Methodologies for specific intron and exon RNA localization in cultured cells by haptenized and fluorochromized probes

Illuminating Genomic Dark Matter with RNA Imaging

In the postgenomic era, it is clear that the human genome encodes thousands of long noncoding RNAs (lncRNAs). Along the way, RNA imaging (e.g., RNA fluorescence in situ hybridization [RNA-FISH]) has been instrumental in identifying powerful roles for lncRNAs based on their subcellular localization patterns. Here, we explore how RNA imaging technologies have shed new light on how, when, and where lncRNAs may play functional roles. Specifically, we will synthesize the underlying principles of RNA imaging techniques by exploring several landmark lncRNA imaging studies that have illuminated key insights into lncRNA biology.

Lipoprotein lipase in non-small cell lung cancer tissue is highly expressed in a subpopulation of tumor-associated macrophages

High lipoprotein lipase (LPL) activity in non-small cell lung cancer (NSCLC) tissue strongly predicts shorter patient survival. We tested the hypothesis that in NSCLC tissue, macrophages are the major site of LPL expression. LPL expression in the entire NSCLC tissue and in the adjacent non-cancer lung tissue was compared to the expression of genes preferentially expressed in macrophages. LPL expression at the cellular level was analyzed by mRNA fluorescence in situ hybridization. In the whole cancer tissue (but not in the adjacent non-cancer tissue), expression of LPL correlated with expression of genes preferentially expressed in macrophages (MSR1, CD163, FOLR2), but not with expression of genes preferentially expressed in tumor cells. All cells in the cancer and adjacent non-cancer tissue exhibit low LPL expression. However, in cancer tissue only, there were individual highly LPL-expressing cells which were macrophages. These LPL-overexpressing cells were approximately 10 times less abundant than anti-CD163-stained, tumor-associated macrophages. To conclude, in NSCLC tissue, a subpopulation of tumor-associated macrophages highly expresses LPL. Because tumor-associated macrophages are pro-tumorigenic, these cells should be further characterized to better understand the underlying nature of the close relationship between high LPL activity in NSCLC tissue and shorter patient survival.

Production of a bovine IL-12p40 probe and application using in situ hybridization on ruminant fixed tissues

Pro-inflammatory cytokines (particularly IL-12) are important for initiating protective T helper 1 (Th1)-type immune responses and hence vital for combating intracellular infections and tumours. In situ hybridization (ISH) provides a powerful diagnostic tool allowing the identification and localization of cells producing these mediators in fixed tissues. The objective of this work was to produce a bovine IL-12p40 probe that allows detection of IL-12p40 mRNA in fixed tissues from different ruminant species. The RNA probe sequence is 447bp in length and from a region with high cross-species-sequence homology (>97.3% homology) to the ovine, cervine, caprine and bubaline IL-12p40 genes. ISH was carried out on paraformaldehyde fixed tissues collected from cattle, sheep and goats. The probe was efficient in identifying IL-12p40 expressing cells in fixed tissues from all these species. In conclusion, the IL-12p40 probe was efficient in identifying and localizing cells that express IL-12p40, and provides a good immuno-diagnostic technique to characterize immune responses in fixed tissues.

Detection of nascent RNA transcripts by fluorescence in situ hybridization

The development of cellular diversity within any organism depends on the timely and correct expression of differing subsets of genes within each tissue type. Many techniques exist which allow a global, average analysis of RNA expression; however, RNA-FISH permits the sensitive detection of specific transcripts within individual cells while preserving the cellular morphology. The technique can provide insight into the spatial and temporal organization of gene transcription as well the relationship of gene expression and mature RNA distribution to nuclear and cellular compartments. It can also reveal the intercellular variation of gene expression within a given tissue. Here, we describe RNA-FISH methodologies that allow the detection of nascent transcripts within the cell nucleus as well as protocols that allow the detection of RNA alongside DNA or proteins. Such techniques allow the placing of gene transcription within a functional context of the whole cell.

Combination DNA/RNA FISH and immunophenotyping

This unit presents methods for combining immunophenotyping with DNA/RNA FISH. The approach is used in so-called genotype/phenotype analysis to identify chromosomal aberrations in sub-populations of cells present in heterogenous populations. Combining RNA and DNA detection with identification of cellular proteins is quite difficult. This series of protocols is provided to enable the successful application of the combination of these techniques.

Similar active genes cluster in specialized transcription factories

How transcription affects the way specific genes are arranged within the nucleus remains to be fully understood. We examine here whether transcription occurs in discrete sites (factories) containing the required machinery and whether these sites specialize in transcribing different genes. We cotransfected plasmids encoding a common origin of replication but different transcription units into cells, where they are assembled into minichromosomes that the cellular machinery replicates and transcribes. In cells containing thousands of minichromosomes, we found (using fluorescence in situ hybridization) active templates concentrated in only a few factories that transcribe particular units depending on the promoter type and the presence of an intron. Close proximity between similar transcription units, whether on two different minichromosomes or on host chromosomes and minichromosomes, is confirmed using chromosome conformation capture. We conclude that factories specialize in producing a particular type of transcript depending on promoter type and whether or not the gene contains an intron.

Simultaneous detection of adenovirus RNA and cellular proteins by fluorescent labeling in situ

Investigating the cell biology of gene expression requires methodologies for localizing RNA relative to proteins involved in RNA transcription, processing, and export. Adenovirus is an important model system for the analysis of eukaryotic gene expression and is also being used to investigate the organization of gene expression within the nucleus. Here are described the combined in situ hybridization and immunofluorescence staining techniques that have been used to study the localization of viral RNA relative to nuclear structures that contain splicing factors.

Stimulated expression of mRNAs in activated T cells depends on a functional CRM1 nuclear export pathway

In metazoans, the nuclear export of bulk mRNAs is mediated by the export receptor TAP, together with its binding partner p15. A number of viral mRNAs, including the unspliced and partially spliced mRNA species of the human immunodeficiency virus (HIV), however, use an alternative export route via the importin beta-related export receptor CRM1. This raises the question of whether a subset of cellular mRNAs might be exported by CRM1 as well. To identify such mRNAs, we performed a systematic screen in different cell lines, using representational difference analyses of cDNA (cDNA-RDA). In HeLa and Cl-4 cells no cellular transcripts could be identified as exported via CRM1. In contrast, we found a number of CRM1-dependent mRNAs in Jurkat T cells, most of which are induced during a T cell response. One of the identified gene products, the dendritic cell marker CD83, was analyzed in detail. CD83 expression depends on a functional CRM1 pathway in activated Jurkat T cells as well as in a heterologous expression system, independent of activation. Our results point to an important role of the CRM1-dependent export pathway for the expression of CD83 and other genes under conditions of T cell activation.

Allele-specific transcription of fetal genes in primary erythroid cell cultures from Lepore and δβ° thalassemia patients

OBJECTIVE

Autonomous gene silencing and gene competition by globin promoters for locus control region (LCR) function have been proposed as mechanisms in developmental regulation of beta-like genes. deltabeta degrees thalassemias are syndromes presenting an increased production of fetal hemoglobin in adult life; the majority of them are due to various deletions in beta-globin gene cluster. We studied samples from double heterozygotes for beta-thalassemia and for Lepore or Sicilian deltabeta degrees deletions, both lacking beta-promoter sequence. Our goal was to address the question of whether the allele carrying the deltabeta degrees deletion is responsible for high level of fetal hemoglobin (HbF) production.

PATIENTS AND METHODS

We analyzed the globin gene transcription in human erythroid cell cultures from peripheral blood stem cells, using primary transcript in situ hybridization. We performed primary erythroid cultures from patients with the following genotypes: Lepore/beta degrees 39, Sicilian deltabeta degrees /beta degrees 39, and, as controls, two thalassemia patients with nondeletional mutations (IVS1,6/IVS1,6; IVS1,6/beta degrees 39), and one normal individual.

RESULTS

The cells where it is possible to unambiguously assign gamma genes transcription in cis with the deletion (gamma:beta) are strongly represented with respect to the nine other combinations of gamma and beta hybridization signals. These cells are at least nine times more represented than those expressing the gamma allele in trans to the deletion.

CONCLUSION

The allele-specific transcription of fetal genes in cis with the deletion is favored in both deletional genotypes. The absence of the adult promoter may influence LCR recruitment by fetal promoter, supporting the hypothesis that competition mechanism and gene silencing can coexist in regulating human globin gene transcription.

Visualizing RNA molecules inside the nucleus of living cells

Fluorescence in situ hybridization is a widely used technique in cell biology providing insight into the spatial organization of specific RNA transcripts in the cell nucleus. However, to further investigate the dynamics of the transcription process and the transport rates of RNAs through the nucleus, RNAs need to be visualized and tracked in the living cell. In past years, various methods have been developed with the aim of tagging specific RNAs with a fluorescent moiety without interfering with cell vitality. These methods include the delivery of probes into a living cell, the in vivo hybridization of fluorescent oligonucleotide probes to endogenous RNAs, and the microscopic imaging of the tagged RNAs in living cells. In this article, we review a number of methods for tagging and visualizing endogenous RNAs in living cells. In addition, a protocol is described that allows detection of various RNA types using fluorochrome-labeled 2(')-O-methyl oligoribonucleotide (2(')-OMe RNA) probes. Compared with conventional oligodeoxynucleotide probes, 2(')-OMe RNA probes are not degraded by nucleases, form stable hybrids with structured RNAs, and do not interfere with cell vitality.

Retrieval of mRNA from paraffin-embedded human infant brain tissue for non-radioactive in situ hybridization using oligonucleotides

In situ hybridization (ISH) is used to examine the spatiotemporal distribution of gene expression in a range of tissues. Neuroscience research in human brain tissue requires techniques that can be used in formalin fixed and paraffin-embedded tissue rather than frozen tissue which is recommended, but difficult to obtain. This study presents a method for non-radioactive (DIG) ISH for detecting NR1 gene expression, in human infant brain tissue. We compared three pre-treatment effects, protease digestion, autoclaving (in citrate and Tris/EDTA buffer) and microwaving (in citrate and Tris/EDTA buffer). Tissue had been fixed in formalin for 2-12 weeks. Results were compared for the hybridization and background signal intensities, and tissue morphology. We found that optimum results were obtained using 12-min microwave pre-treatment in Tris/EDTA buffer. This method produced optimum signal to background ratio in infant and adult tissue, preserved tissue morphology, and was suitable for use across a broad range of fixation times.

Kinetics of HCMV immediate early mRNA expression in stably transfected fibroblasts

Compelling evidence supports an intimate link in time and space between eukaryotic pre-mRNA synthesis and processing and nucleocytoplasmic transport of mature mRNA. In this study, we analyzed the kinetic behavior of these processes in a quantitative manner. We used FISH and confocal scanning laser microscopy to detect transcripts produced by an inducible human cytomegalovirus immediate early (HCMV-IE) expression system. Upon induction, a large amount of pre-mRNA accumulated in nuclear foci at or near their transcription sites and, at later time, throughout the nucleoplasm. Inhibition of RNA polymerase II activity resulted in a rapid decrease in the number of transcripts in the nuclear RNA foci (half time ∼two minutes), indicating that accumulated transcripts were rapidly spliced and then released. The dispersed nucleoplasmic transcripts exited the nucleus with a half time of ∼10 minutes. Both processes were temperature dependent, suggesting that mRNA export is an active process. RNA polymerase II activation revealed that production of mature HCMV IE mRNAs required less than five minutes. Transcripts radiated from the gene at an average speed of ∼0.13 μm2/sec from this time on. Thus, it appears that these processes are tightly linked in time and space, with the splicing reaction as a rate-limiting factor.

Induction of p21 mRNA synthesis after short-wavelength UV light visualized in individual cells by RNA FISH

Expression of the cyclin-dependent kinase inhibitor gene p21 is induced after DNA damage and plays a role in cell survival. The exact mechanism of induction is not known, but enhancement of mRNA stability has recently been implicated as an important factor. To obtain further insight into the dynamics of p21 gene expression at the individual cell level, normal fibroblasts, GM1492 fibroblasts from a Bloom's syndrome patient, and U2OS osteosarcoma cells were UVC irradiated, fixed at different time points, and subjected to mRNA fluorescence in situ hybridization (FISH) and immunocytochemical staining. In mock-irradiated normal fibroblasts, a subfraction of cells revealed low levels of p21 mRNA synthesis. After UVC treatment, p21 transcripts accumulated over time in nuclear locations other than transcription foci. At 6 hr after irradiation, almost 50% of the cells displayed p21 mRNA in three different distribution patterns within the nuclei. The highest frequency of cells with cytoplasmic accumulation of p21 mRNA was seen at 17 hr after UVC treatment. We conclude that increased p21 gene transcription and possibly stabilization of newly synthesized p21 mRNA contribute to elevated levels of p21 protein after UVC irradiation. (J Histochem Cytochem 50:81-89, 2002)

Molecular cytogenetics

Refinements in cytogenetic techniques over the past 30 years have allowed the increasingly sensitive detection of chromosome abnormalities in haematological malignancies. In particular, the advent of fluorescence in situ hybridization techniques has provided significant advances in both diagnosis and research of leukaemias. The application of new multicolour karyotyping techniques has allowed the complete dissection of complex chromosome rearrangements and provides the prospect of identifying new recurrent chromosome rearrangements. Both comparative genomic hybridization and interphase fluorescence in situ hybridization avoid the use of metaphase chromosomes altogether and have allowed the genetic analysis of previously intractable targets. Recent developments in comparative genomic hybridization to DNA microarrays provide the promise of high resolution and automated screening for chromosomal imbalances. Rather than replacing conventional cytogenetics, however, these techniques have extended the range of cytogenetic analyses when applied in a complementary fashion.

Overview of fluorescence in situ hybridization techniques for molecular cytogenetics

This unit presents an overview of the FISH methodology. It covers such topics as direct versus indirect methods, sensitivity, multiplicity, resolution, and applications.

A Rett syndrome patient with a ring X chromosome: further evidence for skewing of X inactivation and heterogeneity in the aetiology of the disease

Rett syndrome (RTT) is an X-linked neurodevelopmental disorder, characterised by regression of development in young females. Recently, mutations in the MECP2 gene were found to be present in 80% of sporadic cases, but in much lower frequency (< 30%) among familial cases. Several reports claim that the pattern of X chromosome inactivation (XCI) relates to the penetrance of RTT; in some cases skewed XCI is seen in Rett patients, and in others it is observed among normal carriers. We present here a case of RTT with a 46,X,r(X) in which complete skewed inactivation of the ring was demonstrated. Further, no mutations were found in the MECP2 gene present on the intact X. Our data, in conjunction with two previously published cases of X chromosome abnormalities in RTT, indicate that X chromosome rearrangements are sporadically associated with RTT in conjunction with extreme skewing of X inactivation. Based on our case and reported data, we discuss the evidence for a second X-linked locus for RTT associated with lower penetrance, and a different pattern of XCI, than for MECP2. This would result in a larger proportion of phenotypically normal carrier women transmitting the mutation for this putative second locus, and account for the minority of sporadic and majority of familial cases that are negative for MECP2 mutations.

Allele-specific detection of nascent transcripts by fluorescence in situ hybridization reveals temporal and culture-induced changes in Igf2 imprinting during pre-implantation mouse development

BACKGROUND

Genomic imprinting causes parental-origin-specific monoallelic transcription of a subset of mammalian genes in the embryo and adult. There is conflicting evidence, however, for the monoallelic transcription of some imprinted genes, such as Igf2, in pre-implantation embryos.

RESULTS

We have developed an allele-specific fluorescence in situ hybridization method which involves a pair of oligonucleotide probes designed to detect an intronic polymorphism. The method, called ASO-RNA-FISH, enabled us to distinguish allelic nascent Igf2 transcripts in the cell nuclei of early mouse embryos, avoiding signals from the stored oocyte-specific transcripts. Igf2 transcription was first detectable in two-cell embryos, and biallelic transcription was predominant up to the morula stage. Then, the maternal allele became silenced during the blastocyst stage. When embryos were cultured in vitro, however, a strong bias to maternal transcription was observed up to the morula stage.

CONCLUSION

ASO-RNA-FISH revealed that a transition of Igf2 from biallelic to monoallelic transcription occurs in the blastocyst stage. This developmental regulation was modified temporarily by in vitro culture, suggesting a possible link between altered imprinting and abnormalities of the foetuses experienced in vitro culture. ASO-RNA-FISH is therefore a powerful technique for the study of allele-specific gene expression.

Treatment-induced decline of human immunodeficiency virus-1 p24 and HIV-1 RNA in lymphoid tissue of patients with early human immunodeficiency virus-1 infection

We report detailed quantitative analysis of human immunodeficiency virus-1 (HIV-1) p24 and HIV-1 RNA in tonsil biopsies from 13 patients with early, asymptomatic HIV infection before and during combination antiretroviral therapy. Using fluorescent microscopy in conjunction with reverse transcriptase-polymerase chain reaction of frozen tissue sections, we show that plasma and tissue viral loads decreased by approximately 3 logs during the 1-year treatment period, with good correlation between the HIV-1 p24 and HIV-1 RNA response in tissue. The decrease of tissue viral load was delayed compared to plasma viral load, possibly explained by the observation that the amount of follicular dendritic cell-associated virus correlated best with the area under the curve of plasma HIV-1 RNA throughout the last 12 weeks. Before and during treatment, the relative proportions of HIV-1 on follicular dendritic cells and within mononuclear cells remained constant, suggesting similar decay characteristics in these two lymphoid tissue compartments. However, viral p24 or RNA remained almost always detectable in tissue despite full suppression of HIV-1 RNA in plasma, and increased even after short-term rebounds in plasma viral load. Thus, full and sustained suppression of viral replication was required to efficiently decrease viral load in lymphoid tissue, but complete abolition of residual viral replication was not achieved.

RNA polymerase II localizes at sites of human cytomegalovirus immediate-early RNA synthesis and processing

Pre-mRNA synthesis in eukaryotic cells is preceded by the formation of a transcription initiation complex and binding of unphosphorylated RNA polymerase II (Pol II) at the promoter region of a gene. Transcription initiation and elongation are accompanied by the hyperphosphorylation of the carboxy-terminal domain (CTD) of Pol II large subunit. Recent biochemical studies provided evidence that RNA processing factors, including those required for splicing, associate with hyperphosphorylated CTDs forming "transcription factories." To directly visualize the existence of such factories, we simultaneously detected human cytomegalovirus immediate-early (IE) DNA and RNA with splicing factors and Pol II in rat 9G cells inducible for IE gene expression. Combined in situ hybridization and immunocytochemistry revealed that, after induction, both splicing factors and Pol II are present at the sites of IE mRNA synthesis and of IE mRNA processing that extend from the transcribing gene. Noninduced cells revealed no such associations. When IE mRNA-synthesizing cells were treated with a transcription inhibitor, these associations disappeared within 30 min. Our results show that the association of Pol II and splicing factors with IE DNA is dependent on its transcriptional activity and furthermore suggest that splicing factors are still associated with Pol II during active splicing.

Sensitive mRNA detection by fluorescence in situ hybridization using horseradish peroxidase-labeled oligodeoxynucleotides and tyramide signal amplification

With the ongoing progress in human genome projects, many genes are discovered whose function and/or expression pattern are not known. Most of these genes are expressed in relatively low abundance compared to housekeeping genes such as elongation factor-1alpha and beta-actin. Gene expression is studied by Northern blot assays or by semiquantitative PCR methods. Another method is the visualization of transcripts in tissue or cell cultures by fluorescence in situ hybridization (FISH). However, for low-abundance RNA detection, this method is hampered by its limited detection sensitivity and by the interference of background signals with specific hybridization signals. Background signals are introduced by nonspecific hybridization of probe sequences or nonspecific binding of antibodies used for visualization. To eliminate background signals derived from both sources and to benefit from the peroxidase-driven tyramide signal amplification (TSA), we directly conjugated horseradish peroxidase (HRP) to oligodeoxynucleotides (ODNs) and used these probes to study in the bladder cancer cell line 5637 the expression of various cytokine genes which, according to Northern hybridization and reverse transcriptase-polymerase chain reaction (RT-PCR) assays, are expressed at levels up to 10,000-fold less than abundantly expressed housekeeping genes. The results show that reduction of probe complexity and the limited use of immunocytochemical detection layers strongly reduces noise signals derived from nonspecific binding of nucleic acid probe and antibodies. The use of the HRP-ODNs in combination with TSA allowed detection of low-abundance cytokine mRNAs by FISH.

Staining of the midbody by an anti-digoxin-specific antibody

Using RNA in situ hybridization to reveal cytoplasmic localization patterns of mRNAs in cultured cells, we noted unexpected staining of a cytoplasmic component in telophase cells. Control experiments revealed that the anti-digoxin-specific antibody was responsible for this staining. Because the staining was observed only at a position where both daughter cells are still connected, we identified the stained component as the midbody. This was confirmed by double staining of cells with anti-digoxin and anti-alpha-tubulin antibodies. We concluded that anti-digoxin-specific antibody shows crossreactivity with a component present in the midbody.

Intergenic transcription and transinduction of the human beta-globin locus

We have identified novel nuclear transcripts in the human beta-globin locus using nuclear run-on analysis in erythroid cell lines and in situ hybridization analysis of erythroid tissue. These transcripts extend across the LCR and intergenic regions but are undetectable in nonerythroid cells. Surprisingly, transient transfection of a beta-globin gene (epsilon, gamma, or beta) induces transcription of the LCR and intergenic regions from the chromosomal beta-globin locus in nonerythroid cell lines. The beta-globin genes themselves, however, remain transcriptionally silent. Induction is dependent on transcription of the globin gene in the transfected plasmid but does not require protein expression. Using in situ hybridization analysis, we show that the plasmid colocalizes with the endogenous beta-globin locus providing insight into the mechanism of transinduction.

Platinum porphyrins as phosphorescent label for time-resolved microscopy

We investigated phosphorescent metalloporphyrins as potential labels for time-resolved microscopy. On the basis of spectroscopic analysis of their physicochemical properties (quantum yield, molar absorption coefficient, decay times) the best candidates were selected. Next, we synthesized antibody and avidin metalloporphyrin conjugates. The optimal F/P ratio with respect to quantum yield, decay time, and retention of biological activity of these immunoreagents was determined. The reagents were then evaluated by in situ hybridization and immunocytochemical procedures for demonstration of hapten-labeled DNA probes, membrane antigens (CD type), and 28S rRNA. All stained samples exhibited bright phosphorescence that could be selectively detected using time-resolved microscopy, especially when glucose/glucose oxidase was added to the embedding medium to deplete oxygen. Applications of time-resolved detection of phosphorescent porphyrins in strongly autofluorescent material (histological sections) are discussed.

Splicing factors associate with nuclear HCMV-IE transcripts after transcriptional activation of the gene, but dissociate upon transcription inhibition: evidence for a dynamic organization of splicing factors

Before being transported to the cytoplasm, intron-containing pre-mRNAs have to be spliced somewhere in the cell nucleus. Efficient splicing requires an ordered assembly of splicing factors onto the pre-mRNAs. To accomplish this, intron containing genes may be preferentially localized at nuclear sites enriched for splicing factors or alternatively, splicing factors may circulate throughout the nucleus and have the ability to associate with randomly positioned nascent transcripts. Combined detection of HCMV-IE mRNA/DNA and splicing factors in rat 9G cells that can be induced for IE gene expression shows that IE genes are not associated with speckled regions enriched for splicing factors when transcriptionally inactive, but ‘attract’ splicing factors when transcriptionally activated. This process proved reversible after transcription inhibition. IE transcripts appeared to be retained near the transcription site in track-like domains by splicing factors associated with them until splicing has been completed. Double-hybridization experiments revealed that a substantial part of the accumulated transcripts contain a poly(A) tail suggesting that most, if not all, IE transcripts are polyadenylated at the site of transcription. These results indicate that RNA processing may occur independent of the position of the gene in the cell nucleus relative to speckle domains.

Detection of mitochondrial DNA deletions in human skin fibroblasts of patients with Pearson's syndrome by two-color fluorescence in situ hybridization

Pearson's marrow/pancreas syndrome is a disease associated with a large mitochondrial DNA (mtDNA) deletion. The various tissues of a patient contain heteroplasmic populations of wild-type (WT) and deleted mtDNA molecules. The clinical phenotype of Pearson's syndrome is variable and is not correlated with the size and position of the deletion. The histo- and cytological distribution of WT and deleted mtDNA molecules may be factors that correlate with the phenotypical expression of the disease. Here we introduce a new application of two-color FISH to visualize WT and deleted mtDNA simultaneously in a cell population of in vitro cultured skin fibroblasts of two patients with Pearson's syndrome. At the third passage of culturing, fibroblasts showed a remarkable heterogeneity of WT and deleted mtDNA: about 90% of the cells contained almost 100% WT mtDNA, and 10% of the cells contained predominantly deleted mtDNA. At the tenth passage of culturing, fibroblasts showed a reduction of intercellular heteroplasmy from 10% to 1%, while intracellular heteroplasmy was maintained. This new approach enables detailed analysis of distribution patterns of WT and deleted mtDNA molecules at the inter- and intracellular levels in clinical samples, and may contribute to a better understanding of genotype-phenotype relationships in patients with mitochondrial diseases.

Bromodeoxyuridine: a diagnostic tool in biology and medicine, Part III. Proliferation in normal, injured and diseased tissue, growth factors, differentiation, DNA replication sites and in situ hybridization

This paper is a continuation of parts I (history, methods and cell kinetics) and II (clinical applications and carcinogenesis) published previously (Dolbeare, 1995 Histochem. J. 27, 339, 923). Incorporation of bromodeoxyuridine (BrdUrd) into DNA is used to measure proliferation in normal, diseased and injured tissue and to follow the effect of growth factors. Immunochemical detection of BrdUrd can be used to determine proliferative characteristics of differentiating tissues and to obtain birth dates for actual differentiation events. Studies are also described in which BrdUrd is used to follow the order of DNA replication in specific chromosomes, DNA replication sites in the nucleus and to monitor DNA repair. BrdUrd incorporation has been used as a tool for in situ hybridization experiments.

RNA molecules lighting up under the microscope

RNA in situ hybridization is a useful method for localizing specific mRNAs and studying the spatial and temporal organization of RNA transcription, processing and transport in cells. In this review, I describe methods of RNA in situ hybridization for tissue sections and cell preparations. Special emphasis is placed on the application of non-radioactive-labeled probes for multiparameter cell analysis. In addition, a summary of RNA in situ hybridization studies on RNA transport in the cytoplasm as well as in the nucleus of cells is given.

Expression patterns of predicted genes from the C. elegans genome sequence visualized by FISH in whole organisms

More than 10 megabases of contiguous genome sequence have been submitted to the databases by the Caenorhabditis elegans Genome Sequencing Consortium. To characterize the genes predicted from the sequence, we have developed high resolution FISH for visualization of mRNA distributions in whole animals. The high resolution and sensitivity afforded by the use of directly fluorescently labelled probes and confocal imaging permitted mRNA distributions to be recorded at the cellular and subcellular level. Expression patterns were obtained for 8 out of 10 genes in an initial test set of predicted gene sequences, indicating that FISH is an effective means of characterizing predicted genes in C. elegans.

Cell-cycle-dependent gene expression studied by two-colour fluorescent detection of a mRNA and histone mRNA

We investigated whether a probe specific for histone H3 mRNA could be used as a marker to study cell-cycle dependency of gene expression by double-fluorescent RNA in situ hybridization (FISH). First, we showed that all S-phase cells in cell cultures having incorporated BrdU revealed histone H3 mRNA expression by RNA FISH, indicating that histone H3 expression is a reliable marker for S-phase cells. Second, we analysed whether the expression of human cytomegalovirus immediate early genes in rat 9G cells, which are known to be induced in an S-phase dependent way by cycloheximide, correlated with the expression of histone H3 mRNA. Double-hybridization experiments with a digoxigenin-labelled probe for IE mRNA and a fluoresceinated probe for histone H3 mRNA revealed that cells expressing IE mRNA also expressed histone H3 mRNA. Third, we examined the cell-cycle dependency of luciferase gene expression in X1 cells. Luciferase mRNA is heterogeneously expressed in X1 cell cultures, but cells expressing luciferase did not necessarily express histone H3 mRNA. This indicates that luciferase gene expression in X1 cells is not induced during S-phase. The results of our study show that histone H3 mRNA expression can be successfully used as a marker to establish cell-cycle dependency of gene expression by double-RNA FISH.

Transcription complex stability and chromatin dynamics in vivo

Distant regulatory sequences affect transcription through long-range chromatin interactions. Visualization of transcriptional activity of genes that compete for distant elements, using the globin locus as a model, has revealed the dynamics of chromatin interactions in vivo. Multiple genes appear to be transcribed alternately rather than at the same time to generate several messenger RNAs in one cell. The regulator may stably complex with one gene at a time and switch back and forth between genes in a flip-flop mechanism.

RNAs radiate from gene to cytoplasm as revealed by fluorescence in situ hybridization

Genes for Epstein-Barr virus, human cytomegalovirus immediate early antigen and luciferase are abundantly transcribed in Namalwa, rat 9G and X1 cells, respectively. The EBV transcripts and HCMV-IE transcripts are extensively spliced, while in the luciferase transcript only a small intron sequence has to be spliced out. EBV transcripts are hardly localized in the cytoplasm while the luciferase and HCMV-IE transcripts are present in the cytoplasm and translated into proteins. We have correlated these characteristics with nuclear RNA distribution patterns as seen by fluorescence in situ hybridization. Transcripts of the HCMV-IE transcription unit were shown to be present in a main nuclear signal in the form of a track or elongated dot and as small nuclear RNA signals that radiate from this site towards the cytoplasm. A similar distribution pattern of small RNA signals was observed for transcripts of the luciferase gene, whereas the main nuclear signal was always observed as a dot and never as a track or elongated dot. In Namalwa cells, EBV transcripts were only present as track-like signals. The results suggest that when the extent for splicing is high, unspliced or partially spliced mRNAs begin to occupy elongated dot or track-like domains in the vicinity of the gene. When the extent of splicing is low, splicing is completed co-transcriptionally, leading to a bright dot-like signal. The presence of small nuclear spots in addition to the main signal correlates with cytoplasmic mRNA expression. The small spots most likely represent, therefore, mRNAs in transport to the cytoplasm.

FISH in genome research and molecular diagnostics

Fluorescence in situ hybridization (FISH) has profoundly altered the aspect of genome research and molecular diagnostics. Deletions of only a few kilobases can be detected by hybridizing probes to naked DNA fibers. Loss or gain of chromosomal material in tumor cells can be visualized using comparative genome hybridization. Further diversification of FISH application will result from new ultrasensitive detection techniques.

Hippocampal loss of N-methyl-D-aspartate receptor subunit 1 mRNA in chronic temporal lobe epilepsy

The hippocampal distribution of mRNA for the N-methyl-D-aspartate (NMDA) receptor subunit 1 (NR1) was examined by non-radioactive in situ hybridization in 21 archival formalin-fixed and paraffin-embedded surgical specimens from patients with pharmacoresistant chronic epilepsy and in normal control specimens obtained at autopsy. Using the digoxigenin-labeling procedure, ribonucleotide probes were found to be significantly more sensitive than synthetic oligonucleotide probes. In normal autopsy specimens and in surgical specimens without Ammon's horn sclerosis there was intense NR1 expression in a great majority of the dentate gyrus granular cells. Many neurons in the hippocampal pyramidal cell layer also revealed a strong signal intensity. The strata oriens and moleculare of Ammon's horn and the molecular layer of the dentate gyrus contained only few labeled neurons. In the subiculum and entorhinal cortex most neurons throughout various layers were positive. In hippocampal specimens of patients with chronic epilepsy there was a loss of NR1-positive cells that was closely related to the overall neuronal loss in the respective specimen and to Ammon's horn sclerosis. These data suggest that the loss of NR1 expression is a secondary phenomenon rather than an event that is relevant for the pathogenesis of epileptic seizures.

Differential expression in blood stages of the gene coding for the 21-kilodalton surface protein of ookinetes of Plasmodium berghei as detected by RNA in situ hybridisation

The developmentally regulated transcription of the gene encoding the ookinete surface protein, Pbs21, has been investigated in the rodent malaria parasite, Plasmodium berghei, by RNA in situ hybridisation using fluorescently labelled DNA probes. We used a procedure that will allow the visualisation of cytoplasmic mRNA in the parasite and of high copy DNA repeats in the nucleus. Specific hybridisation to Pbs21 mRNA occurred in the cytoplasm of female gametocytes, zygotes and ookinetes, while asexual blood stages, male gametocytes and gametes showed no fluorescence. Analysis of the transcription of the Pbs21 gene during blood stage development in two tightly synchronised parasite clones using the same methodology revealed that transcription is restricted to sexual stages and is initiated in immature gametocytes at 19 h post invasion (hpi). At this point in development it is not yet possible to discriminate between the morphology of asexual trophozoites and immature gametocytes. At 24 hpi approximately 50% of the gametocytes transcribed the Pbs21 gene and the morphology of these gametocytes was identical and female. The distribution of the mRNA encoding Pbs21 confirmed that post-transcriptional control of expression occurred in the cytoplasm by repression of translation and not through delayed transport of the message to the cytoplasm. The transcription of the Pbs21 gene is the earliest demonstrated event in gametocytogenesis in rodent malaria species to date.

Expression of nicotinic acetylcholine receptors in the rat superior cervical ganglion on mRNA and protein level

The expression of nicotinic acetylcholine receptors (nAChR) in the rat superior cervical ganglion was investigated by Western blotting, immunohistochemistry and non-radioactive in situ hybridization applying probes for the alpha 4-1 and beta 2 subunit mRNA. Immunoblot analysis of homogenized ganglia using the anti-nAChRs antibody WF6 revealed a labeled protein band of apparent molecular weight of 40 kDa which is typical for the alpha subunit of nAChRs. Applying double-labeling immunofluorescence with antibodies against tyrosine hydroxylase, nAChR-like molecules were identified in most postganglionic neurons and in a subpopulation of small intensely fluorescent (SIF) cells. alpha 4-1 and beta 2 subunit mRNAs were detected in all perikarya of postganglionic sympathetic neurons but not in SIF cells. These results suggest that antibodies raised against purified Torpedo AChR bind to nAChR in sympathetic ganglia and indicate that alpha 4-1 and beta 2 subunits are constituents of nAChRs in sympathetic postganglionic neurons but not of SIF cells.

Cellular distribution of nicotinic acetylcholine receptor subunit mRNAs in the human cerebral cortex as revealed by non-isotopic in situ hybridization

The pharmacology of telencephalic nicotinic acetylcholine receptors (nAChRs) has become an important issue in recent years. While in the human brain a direct pharmacological assessment is difficult to achieve the visualization of nAChRs has been enabled by histochemical techniques providing an ever increasing and improving resolution. Receptor autoradiography was used to visualize binding sites on the level of cortical layers whereas immunohistochemistry has allowed for the cell type-specific and ultrastructural localization of receptor protein. Further investigations have to elucidate the cellular sites of NAChR biosynthesis by visualizing subunit-specific transcripts. Using autopsy samples of the human precentral cortex (Area 4) as a paradigm we have applied digoxigenin-labeled cRNA probes to localize transcripts for the alpha 3- and alpha 4-1-subunits of the nAChR. In accordance with findings in the monkey cortex, the alpha 3-subunit seems to be expressed mainly in pyramidal neurons of layers III-VI of the human cerebral cortex. Transcripts for the alpha 4-1-subunit, by contrast, appear to be present in a large number of neurons throughout all layers of the cerebral cortex, consonant with its ubiquitous distribution in the rodent brain. The present findings show that also in human autopsy brains the cell type-specific detection of nAChR transcripts is possible. For the future, this technique will enable to investigate the expression of receptor transcripts in diseased human brains as compared to controls.