Intercalary heterochromatin in Drosophila

Sites of intercalary heterochromatin (IH) in the complete set of Drosophila melanogaster polytene chromosomes were localized and studied according to the following criteria: tendency to break (weak points), ectopic pairing and late replication, the existence of repeats (in X and 2R) including those enriched with A-T bases. Correlation between these features investigated, the highest correlation coefficients found between weak point behavior, late replication, and ectopic pairing. The frequency of breaks in weak points in some IH bands was shown to be different in different tissues, strains and closely related Drosophila species. Sexual differences in morphology and manifestation of IH features were found in bands of the X chromosome: weak point behavior and participation in ectopic pairing of IH bands are an order of magnitude less frequent in male X chromosomes than in female X chromosomes. In autosomes such differences have not been observed. IH bands in male X chromosomes look more massive than the homologous ones in female X chromosomes: the DNA content of the 11A6-9 region is four times less in females than in males. The hypothesis is proposed that the specific features of intercalary heterochromatin bands are determined by tandem repetitiveness and late replication. The latter, if it occurs in a cluster of repetitions, could cause incomplete polytenization of the region and, as a consequence, breaks (or weak points) and the appearance of adhesive ends which may take part either in realization of ectopic contacts or in fixation of those occurring previously. Breaks caused by chromosome aberrations in regions with repeats may not result in a sharp decline of viability, so that break points of chromosome rearrangements in intercalary heterochromatin may be more frequent than in other regions.     

Intercalary heterochromatin in Drosophila

The relative amount of DNA in defined segments of salivary gland chromosomes of Drosophila melangogaster from the Oregon R stock was determined by autoradiography. The data obtained were then used to estimate the possible correlation between DNA content and the degree of manifestation of charcters such as weak-point behavior, late replication, strong synapsis, breaks of chromosome rearrangements, hybridization with cRNA, and localization of mobile elements. Of 380 regions investigated 274 have showed deviations in the degree of manifestation of these features from that predicted on the basis of the DNA content of these regions. Regions, previously shown to consist of intercalary heterochromatin (IH, Zhimulev et al. 1982), were found to have a significantly higher frequency of the simultaneous manifestation of several of the above-mentioned features, with the exception of localization of mobile elements. These findings support the earlier suggestion that a high frequency and a simultaneous manifestation of IH features depend on some peculiarities of the molecular organization of IH regions, but not on a high DNA content.     

Intercalary heterochromatin in Drosophila melanogaster polytene chromosomes and the problem of genetic silencing

The morphological characteristics of intercalary heterochromatin (IH) are compared with those of other types of silenced chromatin in the Drosophila melanogaster genome: pericentric heterochromatin (PH) and regions subject to position effect variegation (PEV). We conclude that IH regions in polytene chromosomes are binding sites of silencing complexes such as PcG complexes and of SuUR protein. Binding of these proteins results in the appearance of condensed chromatin and late replication of DNA, which in turn may result in DNA underreplication. IH and PH as well as regions subject to PEV have in common the condensed chromatin appearance, the localization of specific proteins, late replication, underreplication in polytene chromosomes, and ectopic pairing.     

Intercalary heterochromatin in polytene chromosomes of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>

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.     

Characterization of Drosophila heterochromatin

A number of preliminary experiments have shown that the fluorescence pattern of Hoechst 33258, as opposed to that of quinacrine, varies with the concentration of dye. The metaphase chromosomes of D. melanogaster, D. simulans, D. virilis, D. texana, D. hydei and D. ezoana have therefore been stained with two concentrations of H 33258 (0.05 and 0.5 mug/ml in phosphate buffer at pH 7) and with a single concentration of quinacrine (0.5% in absolute alcohol). The three fluorescence patterns so obtained were shown to be somewhat different in some of the species and the coincide in others. All three stainings gave an excellent longitudinal differentiation of heterochromatin while euchromatin fluoresced homogeneously. Living ganglion cells of the six species mentioned above were treated with quinacrine and H 33258. Quinacrine induced a generalized lengthening and swelling of the chromosomes and H 33258 the decondensation of specific heterochromatic regions. A correlation of the base composition of the satellite DNAs contained in the heterochromatin of the species studied with the relative fluorescence and decondensation patterns showed that: 1) the extremely fluorochrome bright areas and those decondensed are present only in species containing AT rich satellite DNA; 2) the opposite is not true since some AT-rich satellite DNAs are neither fluorochrome bright nor decondensed; 3) there is no good correspondence between Hoechst bright areas and the decondensed ones. AT richness therefore appears to be a necessary but not sufficient condition both for bright fluorescence and decondensation. Some cytological evidence suggests that similarly AT rich satellite DNAs respond differently in fluorescence and decondensation because they are bound to different chromosomal proteins. A combination of the results of fluorescence and decondensation revealed at least 14 types of heterochromatin; 4-7 of which are simultaneously present in the same species. Since closely related species (i.e. D. melanogaster and D. simulans; D. virilis and D. texana) show marked differences in the heterochromatic types they contain, it can be suggested that within the genus Drosophila qualitative variations of heterochromatin have played an important role in speciation.     

Characterization of Drosophila heterochromatin

The C- and N-banding patterns of D. melanogaster, D. simulans, D. virilis, D. texana, D. ezoana and D. hydei were studied in comparison with quinacrine and Hoechst banding patterns. In all these Drosophila species the C bands correspond to the heterochromatin as revealed by the positive heteropycnosis in the prometaphase chromosomes. The N bands have the following characteristics: 1) they are always localized on the heterochromatin and generally do not correspond to the C bands; 2) they do not correspond to the nucleolar organizing regions; 3) they are inversely correlated with fluorescence, i.e., they correspond to regions which are scarcely, if at all, fluorescent after Hoechst 33258 or quinacrine staining; 4) they are localized both on regions containing AT rich satellite DNA and on those containing GC rich satellite DNA.     

Interstrain heterochromatin polymorphisms in Drosophila melanogaster

Neuroblast chromosomes of 16 Drosophila melanogaster laboratory stocks (15 wild type and 1 carrying the mutant vermilion) were carefully analyzed for Q-banding patterns and morphological characteristics, in all the mitotic phases. Two forms of intraspecific heterochromatin variations, involving three types of chromosomes, are described: 1) differences in the fluorescence pattern with regard to the Y chromosome and the centromeric heterochromatin of the pair II; 2) differences in the size of the heterochromatic segment of the X chromosome. An unambigous evidence of such variants was obtained by comparing homologous chromosomes in the F1 hybrids, as well as in the F2 offspring, where differences in appearance of the heteromorphic chromosomes was readily identified as to the parental origin. The possible evolutionary significance and the usefulness of such cytologically detectable genetic differences between various strains, are considered.This paper is dedicated to Prof. Claudio Barigozzi with gratitude for his guidance and the long collaboration     

Constitutive heterochromatin and transposable elements in Drosophila melanogaster

Several families of transposable elements (TEs), most of them belonging to the retrotransposon catagory, are particularly enriched in Drosophila melanogaster constitutive heterochromatin. The enrichment of TE-homologous sequences into heterochromatin is not a peculiar feature of the Drosophila genome, but appears to be widespread among higher eukaryotes. The constitutive heterochromatin of D. melanogaster contains several genetically active domains; this raises the possibility that TE-homologous sequences inserted into functional heterochromatin compartments may be expressed. In this review, I present available data on the genetic and molecular organization of D. melanogaster constitutive heterochromatin and its relationship with transposable elements. The implications of these findings on the possible impact of heterochromatic TEs on the function and evolution of the host genome are also discussed. This revised version was published online in August 2006 with corrections to the Cover Date.     

Further evidence of intraspecific heterochromatin variants in Drosophila melanogaster

The analysis of inter-strain heterochromatin polymorphism in mitotic chromosomes of Drosophila melanogaster was extended to some stocks characterized by chromosomal mutations. In particular, the present investigation aims to compare, in the same cell, the quinacrine banding of two different Y chromosomes of male hybrids derived from crosses using special stocks. A direct comparison of homologous heteromorphic chromosomes in F₁ hybrids provided additional evidence of differences in the fluorescence pattern of the Y chromosome, as well as in the length of the heterochromatin segment of the X chromosome.     

Characterization of heterochromatin in the B chromosomes of Drosophila nasuta albomicana

The number of B chromosomes in the Chiangmai strain of Drosophila nasuta albomicana varies from one to eight. They are C-band and Ag-As positive, but G-band negative. The implications of these findings are discussed.     

The Drosophila genome

The past year has been a spectacular one for Drosophila research. The sequencing and annotation of the Drosophila melanogaster genome has allowed a comprehensive analysis of the first three eukaryotes to be sequenced-yeast, worm and fly-including an analysis of the fly's influences as a model for the study of human disease. This year has also seen the initiation of a full-length cDNA sequencing project and the first analysis of Drosophila development using high-density DNA microarrays containing several thousand Drosophila genes. For the first time homologous recombination has been demonstrated in flies and targeted gene disruptions may not be far off.     

Euchromatin and pericentromeric heterochromatin: comparative composition in the tomato genome

Eleven sequenced BACs were annotated and localized via FISH to tomato pachytene chromosomes providing the first global insights into the compositional differences of euchromatin and pericentromeric heterochromatin in this model dicot species. The results indicate that tomato euchromatin has a gene density (6.7 kb/gene) similar to that of Arabidopsis and rice. Thus, while the euchromatin comprises only 25% of the tomato nuclear DNA, it is sufficient to account for approximately 90% of the estimated 38,000 nontransposon genes that compose the tomato genome. Moreover, euchromatic BACs were largely devoid of transposons or other repetitive elements. In contrast, BACs assigned to the pericentromeric heterochromatin had a gene density 10-100 times lower than that of the euchromatin and are heavily populated by retrotransposons preferential to the heterochromatin-the most abundant transposons belonging to the Jinling Ty3/gypsy-like retrotransposon family. Jinling elements are highly methylated and rarely transcribed. Nonetheless, they have spread throughout the pericentromeric heterochromatin in tomato and wild tomato species fairly recently-well after tomato diverged from potato and other related solanaceous species. The implications of these findings on evolution and on sequencing the genomes of tomato and other solanaceous species are discussed.     

Neurobiology and the Drosophila genome

The sequencing and annotation of the euchromatin of the Drosophila melanogaster genome provides an important foundation that allows neurobiologists to work back from the complete gene set of neuronal proteins to an eventual understanding of how they function to produce cognition and behavior. Here we provide a brief survey of some of the key insights that have emerged from analyzing the complete gene set in Drosophila. Not surprisingly, both the Caenorhabditis elegans and Drosophila genomes contain a conserved repertoire of neuronal signaling proteins that are also present in mammals. This includes a large number of neuronal cell adhesion receptors, synapse-organizing proteins, ion channels and neurotransmitter receptors, and synaptic vesicle-trafficking proteins. In addition, there are a significant number of fly homologs of human neurological disease loci, suggesting that Drosophila is likely to be an important disease model for human neuropathology in the near future. The experimental analysis of the Drosophila neuronal gene set will provide important insights into how the nervous system functions at the cellular level, allowing the field to integrate this information into the framework of ultimately understanding how neuronal ensembles mediate cognition and behavior. Electronic Publication