Ultrastructural localization of defined sequences of viral RNA and DNA by in situ hybridization of biotinylated DNA probes on sections of herpes simplex virus type 1 infected cells

Highly ordered spatial organization of the structural long noncoding NEAT1 RNAs within paraspeckle nuclear bodies

Paraspeckles (PSPs) are nuclear bodies associated with the retention in the nucleus of specific mRNAs. Two isoforms of a long noncoding RNA (NEAT1_v1/Menε and NEAT1_v2/Menβ) are required for the integrity of PSPs. Here, we analyzed the molecular organization of PSPs by immuno- and in situ hybridization electron microscopy. Detection of the paraspeckle markers PSPC1 and P54NRB/NONO confirm the identity between PSPs and the previously described interchromatin granule-associated zones (IGAZs). High-resolution in situ hybridization of NEAT1 transcripts revealed a highly ordered organization of IGAZ/PSPs. Although the 3.7-kb NEAT1_v1 and the identical 5' end of the 22.7-kb NEAT1_v2 transcripts are confined to the periphery, central sequences of NEAT1_v2 are found within the electron-dense core of the bodies. Moreover, the 3' end of NEAT1_v2 also localize to the periphery, indicating possible architectures for IGAZ/PSPs. These results further suggest that the organization of NEAT1 transcripts constrains the geometry of these bodies. Accordingly, we observed in HeLa and NIH 3T3 cells that IGAZ/PSPs are elongated structures with a well-defined diameter. Our results provide new insight on the ability of noncoding RNAs to form subcellular structures.

Elucidation of Nipah virus morphogenesis and replication using ultrastructural and molecular approaches

Nipah virus, which was first recognized during an outbreak of encephalitis with high mortality in Peninsular Malaysia during 1998-1999, is most closely related to Hendra virus, another emergent paramyxovirus first recognized in Australia in 1994. We have studied the morphologic features of Nipah virus in infected Vero E6 cells and human brain by using standard and immunogold electron microscopy and ultrastructural in situ hybridization. Nipah virions are enveloped particles composed of a tangle of filamentous nucleocapsids and measured as large as 1900 nm in diameter. The nucleocapsids measured up to 1.67 microm in length and had the herringbone structure characteristic for paramyxoviruses. Cellular infection was associated with multinucleation, intracytoplasmic nucleocapsid inclusions (NCIs), and long cytoplasmic tubules. Previously undescribed for other members of the family Paramyxoviridae, infected cells also contained an inclusion formed of reticular structures. Ultrastructural ISH studies suggest these inclusions play an important role in the transcription process.

Intracellular virus DNA distribution and the acquisition of the nucleoprotein core during African swine fever virus particle assembly: ultrastructural in situ hybridisation and DNase-gold labelling

African swine fever virus (ASFV) is a large complex icosahedral double-stranded DNA virus that replicates in the cytoplasm of susceptible cells. Assembly of new virus particles occurs within the perinuclear viroplasm bodies known as virus factories. Two types of virus particle are routinely observed: "fulls," which are particles with an electron-dense DNA-containing nucleoid, and "empties," which consist of the virus protein and membrane icosahedral shell but are without the incorporation of the virus genome. The objective of this study was to understand ASFV morphogenesis by determining the distribution of intracellular viral DNA in the virus factory and during virus particle assembly. The ultrastructural localisation of DNA within ASFV-infected cells was achieved using two complementary methods: with an ASFV-specific DNA probe to the major capsid protein (p73) gene (B646L) hybridised in situ or through detection of all forms of DNA (viral and cellular) with gold-labelled DNase. Conditions for in situ hybridisation at the electron microscopic level were optimised for infected cells in two Lowicryl resins (K4M and HM20) and using two nonradioactive probe labels (digoxygenin and biotin). The morphological data indicate that the viral DNA, perhaps from specialised storage sites within the factory, begins to condense into a pronucleoid and is then inserted, at a single vertex, into an "empty" particle. Further maturation of the viral particle, including closure of the narrow opening in the icosahedron, gives rise to "intermediate" particles, where the nucleoprotein core undergoes additional consolidation to produce the characteristic mature or "full" virions. The site of particle closure may represent a "weak point" at one vertex, but the mechanisms and structures involved in the packaging and release of the virus genome via such a port are yet to be determined.

Biotin and digoxigenin as labels for light and electron microscopy in situ hybridization probes: where do we stand?

Biotin was recently applied to detect cellular DNA or RNA. In combination with avidin, streptavidin or antibody, it can be conjugated with fluorescent dye, enzyme, ferritin, or gold. However, emphasis has recently been placed on the false-positive results that are obtained when this probe is used, because endogenous biotin may sometimes interfere with specific signals. Digoxigenin appears to be an interesting alternative because it is present exclusively in Digitalis plants as a secondary metabolite. We discuss in this review the efficiency and the respective advantages and disavantages of these two probes for in situ hybridization, mainly at the electron microscopic level.

Nuclear targeting of incoming human foamy virus Gag proteins involves a centriolar step

The pathways used in the transport of retroviral genomes to the nucleus are poorly identified. Analyzing the intracellular localization of incoming foamy viruses, we have found that the Gag antigens and the viral genome accumulate in a distinct perinuclear domain identified as the centrosome. Colchicine treatment completely abolished pericentriolar targeting of human foamy virus (HFV) proteins, suggesting a role for microtubules in the transport of the incoming viral proteins to the centrioles. Finally, we demonstrate that, similarly to human immunodeficiency virus DNA, HFV DNA can enter the nucleus of G1/S-phase-arrested cells, although no viral gene expression can be observed. Recent observations have demonstrated that foamy viruses have several features not shared by other retroviruses. The intracellular route of the incoming Gag antigens may constitute a new specificity of this class of viruses.

Non-isotopic electron microscope in situ hybridization for studying the functional sub-compartmentalization of the cell nucleus

Post-embedding electron microscope in situ hybridization using gold particles as label permits the clear identification of the cellular structures which contain the nucleic acid molecules under study. It has yielded information on the distribution of defined nucleic acid sequences of different origins-cellular or viral, DNA or RNA, single- or double-stranded molecules-which has revolutionized the study of the nucleus. Application of this powerful technique in combination with other refined techniques to studies on transcription and replication of cellular and viral genes has augmented our knowledge of the functional organization of the cell nucleus. One can now ask mechanistically meaningful questions concerning the successive steps of gene replication and expression not only under normal conditions of cell growth, but also when the cellular metabolism is altered by a drug treatment or a viral infection. This chapter aims (a) to present the established methods of post-embedding electron microscope in situ hybridization for localizing, precisely and specifically, a nucleic acid target in its normal environment and (b) to present some contributions of this technique to investigations of the functional compartmentalization of the cell nucleus and to elucidate the cell-virus relationships in infected cells.

In situ hybridization and immuno-electron microscope analyses of the Us11 gene of herpes simplex virus type 1 during transient expression

The distribution of Us11 RNA and of its encoded protein have been investigated at the ultrastructural level in HeLa cells transiently expressing the Us11 gene of herpes simplex virus type 1. In these transfected cells, Us11 protein accumulates at sites identical to those of lytically infected cells, i.e., in nucleoli and in regions of the cytoplasm that contain ribosomes. Us11 RNA and polyadenylated RNA are scattered over the ribosome-rich areas of the cytoplasm. They also accumulate in the nucleoplasm on clustered ribonucleoprotein (RNP) fibrils but also in clusters of interchromatin granules, some of them contiguous to nucleoli. However they are never found in nucleoli. These data reveal the involvement of interchromatin granules in some steps of Us11 mRNA maturation and/or transport.

Intranuclear retention of ribosomal RNAs in response to herpes simplex virus type 1 infection

The localization of ribosomal RNA (rRNA) was investigated at the ultrastructural level in herpes simplex virus type 1 infected HeLa cells using three distinct biotinylated probes which bind in sequence to three different segments of the ribosomal genes. Comparison of the above with the signal levels obtained from non-infected cells reveals information about the effects of HSV-1 infection on ribosome biogenesis. A probe specific for the 5′ end portion of pre-rRNA labeled all nucleoli of both non-infected and infected cells in the same way, that is, it mainly labeled the dense fibrillar component and the border of the fibrillar centers but only slightly labeled the granular component. This indicates that the initial cleavage of pre-rRNA in herpes infection still occurs in the 5′ region of the 5′ external transcribed spacer. However, a probe specific for 18 S rRNA labeled the granular component of the nucleoli more intensely after infection. In addition, significant amounts of rRNA molecules were present within the intranuclear viral region, except over the enclosed viral dense bodies, and within the virus-enlarged clusters of interchromatin granules. The data indicate that the still enigmatic viral dense bodies, which are nucleolus-related structures, are excluded from the marked intranuclear retention of ribosomal RNAs and, in addition, reveal a possible role for the interchromatin granules of infected cells in the regulation of the export of the ribosomal subunits towards the cytoplasm.

Non-isotopic in situ hybridization at the ultrastructural level

Non-isotopic in situ hybridization techniques are becoming increasingly widely used at the ultrastructural level, permitting rapid localization of nucleic acid targets with a high degree of resolution. Technical considerations dictate that the great specificity of the method cannot be matched by a similar degree of sensitivity; the value of non-isotopic ultrastructural in situ hybridization lies in its unique ability to localize nucleic acid targets in relation to submicroscopic cellular structures. This article presents an overview of non-isotopic ultrastructural hybridization methods and applications.

Immunocytochemistry, autoradiography, in situ hybridization, selective stains: complementary tools for ultrastructural study of structure-function relationships in the nucleus. Applications to adenovirus-infected cells

A significant amount of new information on structure-function relationships in nuclei of adenovirus-infected cells has accumulated during the last decade as a result of the combined use of several new cytochemical techniques. Localization of viral DNA on ultrathin sections of infected cells has been investigated at the ultrastructural level by using specific DNA staining and immunocytochemistry with monoclonal anti-DNA antibodies. Both techniques, however, concomitantly visualize cellular and viral DNA. The specific stain for DNA reveals the configuration of the DNA molecules in the different nuclear substructures, whatever their synthetic activities. The immunodetection of DNA reveals that specific antibodies strongly bind to DNA of condensed host chromatin and to both encapsidated and nonencapsidated inactive viral genomes. However, the observation of an abnormally low level of labeling over the substructures in which synthetic activities of viral genomes are known to be intense demonstrates a serious limitation of this technique for the detection of active DNA. Postembedding in situ hybridization is the most useful method for identifying with certainty the structures containing defined nucleic acid sequences. By using a biotinylated viral DNA probe, in situ hybridization provides specific identification of structures containing either viral DNA or viral RNA molecules. In addition, with appropriate pretreatment of the sections, it is possible to reveal either all the viral DNA--that is, both double- and single-stranded DNA molecules (dsDNA, ssDNA)--or more specific species such as only ssDNA or only dsDNA molecules. The replicative and transcriptional activities of viral genomes are determined by high-resolution autoradiography. Autoradiography after a short pulse incorporation of appropriate radioactive precursors by infected cells reveals the sites of cellular and viral DNA replication or transcription. A short pulse followed by chase periods of different durations reveals the progressive migration of the cellular and viral synthesized products. The in situ distribution of the viral 72 kDa DNA-binding protein, a highly phosphorylated protein which protects the viral ssDNA, is revealed either by immunocytochemistry with specific antibodies or by the bismuth staining method which stains all highly phosphorylated proteins, including both cellular and viral proteins. The combined results of all these cytochemical procedures reveal the composition and functions of some of the structures induced by adenovirus infection. They demonstrate that viral genomes engaged in replication lead to the formation of the replicative foci in which two compartments rapidly develop, one of which results from the aggregation of single strands of viral DNA and their accompanying 72 kDa protein.(ABSTRACT TRUNCATED AT 400 WORDS)

Ultrastructural in situ hybridization to nascent transcripts of highly transcribed rRNA genes in chromatin spreads

The amplified rRNA genes of amphibian oocytes were used as a model system for the development of an in situ hybridization technique to label nascent transcripts in dispersed chromatin. A biotinylated complementary RNA probe was hybridized to nascent transcripts from dispersed nucleoli, and detected by a two step antibody technique utilizing colloidal gold as an electron dense marker. A specific sequence on the rRNA nascent transcript was labeled in a pattern consistent with its location; however, gene morphology was difficult to analyze following in situ hybridization owing to low sample contrast. Proteins associated with the transcripts were apparently lost during the procedure, leading to decreased electron density of the transcripts. The technique was systematically modified in an attempt to identify conditions that preserved gene morphology adequately for ultrastructural analysis, while simultaneously maintaining sufficient levels of specific labeling.

Intracellular localization of parvovirus B19 nucleic acid at the ultrastructural level by in situ hybridization with digoxigenin-labelled probes

Conditions suitable for immunogold detection of digoxigenin-labelled DNA probes hybridized to parvovirus B19-infected erythroid cells embedded in Lowicryl K4M and LR White acrylic resins were established at the electron microscope level. The protocol was initially optimized using a positive control probe for whole human DNA which produced signal over the heterochromatin of all nucleated cells. In cultures harvested 2 days postinfection, B19 nucleic acid was detected mainly within the centrinuclear region of erythroid cells exhibiting characteristic margination of the chromatin. The B19 hybridization signal was largely unaffected by denaturation and was resistant to RNase digestion but sensitive to DNase digestion, indicating that it was mainly single-stranded B19 DNA. Relatively few gold particles were found over crystalline arrays of viral capsids, consistent with the observation that they are composed of mainly 'empty' capsids. B19 nucleic acid was detected in apparent transit from nucleus to cytoplasm through pores in the nuclear membrane. While the sensitivity of this system is limited by the fact that hybridization occurs only at the surface of the section, it is a rapid and specific means of localizing viral nucleic acids with a high degree of resolution.

Protocol of electron microscope in situ nucleic acid hybridization for the exclusive detection of double-stranded DNA sequences in cells containing large amounts of homologous single-stranded DNA and RNA sequences: application to adenovirus type 5 infected HeLa cells

In order to gain a further insight into the relationships of the complex process of replication of adenovirus genomes to the substructures which occur in the nuclei of adenovirus type 5 (Ad5) infected HeLa cells, we have visualized directly, at the electron microscopic level, viral double-stranded DNA (dsDNA) in late infected nuclei by the use of a post-embedding in situ hybridization technique with a biotinylated specific DNA probe. The procedure is based on the removal of single-stranded (ss) nucleic acids by S1 nuclease. The highest levels of signal density for viral dsDNA were detected over the fibrils of the large, centrally located viral genome storage site and over the viral nucleoids of both clustered and isolated viruses. Lower but significant signals were observed over the fibrillo-granular network of the peripheral replicative zones, where both transcription and replication of viral DNA occur. On the other hand, the labeling of the enclosed viral ssDNA accumulation sites, also involved in viral replication but not transcription, was negligible, which suggests that, in the latter, the newly synthesized viral dsDNA immediately extends into the adjacent peripheral replicative zone to be transcribed and/or replicated.

Adaptation of a non-radioactive in situ hybridization method to electron microscopy: detection of tenascin mRNAs in mouse cerebellum with digoxigenin-labelled probes and gold-labelled antibodies

In this study we describe a method for the detection of mRNAs at the ultrastructural level using a non-radioactive in situ hybridization method based on digoxigenin-labelled cRNA probes and gold-labelled digoxigenin-specific antibodies. We applied this protocol to an analysis of the expression of the extracellular matrix protein tenascin in the developing cerebellar cortex of the mouse. To gain an impression of the sensitivity attainable with digoxigenin-labelled probes, we first established at the light microscopic level that the hybridization signal obtained with the non-radioactive probe is as sensitive as that obtained with a 35S-labelled probe. The non-radioactive hybridization protocol was then combined with electron microscopic post-embedding and immunogold detection techniques. Tenascin-specific, digoxigenin-labelled cRNA probes were hybridized to ultrathin sections of Lowicryl K4M-embedded tissue and the probe/target mRNA hybrids were detected using gold-labelled antibodies to digoxigenin. In agreement with the observations from in situ hybridization at the light microscopic level, specific labelling was observed in Golgi epithelial cells in the region of the Purkinje cell layer and cells in the internal granular layer, which could be identified as astrocytes by ultrastructural criteria. Labelling was detectable in association with free ribosomes and ribosomes of the rough endoplasmic reticulum. In addition, focal hybridization signals were occasionally found in the nucleus. No signal was observed in Golgi epithelial cells or astrocytes using sense or in any other cerebellar cell type using either sense or anti-sense probes. The described in situ hybridization technique uses ultrastructural criteria to associate the presence of a given mRNA species with a particular cell type. Additionally, it provides information about the target mRNA's subcellular distribution, thus offering the possibility to study intracellular transport of particular mRNAs.

Distribution of viral RNA molecules during the adenovirus type 5 infectious cycle in HeLa cells

Viral RNA was localized ultrastructurally by in situ hybridization with a biotinylated viral DNA probe and colloidal gold label in HeLa cells during infection with adenovirus type 5. Transcription was monitored by high-resolution autoradiography after short pulses with tritiated uridine. At the earliest stage of virus-induced nuclear transformation, viral RNA was restricted to the small compact fibrillar "early replicative sites" which we had previously demonstrated to be the site of viral DNA replication (Puvion-Dutilleul and Puvion, 1990b). Protease-DNase-treated sections revealed that these fibrillar masses rapidly enlarged and gave rise to a juxtaposed loose fibrillogranular structure devoid of viral RNA. Subsequently, the function of the compact fibrillar zones changed to become the sites of accumulation of single-stranded (ss) viral DNA molecules, and the contiguous new fibrillogranular zones (previously named the peripheral replicative zones, Puvion-Dutilleul and Puvion, 1990a) became not only the centers of replicating viral double-stranded DNA but also the only sites of viral RNA molecules including the elongating RNA transcripts. Pulse-chase experiments revealed an unexpected accumulation of RNA molecules in these extranucleolar regions of infected nuclei.

Nucleolar organization of HeLa cells as studied by in situ hybridization

The distribution of the ribosomal genes and their ribosomal RNA (rRNA) products in the different compartments of the nucleolus of HeLa cells was examined on thin sections of Lowicryl embedded material. The ribosomal nucleic acids were visualized after hybridization with a set of biotinylated double-stranded ribosomal DNA (rDNA) probes from different locations along the gene, followed by immunogold labelling of biotin. Ribosomal genes were detected over both the entire fibrillar centres (FCs) and some masses of intranucleolar condensed chromatin. As for the rRNA components, comparison of the signal levels obtained with the different probes provides some information about the compartmentalization of distinct stages of ribosome biogenesis. Thus a probe specific for the 5' external transcribed spacer (5'ETS) portion of pre-rRNA labels almost exclusively the dense fibrillar component (DFC) and the border of the FCs, while the interior of the FCs appears devoid of any kind of rRNA species. By contrast, probes recognizing either 18S or 28S mature rRNA sequences label both the DFC and the granular component (GC). Moreover, mature 18S rRNA sequences are markedly under-represented relative to mature 28S rRNA sequences in the GC, as compared with the other nucleolar compartments. Our observations are consistent with the view that DFCs contain elongating and 47S-45S precursor rRNA molecules whereas the subsequent various rRNA processing intermediates are mainly located within the GC. Since the border of FCs is the only site where both rDNA and newly synthesized pre-rRNA coexist, the transcription of ribosomal genes seems to take place at the periphery of the FCs, and not in the DFC, suggesting that elongating and newly completed transcripts are immediately transferred into the surrounding DFC where they transiently accumulate before undergoing processing reactions and transfer to the GC.