The unusual structure of heat shock locus 2-48B in Drosophila hydei

From Heterochromatin to Long Noncoding RNAs in Drosophila: Expanding the Arena of Gene Function and Regulation

Recent years have witnessed a remarkable interest in exploring the significance of pervasive noncoding transcripts in diverse eukaryotes. Classical cytogenetic studies using the Drosophila model system unraveled the perplexing attributes and "functions" of the "gene"-poor heterochromatin. Recent molecular studies in the fly model are likewise revealing the very diverse and significant roles played by long noncoding RNAs (lncRNAs) in development, gene regulation, chromatin organization, cell and nuclear architecture, etc. There has been a rapid increase in the number of identified lncRNAs, although a much larger number still remains unknown. The diversity of modes of actions and functions of the limited number of Drosophila lncRNAs, which have been examined, already reflects the profound roles of such RNAs in generating and sustaining the biological complexities of eukaryotes. Several of the known Drosophila lncRNAs originate as independent sense or antisense transcripts from promoter or intergenic, intronic, or 5'/3'-UTR regions, while many of them are independent genes that produce only lncRNAs or coding as well as noncoding RNAs. The different lncRNAs affect chromatin organization (local or large-scale pan-chromosomal), transcription, RNA processing/stability, or translation either directly through interaction with their target DNA sequences or indirectly by acting as intermediary molecules for specific regulatory proteins or may act as decoys/sinks, or storage sites for specific proteins or groups of proteins, or may provide a structural framework for the assembly of substructures in nucleus/cytoplasm. It is interesting that many of the "functions" alluded to heterochromatin in earlier cytogenetic studies appear to find correlates with the known subtle as well as far-reaching actions of the different small and long noncoding RNAs. Further studies exploiting the very rich and powerful genetic and molecular resources available for the Drosophila model are expected to unravel the mystery underlying the long reach of ncRNAs.

Unusual Drosophila virilis stress-puff at 20CD: cytological localization of a heat sensitive locus and some peculiarities of the heat shock response

Using a series of chromosome aberrations a heat shock (hs) inducible site of the Drosophila virilis heat shock puff 20CD has been cytologically localized in the distal 20C subdivision: the hs puff was not observable in chromosome 2 carrying the Df(2)ebTG-52 deficiency; the bands in the proximal 20D subdivision could not autonomously be activated by hs in aberrant chromosomes that have this deficiency or the In(2)ebPC-19 inversion. An electron microscopy (EM) analysis of the successive stages of puff development in the 20CD and 20F regions shows that the 20CD puff is intially formed from the right part of the 20C6-7 band. In the maximally developed puff, the neighboring bands of the 20C and 20D regions are only partially decondensed; they are seen as discrete compact chromatin clumps. Specific differences in the ultrastructural organization and in response to hs have been found between the D. virilis "unusual" 20CD and typical 20F hs puffs.

Low occurrence of gene transposition events during the evolution of the genus Drosophila

The role played by gene transpositions during the evolution of eukaryotic genomes is still poorly understood and indeed has been analyzed in detail only in nematodes. In Drosophila, a limited number of transpositions have been detected by comparing the chromosomal location of genes between different species. The relative importance of gene transposition versus other types of chromosomal rearrangements, for example, inversions, has not yet been evaluated. Here, we use physical mapping to perform an extensive search for long-distance gene transpositions and assess their impact during the evolution of the Drosophila genome. We compare the relative order of 297 molecular markers that cover 60% of the euchromatic fraction of the genome between two related Drosophila species and conclude that the frequency of gene transpositions is very low, namely one order of magnitude lower than that of nematodes. In addition, gene transpositions seem to be events almost exclusively associated with genes of repetitive nature such as the Histone gene complex (HIS-C).

How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila

During the evolution of the genus Drosophila, the molecular organization of the major chromosomal elements has been repeatedly rearranged via the fixation of paracentric inversions. Little detailed information is available, however, on the extent and effect of these changes at the molecular level. In principle, a full description of the rate and pattern of change could reveal the limits, if any, to which the eukaryotic genome can accommodate reorganizations. We have constructed a high-density physical map of the largest chromosomal element in Drosophila repleta (chromosome 2) and compared the order and distances between the markers with those on the homologous chromosomal element (3R) in Drosophila melanogaster. The two species belong to different subgenera (Drosophila and Sophophora, respectively), which diverged 40-62 million years (Myr) ago and represent, thus, the farthest lineages within the Drosophila genus. The comparison reveals extensive reshuffling of gene order from centromere to telomere. Using a maximum likelihood method, we estimate that 114 +/- 14 paracentric inversions have been fixed in this chromosomal element since the divergence of the two species, that is, 0.9-1.4 inversions fixed per Myr. Comparison with available rates of chromosomal evolution, taking into account genome size, indicates that the Drosophila genome shows the highest rate found so far in any eukaryote. Twenty-one small segments (23-599 kb) comprising at least two independent (nonoverlapping) markers appear to be conserved between D. melanogaster and D. repleta. These results are consistent with the random breakage model and do not provide significant evidence of functional constraint of any kind. They support the notion that the Drosophila genome is extraordinarily malleable and has a modular organization. The high rate of chromosomal change also suggests a very limited transferability of the positional information from the Drosophila genome to other insects.

Chromosomal homology and molecular organization of Muller's elements D and E in the Drosophila repleta species group

Thirty-three DNA clones containing protein-coding genes have been used for in situ hybridization to the polytene chromosomes of two Drosophila repleta group species, D. repleta and D. buzzatii. Twenty-six clones gave positive results allowing the precise localization of 26 genes and the tentative identification of another nine. The results were fully consistent with the currently accepted chromosomal homologies and in no case was evidence for reciprocal translocations or pericentric inversions found. Most of the genes mapped to chromosomes 2 and 4 that are homologous, respectively, to chromosome arms 3R and 3L of D. melanogaster (Muller's elements E and D). The comparison of the molecular organization of-these two elements between D. melanogaster and D. repleta (two species that belong to different subgenera and diverged some 62 million years ago) showed an extensive reorganization via paracentric inversions. Using a maximum likelihood procedure, we estimated that 130 paracentric inversions have become fixed in element E after the divergence of the two lineages. Therefore, the evolution rate for element E is approximately one inversion per million years. This value is comparable to previous estimates of the rate of evolution of chromosome X and yields an estimate of 4.5 inversions per million years for the whole Drosophila genome.

The 93D (hsr-omega) locus of Drosophila: non-coding gene with house-keeping functions

The 93D, or hsr-omega (heat-shock RNA-omega), locus of Drosophila melanogaster and other species of Drosophila, besides being induced as a member of the heat shock gene family, is also selectively and singularly inducible by a variety of agents, notably benzamide, colchicine and vitamin B6 (in species other than D. melanogaster). The genomic structure of this locus is highly conserved in all species, although the primary base sequence has diverged rapidly between species. Three transcripts (two nuclear and one cytoplasmic) are produced by this locus but none of them has any significant protein coding capacity. The profile of the three transcripts varies in a developmental and inducer-specific manner. This locus is developmentally active in nearly all cell types and is essential for viability of flies. Its induction during heat shock is independent of the other members of the heat shock gene family. The other selective inducers act on this locus through separate response elements. hsr-omega activity has a characteristic effect on transcription/turnover of the heat shock induced hsp70 and the alpha-beta transcripts in D. melanogaster. It appears that the hsr-omega locus has important house-keeping functions in transport and turnover of some transcripts and in monitoring the 'health' of the translational machinery of the cell.

Multiple inducers of the Drosophila heat shock locus 93D (hsr omega): inducer-specific patterns of the three transcripts

The Drosophila hsr omega locus produces one of the largest and most active heat shock puffs, yet it does not encode a heat shock protein. Instead, this locus produces a distinctive set of three transcripts, all from the same start site. The largest transcript, omega 1, is limited to the nucleus and appears to have a role there. A second nuclear transcript, omega 2, is produced by alternative termination and contains the sequence found in the 5' 20-25% of omega 1 (depending on the Drosophila species). The cytoplasmic transcript, omega 3, is produced by removal of a 700-bp intron from omega 2. All three hsr omega RNAs are produced constitutively and production is enhanced by heat shock. In addition to being a member of the set of heat shock puffs, the hsr omega puff is induced by agents that do not affect other heat shock loci, suggesting that hsr omega is more sensitive to environmental changes than other loci. We report here that agents that induce puffing of hsr omega loci in polytene nuclei also lead to an increase in hsr omega transcripts in diploid cells. We also show that the relative levels of omega 1 and omega 3 can be modulated independently by several agents. All drugs that inhibit translation, either initiation or elongation, stabilize the omega 3 transcript, which normally turns over within minutes in control cells. Drugs (such as benzamide and colchicine) that induce puffing of hsr omega, but not other heat shock loci, lead to large increases in omega 1. Although the constitutive level of omega 1 is relatively stable, the drug-induced excess is lost rapidly when the drug is withdrawn. The relative levels of hsr omega transcripts may reflect different states in cellular metabolism.

Heat shock loci 93D of Drosophila melanogaster and 48B of Drosophila hydei exhibit a common structural and transcriptional pattern

A comparison of gene structure, sequence, and transcription pattern of heat shock loci 93D of Drosophila melanogaster and 48B of Drosophila hydei has been performed. Both heat shock loci consist of an unique region that is flanked by an internally repetitive element. Different members of these elements are highly conserved, repeat unit length, however, and primary sequence diverged totally. Whereas the overall gene structure in both species is substantially related, sequence conservation is only observed at very few sites in the unique region. These represent primarily sequences that are identified as regulatory elements for faithful transcription and processing. The number and size of transcripts obtained from heat shock locus 48B in third instar larvae closely resembles the pattern of heat shock locus 93D. Thus their quite alike structure and transcription pattern suggest strongly a conserved hitherto unknown function.

Heat shock locus 93D of Drosophila melanogaster: a spliced RNA most strongly conserved in the intron sequence

The Drosophila melanogaster heat shock locus at 93D encodes at least three overlapping transcripts, 10-12 kilobases (kb), 1.9 kb, and 1.2 kb. The abundance of the three transcripts is significantly increased during heat shock; however, all are also found in non-heat-shocked cells. The 1.2-kb transcript is found in the cytoplasm. Sequence analysis of a 1.1-kb cDNA clone representing sequences within the 1.2-kb transcript and comparison to genomic sequences indicate that it is spliced; 700 base pairs of sequence found in genomic DNA are removed from the middle of the transcript. Sequence analysis further suggests that this RNA does not encode a heat shock protein. The largest open reading frame beginning with a methionine codon would encode a polypeptide of 34 amino acids. We have not been able to detect a heat shock-induced polypeptide of this size. A DNA clone from the analogous heat shock puff of Drosophila hydei has been analyzed by hybridization with the small subclones used to sequence the D. melanogaster cDNA plus a genomic fragment containing the 700-base-pair intron. Results of this hybridization indicated strong homology of the intron fragment. Weaker homology was detected with the two small fragments flanking the intron. Other fragments of the D. melanogaster cDNA showed no hybridization to the cloned D. hydei puff DNA.

Two major RNA products are transcribed from heat-shock locus 93D of Drosophila melanogaster

The heat-shock locus 93D from Drosophila melanogaster has recently become available for a molecular analysis. We established a restriction site map of a recombinant DNA clone covering the major part of heat-shock locus 93D. This clone includes part of a repetitive Taq I region and neighbouring unique sequences. The portion of the Taq I repeat analysed consists of tandemly arranged sequence blocks of about 280 base pairs (bp) in length. Using genomic and cDNA as hybridization probes we examined the transcription of 93D in 2- to 4-day-old flies. We identified two major RNA classes enhanced after heat shock, namely nonpolyadenylated transcripts of heterogeneous length derived from the repetitive region and one discrete polyadenylated transcript in spliced and unspliced form from the neighbouring unique region. The occurrence of a highly heterogeneous poly(A)- transcript and high levels of an unspliced discrete poly(A)+ species suggests unusual mechanisms of transcription regulation in the 93D region.