Modifiers of solid RNP granules control normal RNP dynamics and mRNA activity in early development

Ribonucleoproteins (RNPs) often coassemble into supramolecular bodies with regulated dynamics. The factors controlling RNP bodies and connections to RNA regulation are unclear. During Caenorhabditis elegans oogenesis, cytoplasmic RNPs can transition among diffuse, liquid, and solid states linked to mRNA regulation. Loss of CGH-1/Ddx6 RNA helicase generates solid granules that are sensitive to mRNA regulators. Here, we identified 66 modifiers of RNP solids induced by cgh-1 mutation. A majority of genes promote or suppress normal RNP body assembly, dynamics, or metabolism. Surprisingly, polyadenylation factors promote RNP coassembly in vivo, suggesting new functions of poly(A) tail regulation in RNP dynamics. Many genes carry polyglutatmine (polyQ) motifs or modulate polyQ aggregation, indicating possible connections with neurodegenerative disorders induced by CAG/polyQ expansion. Several RNP body regulators repress translation of mRNA subsets, suggesting that mRNAs are repressed by multiple mechanisms. Collectively, these findings suggest new pathways of RNP modification that control large-scale coassembly and mRNA activity during development.     

Evolution of proteins and gene expression levels are coupled in Drosophila and are independently associated with mRNA abundance, protein length, and number of protein-protein interactions

Organismic evolution requires that variation at distinct hierarchical levels and attributes be coherently integrated, often in the face of disparate environmental and genetic pressures. A central part of the evolutionary analysis of biological systems remains to decipher the causal connections between organism-wide (or genome-wide) attributes (e.g., mRNA abundance, protein length, codon bias, recombination rate, genomic position, mutation rate, etc) as well as their role-together with mutation, selection, and genetic drift-in shaping patterns of evolutionary variation in any of the attributes themselves. Here we combine genome-wide evolutionary analysis of protein and gene expression data to highlight fundamental relationships among genomic attributes and their associations with the evolution of both protein sequences and gene expression levels. Our results show that protein divergence is positively coupled with both gene expression polymorphism and divergence. We show moreover that although the number of protein-protein interactions in Drosophila is negatively associated with protein divergence as well as gene expression polymorphism and divergence, protein-protein interactions cannot account for the observed coupling between regulatory and structural evolution. Furthermore, we show that proteins with higher rates of amino acid substitutions tend to have larger sizes and tend to be expressed at lower mRNA abundances, whereas genes with higher levels of gene expression divergence and polymorphism tend to have shorter sizes and tend to be expressed at higher mRNA abundances. Finally, we show that protein length is negatively associated with both number of protein-protein interactions and mRNA abundance and that interacting proteins in Drosophila show similar amounts of divergence. We suggest that protein sequences and gene expression are subjected to similar evolutionary dynamics, possibly because of similarity in the fitness effect (i.e., strength of stabilizing selection) of disruptions in a gene's protein sequence or its mRNA expression. We conclude that, as more and better data accumulate, understanding the causal connections among biological traits and how they are integrated over time to constrain or promote structural and regulatory evolution may finally become possible.     

Neurotrophin expression in rat hippocampal slices: a stimulus paradigm inducing LTP in CA1 evokes increases in BDNF and NT-3 mRNAs.

We report that stimulation inducing long-term potentiation (LTP) in the CA1 pyramidal cell layer of the hippocampus evokes significant increases in both BDNF and NT-3 mRNAs in CA1 neurons. No changes in BDNF or NT-3 mRNA levels were seen in the nonstimulated regions of the pyramidal cell layer or the dentate. No change was seen in the levels of NGF mRNA at the time point examined. These results suggest that relatively normal levels of activity may regulate region-specific neurotrophin levels in the hippocampus. Given that known effects of NGF (and presumably of BDNF and NT-3) include elevation of neurotransmitter levels, elevation of sodium channels, and promotion of axonal terminal sprouting, activity-associated changes in neurotrophin levels may play a role in regulating neural connections in the adult as well as the developing nervous system.     

Upregulation by KCl treatment of eukaryotic translation elongation factor 1A (eEF1A) mRNA in the dendrites of cultured rat hippocampal neurons

Activity-dependent local translation in the dendrites of brain neurons plays an important role in the synapse-specific provision of proteins necessary for strengthening synaptic connections. In this study we carried out combined fluorescence in situ hybridization (FISH) and immunocytochemistry (IC) and showed that more than half of the eukaryotic elongation factor 1A (eEF1A) mRNA clusters overlapped with or were immediately adjacent to clusters of PSD-95, a postsynaptic marker, in the dendrites of cultured rat hippocampal neurons. Treatment of the neurons with KCl increased the density of the dendritic eEF1A mRNA clusters more than two-fold. FISH combined with IC revealed that the KCl treatment increased the density of eEF1A mRNA clusters that overlapped with or were immediately adjacent to PSD-95 clusters. These results indicate that KCl treatment increases both the density of eEF1A mRNA clusters and their synaptic association in dendrites of cultured neurons.     

EphB3 receptor and ligand expression in the adult rat brain

Summary Eph receptors and ligands are two families of proteins that control axonal guidance during development. Their expression was originally thought to be developmentally regulated but recent work has shown that several EphA receptors are expressed postnatally. The EphB3 receptors are expressed during embryonic development in multiple regions of the central nervous system but their potential expression and functional role in the adult brain is unknown. We used in situ hybridization, immunohistochemistry, and receptor affinity probe in situ staining to investigate EphB3 receptors mRNA, protein, and ligand (ephrin-B) expression, respectively, in the adult rat brain. Our results indicate that EphB3 receptor mRNA and protein are constitutively expressed in discrete regions of the adult rat brain including the cerebellum, raphe pallidus, hippocampus, entorhinal cortex, and both motor and sensory cortices. The spatial profile of EphB3 receptors was co-localized to regions of the brain that had a high level of EphB3 receptor binding ligands. Its expression pattern suggests that EphB3 may play a role in the maintenance of mature neuronal connections or re-arrangement of synaptic connections during late stages of development.     

Expression of Bmp ligands and receptors in the developing Xenopus retina

Bone morphogenetic proteins (BMPs) act repeatedly in the development of nervous system tissues. While BMP signaling is critical for the early growth and patterning of the eye, we are interested in possible later functions of BMPs in the morphological development of retinal neurons and formation of synaptic connections. Therefore, we conducted an in situ hybridization analysis of the mRNA expression for the ligands Bmp2, -4 and 7 and the type Ia, Ib and II receptors (BmprIa, BmprIb and BmprII) during development of the retina of Xenopus laevis. Bmp4 mRNA is expressed in the dorsal retina and Bmp7 in the distal peripheral retina during the period of cell differentiation, while Bmp2 is not present in the eye. The type I receptors are expressed predominantly ventrally, from the optic vesicle stage until at least stage 35/36, after most cells have differentiated and many synaptic connections have formed. BmprII mRNA, however, is distributed evenly across the dorsoventral axis, with highest expression in retinal ganglion cell and inner nuclear layers.     

Linking nuclear mRNP assembly and cytoplasmic destiny

From the very beginning, mRNAs have a complex existence. They are transcribed, capped, spliced, modified at the 3'end, exported from the nucleus, translated, and eventually degraded. These many events not only affect the overall survival and properties of an mRNA, but are also carefully co-ordinated and integrated with quality control mechanisms that function to ensure that only 'proper' mRNAs are translated at the correct developmental time and place. This does not mean that all mRNAs follow a single or uniform path from synthesis to death. Instead, there are diverse means by which the activities of specific mRNAs are regulated, and these controls often depend upon multiple events in the mRNA's life. mRNAs are not found naked in the cell, instead they are part of complex RNPs (ribonucleoproteins) that consist of many factors. These RNPs are highly dynamic structures that change during the lifetime of a given RNA; linking events such as synthesis and processing to the final fate of the mRNA. Here, we will discuss what is known of the assembly of RNPs in general, with specific reference to the myriad of connections between different nuclear events and the cytoplasmic activity of an mRNA. Due to space limitations this review is not comprehensive, instead we focus on specific examples to illustrate these emerging themes in gene expression.     

Synaptic connections of the common inhibitory motoneurone within the fifth thoracic ganglion of crayfish

The common inhibitor (CI) has been studied morphologically and electrophysiologically in the fifth thoracic ganglion of crayfish (Procambarus clarkii). It has a large soma and possesses two separate dendritic fields arising from distinct integrative segments.In vitro preparations display motor outputs ranging from tonic activity to fictive locomotion. The CI's tonic firing frequency increases as more excitors are recruited, and displays two peaks of frequency during fictive locomotion, one during stance, the other during swing.Paired intracellular recordings have been used to demonstrate the different central synaptic connections received or made by the CI. At least 27% of the proximal excitors receive monosynaptic connections from the CI corresponding to post-synaptic depolarizations of small amplitude mediated by GABA. However as they do not change the overall activities of the excitors which receive them, they may be used for local inhibition within the dendrites. Besides, electrical synapses between several proximal excitors and the CI may synchronize their activity.The CI receives synaptic connections arising from interneurones. Some are direct either by inhibitory monosynaptic connections or by electrical couplings whereas others arise through polysynaptic pathways. All these connections are functionally significant in the control of the CI firing activity and in its motor coordinations.     

Chromocentral nature of interchromosome connections coorienting nonhomologous chromosomes in meiosis of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis> females

Data are presented in favor of universal significance of physical connections between pericentromeric regions of homologs in their orientation to the opposite poles of the first meiotic division in Drosophila melanogaster. Disturbances in the formation of such connections caused by structural or locus mutations are compensated for by the presence of pericentromeric chiasmata between homologs or (in the case of their absence) by chromocentral connections between nonhomologs being preserved up to the prometaphase. In the latter case, an interchromosome effect on chromosome disjunction and nonhomologous pairing is registered by genetic methods. Inhibition of the formation of the division spindle fibers during prometaphase of meiosis 1 by the long-term action of colcemide promotes the retention of connections between paired nonexchanged homologs and between nonhomologous chromosomes with abnormal homologous pairing because of heterozygosity for numerous inversions and transpositions (X and autosome 2). These connections are registered cytologically. Cytologically registered are also connections between normal X chromosomes and metacentric compounds by the arms of autosome 2 (C(2L)RM, C(2R)RM), which is the known case of the interchromosome effect on chromosome nondisjunction. It is supposed that cytologically detected associations between compounds are realized through a normal mechanism, as a result of interaction and formation of orienting connections between the homologous pericentromeric regions of these compounds. Cytological evidence is presented for colocation of compounds in the chromocentrally organized nucleus of somatic and germline cells.     

Highly nonrandom features of synaptic connectivity in local cortical circuits

How different is local cortical circuitry from a random network? To answer this question, we probed synaptic connections with several hundred simultaneous quadruple whole-cell recordings from layer 5 pyramidal neurons in the rat visual cortex. Analysis of this dataset revealed several nonrandom features in synaptic connectivity. We confirmed previous reports that bidirectional connections are more common than expected in a random network. We found that several highly clustered three-neuron connectivity patterns are overrepresented, suggesting that connections tend to cluster together. We also analyzed synaptic connection strength as defined by the peak excitatory postsynaptic potential amplitude. We found that the distribution of synaptic connection strength differs significantly from the Poisson distribution and can be fitted by a lognormal distribution. Such a distribution has a heavier tail and implies that synaptic weight is concentrated among few synaptic connections. In addition, the strengths of synaptic connections sharing pre- or postsynaptic neurons are correlated, implying that strong connections are even more clustered than the weak ones. Therefore, the local cortical network structure can be viewed as a skeleton of stronger connections in a sea of weaker ones. Such a skeleton is likely to play an important role in network dynamics and should be investigated further.     

Human connectomics

Recent advances in non-invasive neuroimaging have enabled the measurement of connections between distant regions in the living human brain, thus opening up a new field of research: Human connectomics. Different imaging modalities allow the mapping of structural connections (axonal fibre tracts) as well as functional connections (correlations in time series), and individual variations in these connections may be related to individual variations in behaviour and cognition. Connectivity analysis has already led to a number of new insights about brain organization. For example, segregated brain regions may be identified by their unique patterns of connectivity, structural and functional connectivity may be compared to elucidate how dynamic interactions arise from the anatomical substrate, and the architecture of large-scale networks connecting sets of brain regions may be analysed in detail. The combined analysis of structural and functional networks has begun to reveal components or modules with distinct patterns of connections that become engaged in different cognitive tasks. Collectively, advances in human connectomics open up the possibility of studying how brain connections mediate regional brain function and thence behaviour.     

Identification of two proteins that bind to a pyrimidine-rich sequence in the 3'-untranslated region of GAP-43 mRNA.

GAP-43 is a membrane phosphoprotein that is important for the development and plasticity of neural connections. In undifferentiated PC12 pheochromocytoma cells, GAP-43 mRNA degrades rapidly ( t = 5 h), but becomes stable when cells are treated with nerve growth factor. To identify trans- acting factors that may influence mRNA stability, we combined column chromatography and gel mobility shift assays to isolate GAP-43 mRNA binding proteins from neonatal bovine brain tissue. This resulted in the isolation of two proteins that bind specifically and competitively to a pyrimidine-rich sequence in the 3'-untranslated region of GAP-43 mRNA. Partial amino acid sequencing revealed that one of the RNA binding proteins coincides with FBP (far upstream element binding protein), previously characterized as a protein that resembles hnRNP K and which binds to a single-stranded, pyrimidine-rich DNA sequence upstream of the c -myc gene to activate its expression. The other binding protein shares sequence homology with PTB, a polypyrimidine tract binding protein implicated in RNA splicing and regulation of translation initiation. The two proteins bind to a 26 nt pyrimidine-rich sequence lying 300 nt downstream of the end of the coding region, in an area shown by others to confer instability on a reporter mRNA in transient transfection assays. We therefore propose that FBP and the PTB-like protein may compete for binding at the same site to influence the stability of GAP-43 mRNA.