Ultrastructural distribution of myosin heavy chain mRNA in cardiac tissue: a comparison of frozen and LR White embedment

Resin embedded multicycle imaging (REMI): a tool to evaluate protein domains

Protein complexes associated with cellular processes comprise a significant fraction of all biology, but our understanding of their heterogeneous organization remains inadequate, particularly for physiological densities of multiple protein species. Towards resolving this limitation, we here present a new technique based on resin-embedded multicycle imaging (REMI) of proteins in-situ. By stabilizing protein structure and antigenicity in acrylic resins, affinity labels were repeatedly applied, imaged, removed, and replaced. In principle, an arbitrarily large number of proteins of interest may be imaged on the same specimen with subsequent digital overlay. A series of novel preparative methods were developed to address the problem of imaging multiple protein species in areas of the plasma membrane or volumes of cytoplasm of individual cells. For multiplexed examination of antibody staining we used straightforward computational techniques to align sequential images, and super-resolution microscopy was used to further define membrane protein colocalization. We give one example of a fibroblast membrane with eight multiplexed proteins. A simple statistical analysis of this limited membrane proteomic dataset is sufficient to demonstrate the analytical power contributed by additional imaged proteins when studying membrane protein domains.

Tracking DNA and RNA sequences at high resolution

In this chapter, the basic principles and protocols of the electron microscopical detections of specific DNA and RNA sequences are described. We focused primarily on a comparison of various methods of electron microscopy in situ hybridization (EM-ISH) with respect to their sensitivity and the structural preservation of the sample with the aim of helping the readers select the appropriate hybridization protocol. As the post-embedding EM-ISH most frequently represents the optimal choice, the protocol for the post-embedding EM-ISH approach is described in detail. Concurrently, the alternative methods based on the enzymatic synthesis of the labeled nucleic acids chains that can be used for the detection of DNA or RNA molecules in situ are mentioned. In this respect, the technique enabling the enzymatic detection of the polyadenylated RNA sequences is described in detail.

Electron microscopy in situ hybridization: tracking of DNA and RNA sequences at high resolution

Electron microscopy in situ hybridization (EM-ISH) represents a powerful method that enables the localization of specific sequences of nucleic acids at high resolution. We provide here an overview of three different nonisotopic EM-ISH approaches that allow the visualization of nucleic acid sequences in cells. A comparison of various methods with respect to their sensitivity and the structural preservation of the sample is presented, with the aim of helping the reader to choose a convenient hybridization procedure. The post-embedding EM-ISH protocol that currently represents the most widely used technique is described in detail, with a special emphasis on the organization of the cell nucleus.

In situ detection of specific gene expression during and immediately after transcription at electron microscopic level

In situ hybridization (ISH) is a widely applied technique used for visualizing specific nucleic acid sequences at chromosomal, cytologic, and histologic levels. It sometimes fails, however, to demonstrate precise cell identity, early stages of gene expression and variants of alternative splicing because of its limited resolution. To overcome this shortcoming, we have developed an improved ISH technique at the electron microscopic (EM) level by conducting en bloc hybridization before embedding (pre-embedding) and immuno-EM detection after ultra-thin sectioning (post-embedding). We applied this technique to demonstrate both the dynamic expression of interleukin (IL)-6 mRNA immediately after lipopolysaccharide (LPS) treatment, and the static expression of osteonectin mRNA in a differentiating osteoblastic cell linage. Tissue samples were diced into 1mm cubes, fixed with 4% paraformaldehyde, and then successively hybridized en bloc with the digoxigenin (DIG)-labeled single-stranded probe measuring 200-300 bp with the aid of microwave treatment. After washing, for EM observation, the cubes were embedded in epon for ultra-thin sectioning, and a gold-colloid-labeled anti-DIG antibody was used for post-embedding immuno-EM; some of the cubes was directly incubated with anti-DIG antibody and developed en bloc for stereoscopic and light microscopic observation. IL-6 mRNA during and immediately after transcription was demonstrated in the nuclei of the alveolar macrophages and in neutrophils of mouse lung tissue as early as 15 min after LPS treatment, which was of better sensitivity than that by Northern blot or nuclear run-on techniques. Moreover, in mouse calvaria tissue, osteonectin mRNA both in the nucleus and the cytoplasm was observed in a differentiating osteoblastic cell linage in a differentiation-specific manner. This technique is useful in identifying specific cell types during and immediately after transcribing specific mRNA based on ultrastructural morphology.

Mechanical activity in heart regulates translation of alpha-myosin heavy chain mRNA but not its localization

Mechanical inactivity depresses protein expression in cardiac muscle tissue and results in atrophy. We explore the mechanical transduction mechanism in spontaneously beating neonatal rat cardiomyocytes expressing the alpha-myosin heavy chain (alpha-MyHC) isoform by interfering with cross-bridge function [2,3-butanedione monoxime (BDM), 7.5 mM] without affecting cell calcium. The polysome content and alpha-MyHC mRNA levels in fractions from a sucrose gradient were analyzed. BDM treatment blocked translation at initiation (162 +/- 12% in the nonpolysomal RNA fraction and 43 +/- 6% in the polysomal fraction, relative to control as 100%; P < 0.05). There was an increase in alpha-MyHC mRNA from the nonpolysomal fraction (120.5 +/- 7.7%; P < 0.05 compared with control) with no significant change in the heavy polysomes. In situ hybridization of alpha-MyHC mRNA was used to estimate message abundance as a function of the distance from the nucleus. The mRNA was dispersed through the cytoplasm in spontaneously beating cells as well as in BDM-treated cells (no significant difference). We conclude that direct inhibition of contractile machinery, but not calcium, regulates initiation of alpha-MyHC mRNA translation. However, calcium, not pure mechanical signals, appears to be important for message localization.

Subcellular localization of mRNA in neuronal cells. Contributions of high-resolution in situ hybridization techniques

The development of technologies for high-resolution nucleic acid localization in cells and tissues has contributed significantly to our understanding of transcriptional and translational regulation in eukaryotic cells. These methods include nonisotopic in situ hybridization methods for light and electron microscopy, and fluorescent tagging for the study of nucleic acid behavior in living cells. In situ hybridization to detect messenger RNA has led to the discovery that individual transcripts may be selectively targeted to particular subcellular domains. In the nervous system, certain species of mRNA have been localized in distal processes in nerve cells and glia. Direct visualization of mRNA and its interactions with subcellular features, such as synaptic specializations, cytoskeletal elements, and nuclear pores, have been achieved. Of particular interest is the presence of mRNA and ribosomes in dendrites, beneath synaptic contacts, suggesting the possibility of synaptic regulation of protein synthesis. The following article will describe the application of high-resolution in situ hybridization and live imaging techniques to the study of mRNA targeting in neurons.

Use of methacrylate De-embedding protocols for in situ hybridization on semithin plastic sections with multiple detection strategies

New plastic resins are gradually replacing traditional paraffin-embedding in situ hybridization (ISH) strategies. One unique resin that has not been fully investigated or exploited with respect to light microscopic ISH is a methacrylate mixture. The advantage of this resin is its ability to be removed from tissues postsectioning, dramatically increasing hybridization signal compared to that obtained in other plastics. The goal of this study was to evaluate the general applicability of the methacrylate embedding acetone de-embedding (MEADE) technique for ISH investigations. Several high-resolution, high-sensitivity ISH protocols are described, using both end-labeled oligonucleotides and randomly primed DNA probes (200-400 BPS), signal amplification by catalyzed reporter deposition (CARD), and chromogenic and fluorescent detection methods. With slight modification, the MEADE ISH technique permitted localization of bacterial symbionts in fragile gill tissue and collagen transcripts in foot tissue of two marine bivalves. MEADE ISH has proved extremely versatile and will likely be suitable for many future applications.

Ultrastructural localization of dendritic messenger RNA in adult rat hippocampus

An ultrastructural examination of mRNA within adult rat CA1 hippocampal dendrites was conducted using two different methods. The messages for the alpha and beta forms of the calcium-calmodulin-dependent protein kinase II were localized in ultracryosections using silver-intensified gold detection of isoform-specific oligonucleotide probes. Labeling for both isoforms was observed within the cell bodies and proximal dendrites of pyramidal neurons, but only the alpha form was observed in more distal dendrites. Unfortunately, the morphological preservation of the tissue was not sufficient to determine the localization of labeling relative to subcellular features such as dendritic spines. To address this issue, a preembedding peroxidase-based method was developed, resulting in better preservation of the neuropil. The total population of polyadenylated [poly(A)] mRNA was localized in hippocampus using a biotinylated poly(dT) probe. Poly(A) mRNA was present in the nucleus and throughout the cell body of all hippocampal cells and within isolated dendrites and glial processes within the neuropil. Within pyramidal neurons, labeling was distributed in a longitudinal pattern in proximal apical dendrites. More distally, the amount of labeling diminished, and smaller foci of labeling were observed, particularly near the plasma membrane. Concentrated labeling was present at the base of dendritic spines and, less frequently, near synapses onto the dendritic shaft. These results suggest that dendritic mRNA is found in the vicinity of postsynaptic sites and provide additional evidence that local protein synthesis may play an important role in establishing and maintaining synaptic specializations.

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.

Evaluation of pepsin treatment for electron microscopic RNA in situ hybridization on ultra-thin cryosections of cultured cells

The in situ hybridization (ISH) technique, as applied to electron microscopic detection of RNAs, was evaluated for ultra-thin cryosections of cultured rat fibroblasts (rat 9G). Experimental variables to balance penetration of detection reagents and preservation of ultrastructural morphology included various strengths of aldehyde fixation and pepsin treatment. We performed ISH for 28S ribosomal RNA (rRNA) followed by ultra-small colloidal gold immunocytochemistry and silver enhancement. An acceptable balance for 28S rRNA ISH detection was obtained using mild cross-linking fixation followed by treatment with a relative high concentration of pepsin for a short time. The ISH method presented in this study was compatible with immunocytochemical detection of protein as demonstrated by double-labeling experiments.

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.

Ultrastructural localization of myoglobin mRNA in human skeletal muscle

The intracellular localization of myoglobin mRNA in the skeletal muscles of normal subjects was examined by in situ hybridization using a biotin-labeled cDNA probe. By phase-contrast microscopy, myoglobin mRNA signals were demonstrated to be located preferentially on the A-band. Two different methods of tissue preparation, i.e., pre-embedding method and post-embedding method, were used for the electron microscopic study. With the pre-embedding method, only a few gold particles were found to be associated with cytoskeletal filaments in the intermyofibrillar space. With the post-embedding method, superior preservation of sections and higher signal intensities were obtained. Although most of the gold particles were localized on the A-band, some were seen in other regions; i.e., in the intermyofibrillar space, perinuclear space, or the I-band, where myoglobin is localized. These findings suggest that myoglobin is primarily synthesized on the A-band, where ribosomes predominantly exist, although myoglobin is also localized on the I-band. The predominant localization of myoglobin mRNA on the A-band may aid in the mRNA transcription and may be related to the regulation of myoglobin synthesis in skeletal muscle cells.

Ribosomes in the skeletal muscle filament lattice

The compartmentalization of myosin isoforms within a muscle cell (Gauthier: J. Cell Biol. 110:693-701, 1990) suggests that myosin might be assembled directly into thick filaments at sites where it is synthesized. We therefore examined myofibrils by immunoelectron microscopy to determine whether ribosomes are associated with thick filaments under conditions in which new myosin can be identified. We used the embryonic chick anterior latissimus dorsi (ALD), a slow muscle that is induced, by curare, to synthesize a fast myosin isoform that is not normally present. Myosin was localized in situ, using a gold-labeled monoclonal antibody that recognizes the new isoform. The gold marker, as expected, was localized preferentially to the A band. There was an overall increase of fivefold in the number of gold particles per micron2 of A band in the curare-treated compared to the normal ALD, indicating that the labeled isoform was largely newly formed. There was a corresponding preferential distribution of ribosomes at the A band, especially in the H-band region, and the number of ribosomes per micron2 of A band was nearly twice as high in the curare-treated as in the normal muscle. Ribosomes were located between thick filaments, often aligned in rows. We conclude that ribosomes are located within the filament lattice, and therefore that they are available for local myosin synthesis.

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.

Mechanisms for intracellular distribution of mRNA: in situ hybridization studies in muscle

The intracellular distribution of mRNA in striated muscle fibers is highly ordered, as is the structural organization of the fibers' contractile apparatus. Results from in situ hybridization of muscle mRNA are reviewed in an attempt to discern the mechanisms involved in mRNA distribution and to determine its relationship to developmental, growth, and repair processes in muscle. Nonradioactively labeled complementary RNA probes allow anatomic localization of mRNA at the light and electron microscopic level. Myosin mRNA in striated muscle is concentrated around transcriptionally active nuclei, myosin mRNA is excluded by the myofibrillar mass, myosin mRNA distribution correlates with that of cytoskeletal elements, and myosin mRNA is concentrated in regions of rapid growth and repair. The even distribution of myosin mRNA along the length of myofibrils gives no indication of specific association with either the thick or thin filaments. Of the possible mechanisms directing mRNA distribution, results from in situ hybridization and other analyses support a restricted diffusion model. Diffusion of mRNA (and polysomes) is severely limited by the myofibrillar lattice. It is possible that myosin mRNA is also associated with a cytoskeletal element, which may direct the mRNA to specific intracellular locations and affect translational activity.