Chromosomal organization of Drosophila tumours

Replication timing in Drosophila and its peculiarities in polytene chromosomes

Drosophila melanogaster is one of the popular model organisms in DNA replication studies. Since the 1960s, DNA replication of polytene chromosomes has been extensively studied by cytological methods. In the recent two decades, the progress in our understanding of DNA replication was associated with new techniques. Use of fluorescent dyes increased the resolution of cytological methods significantly. High-throughput methods allowed analysis of DNA replication on a genome scale, as well as its correlation with chromatin structure and gene activi ty. Precise mapping of the cytological structures of polytene chromosomes to the genome assembly allowed comparison of replication between polytene chromosomes and chromosomes of diploid cells. New features of replication characteristic for D. melanogaster were described for both diploid and polytene chromosomes. Comparison of genomic replication profiles revealed a significant similarity between Drosophila and other well-studi ed eukaryotic species, such as human. Early replication is often confined to intensely transcribed gene-dense regions characterized by multiple replication initiation sites. Features of DNA replication in Drosophila might be explained by a compact genome. The organization of replication in polytene chromosomes has much in common with the organization of replication in chromosomes in diploid cells. The most important feature of replication in polytene chromosomes is its low rate and the dependence of S-phase duration on many factors: external and internal, local and global. The speed of replication forks in D. melanogaster polytene chromosomes is affected by SUUR and Rif1 proteins. It is not known yet how universal the mechanisms associated with these factors are, but their study is very promising.

Banding Pattern of Polytene Chromosomes as a Representation of Universal Principles of Chromatin Organization into Topological Domains

Drosophila polytene chromosomes are widely used as a model of eukaryotic interphase chromosomes. The most noticeable feature of polytene chromosome is transverse banding associated with alternation of dense stripes (dark or black bands) and light diffuse areas that encompass alternating less compact gray bands and interbands visible with an electron microscope. In recent years, several approaches have been developed to predict location of morphological structures of polytene chromosomes based on the distribution of proteins on the molecular map of Drosophila genome. Comparison of these structures with the results of analysis of the three-dimensional chromatin organization by the Hi-C method indicates that the morphology of polytene chromosomes represents direct visualization of the interphase nucleus spatial organization into topological domains. Compact black bands correspond to the extended topological domains of inactive chromatin, while interbands are the barriers between the adjacent domains. Here, we discuss the prospects of using polytene chromosomes to study mechanisms of spatial organization of interphase chromosomes, as well as their dynamics and evolution.

DNA replication in nurse cell polytene chromosomes of Drosophila melanogaster otu mutants

Drosophila cell lines are used extensively to study replication timing, yet data about DNA replication in larval and adult tissues are extremely limited. To address this gap, we traced DNA replication in polytene chromosomes from nurse cells of Drosophila melanogaster otu mutants using bromodeoxyuridine incorporation. Importantly, nurse cells are of female germline origin, unlike the classical larval salivary glands, that are somatic. In contrast to salivary gland polytene chromosomes, where replication begins simultaneously across all puffs and interbands, replication in nurse cells is first observed at several specific chromosomal regions. For instance, in the chromosome 2L, these include the regions 31B-E and 37E and proximal parts of 34B and 35B, with the rest of the decondensed chromosomal regions joining replication process a little later. We observed that replication timing of pericentric heterochromatin in nurse cells was shifted from late S phase to early and mid stages. Curiously, chromosome 4 may represent a special domain of the genome, as it replicates on its own schedule which is uncoupled from the rest of the chromosomes. Finally, we report that SUUR protein, an established marker of late replication in salivary gland polytene chromosomes, does not always colocalize with late-replicating regions in nurse cells.

Paucity and preferential suppression of transgenes in late replication domains of the D. melanogaster genome

Background

Eukaryotic genomes are organized in extended domains with distinct features intimately linking genome structure, replication pattern and chromatin state. Recently we identified a set of long late replicating euchromatic regions that are underreplicated in salivary gland polytene chromosomes of D. melanogaster.

Results

Here we demonstrate that these underreplicated regions (URs) have a low density of P-element and piggyBac insertions compared to the genome average or neighboring regions. In contrast, Minos-based transposons show no paucity in URs but have a strong bias to testis-specific genes. We estimated the suppression level in 2,852 stocks carrying a single P-element by analysis of eye color determined by the mini-white marker gene and demonstrate that the proportion of suppressed transgenes in URs is more than three times higher than in the flanking regions or the genomic average. The suppressed transgenes reside in intergenic, genic or promoter regions of the annotated genes. We speculate that the low insertion frequency of P-elements and piggyBacs in URs partially results from suppression of transgenes that potentially could prevent identification of transgenes due to complete suppression of the marker gene. In a similar manner, the proportion of suppressed transgenes is higher in loci replicating late or very late in Kc cells and these loci have a lower density of P-elements and piggyBac insertions. In transgenes with two marker genes suppression of mini-white gene in eye coincides with suppression of yellow gene in bristles.

Conclusions

Our results suggest that the late replication domains have a high inactivation potential apparently linked to the silenced or closed chromatin state in these regions, and that such inactivation potential is largely maintained in different tissues.

Localization and characteristics of DNA underreplication zone in the 75C region of intercalary heterochromatin in Drosophila melanogaster polytene chromosomes

In Drosophila polytene chromosomes, regions of intercalary heterochromatin are scattered throughout the euchromatic arms. Here, we present data on the first fine analysis of the individual intercalary heterochromatin region, 75C1-2, located in the 3L chromosome. By using electron microscopy, we demonstrated that this region appears as three closely adjacent condensed bands. Mapping of the region on the physical map by means of the chromosomal rearrangements with known breakpoints showed that the length of the region is about 445 kb. Although it seems that the SUUR protein binds to the whole 75C1-2 region, the proximal part of the region is fully polytenized, so the DNA underreplication zone is asymmetric and located in the distal half of the region. Finally, we speculate that intercalary heterochromatin regions of Drosophila polytene chromosomes are organized into three different types with respect to the localization of the underreplication zone.

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.

The SuUR gene influences the distribution of heterochromatic proteins HP1 and SU(VAR)3–9 on nurse cell polytene chromosomes of Drosophila melanogaster

We have investigated the distribution of three heterochromatic proteins [SUppressor of UnderReplication (SUUR), heterochromatin protein 1 (HP1), and SU(VAR)3-9] in chromosomes of nurse cells (NCs) and have compared the data obtained with the distribution of the same proteins in salivary gland (SG) chromosomes. In NC chromosomes, the SU(VAR)3-9 protein was found in pericentric heterochromatin and at 223 sites on euchromatic arms, while in SG chromosomes, it was mainly restricted to the chromocenter. In NC chromosomes, the HP1 and SUUR proteins bind to 331 and 256 sites, respectively, which are almost twice the number of sites in SG chromosomes. The distribution of the HP1 and SU(VAR)3-9 proteins depends on the SuUR gene. A mutation in this gene results in a dramatic decrease in the amount of SU(VAR)3-9 binding sites in autosomes. In the X chromosome, these sites are relocated in comparison to the SuUR (+), and their total number only varies slightly. HP1 binding sites are redistributed in chromosomes of SuUR mutants, and their overall number did not change as considerably as SU(VAR)3-9. These data together point to an interaction of these three proteins in Drosophila NC chromosomes.

Polytene chromosomes show normal gene activity but some mRNAs are abnormally accumulated in the pseudonurse cell nuclei of Drosophila melanogaster otu mutants

Certain mutant alleles of the ovarian tumor (otu) locus give rise to polytene chromosomes in the pseudonurse cells (PNCs). We have previously shown that the banding pattern of these germ line-derived chromosomes is similar to that in the larval salivary gland chromosomes. In this study, we have examined the gene activity of these chromosomes. General gene expression from these chromosomes was studied by uridine autoradiography. The expression of specific genes was monitored by in situ hybridisation to mRNA and also by combining enhancer trap lines with otu mutants. We found that most of the genes studied were expressed in the PNCs as they were in the wild-type nurse cells. Four out of the 12 mRNAs studied accumulated in the nuclei instead of migrating to the cytoplasm. The intensity of accumulation directly correlated with the extent of polytenisation in the PNC nuclei. We suggest that the otu mRNA remains partly attached to the polytene chromosome template after transcription and discuss the effects of this phenomenon on polytenisation of the PNC chromosomes.

Genome reorganization from polyteny to polyploidy in the nurse cells found in onion fly (Delia antiqua) and cabbage root fly (Delia radicum) ovaries (Diptera, Anthomyiidae)

The material required to ensure successful embryogenesis in the onion fly (Delia antiqua) and the cabbage root fly (Delia radicum) (Diptera, Anthomyiidae) is supplied by 15 nurse cells, while the oocyte chromosomes enter a quiescent stage during prophase I of meiosis. This level of transcription is achieved by the polyploidization of the nurse cell DNA. Elongate polytene chromosomes form in both species, but lack the banding and conspicuous puffing commonly seen in other dipteran tissues. The polytene chromosomes contract until they finally appear as small, densely staining spheres. These fragment into large numbers of endochromosomes that are much smaller than their mitotic counterparts, which then despiralize, resulting in the flocculate appearance of the nurse cell nucleus. Photodensitometry revealed a gradient of DNA values between nurse cells near the oocytes and those further away. Final DNA values 1000 times the haploid level were recorded in the nurse cell nearest to the oocyte compared with 336 times the C-value in the most distal cell. At lower temperatures (< 10 degrees C), the polytene chromosomes become banded and longer. None of the onion flies kept in these conditions produced viable eggs, though there was some reproductive success among the cabbage root flies.

General characteristics of the polytene chromosome from ovarian pseudonurse cells of the Drosophila melanogaster otu11 and fs(2)B mutants

Polytene chromosomes of good cytological quality from pseudonurse cells (PNCs) of fs(2)B and otu11 mutants were obtained, photomaps for otu11 mutants were constructed and the general characteristics of polytene chromosomes from salivary glands (SGs) and PNCs were compared. Three conditions were found to improve the cytological quality of PNC chromosomes: temperature below 18 degrees C, a protein-rich medium and presence of the Y-chromosome. Detailed comparison of the chromosome banding pattern from SGs and PNCs has shown only minor differences between them. The frequency of asynapsis appeared to be 10 times higher for PNC chromosomes. Despite previous reports, features such as breaks and ectopic contacts turned out to be also typical for PNC chromosomes, but with remarkably lower frequencies.

Polytene chromosomes from ovarian pseudonurse cells of the Drosophila melanogaster otu mutant. II. Photographic map of the X chromosome

The banding pattern of the polytene chromosomes of the ovarian pseudonurse cells (PNC) of the Drosophila melanogaster otu mutant were compared with larval salivary gland (SG) polytene chromosomes. The X chromosome was studied and no significant differences were found in the banding pattern between these functionally very different tissues. Most of the differences result from differential puffing activity. In situ hybridisation with five different DNA probes located along the X chromosome was used to cross-check the results obtained by morphological mapping. The constrictions present in the SG chromosomes were found to be absent in the germ line derived PNC chromosomes. There are prominent puffs in the PNC chromosomes at certain locations where genes known to be transcriptionally active in the germ line reside. This suggests that at least some of the genes active in the wild-type nurse cells may also be active in the PNC cells.

Polytene chromosomes from ovarian pseudonurse cells of the Drosophila melanogaster otu mutant. I. Photographic map of chromosome 3

Certain mutant alleles of the otu locus in Drosophila melanogaster produce abnormal nurse cells in the ovaries. These cells are called pseudonurse cells (PNC), since they generate polytene chromosomes instead of endopolyploid ones and do not normally have an oocyte to nurse. The banding pattern of polytene chromosome 3 from the salivary glands (SG) and from PNCs of homozygous otu1 females was compared and a detailed photomap of PNC chromosomes with different degrees of polyteny is presented. The banding pattern was found to be strikingly similiar in the two tissues. The puffing pattern of the PNC chromosomes is discussed. No constrictions or breaks were found in the PNC chromosomes which seems to indicate that these sites, which are known to be underreplicated in the SG chromosomes, are equally replicated along with the rest of the chromosomes in the PNC nuclei.

Mitotic chromosome organization of neuroblastomas induced by the recessive oncogene Lethal(2)giant larvae4 of Drosophila melanogaster

Mitotic chromosomes in neuroblastomas of Drosophila melanogaster homozygous for the recessive oncogene Lethal(2)giant larvae4 were studied at different larval ages. There was a progressive increase in mitotically active cells with increasing period of tumorous growth. The karyotype of the neuroblastomas generally remained stable. The metaphase chromosomes of the neuroblastomas, however, showed widely varying levels of condensation ranging from highly condensed to highly extended. Staining with the AT-specific fluorescent dye Hoechst 33258 showed extensive resolution of AT-rich heterochromatic blocks in the third and Y chromosomes suggesting their lack of coalescence in the extended metaphases of neuroblastomas. Our results suggest aberrant condensation as a major chromosomal lesion in Drosophila neuroblastomas.