mRNA structure, in situ, as assessed by microscopic techniques

Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput

We argue that the study of single-cell subcellular organelle omics is needed to understand and regulate cell function. This requires and is being enabled by new technology development.

Drug targets: single-cell transcriptomics hastens unbiased discovery

Drug discovery in neuro- and psychopharmacology is lagging, and the most commonly mentioned cause is the scarcity of drug targets. Using NextGen 'sequencing based single-cell transcriptomics' (SBSCT), several hundred different receptors and channels can be identified in individual neurons, and the functional gene product can subsequently be validated. The use of single-cell transcriptome data to reveal the entire receptor repertoire is crucial, as the copy numbers of mRNAs encoding receptors are low, and when cells are pooled dilution of rare mRNAs leads to loss of signal. These overlooked receptors on key neurons often mediate robust effects that may be therapeutically useful. SBSCT also enables the identification of orphan receptors and can provide strong evidence for receptor heterodimers. Here, we compare SBSCT to other single-cell profiling methods. We argue that the unbiased nature of SBSCT makes it a powerful tool for the identification of new drug targets.

Single neurons as experimental systems in molecular biology

The cellular and the inter-connective complexity of the central nervous system (CNS) necessitate's analysis of functioning at both the system and single cell levels. Systems neuroscience has developed procedures that facilitate the analysis of multicellular systems including multielectrode arrays, dye tracings and lesioning assays, and at the single cell level there have been significant strides in assessing the physiology and morphology of individual cells. Until recently little progress had been made in understanding the molecular biology of single neuronal cells. This review will highlight the development of PCR and aRNA procedures for analysis of mRNA abundances in single cells. Also, other procedures for the analysis of protein abundances as well as the association of RNA with proteins will also be summarized. These procedures promise to provide experimental insights that will help unravel the functional mechanisms regulating the cellular components of the CNS.

Analysis of subcellularly localized mRNAs using in situ hybridization, mRNA amplification, and expression profiling

Targeting of mRNAs to distinct subcellular regions occurs in all polarized cells. The mechanisms by which RNA transport occurs are poorly understood. With the advent of RNA amplification methodologies and expression profiling it is now possible to catalogue the RNAs that are targeted to particular subcellular regions. In particular, neurons are polarized cells in which dendrites receive signals from presynaptic neurons. Upon stimulation (information receipt) the dendrite processes the information such that an immediate dendritic response is generated as well as a longer-term somatic response. The integrated cellular response results in a signal that can be propagated through the axon to the next post-synaptic neuron. Much previous work has shown that mRNAs can be localized in dendrites and that local translation in dendrites can occur. In this chapter the methods for analysis of RNAs that are localized to dendrites are reviewed and a partial list of dendritically localized RNAs is presented. This information may be useful in identifying RNA regulatory regions that are responsible for specifying rate of RNA transport and the dendritic sites at which targeted RNAs dock so that they can be translated.

Cytoplasmic proteins interact with a translational control element in the protein-coding region of proopiomelanocortin mRNA

Previous studies have indicated that proopiomelanocortin (POMC) is translationally regulated. We proposed that the regulatory mechanism involves an interaction between trans-acting protein factors and a cis-acting stem-loop structure in the coding region of POMC mRNA. Functional interactions were tested by examining the translation of mouse POMC mRNA in a rabbit reticulocyte system. Specific binding was demonstrated with ultraviolet-crosslinking and RNA gel mobility shift assays. The evidence presented supports our hypothesis that the translational regulation of POMC gene expression involves recognition of the stem-loop by RNA-binding proteins. Furthermore, POMC stem-loop RNA-binding proteins specifically recognized a predicted stem-loop found in the coding region of corticotropin-releasing hormone, suggesting a novel mechanism of gene regulation that may extend to other neuropeptides as well.

Immunoautoradiographic and in situ hybridization analysis of corticotropin-releasing hormone biosynthesis in the hypothalamic paraventricular nucleus

Corticotropin-releasing hormone (CRH) gene transcription and mRNA expression are keyed to stimuli activating the pituitary-adrenocortical axis, suggesting a connection between neuronal activation and synthesis of active peptide. However, the relationship between CRH mRNA and levels of CRH peptide remains to be definitively established. The present report characterizes an immunoautoradiographic (IAR) strategy to assess CRH peptide expression in an anatomical context. Non-fixed tissue sections through the rat hypothalamus were reacted with a primary antibody against rat CRH, followed by incubation with [35S] or [125I] labeled secondary antibody. Autoradiography performed on reacted sections revealed that CRH immunoreactivity could be detected in CRH-containing regions of the hypothalamus and amygdala. Generation of CRH signal was blocked by preabsorption of primary antibody with CRH peptide, demonstrating antibody specificity. IAR performed on nitrocellulose blotted with synthetic CRH peptide revealed a linear relationship between peptide quantity and intensity of autoradiographic signal, verifying that this method is appropriate for semi-quantitative analysis of CRH peptide regulation. Assessment of CRH peptide regulation revealed a significant increase in CRH content in adrenalectomized rats (ADX) relative to sham-adrenalectomized (SHAM) controls (196%). In situ hybridization performed on adjacent sections revealed a similar increase in CRH mRNA expression in ADX rats (256%), and a significant correlation between CRH peptide and mRNA measures (r = 0.68). No ADX induced changes were seen in median eminence, dorsomedial hypothalamus or central amygdaloid nucleus. The results of this study indicate that CRH biosynthesis appears to be driven by amount of available mRNA, rather than changes in translational efficacy. In addition, the IAR technique appears ideally suited to allow concomitant assessment of mRNA and protein expression within defined populations of CNS neurons.

On the nature and differential distribution of mRNAs in hippocampal neurites: implications for neuronal functioning

Neurons are highly polarized cells with a mosaic of cytoplasmic and membrane proteins differentially distributed in axons, dendrites, and somata. In Drosophila and Xenopus, mRNA localization coupled with local translation is a powerful mechanism by which regionalized domains of surface or cytoplasmic proteins are generated. In neurons, there is substantial ultrastructural evidence positing the presence of protein synthetic machinery in neuronal processes, especially at or near postsynaptic sites. There are, however, remarkably few reports of mRNAs localized to these regions. We now present direct evidence that an unexpectedly large number of mRNAs, including members of the glutamate receptor family, second messenger system, and components of the translational control apparatus, are present in individual processes of hippocampal cells in culture.