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

Electron microscopic photomap of divisions 64 through 70 of the salivary gland 3L chromosome in Drosophila melanogaster

The study is a part of an electron microscopic mapping project on the salivary gland chromosomes of D. melanogaster. Chromosomes were fixed with acetic methanol and, alternatively, with formaldehyde-Ringer solution, squashed and thin sectioned for electron microscopy. The banding pattern was compared with the drawn light microscopic map of Bridges, which shows 209 single and 93 double bands within the divisions 64 through 70. Thirteen Bridges' singlets could not be consistently documented in the electron micrographs. About 50 new, mainly very faint bands were found, most of them following formaldehyde fixation. Again, about 40 bands marked double by Bridges were interpreted to be two separate single bands. This paper completes the electron microscopic mapping of the 3L chromosome.

Evolution of 5S rRNA gene families in Drosophila

In Drosophila virilis, the three clusters of 5S rRNA genes on chromosome 5 comprise two different gene families (B and C), which differ profoundly in the organization of their spacer sequences. While C-type genes, which are found in two of the clusters, exhibit a true repetitive character, the B-type genes of the third cluster are each embedded in completely different genomic environments. Southern blots of genomic DNA of different D. virilis subspecies, D. hydei and D. melanogaster probed with 5S rRNA gene spacer and coding sequences demonstrate the specificity of C-type sequences for the D. virilis species group. The comparative analysis of flanking sequences of 5S rRNA genes of D. virilis, members of the D. melanogaster species subgroup and of the blowfly Calliphora erythrocephala reveals the existence of conserved sequence motifs both in the 5' upstream and 3' downstream flanking regions. Their possible roles in the control of expression and processing of the 5S rRNA precursor molecule are discussed.

Chromosomal localization links the SIN3-RPD3 complex to the regulation of chromatin condensation, histone acetylation and gene expression

Acetylation of core histone N-terminal tails influences chromatin condensation and transcription. To examine how the SIN3-RPD3 deacetylase complex contributes to these events in vivo, we examined binding of SIN3 and RPD3 to Drosophila salivary gland polytene chromosomes. The binding patterns of SIN3 and RPD3 were highly coincident, suggesting that the SIN3-RPD3 complex is the most abundant chromatin-bound RPD3 complex in salivary gland cells. SIN3- RPD3 binding was restricted to less condensed, hypoacetylated euchromatic interbands and was absent from moderately condensed, hyperacetylated euchromatic bands and highly condensed, differentially acetylated centric heterochromatin. Consistent with its demonstrated role in transcriptional repression, SIN3-RPD3 did not co-localize with RNA polymer ase II. Chromatin binding of the complex, mediated by SMRTER, decreased upon ecdysone-induced transcriptional activation but was restored when transcription was reduced. These results implicate SIN3-RPD3 in maintaining histone acetylation levels or patterns within less condensed chromatin domains and suggest that SIN3-RPD3 activity is required, in the absence of an activation signal, to repress transcription of particular genes within transcriptionally active chromatin domains.

Electron microscopic in situ hybridization of digoxigenin-dUTP-labelled DNA probes with Drosophila melanogaster polytene chromosomes

We report a simplified method of electron microscopic (EM) in situ hybridization for standard squashes of Drosophila melanogaster polytene chromosomes using digoxigenin-11-dUTP labelled DNA probes. The method is efficient and reproducible: its high resolution and specificity were demonstrated for the transformed strain 148, in which the insertion was localized precisely as a new thin band both by conventional EM and according to our method. In addition, the method was applied to the fine mapping of the developmentally regulated gene muscle-blind (mbl). On the one hand, mbl was shown to cover the 54B1-2 large band and the adjacent interbands in the 2R polytene chromosome. On the other hand, the use of distantly located DNA probes in the mbl gene allowed us to orientate the transcription unit in the chromosome.

Sequence, molecular organization and products of the Drosophila virilis homologs of the D. melanogaster nested genes lethal(2) tumorous imaginal discs [1(2)tid] and lethal(2) neighbour of tid [1(2)not]

In this study, we describe the isolation of the Drosophila virilis (Dvir) 6201-bp genomic fragment homologous to a 7047-bp genomic region of D. melanogaster (Dmel) that harbors the nested genes lethal(2) tumorous imaginal discs (l(2)tid), lethal(2) neighbour of tid (l(2)not) and lethal(2) relative of tid (l(2)rot). The isolated fragment, which maps at the cytogenetic position 50A5 on chromosome 5, carries the Dvir homologs of the Dmel genes l(2)tid and l(2)not. In both cases, the interspecific comparison of the determined sequences reveals a high homology regarding the protein coding regions and a high degree of evolutionary divergence concerning the intronic parts of the genes. In the two distantly related species, the particular gene within gene arrangement of the two genes is conserved, namely, Dvir tid is located in the intron of Dvir not, on the non-coding DNA strand. Interestingly, the Dvir homolog of the Dmel l(2)rot gene residing in the l(2)not intron on its coding strand, opposite l(2)tid, is not present in the 6201-bp genomic fragment. The protein predicted from the Dvir tid sequence, Dvir Tid58, exhibits 76.5% identity with the putative Tid56 protein of Dmel. The putative Dvir Not58 protein shows 71% identity with its Dmel homolog Not56. The developmental transcript and protein patterns, as well as the characteristics of the protein products encoded by the genes Dvir tid and Dvir not are similar to those identified for their Dmel homologs.

Ultrastructure of in situ hybridization

Techniques for the ultrastructural localization of structures identified by in situ hybridization are being developed for both preembedding labeling and labeling on thin sections (postembedding). Successful labeling of both RNA and DNA sequences has been reported in recent years. Biotinylated nucleic acid probes are becoming increasing available. Colloidal gold is the only successful ultrastructural label with meaningful spatial localization, and the best results have been obtained with small (20-5 nm) gold particles. The link between biotinylated nucleic acid probes and gold has been protein A, antibiotin, or avidin binding. The size of the target nucleotide sequence, the size of the probe, and the number of gold particles attached to the labeling protein must be understood before there can be meaningful interpretation of micrographs. In addition, the spatial considerations depend on whether preembedding or postembedding is used.

The faint band/interband region 28C2 to 28C4-5(-) of the Drosophila melanogaster salivary gland polytene chromosomes is rich in transcripts

Urate oxidase mRNA and five other transcripts map along 38 kb of DNA in the region 28C on the Drosophila melanogaster second chromosome. Three biotinylated restriction fragments from this 38 kb of DNA, one from each end and one from the middle, were individually hybridized in situ to slightly stretched salivary gland polytene chromosomes. The data from these in situ hybridizations in combination with the transcription map of the 38 kb of DNA indicate that: (i) there are six discrete RNA species encoded along the 38 kb of DNA and (ii) these six transcripts map to the faint band/interband region which includes the proximal edge of 28C1, the three faint bands, 28C2, 28C3 and 28C4-5(-), and the adjacent interband chromatin. Our data are consistent with the few published studies directly demonstrating that faint band/interband regions of the Drosophila melanogaster salivary gland polytene chromosomes code for a high density of transcripts.

Localizing DNA and RNA within nuclei and chromosomes by fluorescence in situ hybridization

The enormous potential of in situ hybridization derives from the unique ability of this approach to directly couple cytological and molecular information. In recent years, there has been a surge of success in powerful new applications, resulting from methodologic advances that bring the practical capabilities of this technology closer to its theoretical potential. A major advance has been improvements that enable, with a high degree of reproducibility and efficiency, precise visualization of single sequences within individual metaphase and interphase cells. This has implications for gene mapping, the analysis of nuclear organization, clinical cytogenetics, virology, and studies of gene expression. This article discusses the current state of the art of fluorescence in situ hybridization, with emphasis on applications to human genetics, but including brief discussions on studies of nuclear DNA and RNA organization, and on applications to clinical genetics and virology. Although a review of all of the literature in this field is not possible here, many of the major contributions are summarized along with recent work from our laboratory.

Ultrastructural analysis of polytene chromatin of Drosophila melanogaster reveals clusters of tightly linked co-expressed genes

Patterns of gene activity on individual chromatids of polytene chromosomes of Drosophila melanogaster white prepupae were ultrastructurally characterized by electron microscopy. The band-interband structure of salivary gland polytene chromosomes is lost when they are dispersed in a low ionic strength detergent solution. Morphologically similar, active genes in close proximity to one another were seen in dispersed white prepupal chromatin. The arrays of genes almost certainly represent sister copies of the same locus. Although lateral register between gene copies on multiple strands was not maintained, analysis of sister transcriptional units of unknown identity was achieved at the periphery of the chromatin arrays. Juxtaposed genes with divergent transcriptional polarity were prevalent. The morphology, size and transcriptional polarity of multiple copies of short, tandemly organized, RNA polymerase dense, co-expressed gene clusters is reported. One highly transcriptionally active region, designated the white prepupal locus (WPP locus), composed of a co-expressed tandem cluster of ten genes within an approximately 50 kb region was analyzed on six separate chromatids. The transcriptional map suggests that the pattern of gene activity for at least one gene within the cluster may not be identical on all homologous strands. The survey of active polytene genes provides ultrastructural correlation with previous molecular data that demonstrate tight linkage of certain developmentally co-regulated Drosophila genes. Our findings are discussed in relation to Drosophila gene organization, clustering, and regulation of gene expression.

Optical sectioning and three-dimensional reconstruction of diploid and polytene nuclei

To build a coherent picture of mitosis and cell fates during blastoderm and through the complex movements of gastrulation, it will be important to localize and follow several markers simultaneously in live specimens, ideally in 3D, using high-resolution, specific, noninjurious staining and observation procedures. The study of early Drosophila development has already profited from the use of fluorescent labeling and low-light-level imaging of live embryos using a CCD camera. Chromosomes in fixed samples have been labeled using DNA-specific dyes, making the pattern of mitotic patches visible. In vivo, 3D microscopy of fluorescently tagged chromosomes, in conjunction with computerized image processing, has permitted the first direct cell lineage analysis in the early Drosophila embryo. Moreover, the techniques adapted to study Drosophila development have been used for analysis of Drosophila chromosome structure, mitosis, and cell cycle, and are general enough to be applied to a myriad of problems in cell biology. "Optical sectioning" has always been used to scrutinize everything from onion roots to frog eggs, focusing up and down through the specimen, with the observer's brain responsible for the image processing. However, the volume of raw data generated by the high-resolution approach detailed above requires the use of sophisticated and adaptable computer systems to analyze and organize the results. Software designed to extract information from these complex images, either automatically or through an interactive approach, will become essential tools for cell and developmental biology. The brain of the experimenter remains the most important component in any image-processing system, but the support of technology will be essential.

Detection and localization of actin mRNA isoforms in chicken muscle cells by in situ hybridization using biotinated oligonucleotide probes

We have developed in situ hybridization methodology for nonisotopically labeled oligonucleotide probes to detect cellular mRNA with improved speed, convenience, and resolution over previous techniques. Previous work using isotopically labeled oligonucleotide probes characterized important parameters for in situ hybridization (Anal Biochem 166:389, 1987). Eleven oligonucleotide probes were made to coding and noncoding regions of chick beta-actin mRNA and one oligonucleotide probe to chick alpha-cardiac actin mRNA. All the probes were 3' end-labeled with bio-11-dUTP using terminal transferase, and the labeled probes were hybridized to chicken myoblast and myotube cultures. The hybridized probe was detected using a streptavidin-alkaline phosphatase conjugate. Our assay for the success of probe hybridization and detection was the demonstration of beta-actin mRNA highly localized in the lamellipodia of single cells (Lawrence and Singer, Cell 45:407, 1986) as well as the expression of alpha-cardiac actin mRNA and the repression of beta-actin mRNA in differentiating myoblasts and in myotubes. With the alpha-cardiac probe, we found that this mRNA was distributed all over the cytoplasm of myotubes and differentiated (bipolar) single cells and negative in undifferentiated single cells and at the ends of myotubes. When beta-actin probes were used, two of 11 probes were highly sensitive, and, in pooling them together, the localization of beta-actin mRNA in fibroblastic single cells was evident at the leading edge of the motile cells, the lamellipodium. beta-Actin mRNA was not detected in myotubes except at the ends where contact was made with substrate. This indicates that both beta and cardiac actin mRNA can coexist in the same myotube cytoplasm but at different locations.

Promoter is an important determinant of developmentally regulated puffing at the Sgs-4 locus of Drosophila melanogaster

Sgs-4 is one of the eight known genes coding for larval secretion proteins in Drosophila melanogaster. High-level transcription of the endogenous Sgs genes in salivary glands is accompanied by chromosome puffing at the Sgs gene loci. Naturally occurring mutations of the Sgs-4 promoter region diminish both the level of Sgs-4 expression and the puff size; in null-producers no puff is formed. P element-mediated transformation experiments were performed to clarify this apparent causal relation between transcription and puffing. Sgs-4 upstream sequences, unchanged or recombined with sequences from differently expressed alleles, were fused with Sgs-4 coding and downstream sequences or with the coding sequence of the viral oncogene v-mil. Analyses of the expression of these fragments at the RNA and protein levels and of their capacity for puff formation demonstrate uncoupling of transcription and puffing. That is, high-level transcription is independent of chromosome puffing and does not necessarily induce puffing, and developmentally regulated chromosome puffing is independent of significant transcriptional activity within the puff. Our results show that the strength of the Sgs-4 promoter located within the upstream region from -1 to -840 determines the formation of a puff. No specific effects could be detected on either transcription or puffing by decondensed versus compact chromatin adjoining the transposed DNA at the sites of insertion in transformants. A model in which trans-acting factors binding to the promoter region initiate puffing is proposed.

Non-isotopic RNA probes. Comparison between different labels and detection systems

Several studies have shown the use of non-radioactive labelled DNA probes for in situ hybridisation, mainly to identify cellular DNA. In this study mRNA in situ hybridisation was performed on rat pituitary with biotinylated complementary (c) RNA probes for rat prolactin and growth hormone (GH), and compared with radioactive 35S-radiolabelled probes. Biotinylated cRNA probes were labelled with either biotin-11-UTP or with allylamine-UTP, the latter method being able to produce a higher yield of labelled RNA. Different detection systems were tested, and hybridisation signal was seen in cells of anterior pituitary with both types of biotinylated probes. The signals were detected using either avidin-biotin-complex with peroxidase (ABC), peroxidase-anti-peroxidase (PAP) or gold-silver methods. ABC peroxidase detected using glucose oxidase-diaminobenzidine (DAB)-nickel solution appeared to be the best method for detecting labelled RNA probes, with very strong signal and low background. The biotinylated probes were comparable in sensitivity to the radiolabelled probes in detecting prolactin and GH mRNAs in the anterior lobe of the rat pituitary. These results indicate an alternative methods of labelling and detection of biotinylated probes which could have a potential role in research and diagnostic techniques.

Precise determination of the molecular limits of a polytene chromosome band: regulatory sequences for the Notch gene are in the interband

We have aligned the molecular map of the Notch locus to the cytological features of the salivary gland polytene chromosomes of D. melanogaster in order to determine the interphase chromatin structure of this gene. Using high-resolution in situ hybridization and computer-aided optical microscope data collection and image analysis, we have determined that the coding portions and introns of the Notch gene, which is not expressed in this tissue, are all contained within the polytene chromosome band 3C7. The portion of the Notch gene that resides 5' to the start of transcription lies in an open chromatin conformation, the interband between bands 3C6 and 3C7. Our data are most consistent with condensation of the chromosomal DNA into 30 nm fibers in this polytene band.

Non-radioactive in situ hybridization. A comparison of several immunocytochemical detection systems using reflection-contrast and electron microscopy

A number of immunocytochemical detection systems for determining the chromosomal localization of specific nucleic acid sequences by non-radioactive in situ hybridization have been compared. The procedures were: 1. the peroxidase/diaminobenzidine (PO/DAB) combination, either or not gold/silver intensificated; 2. alkaline phosphatase marking using the nitro-blue tetrazolium plus bromochloro-indolyl phosphate substrate combination (AP/NBT + BCIP); and 3. immunogold with or without silver enhancement. The procedures were first tested and optimized in dot blot experiments and then applied to in situ hybridization. As hybridization probes, both a middle-repetitive and a unique sequence (modified with 2-acetylaminofluorene (AAF] were used. The advantages and disadvantages of the various methods for reflection contrast (RC) or transmission electron microscopic (TEM) visualization of hybrids are discussed.

Chromosome structure in four wild-type polytene tissues of Drosophila melanogaster. The 87A and 87C heat shock loci are induced unequally in the midgut in a manner dependent on growth temperature

A systematic screen of wild-type Drosophila melanogaster larval organs has revealed three tissues besides the salivary gland with suitable polyteny for detailed cytogenetic analysis: the prothoracic gland, hindgut, and middle midgut. Chromosome banding patterns are very similar between tissues, but puffing patterns show considerable differences. In intact nuclei, oblique substructural elements can sometimes be detected in bands from some of the tissues. As a way of exploiting these newly characterized chromosomes, the heat shock puff response in midgut cells has been studied in detail. The puffing pattern is very similar to that in salivary glands, but an unexpected difference is found in the relative activity of the 87A7 and 87C1 loci, which contain the hsp70 genes. When larvae are raised at 16 degrees C, heat shocks ranging from 10 to 60 min induce only a weak midgut puff at 87A7 that is much smaller than that at 87C1, in contrast to other tissues where both are strongly induced. In pulse-labeled nuclei, an approximately five fold difference in transcriptional activity at the two loci is observed. However, when larvae are raised at 25 degrees C, the converse is found: the 87A7 puff is large, and little or no puffing is detectable at 87C1. Thus, in the midgut, heat shock induced puffing at these two loci is inversely modulated by a mechanism dependent on growth temperature.

Gene mapping on human metaphase chromosomes by in situ hybridization with 3H, 35S, and 32P labeled probes and transmission electron microscopy

A method based on in situ hybridization, autoradiography and transmission electron microscopy for mapping genes on human metaphase chromosomes is presented. Successful mapping of the tandemly repeated rDNA genes and of two nucleic acid probes, N-myc and probe 3 (Kanda et al. 1983), that are amplified in a homogeneously staining region (HSR) of the neuroblastoma cell line, IMR-32 is described. By using sufficiently thin AgBr emulsions, it is possible to obtain observable grains and good resolution with probes radiolabeled with 3H, 35S, or 32P, but the former gives the best results. We observe that neither of the two probes, N-myc and probe 3, has a uniform spatial distribution along the HSR and that the distributions of the two probes differ from each other. These observations support previous studies which indicated that the formation of an HSR is a more complex process than uniform amplification of a single DNA segment to form an n-fold set of perfect tandem repeats. The present study shows that the electron microscopic method is useful for extending the results of light microscopic studies for problems where higher resolution mapping is needed.