary heterochromatic and pericentric heterochromatic regions. No support has been found for the view that the frequency of chromosome aberrations is elevated in intercalary heterochromatin.

Histone modification and the control of heterochromatic gene silencing in Drosophila

Covalent modifications of histones index structurally and functionally distinct chromatin domains in eukaryotic nuclei. Drosophila with its polytene chromosomes and developed genetics allows detailed cytological as well as functional analysis of epigenetic histone modifications involved in the control of gene expression pattern during development. All H3K9 mono- and dimethylation together with all H3K27 methylation states and H4K20 trimethylation are predominant marks of pericentric heterochromatin. In euchromatin, bands and interbands are differentially indexed. H3K4 and H3K36 methylation together with H3S10 phosphorylation are predominant marks of interband regions whereas in bands different H3K27 and H4K20 methylation states are combined with acetylation of H3K9 and H3K14. Genetic dissection of heterochromatic gene silencing in position-effect variegation (PEV) by Su(var) and E(var) mutations allowed identification and functional analysis of key factors controlling the formation of heterochromatin. SU(VAR)3-9 association with heterochromatic sequences followed by H3K9 methylation initiates the establishment of repressive SU(VAR)3-9/HP1/SU(VAR)3-7 protein complexes. Differential enzymatic activities of novel point mutants demonstrate that the silencing potential of SU(VAR)3-9 is mainly determined by the kinetic properties of the HMTase reaction. In Su(var)3-9ptn a significantly enhanced enzymatic activity results in H3K9 hypermethylation, enhanced gene silencing and extensive chromatin compaction. Mutations in factors controlling active histone modification marks revealed the dynamic balance between euchromatin and heterochromatin. Further analysis and definition of Su(var) and E(var) genes in Drosophila will increase our understanding of the molecular hierarchy of processes controlling higher-order structures in chromatin.

Varied expression of a Y-linked P[w+] insert due to imprinting in Drosophila melanogaster

During gametogenesis, a gene can become imprinted affecting its expression in progeny. We have used the expression of a Y-linked P[w+]YAL transposable DNA element as a reporter system to investigate the effect of parental origination on the expression of the w+ insert. Expression of w+ was greater in male progeny when the Y chromosome, harboring the insert, was inherited from the parental male rather than from the parental female. Imprinting was not due to a genetic background influence in the males, since the only difference among the males was the parental origin of the Y chromosome. It was also observed that the genetic background can affect imprinting, since w+ expression was also higher in males when the Y was derived from C(1)DX attached-X parental females rather than from C(1)RM attached-X parental females. Though the heterochromatic imprinting mechanism is unknown, a mutated Heterochromatin Protein 1 (HP1) gene, which is associated with suppression of position-effect variegation, increases expression of the w+ locus in the P[w+]YAL insert, indicating that HP1 may play a role in Y chromosome packaging.

Genomic imprinting and position-effect variegation in Drosophila melanogaster

Genomic imprinting is a phenomenon in which the expression of a gene or chromosomal region depends on the sex of the individual transmitting it. The term imprinting was first coined to describe parent-specific chromosome behavior in the dipteran insect Sciara and has since been described in many organisms, including other insects, plants, fish, and mammals. In this article we describe a mini-X chromosome in Drosophila melanogaster that shows genomic imprinting of at least three closely linked genes. The imprinting of these genes is observed as mosaic silencing when the genes are transmitted by the male parent, in contrast to essentially wild-type expression when the same genes are maternally transmitted. We show that the imprint is due to the sex of the parent rather than to a conventional maternal effect, differential mitotic instability of the mini-X chromosome, or an allele-specific effect. Finally, we have examined the effects of classical modifiers of position-effect variegation on the maintenance and the establishment of the imprint. Factors that modify position-effect variegation alter the somatic expression but not the establishment of the imprint. This suggests that chromatin structure is important in maintenance of the imprint, but a separate mechanism may be responsible for its initiation.

Position effect variegation and chromatin proteins

Variegated phenotypes often result from chromosomal rearrangements that place euchromatic genes next to heterochromatin. In such rearrangements, the condensed structure of heterochromatin can spread into euchromatic regions, which then assume the morphology of heterochromatin and become transcriptionally inactive. In position-effect variegation (PEV) therefore, gene inactivation results from a change in chromatin structure. PEV has been intensively investigated in the fruitfly Drosophila, where the phenomenon allows a genetic dissection of chromatin components. Consequently, many genes have been identified which, when mutated, act as dominant modifiers (suppressors or enhancers) of PEV. Data available already demonstrate that genetic, molecular and developmental analysis of these genes provides an avenue to the identification of regulatory and structural chromatin components, and hence to fundamental aspects of chromosome structure and function.

Reduced DNA polytenization of a minichromosome region undergoing position-effect variegation in Drosophila

Molecular analysis of a Drosophila minichromosome, Dp(1;f)1187, revealed a relationship between position-effect variegation and the copy number reductions of heterochromatic sequences that occur in polytene cells. Heterochromatin adjacent to a defined junction with euchromatin underpolytenized at least 60-fold. Lesser reductions were observed in euchromatic sequences up to 103 kb from the breakpoint. The copy number changes behaved in all respects like the expression of yellow, a gene located within the affected region. Both copy number and yellow expression displayed a cell-by-cell mosaic pattern of reduction, and adding a Y chromosome, a known suppressor of variegation, increased both substantially. We discuss the possibility that changes in replication alter copy number locally and also propose an alternative model of position-effect variegation based on the somatic elimination of heterochromatic sequences.

The isolation of the acid phosphatase-1 gene of Drosophila melanogaster and a chromosomal breakpoint inducing its position effect variegation

Over 120 kb of contiguous genomic DNA sequence derived from the 99C-99D region of the Drosophila melanogaster third chromosome were isolated by molecular cloning. Sequences within this region required for the expression of the lysosomal gene-enzyme system acid phosphatase-1 (Acph-1) were identified by both P element-mediated germline transformation and transient expression and lie within a single 5 kb fragment. Acph-1 is encoded by a 2.1 kb poly(A)+ RNA transcript, which is expressed throughout development. Enzyme activity peaks also correlate with increases in RNA abundance. The ca-74 deletion, which exhibits position effect variegation at the Acph-1 gene (Frisardi and MacIntyre 1984), was also partially characterized. The variegating ca-74 breakpoint is located approximately 20 kb proximal to the Acph-1 gene. Results suggest that the heterochromatin at this breakpoint comprises highly repetitive or satellite DNA.

The genetics of position-effect variegation modifying loci in Drosophila melanogaster

The dose dependent effects of position-effect variegation (PEV) modifying genes were studied in chromosome arms 2L, 2R and 3R. Four groups of PEV modifying genes can be distinguished: haplo-abnormal suppressor and enhancer loci with or without a triplo-effect. Using duplications four triplo-abnormal suppressor and four triplo-abnormal enhancer functions were localized. In two cases we proved that these functions correspond to a converse haplo-abnormal one. Altogether 43 modifier loci were identified. Most of these loci proved not to display significant triplo-effects (35). The group of haplo-abnormal loci with a triplo-effect may represent genes which play an important role in heterochromatin packaging.

The effects of two mutations connected with chromatin functions on female germ-line cells of Drosophila

We have studied the developmental effects of two dominant suppressor mutations of position-effect variegation mutations on female germ-line cells. Su-var(2)1(01), which has been shown to affect chromatin structure though altering histone deacetylation, and Su-var(3)3(03) are recessive female steriles and zygotic lethals in the presence of butyrate or an additional Y chromosome. We have analysed mosaic females with mutant germ-line and normal soma and concluded that intact functions of the Su-var(2)1 and the Su-var(3)3 genes are required for development of both the soma and the germ-line and that as indirect evidence suggest, their maternally provided products are needed for normal embryonic development. It is suggested that there is possibly a common control of chromatin structure and gene expression in the soma, female germ-line and embryonic cells of Drosophila.

Variegated expression of the Sgs-4 locus in Drosophila melanogaster

Experiments on T(1;4)wm258-21 larvae of Drosophila melanogaster are described which establish the existence of a salivary gland specific marker for position-effect variegation. The marker is a glue protein gene called Sgs-4 which is expressed during the third larval instar. Using temperature as a variegation modifier, we showed that cytological compaction for the Sgs-4 chromosomal locus is enhanced at 17 degrees C and reduced at 29 degrees C. We also found that the Sgs-4 protein and transcript from salivary glands at 17 degrees C accumulate to roughly half the levels found in salivary glands at 29 degrees C. Southern analysis suggested that the Sgs-4 locus at 17 degrees C is polytenized to roughly one-third the level at 29 degrees C. The results are discussed with respect to alternative models of variegation.

Butyrate sensitive suppressor of position-effect variegation mutations in Drosophila melanogaster

Mutations at a locus on chromosome II of D. melanogaster suppressing position-effect variegation mutations have been identified which display recessive butyrate sensitivity. Survival of homozygous mutant flies is significantly reduced on medium containing sodium n-butyrate. The butyrate sensitive suppressor mutations are further characterized by recessive female sterility and reduced survival of homozygotes. Complementation analysis showed their allelism. The locus of these mutations, Su-var (2) 1, has been localized to 40.5 +/- 0.2 and, by using interstitial duplications, to region 31CD on the cytogenetic map. Moreover, the mutant alleles of the Su-var (2) 1 locus display a lethal interaction with the heterochromatic Y chromosome. The presence or absence of a Y chromosome in males or females has a strong influence on the viability of homozygous or transheterozygous suppressor flies. All the genetic properties of Su-var (2) 1 mutants suggest strongly that this locus affects chromosome condensation.

Mutants affecting position-effect heterochromatinization in Drosophila melanogaster

The dominant suppressor Su(var)b101 and the dominant enhancer En(var)c101 were found to affect significantly white variegation in a strongly variegating line of the Wm4 chromosome (Wm4h) which has been used as standard rearrangement for a genetic dissection of position-effect variegation (Reuter and Wolff, 1981). Both mutations were also shown to affect position-effect heterochromatisation in T (1 ; 4)Wm258-21 and variegation in all the rearrangements tested (white, brown, scute and bobbed variegation). These results suggest that the genes identified encode functions essential for the manifestation of gene inactivation in position-effect rearrangements. It seems also reasonable to assume that in all the rearrangements tested identical heterochromatisation processes lead to inactivation of the genes whose phenotype is variegated.

Isolation of dominant suppressor mutations for position-effect variegation in Drosophila melanogaster

Dominant suppressor mutations for position-effect variegation have been isolated by using a strongly variegated line carrying the wm4 chromosome (wm4h) and the dominant enhancer mutant En(var)c101. The use of an effective genetic test system made it possible to isolate more than 100 strongly dominant suppressor mutations for position-effect variegation. This suggests that the phenomenon of position-effect variegation is characterised by a complex genetic basis. The significance of the isolated mutants to genetic dissection of structural and regulatory functions of the eukaryotic chromosome is discussed.

Modification of the DNA content in translocated regions of Drosophila polytene chromosomes

The DNA content of translocated polytene chromosome regions in Drosophila melanogaster is affected by heterochromatic position effect. Microdensitometric studies on wm258-21 translocation heterozygotes showd (Hartmann-Goldstein and Cowell, 1976; Cowell and Hartmann-Goldstein, 1980) that band region 3D1-E2, adjacent to the breakpoint, contained less DNA than the homologous non-translocated region whereas the neighbouring 3C1-10 region contained more DNA than its non-translocated counterpart. In the nuclei selected for measurement the translocated X chromosome was morphologically euchromatic, but both regions undergo heterochromatisation in other nuclei within the same salivary gland. To explore the relationship between changes in DNA content and heterochromatisation, the effect on DNA content of two known modifiers of heterochromatisation has now been studied. Larvae cultured at 15 degrees C, which exhibit more heterochromatisation than those grown in 25 degrees C, have the same relative DNA contents as at the higher temperature. The addition of a Y chromosome markedly reduced heterochromatisation; in XXY larvae there was no difference between the DNA contents of translocated and non-translocated 3D1-E2 regions, and in region 3C1-10 the percentage excess of DNA in the translocated homolgue was approximately double that found in XX larvae. The relationship between replication behaviour and compaction suggested by these results is discussed.

The effects of temperature on genetic instability in Aspergillus nidulans

Previous work has shown that strains of Aspergillus nidulans with a chromosome segment in duplicate (one in normal position, one translocated to another chromosome) are unstable. Deletions occur from either duplicate segment. The present work has shown that most deletions occur from the translocated duplicate segment. Furthermore, it has been found that the overall frequency of deletions from a duplication is dependent upon the temperature of growth. The overall frequency of deletions from a chromosome III duplication is greatly enhanced by low temperatures, while the overall frequency of deletions from a chromosome I duplication is markedly enhanced by high temperatures. A temperature of 39.5 degrees C appears to enhance to overall frequency of deletions from the I duplication to the greatest extent. With regard to the non-translocated duplicate I segment, an increase in temperature progressively enhances the frequency of those deletions to which it is subject to far more deletions during a particular period of growth than during any other period, and at 42 degrees C, a section of the III duplication is subject to far more deletions during a given period of growth than during any other period. Comparisons with other cases of genetic instability are made and common underlying connections are proposed.

The appearance of new structures and functions in proteins during evolution

The likelihood of a de novo generation of classes of efficient proteins through neoformation of DNA, through modification of expressed DNA, and through modification of nonexpressed DNA is examined. So is the likelihood that newly formed inefficient enzymes be turned into efficient enzymes. The conclusions are that neither gene duplicates nor dormant genes represent promising materials for a de novo generation of protein classes, that (with exceptions) such generation is unlikely to have taken place in recent evolution, that new structural genes must nearly consistently derive from preexisting structural genes, and that new functions can be evolved only on the basis of old proteins. Conditions of protein evolution in prokaryotes suggest that the saltatory formation of protein classes is as unlikely in prokaryotes as in eukaryotes. Data on the history of a few protein classes are reviewed to illustrate the preceding inferences. The analysis leads to the hypothesis that most protein classes originated before the major elements of the translation apparatus of modern cells were fully evolved. If simple sequence DNA is turned into structural genes by evolution, this process (again with exceptions) is considered to have taken place only at that very remote period. A polyphyletic origin of proteins is thought to date back to the same era. It is proposed that the development of genic multiplicity and of marked structural and functional diversity of proteins may have come about in the earliest cells primarily through the independent generation of structurally different polymerases in different protocells, followed by cell conjugation and the subsequent use by enriched cells of supernumerary types of polymerase for evolving further functions. Functional growth, as it took place at early times, is briefly discussed as well as functional change. The foundations for new functional developments in old proteins are analyzed. In considering the evolutionary recovery of lost functions, aspects of cell differentiation and gene regulation are linked with the evolutionary picture. The distinction between eurygenic and stemogenic control of gene activity is used. Next to gene deletion, cell and tissue deletion is held to be an event of general evolutionary significance, through cell and tissue origination that presumably accompanies the restoration of a lost molecular function.

On the relationship between heterochromatization and variegation in Drosophila, with special reference to temperature-sensitive periods

Using a strain ofD. melanogastercarrying an X-4 translocation, comparison between groups of individuals cultured at 14°, 19° and 25°C. showed good correlation between heterochromatization, variegation in malpighian tubules andNotch. All these phenomena are enhanced by low temperatures. Correlation was less good within each temperature group, and considerable variability was observed between individuals within the group, and between nuclei from one individual.

Experiments involving a temperature change during the embryonic period indicate that (1) heterochromatization is especially temperature-sensitive during the early embryonic period but may be increased by low temperature later, (2) larval malpighian tubules are sensitive to temperature only during the early embryonic stage, and (3)Nis influenced by temperature during early embryonic life and also during the larval period.

Our observations, in conjunction with those of other workers, could be explained as follows: exposure of individuals to low temperature at a time when a specific system is beginning to differentiate will cause the processes concerned to be blocked in some cells. At least during the early embryonic stages this appears to involve heterochromatization of the relevant locus. Once the processes are established which will lead to the formation of a character, further heterochromatization has no effect on the phenotype. Temperature may affect pupal or adult phenotype in this way or by a direct action on the metabolic processes of cells.

Further experiments showed: (1) the greatest temperature-sensitivity of all three phenomena within the first 6 hours of embryonic life; (2) striking fluctuations of the effect of temperature, especially within the early embryonic period; (3) close correspondence between all three phenomena in time of response to temperature. Some alternative interpretations are considered.