Cytological localization of DNA complementary to ribosomal RNA in polytene chromosomes of Diptera

Non-random chromosome segregation and chromosome eliminations in the fly Bradysia (Sciara)

Mendelian inheritance is based upon random segregation of homologous chromosomes during meiosis and perfect duplication and division of chromosomes in mitosis so that the entire genomic content is passed down to the daughter cells. The unusual chromosome mechanics of the fly Bradysia (previously called Sciara) presents many exceptions to the canonical processes. In male meiosis I, there is a monopolar spindle and non-random segregation such that all the paternal homologs move away from the single pole and are eliminated. In male meiosis II, there is a bipolar spindle and segregation of the sister chromatids except for the X dyad that undergoes non-disjunction. The daughter cell that is nullo-X degenerates, whereas the sperm has two copies of the X. Fertilization restores the diploid state, but there are three copies of the X chromosome, of which one or two of the paternally derived X chromosomes will be eliminated in an early cleavage division. Bradysia (Sciara) coprophila also has germ line limited L chromosomes that are eliminated from the soma. Current information and the molecular mechanisms for chromosome imprinting and eliminations, which are just beginning to be studied, will be reviewed here.

High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing

BACKGROUND

The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination in Sciara was the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence for Sciara coprophila to take a large step forward in addressing these features.

RESULTS

We assembled the Sciara genome using PacBio, Nanopore, and Illumina sequencing. To find an optimal assembly using these datasets, we generated 44 short-read and 50 long-read assemblies. We ranked assemblies using 27 metrics assessing contiguity, gene content, and dataset concordance. The highest-ranking assemblies were scaffolded using BioNano optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. A set of 66 metrics was used to select the first draft assembly for Sciara. Nearly half of the Sciara genome sequence was anchored into chromosomes, and all scaffolds were classified as X-linked or autosomal by coverage.

CONCLUSIONS

We determined that X-linked genes in Sciara males undergo dosage compensation. An entire bacterial genome from the Rickettsia genus, a group known to be endosymbionts in insects, was co-assembled with the Sciara genome, opening the possibility that Rickettsia may function in sex determination in Sciara. Finally, the signal level of the PacBio and Nanopore data support the presence of cytosine and adenine modifications in the Sciara genome, consistent with a possible role in imprinting.

Dramatic nucleolar dispersion in the salivary gland of Schwenkfeldina sp. (Diptera: Sciaridae)

Micronucleoli are among the structures composing the peculiar scenario of the nucleolus in salivary gland nuclei of dipterans representative of Sciaridae. Micronucleolar bodies contain ribosomal DNA and RNA, are transcriptionally active and may appear free in the nucleoplasm or associated with specific chromosome regions in salivary gland nuclei. This report deals with an extreme case of nucleolar fragmentation/dispersion detected in the salivary gland of Schwenkfeldina sp. Such a phenomenon in this species was found to be restricted to cell types undergoing polyteny and seems to be differentially controlled according to the cell type. Furthermore, transcriptional activity was detected in virtually all the micronucleolar bodies generated in the salivary gland. The relative proportion of the rDNA in polytene and diploid tissues showed that rDNA under-replication did not occur in polytene nuclei suggesting that the nucleolar and concomitant rDNA dispersion in Schwenkfeldina sp. may reflect a previously hypothesised process in order to counterbalance the rDNA loss due to the under-replication. The chromosomal distribution of epigenetic markers for the heterochromatin agreed with early cytological observations in this species suggesting that heterochromatin is spread throughout the chromosome length of Schwenkfeldina sp. A comparison made with results from another sciarid species argues for a role played by the heterochromatin in the establishment of the rDNA topology in polytene nuclei of Sciaridae.

Transposable elements in Drosophila

Drosophila has been studied as a biological model for many years and many discoveries in biology rely on this species. Research on transposable elements (TEs) is not an exception. Drosophila has contributed significantly to our knowledge on the mechanisms of transposition and their regulation, but above all, it was one of the first organisms on which genetic and genomic studies of populations were done. In this review article, in a very broad way, we will approach the TEs of Drosophila with a historical hindsight as well as recent discoveries in the field.

The path from student to mentor and from chromosomes to replication to genomics

The American Society for Cell Biology Women in Cell Biology Sandra Masur Senior Award recognizes leadership in scientific accomplishments and in mentoring, which are intertwined. My development as a scientist reflects important mentors in my life, including my father and Joe Gall, who is my “Doktor Vater.” In turn, as an established investigator, my scientific successes in researching 1) chromosomes, their replication and genomics, and 2) ribosomes, their structure, evolution, and biogenesis, reflects the hard work of my students and postdocs, for whom I act as a mentor, guiding them in their research and along their career paths.

Beyond DNA puffs: What can we learn from studying sciarids?

Members of the Sciaridae family attracted the interest of researchers because of the demonstration that the DNA puff regions, which are formed in the salivary gland polytene chromosomes at the end of the fourth larval instar, constitute sites of developmentally regulated gene amplification. Besides contributing to a deeper understanding of the process of gene amplification, the study of sciarids has also provided important insights on other biological processes such as sex determination, programmed cell death, insect immunity, telomere maintenance, and nucleolar organizing regions (NOR) formation. Open questions in sciarids include among others, early development, the role of noncoding RNAs in gene amplification and the relationship between gene amplification and transcription in DNA puff forming regions. These and other questions can now be pursued with next generation sequencing techniques and experiments using RNAi experiments, since this latter technique has been shown to be feasible in sciarids. These new perspectives in the field of sciarid biology open the opportunity to consolidate sciarid species as important emerging models. genesis 54:361-378, 2016. © 2016 Wiley Periodicals, Inc.

The origin of in situ hybridization - A personal history

In situ hybridization is the technique by which specific RNA or DNA molecules are detected in cytological preparations. Basically it involves formation of a hybrid molecule between an endogenous single-stranded RNA or DNA in the cell and a complementary single-stranded RNA or DNA probe. In its original form the probe was labeled with (3)H and the hybrid was detected by autoradiography. The first successful experiments in 1968 involved detection of the highly amplified ribosomal DNA in oocytes of the frog Xenopus, followed soon after by the reiterated "satellite DNA" in mouse and Drosophila chromosomes. Fluorescent probes were developed about ten years later.

Chromatin structure of ribosomal RNA genes in dipterans and its relationship to the location of nucleolar organizers

Nucleoli, nuclear organelles in which ribosomal RNA is synthesized and processed, emerge from nucleolar organizers (NORs) located in distinct chromosomal regions. In polytene nuclei of dipterans, nucleoli of some species can be observed under light microscopy exhibiting distinctive morphology: Drosophila and chironomid species display well-formed nucleoli in contrast to the fragmented and dispersed nucleoli seen in sciarid flies. The available data show no apparent relationship between nucleolar morphology and location of NORs in Diptera. The regulation of rRNA transcription involves controlling both the transcription rate per gene as well as the proportion of rRNA genes adopting a proper chromatin structure for transcription, since active and inactive rRNA gene copies coexist in NORs. Transcription units organized in nucleosomes and those lacking canonical nucleosomes can be analyzed by the method termed psoralen gel retarding assay (PGRA), allowing inferences on the ratio of active to inactive rRNA gene copies. In this work, possible connections between chromosomal location of NORs and proportion of active rRNA genes were studied in Drosophila melanogaster, and in chironomid and sciarid species. The data suggested a link between location of NORs and proportion of active rRNA genes since the copy number showing nucleosomal organization predominates when NORs are located in the pericentric heterochromatin. The results presented in this work are in agreement with previous data on the chromatin structure of rRNA genes from distantly related eukaryotes, as assessed by the PGRA.

Chromosome odds and ends

Here I give a brief history of my scientific career, beginning with my early interest in natural history and my introduction to the microscope and the wonderful world of the cell. My studies have focused on chromosomes, nucleoli, and other nuclear structures, with a few forays into the cytoplasm. In each case, I have tried to understand how proteins and nucleic acids are physically organized to give rise to the structures seen under the microscope. I describe how studies in my laboratory on amplified ribosomal RNA genes led to the development of in situ hybridization, a technique that permitted us to localize specific nucleic acid sequences with high precision. My early exposure to the diversity of animals and plants made it seem natural to choose organisms best suited to a particular problem, hence the use of salamanders, frogs, and mice, as well as protozoa, fruit flies, and other invertebrates.

Chromosomal localization and copy number of 18S + 28S ribosomal RNA genes in evolutionarily diverse mosquitoes (Diptera, Culicidae)

In situ hybridization using 3H-labeled 18S and 28S ribosomal DNA (rDNA) probes from Aedes albopictus was performed on the mitotic chromosomes of 20 species of mosquitoes belonging to 8 genera of subfamilies Culicinae and Anophelinae. In all but one species examined, the rDNA family was localized to a single chromosome per haploid genome. Aedes triseriatus was the only exception, with the rDNA cistrons present on chromosome 1 and on chromosome 3. The ribosomal RNA genes were located on chromosome 1 in Ae. albopictus, Ae. aegypti, Ae. flavopictus, Ae. seatoi, A. polynesiensis, Ae. alcasidi, Ae. annandalei, Ae. mascarensis, Ae. hendersoni, Ae. atropalpus, Ae. epactius, Culex pipiens quinquefasciatus, Wyeomyia smithii, and Sabethes cyaneus; chromosome 2 in Ae. mediovittatus and Haemagogus equinus; chromosome 3 in Armigeres subalbatus and Tripteroides bambusa; and the heteromorphic X and Y chromosomes in Anopheles quadrimaculatus. The variation in the location of ribosomal RNA genes on the different chromosomes and at different positions on the chromosome arm among the mosquito species examined is suggestive of considerable chromosome repatterning through translocations and inversions in the karyotypic evolution of mosquitoes. Dot-blot hybridization was used to estimate copy number of rRNA genes; the copy number per haploid genome ranged from 39 +/- 3.27 in Sa. cyaneus to 1023 +/- 68.14 in Ae. flavopictus.

Following the Chromosome Path to the Garden of the Genome

I have been fascinated by chromosomes for longer than I care to mention; their beautiful structure, cell-type-specific changes in morphology, and elegant movements delight me. Shortly before I began graduate study, the development of nucleic acid hybridization made it possible to compare two nucleic acids whether or not their sequences were known. From this stemmed a progression of development in tools and techniques that continues to enhance our understanding of how chromosomes function. As my PhD project I contributed to this progression by developing in situ hybridization, a technique for hybridization to nucleic acids within their cellular context. Early studies with this technique initiated several lines of research, two of which I describe here, that I have pursued to this day. First, analysis of RNA populations by hybridization to polytene chromosomes (a proto-microarray-type experiment) led us to characterize levels of regulation during heat shock beyond those recognizable by puffing studies. We found also that one still-undeciphered major heat shock puff encodes a novel set of RNAs for which we propose a regulatory role. Second, localization of various multicopy DNA sequences has suggested roles for them in chromosome structure: Most recently we have found that Drosophila telomeres consist of and are maintained by special non-LTR (long terminal repeat) retrotransposons.

The localization of ribosomal DNA in Sciaridae (Diptera: Nematocera) reassessed

The chromosomal localization of ribosomal DNA (rDNA) was studied in polytene and diploid tissues of four sciarid species, Trichosia pubescens, Rhynchosciara americana, R. milleri and Schwenkfeldina sp. While hybridization to mitotic chromosomes showed the existence of a single rDNA locus, ribosomal probes hybridized to more than one polytene chromosome region in all the species analyzed as a result of micronucleolar attachment to specific chromosome sites. Micronucleoli are small, round bodies containing transcriptionally active, probably extrachromosomal rDNA. In T. pubescens the rDNA is predominantly localized in chromosome sections X-10 and X-8. In R. americana the rDNA is frequently found associated with centromeric heterochromatin of the chromosomes X, C, B and A, and also with sections X-1 and B-13. Ribosomal probes in R. milleri hybridized with high frequency to pericentric and telomeric regions of its polytene complement. Schwfenkfeldina sp. displays a remarkably unusual distribution of rDNA in polytene nuclei, characterized by the attachment of micronucleoli to many chromosome regions. The results showed that micronucleoli preferentially associate with intercalary or terminal heterochromatin of all sciarid flies analyzed and, depending on the species, are attached to a few (Trichosia), moderate (Rhynchosciara) or a large (Schwenkfeldina sp.) number of polytene chromosome sites.

Patient with trisomy 9p and a hypoplastic left heart with a tricentric chromosome 9

We present a patient with a hypoplastic left heart (HLH), dislocations of the hips and knees, and minor dysmorphic features, who had an abnormal karyotype that resulted in trisomy for 9p and a portion of 9q: 46,((, dic(or tri?)(9)(9pter --> 9q34::9q21 --> 9pter).ish(WCP9++).ish(D9Z5X4 +/+++). The derivative chromosome consisted of an additional copy of the proximal q arm and p arm attached to 9qter in an inverted fashion. Fluorescence in situ hybridization (FISH) using a chromosome 9 beta-satellite probe revealed three signals on the abnormal chromosome 9, suggesting the presence of 3 pericentromeric regions on the der(9). The 9q subtelomere was present on both the normal and derivative chromosome 9, suggesting that very little material, if any, is deleted.

Location of ribosomal genes in the chromosomes of Anopheles darlingi and Anopheles nuneztovari (Diptera, Culicidae) from the Brazilian Amazon

Fluorescence in situ hybridization of Anopheles darlingi and A. nuneztovari demonstrated nucleolar organizer region activity at the end of the fourth larval instar, when the nucleolar organizer regions underwent gradual condensation. The heteromorphic sex chromosomes showed intraindividual size variation in the rDNA blocks located in the pericentromeric region and this coincided with the location of constitutive heterochromatin (C-banding).

The promoter of the heterochromatic Drosophila telomeric retrotransposon, HeT-A, is active when moved into euchromatic locations

The Drosophila telomeric retrotransposon, HeT-A, is found only in heterochromatin; therefore, its promoter must function in this chromatin environment. Studies of position effect variegation suggest that promoters of heterochromatic genes are very different from euchromatic promoters, but this idea has not been tested with isolated promoter sequences. The HeT-A promoter is the first heterochromatin promoter to be isolated and it is of interest to investigate its activity when removed from telomeric heterochromatin. This promoter was initially characterized by testing reporter constructs in transient transfection of cultured cells, an environment that may approximate its endogenous heterochromatin. We now report P-element-mediated transpositions of these constructs, testing the function of different parts of the putative promoter in euchromatin. Expression of endogenous HeT-A RNA shows marked developmental regulation and accumulates preferentially in replicating diploid tissues. HeT-A promoter constructs are active in all euchromatic locations tested and some display aspects of endogenous HeT-A stage- and cell-type expression programs. The activity of each promoter construct in euchromatic locations is also generally consistent with its activity in the transient transfection tests; a possibly significant exception is one sequence segment that appreciably enhanced activity in transient transfection but repressed promoter activity in euchromatin.

Localizing genes in Drosophila melanogaster polytene chromosomes by fluorescence in situ hybridization

This paper describes a method for the identification of single copy genes in Drosophila melanogaster polytene chromosomes, using fluorescence in situ hybridization (FISH). We demonstrate the detection of white (w), a gene previously mapped to 1-1.5 region of the linkage map, and to 3C2 region of the cytogenetic map of X chromosome. Squash preparations of polytene chromosomes from salivary glands dissected out from third instar larvae of Drosophila melanogaster were denatured and subjected to hybridization with a digoxigenin labeled probe, corresponding to mini-white gene. The preparations were then washed and incubated with anti-digoxigenin-fluorescein antibodies. After removal of the nonspecifically bound antibodies, the polytene chromosomes were counterstained with propidium iodide. Fluorescence microscopy revealed white locus in the X chromosome in a subterminal location, in agreement with the above mentioned maps. The protocol is efficient and adaptable for simultaneously multiple signal detection.

Epigenetic silencing of RNA polymerase I transcription: a role for DNA methylation and histone modification in nucleolar dominance

Nucleolar dominance is an epigenetic phenomenon that describes nucleolus formation around rRNA genes inherited from only one progenitor of an interspecific hybrid or allopolyploid. The phenomenon is widespread, occurring in plants, insects, amphibians, and mammals, yet its molecular basis remains unclear. We have demonstrated nucleolar dominance in three allotetraploids of the plant genus Brassica. In Brassica napus, accurately initiated pre-rRNA transcripts from one progenitor, Brassica rapa are detected readily, whereas transcripts from the approximately 3000 rRNA genes inherited from the other progenitor, Brassica oleracea, are undetectable. Nuclear run-on confirmed that dominance is controlled at the level of transcription. Growth of B. napus seedlings on 5-aza-2'-deoxycytidine to inhibit cytosine methylation caused the normally silent, under-dominant B. oleracea rRNA genes to become expressed to high levels. The histone deacetylase inhibitors sodium butyrate and trichostatin A also derepressed silent rRNA genes. These results reveal an enforcement mechanism for nucleolar dominance in which DNA methylation and histone modifications combine to regulate rRNA gene loci spanning tens of megabase pairs of DNA.

Around the genomes: the Drosophila genome project

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Ribosomal RNA genes in mosquitoes: localization by fluorescence in situ hybridization (FISH)

Fluorescence in situ hybridization (FISH) was used to localize the 18S-28S ribosomal RNA gene clusters on the chromosomes of 15 mosquito species belonging to the Anophelinae and Culicinae subfamilies. In the genus Anopheles the rRNA genes are localized on the heterochromatic arm of both sex chromosomes. The association between rRNA genes and sex determining chromosomes also applies to the homomorphic karyotype of Culicinae mosquitoes, at least in those cases in which localization of the sex locus/loci has been determined. In these species ribosomal genes are often found within or adjacent to heterochromatic regions (C bands). Differences in the location of rRNA genes among and within genera suggest the occurrence of several chromosomal rearrangements during the evolution of mosquitoes.

The introduction of a transpositionally active copy of retrotransposon GYPSY into the Stable Strain of Drosophila melanogaster causes genetic instability

A previously described genetic system comprising a Mutator Strain (MS) and the Stable Strain (SS) from which it originated is characterized by genetic instability caused by transpositions of the retrotransposon gypsy. A series of genetic crosses was used to obtain three MS derivatives, each containing one MS chromosome (X, 2 or 3) in the environment of SS chromosomes. All derivatives are characterized by elevated frequencies of spontaneous mutations in both sexes. Mutations appear at the premeiotic stage and are unstable. Transformed derivatives of SS and another stable strain 208 were obtained by microinjection of plasmid DNA containing transpositionally active gypsy inserted into the Casper vector. In situ hybridization experiments revealed amplification and active transposition of gypsy in SS derivatives, while the integration of a single copy of gypsy into the genome of 208 does not change the genetic properties of this strain. We propose that genetic instability in the MS system is caused by the combination of two factors: mutation(s) in gene(s) regulating gypsy transposition in SS and its MS derivatives, and the presence of transpositionally active gypsy copies in MS but not SS.

A molecular and cytogenetic analysis of lambda 20p7 fragment DNA from the proximal beta-heterochromatin of Drosophila melanogaster

A DNA fragment from the Drosophila melanogaster genome, cloned in lambda 20p7, was derived independently from clones lambda 20 and lambda L [Baiborodin et al., Genetika 29 (1993) 403-416; Sharakhov et al., Genetika 29 (1993) 392-402]. In situ hybridization of lambda 20p7 DNA to the chromosomes of D. melanogaster demonstrated preferential hybridization of the fragment to the chromocenter of polytene chromosomes and to pericentric heterochromatin of chromosomes II, IV and X at the metaphase plate. Copy number per haploid genome for lambda 20p7 was estimated as approximately 200. Based on Southern blotting, the major portion of this moderate repeat was localized in the region of a 5.5-kb HindIII digest. In situ hybridization to polytene chromosomes from strain fs(2)B trophocytes revealed that repeats homologous to lambda 20p7 are located in the proximal heterochromatin which undergoes structural reorganization during tissue differentiation. The nucleotide sequence of two segments of the clone lambda 20p7, Dm0.9 and Dm270, was determined. Sequence analysis of the 300-bp Dm0.9 clone revealed that it contains 21-bp and 30-bp d(GT/CA) sequences, a 12-bp AT box, recognition sites for nuclear factors NFI and SpI, and a set of inverted repeats. Clone Dm270 contains an open reading frame (ORF). The deduced amino acid (aa) sequence shares homology with the gag-like gene from type-I (R1) ribosomal DNA insertion and may code for a polypeptide of 10 kDa. The Dm270 sequence was found to contain two direct repeats showing homology to the human CENP-B box.

Localization of ribosomal DNA in Rhagoletis pomonella (Diptera: Tephritidae) by in situ hybridization

The ribosomal DNA (rDNA) of Rhagoletis pomonella was localized within both salivary gland polytene chromosomes and somatic cell mitotic chromosomes by in situ hybridization using the heterospecific Drosophila melanogaster rDNA clone, Dm238. In situ hybridization analysis of polytene nuclei showed that R. pomonella rDNA is located in the nucleolus and adjacent granular network of chromosome 1. The site of origin of rDNA is within this isomorphic granular network. The preservation of nucleolar ultrastructure in some polytene chromosome preparations allowed light microscope localization of R. pomonella rDNA to the apparent periphery of fibrillar centres within fibrillar complexes. In somatic cell nuclei, DM238 hybridized to the nucleolus organizing region (NOR) located on chromosome 1 at the site of the secondary constriction. The frequency distribution of heteromorphisms for rDNA content, differential appearance of secondary constrictions, non-pairing of the NOR and differences in homologue lengths suggests that the structural differentiation of this region in chromosome 1 is sex linked. This the first published description of the salivary gland polytene chromosomes from R. pomonella, and we include a tentative karyotype description, polytene chromosome maps and comments on their suitability for banding and molecular analysis.

Transposition of mobile elements gypsy (mdg4) and hobo in germ-line and somatic cells of a genetically unstable mutator strain of Drosophila melanogaster

Using the in situ hybridization technique, we have analysed the distribution of mobile elements in the X chromosomes of male offspring of individual mutator strain (MS) males crossed to attached-X females. The experiments demonstrate varying cytological localization of the mobile elements gypsy (mdg4) and hobo among different individuals. The other mobile elements investigated (mdg1, mdg3, 412, 297, copia, 17.6, Doc, H. M. S. Beagle, Springer, FB) display no changes in insertion sites. Such an experiment is equivalent to analysis of separate gametes of an MS individual. Thus, the ability of gypsy and hobo to transpose in germ-line cells is demonstrated directly. Transpositions occur at premeiotic stages of germ cell development, since they appear in clusters. Analysis of gypsy and hobo transposition events shows that they occur independently. The same experiment demonstrates that gypsy localization varies significantly between different salivary gland cells of an MS individual. Two types of gypsy hybridization sites can be distinguished: "permanent" sites, common to all cells, and "additional" ones varying between neighbouring salivary gland cells. These additional sites indicate gypsy transposition in somatic cells of the MS. Transposition of the hobo element in somatic cells has also been observed.

Towards a physical map of the Drosophila melanogaster genome: mapping of cosmid clones within defined genomic divisions

A physical map of the D. melanogaster genome is being constructed, in the form of overlapping cosmid clones that are assigned to specific polytene chromosome sites. A master library of ca. 20,000 cosmids is screened with probes that correspond to numbered chromosomal divisions (ca. 1% of the genome); these probes are prepared by microdissection and PCR-amplification of individual chromosomes. The 120 to 250 cosmids selected by each probe are fingerprinted by Hinfl digestion and gel electrophoresis, and overlaps are detected by computer analysis of the fingerprints, permitting us to assemble sets of contiguous clones (contigs). Selected cosmids, both from contigs and unattached, are then localized by in situ hybridization to polytene chromosomes. Crosshybridization analysis using end probes links some contigs, and hybridization to previously cloned genes relates the physical to the genetic map. This approach has been used to construct a physical map of the 3.8 megabase DNA in the three distal divisions of the x chromosome. The map is represented by 181 canonical cosmids, of which 108 clones in contigs and 32 unattached clones have been mapped individually by in situ hybridization to chromosomes. Our current database of in situ hybridization results also includes the beginning of a physical map for the rest of the genome: 162 cosmids have been assigned by in situ hybridization to 129 chromosomal subdivisions elsewhere in the genome, representing 5 to 6 megabases of additional mapped DNA.

Two puff-specific proteins bind within the 2.5 kb upstream region of the Drosophila melanogaster Sgs-4 gene

The Drosophila nuclear proteins Bj6 and Bx42 characterized previously are detected in a series of developmentally active puffs on salivary gland chromosomes. Here the binding of both proteins at puff 3C11-12 containing the glue protein gene Sgs-4 is described in more detail. By deletion analysis we show that both proteins bind within a chromosomal segment containing 17-19 kb of DNA surrounding the Sgs-4 gene. They are detectable at this site during the intermoult stages, before the puff regresses in response to the moulting hormone ecdysone. If the Sgs-4 gene together with flanking DNA sequences is brought into a different chromosomal position by P element transfer, both proteins are detected at this new location. Both proteins are bound to the chromosome within the range of 2.5 kb DNA upstream of the Sgs-4 gene. A strain containing a 52 bp deletion within this region fails to bind Bx42 protein suggesting that the missing DNA, which overlaps a hypersensitive region, may be required for the binding of the Bx42 protein.

Studies of He-T DNA sequences in the pericentric regions of Drosophila chromosomes

He-T DNA is a complex set of repeated DNA sequences with sharply defined locations in the polytene chromosomes of Drosophila melanogaster. He-T sequences are found only in the chromocenter and in the terminal (telomere) band on each chromosome arm. Both of these regions appear to be heterochromatic and He-T sequences are never detected in the euchromatic arms of the chromosomes (Young et al. 1983). In the study reported here, in situ hybridization to metaphase chromosomes was used to study the association of He-T DNA with heterochromatic regions that are under-replicated in polytene chromosomes. Although the metaphase Y chromosome appears to be uniformly heterochromatic, He-T DNA hybridization is concentrated in the pericentric region of both normal and deleted Y chromosomes. He-T DNA hybridization is also concentrated in the pericentric regions of the autosomes. Much lower levels of He-T sequences were found in pericentric regions of normal X chromosomes; however compound X chromosomes, constructed by exchanges involving Y chromosomes, had large amounts of He-T DNA, presumably residual Y sequences. The apparent co-localization of He-T sequences with satellite DNAs in pericentric heterochromatin of metaphase chromosomes contrasts with the segregation of satellite DNA to alpha heterochromatin while He-T sequences hybridize to beta heterochromatin in polytene nuclei. This comparison suggests that satellite sequences do not exist as a single block within each chromosome but have interspersed regions of other sequences, including He-T DNA. If this is so, we assume that the satellite DNA blocks must associate during polytenization, leaving the interspersed sequences looped out to form beta heterochromatin. DNA from D. melanogaster has many restriction fragments with homology to He-T sequences. Some of these fragments are found only on the Y. Two of the repeated He-T family restriction fragments are found entirely on the short arm of the Y, predominantly in the pericentric region. Under conditions of moderate stringency, a subset of He-T DNA sequences cross-hybridizes with DNA from D. simulans and D. miranda. In each species, a large fraction of the cross-hybridizing sequences is on the Y chromosome.

Two proteins from Drosophila nuclei are bound to chromatin and are detected in a series of puffs on polytene chromosomes

Immunizing chromatin protein fractions from Drosophila melanogaster embryos, monoclonal antibodies have been generated against two nuclear proteins of different molecular weight. These proteins are present in a chromatin fraction of Drosophila Kc-cell nuclei and both proteins could be shown to cosediment with nucleosomes following separation on sucrose gradients. Early in development both proteins are located in the embryo cytoplasm. Later, at times when transcription starts at blastoderm, they become redistributed into the nuclei. On salivary gland chromosomes both proteins are detected in a series of developmentally active puffs. The number of sites where these antigens can be detected, as well as the qualitative properties of the antigens at these sites differ between both proteins.

Sensitivity of in situ hybridization techniques using biotin- and 35S-labeled human papillomavirus (HPV) DNA probes

In order to evaluate the sensitivity of our modified in situ DNA hybridization technique using biotinylated probes, formalin fixed, paraffin embedded biopsies from 20 cervical lesions known to contain human papillomavirus (HPV) DNA were re-examined by the technique using both 35S-labeled- and biotinylated HPV DNA probes. The probe concentrations as well as the detection limits of biotin probing were screened by spotting known amounts of HPV 16 DNA on nylon filter, and allowed to hybridize with biotinylated HPV 16 DNA probe. By this method, 4 pg of HPV 16 DNA could be detected using a probe concentration of 0.2 micrograms/ml. HPV DNA could be demonstrated in all 20 biopsies with both hybridization techniques. However, signals in subrabasal cells were detected more frequently with biotin- than with 35S-labeled probes. Additional experiments were performed using three cervical cancer cell lines (with known copy numbers of HPV DNA), to assess the detection limits of HPV infections by the in situ hybridization techniques. The CaSki cells (500-600 HPV 16 copies/cell) were unequivocally positive with both labelling systems. HeLa cells (10-50 HPV 18 copies/cell) were positive with the biotin probing in 10/10 smears, as compared to 7/10 smears when 35S-labeled probes were used. Radioactive probing was inferior to biotinylated probing in detecting the signals in SiHa cells (1-2 HPV 16 copies/cell). This is because even weak background signals could mask true positive signals when 35S-labeled probes are used. In contrast, no background is generated with the biotinylated probes, detected with streptavidin-biotinylated alkaline phosphatase complex. In situ hybridization with biotinylated DNA probes is as sensitive as techniques using 35S-labeled probes for detecting HPV infections in routine cervical biopsies or smears.

Three-dimensional organization of Drosophila melanogaster interphase nuclei. II. Chromosome spatial organization and gene regulation

In the preceding article we compared the general organization of polytene chromosomes in four different Drosophila melanogaster cell types. Here we describe experiments aimed at testing for a potential role of three-dimensional chromosome folding and positioning in modulating gene expression and examining specific chromosome interactions with different nuclear structures. By charting the configurations of salivary gland chromosomes as the cells undergo functional changes, it is shown that loci are not repositioned within the nucleus when the pattern of transcription changes. Heterologous loci show no evidence of specific physical interactions with one another in any of the cell types. However, a specific subset of chromosomal loci is attached to the nuclear envelope, and this subset is extremely similar in at least two tissues. In contrast, no specific interactions between any locus and the nucleolus are found, but the base of the X chromosome, containing the nucleolar organizer, is closely linked to this organelle. These results are used to evaluate models of gene regulation that involve the specific intranuclear positioning of gene sequences. Finally, data are presented on an unusual class of nuclear envelope structures, filled with large, electron-dense particles, that are usually associated with chromosomes.

Three-dimensional organization of Drosophila melanogaster interphase nuclei. I. Tissue-specific aspects of polytene nuclear architecture

Interphase chromosome organization in four different Drosophila melanogaster tissues, covering three to four levels of polyteny, has been analyzed. The results are based primarily on three-dimensional reconstructions from unfixed tissues using a computer-based data collection and modeling system. A characteristic organization of chromosomes in each cell type is observed, independent of polyteny, with some packing motifs common to several or all tissues and others tissue-specific. All chromosomes display a right-handed coiling chirality, despite large differences in size and degree of coiling. Conversely, in each cell type, the heterochromatic centromeric regions have a unique structure, tendency to associate, and intranuclear location. The organization of condensed nucleolar chromatin is also tissue-specific. The tightly coiled prothoracic gland chromosomes are arrayed in a similar fashion to the much larger salivary gland chromosomes described previously, having polarized orientations, nonintertwined spatial domains, and close packing of the arms of each autosome, whereas hindgut and especially the unusually straight midgut chromosomes display striking departures from these regularities. Surprisingly, gut chromosomes often appear to be broken in the centric heterochromatin. Severe deformations of midgut nuclei observed during gut contractions in living larvae may account for their unusual properties. Finally, morphometric measurements of chromosome and nuclear dimensions provide insights into chromosome growth and substructure and also suggest an unexpected parallel with diploid chromatin organization.

High resolution mapping of in situ hybridized biotinylated DNA to surface-spread Drosophila polytene chromosomes

We describe a method of mapping genes or transcripts on polytene chromosomes by transmission electron microscopy. We present several applications which illustrate that, in favorable cases, the method has a resolution of ca. 10 kg, and that high resolution mapping of hybridization sites relative to bands and puffs can be achieved. We mapped sites of transcription for poly-(A) RNA and present evidence which shows that these sites are localized in some bands and puffs, but are also found in interbands.

Nonselective amplification of ribosomal DNA repeat units in compensating genotypes of Drosophila melanogaster

Compensation is a mechanism by which the X-chromosome nucleolus organizer region of Drosophila melanogaster can increase its ribosomal DNA content up to twofold. It occurs in somatic cells under specific genetic conditions and is mediated by a defined genetic site, the compensatory response locus. The In- and various type I ribosomal DNA repeat units were separated by restriction endonuclease digestion. Comparison of the percentages of these repeat unit types between compensating and noncompensating genotypes showed the same distribution. Therefore no selective amplification of these repeat unit types occurs during ribosomal DNA compensation. These results demonstrate that two processes of rDNA amplification in somatic cells, compensation and independent rDNA polytenization, are exclusive events.