Inhibition of glutamate receptor 2 translation by a polymorphic repeat sequence in the 5'-untranslated leaders

Splicing and editing of ionotropic glutamate receptors: a comprehensive analysis based on human RNA-Seq data

Ionotropic glutamate receptors (iGluRs) play key roles for signaling in the central nervous system. Alternative splicing and RNA editing are well-known mechanisms to increase iGluR diversity and to provide context-dependent regulation. Earlier work on isoform identification has focused on the analysis of cloned transcripts, mostly from rodents. We here set out to obtain a systematic overview of iGluR splicing and editing in human brain based on RNA-Seq data. Using data from two large-scale transcriptome studies, we established a workflow for the de novo identification and quantification of alternative splice and editing events. We detected all canonical iGluR splice junctions, assessed the abundance of alternative events described in the literature, and identified new splice events in AMPA, kainate, delta, and NMDA receptor subunits. Notable events include an abundant transcript encoding the GluA4 amino-terminal domain, GluA4-ATD, a novel C-terminal GluD1 (delta receptor 1) isoform, GluD1-b, and potentially new GluK4 and GluN2C isoforms. C-terminal GluN1 splicing may be controlled by inclusion of a cassette exon, which shows preference for one of the two acceptor sites in the last exon. Moreover, we identified alternative untranslated regions (UTRs) and species-specific differences in splicing. In contrast, editing in exonic iGluR regions appears to be mostly limited to ten previously described sites, two of which result in silent amino acid changes. Coupling of proximal editing/editing and editing/splice events occurs to variable degree. Overall, this analysis provides the first inventory of alternative splicing and editing in human brain iGluRs and provides the impetus for further transcriptome-based and functional investigations.

RNA biology of disease-associated microsatellite repeat expansions

Microsatellites, or simple tandem repeat sequences, occur naturally in the human genome and have important roles in genome evolution and function. However, the expansion of microsatellites is associated with over two dozen neurological diseases. A common denominator among the majority of these disorders is the expression of expanded tandem repeat-containing RNA, referred to as xtrRNA in this review, which can mediate molecular disease pathology in multiple ways. This review focuses on the potential impact that simple tandem repeat expansions can have on the biology and metabolism of RNA that contain them and underscores important gaps in understanding. Merging the molecular biology of repeat expansion disorders with the current understanding of RNA biology, including splicing, transcription, transport, turnover and translation, will help clarify mechanisms of disease and improve therapeutic development.

Rootin, a compound that inhibits root development through modulating PIN-mediated auxin distribution

Plant roots anchor the plant to the soil and absorb water and nutrients for growth. Understanding the molecular mechanisms regulating root development is essential for improving plant survival and agricultural productivity. Extensive molecular genetic studies have provided important information on crucial components for the root development control over the last few decades. However, it is becoming difficult to identify new regulatory components in root development due to the functional redundancy and lethality of genes involved in root development. In this study, we performed a chemical genetic screen to identify novel synthetic compounds that regulate root development in Arabidopsis seedlings. The screen yielded a root growth inhibitor designated as 'rootin', which inhibited Arabidopsis root development by modulating cell division and elongation, but did not significantly affect shoot development. Transcript analysis of phytohormone marker genes revealed that rootin preferentially altered the expression of auxin-regulated genes. Furthermore, rootin reduced the accumulation of PIN1, PIN3, and PIN7 proteins, and affected the auxin distribution in roots, which consequently may lead to the observed defects in root development. Our results suggest that rootin could be utilized to unravel the mechanisms underlying root development and to investigate dynamic changes in PIN-mediated auxin distribution.

FXR1P limits long-term memory, long-lasting synaptic potentiation, and de novo GluA2 translation

Translational control of mRNAs allows for rapid and selective changes in synaptic protein expression that are required for long-lasting plasticity and memory formation in the brain. Fragile X Related Protein 1 (FXR1P) is an RNA-binding protein that controls mRNA translation in nonneuronal cells and colocalizes with translational machinery in neurons. However, its neuronal mRNA targets and role in the brain are unknown. Here, we demonstrate that removal of FXR1P from the forebrain of postnatal mice selectively enhances long-term storage of spatial memories, hippocampal late-phase long-term potentiation (L-LTP), and de novo GluA2 synthesis. Furthermore, FXR1P binds specifically to the 5' UTR of GluA2 mRNA to repress translation and limit the amount of GluA2 that is incorporated at potentiated synapses. This study uncovers a mechanism for regulating long-lasting synaptic plasticity and spatial memory formation and reveals an unexpected divergent role of FXR1P among Fragile X proteins in brain plasticity.

Synthesis of two SAPAP3 isoforms from a single mRNA is mediated via alternative translational initiation

In mammalian neurons, targeting and translation of specific mRNAs in dendrites contribute to synaptic plasticity. After nuclear export, mRNAs designated for dendritic transport are generally assumed to be translationally dormant and activity of individual synapses may locally trigger their extrasomatic translation. We show that the long, GC-rich 5′-untranslated region of dendritic SAPAP3 mRNA restricts translation initiation via a mechanism that involves an upstream open reading frame (uORF). In addition, the uORF enables the use of an alternative translation start site, permitting synthesis of two SAPAP3 isoforms from a single mRNA. While both isoforms progressively accumulate at postsynaptic densities during early rat brain development, their levels relative to each other vary in different adult rat brain areas. Thus, alternative translation initiation events appear to regulate relative expression of distinct SAPAP3 isoforms in different brain regions, which may function to influence synaptic plasticity.

Polymorphisms in the GluR2 gene are not associated with amyotrophic lateral sclerosis

Excitotoxicity is thought to play a pathogenic role in amyotrophic lateral sclerosis (ALS). Excitotoxic motor neuron death is mediated through the Ca(2+)-permeable α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)-type of glutamate receptors and Ca(2+) permeability is determined by the GluR2 subunit. We investigated whether polymorphisms or mutations in the GluR2 gene (GRIA2) predispose patients to ALS. Upon sequencing 24 patients and 24 controls no nonsynonymous coding variants were observed but 24 polymorphisms were identified, 9 of which were novel. In a screening set of 310 Belgian ALS cases and 794 healthy controls and a replication set of 3157 cases and 5397 controls from 6 additional populations no association with susceptibility, age at onset, or disease duration was observed. We conclude that polymorphisms in the GluR2 gene (GRIA2) are not a major contributory factor in the pathogenesis of ALS.

AMPA receptor regulation at the mRNA and protein level in rat primary cortical cultures

Ionotropic glutamate α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptors are the major mediators of fast synaptic neurotransmission. In this work, we used primary cortical cultures from rats as a model system to study AMPA receptor regulation during in vitro cell maturation and after synaptic activity modifications. The levels of AMPA receptor mRNA and protein, along with the alternative splicing and RNA editing of the AMPA receptor subunit (GluR1-4) mRNAs, were analyzed in immature (DIV5) and mature (DIV26) rat neuronal cultures. We observed an increase in the expression of all four AMPA receptor subunits during in vitro neuronal maturation. This finding might be due to the formation of new synapses between neurons during the development of a complex neuronal network. We also analyzed the effects of stimulation (KCl and glutamate) and inhibition (APV/TTX) on rat mature neuronal cultures (DIV26): stimulation with KCl led to an overall down-regulation of GluR1 and GluR3 AMPA receptor subunits and an up-regulation of the GluR2 subunit. Similarly, glutamate treatment induced a significant down-regulation of GluR1 together with an up-regulation of GluR2. In contrast, the chronic blockade of neuronal activity that resulted from APV/TTX treatment up-regulated GluR1 and GluR3 with a parallel down-regulation of GluR2 and GluR4. RNA editing at the R/G site increased during neuronal cell maturation for all AMPA receptors (from 8–39% at DIV5 to 28–67% at DIV26). Unexpectedly, all the treatments tested induced a marked reduction (ranging from −9% to −52%) of R/G editing levels in mature neurons, primarily for the mRNA flip variant.

In summary, we showed that cultured rat cortical neurons are able to vary the stoichiometric ratios of the AMPA receptor subunits and to control post-transcriptional processes to adapt fast synaptic transmission under different environmental conditions.

Glutamate receptor ion channels: structure, regulation, and function

The mammalian ionotropic glutamate receptor family encodes 18 gene products that coassemble to form ligand-gated ion channels containing an agonist recognition site, a transmembrane ion permeation pathway, and gating elements that couple agonist-induced conformational changes to the opening or closing of the permeation pore. Glutamate receptors mediate fast excitatory synaptic transmission in the central nervous system and are localized on neuronal and non-neuronal cells. These receptors regulate a broad spectrum of processes in the brain, spinal cord, retina, and peripheral nervous system. Glutamate receptors are postulated to play important roles in numerous neurological diseases and have attracted intense scrutiny. The description of glutamate receptor structure, including its transmembrane elements, reveals a complex assembly of multiple semiautonomous extracellular domains linked to a pore-forming element with striking resemblance to an inverted potassium channel. In this review we discuss International Union of Basic and Clinical Pharmacology glutamate receptor nomenclature, structure, assembly, accessory subunits, interacting proteins, gene expression and translation, post-translational modifications, agonist and antagonist pharmacology, allosteric modulation, mechanisms of gating and permeation, roles in normal physiological function, as well as the potential therapeutic use of pharmacological agents acting at glutamate receptors.

Control of glutamate receptor 2 (GluR2) translational initiation by its alternative 3' untranslated regions

Four major glutamate receptor 2 (GluR2) transcripts differing in size (approximately 4 and approximately 6 kilobases) due to alternative 3' untranslated regions (UTRs), and also containing alternative 5'UTRs, exist in the brain. Both the long 5'UTR and long 3'UTR repress translation of GluR2 mRNA; repression by the 3'UTR is relieved after seizures. To understand the mechanism of translational repression, we used rabbit reticulocyte lysates as an in vitro translation system to examine the expression profiles of firefly reporter mRNAs bearing alternative combinations of GluR2 5'UTR and 3'UTR in the presence of inhibitors of either translational elongation or initiation. Translation of reporter mRNAs bearing the long GluR2 3'UTR was insensitive to low concentrations of the translation elongation inhibitors cycloheximide (0.7-70 nM) and anisomycin (7.5-750 nM), in contrast to a reporter bearing the short 3'UTR, which was inhibited. These data suggest that the rate-limiting step for translation of GluR2 mRNA bearing the long 3'UTR is not elongation. Regardless of the GluR2 UTR length, translation of all reporter mRNAs was equally sensitive to desmethyl-desamino-pateamine A (0.2-200 nM), an initiation inhibitor. Kasugamycin, which can facilitate recognition of certain mRNAs by ribosomes leading to alternative initiation, had no effect on translation of a capped reporter bearing both short 5'UTR and short 3'UTR, but increased the translation rate of reporters bearing either the long GluR2 5'UTR or long 3'UTR. Our findings suggest that both the long 5'UTR and long 3'UTR of GluR2 mRNA repress translation at the initiation step.

Regulation of Translational Efficiency by Disparate 5' UTRs of PPARgamma Splice Variants

The PPAR-gamma gene encodes for at least 7 unique transcripts due to alternative splicing of five exons in the 5'-untranslated region (UTR). The translated region is encoded by exons 1-6, which are identical in all isoforms. This study investigated the role of the 5'-UTR in regulating the efficiency with which the message is translated to protein. A coupled in vitro transcription-translation assay demonstrated that PPAR-gamma1, -gamma2, and -gamma5 are efficiently translated, whereas PPAR-gamma4 and -gamma7 are poorly translated. An in vivo reporter gene assay using each 5'-UTR upstream of the firefly luciferase gene showed that the 5'-UTRs for PPAR-gamma1, -gamma2, and -gamma4 enhanced translation, whereas the 5'-UTRs for PPAR-gamma5 and -gamma7 inhibited translation. Models of RNA secondary structure, obtained by the mfold software, were used to explain the mechanism of regulation by each 5'-UTR. In general, it was found that the translational efficiency was inversely correlated with the stability of the mRNA secondary structure, the presence of base-pairing in the consensus Kozak sequence, the number of start codons in the 5'-UTR, and the length of the 5'-UTR. A better understanding of posttranscriptional regulation of translation will allow modulation of protein levels without altering transcription.

Knockdown of Cav2.1 calcium channels is sufficient to induce neurological disorders observed in natural occurring Cacna1a mutants in mice

The CACNA1A gene encodes the poreforming, voltage-sensitive subunit of the voltage-dependent Ca(v)2.1 calcium channel. Mutations in this gene have been linked to several human disorders, including familial hemiplegic migraine type 1, episodic ataxia type 2, and spinocerebellar ataxia type 6. In mice, mutations of the homolog Cacna1a cause recessively inherited phenotypes in tottering, rolling Nagoya, rocker, and leaner mice. Here we describe two knockdown mice with 28.4+/-3.4% and 13.8+/-3.3% of the wild-type Ca(v)2.1 quantity. 28.4+/-3.4% level mutants displayed ataxia, absence-like seizures and progressive cerebellar atrophy, although they had a normal life span. Mutants with 13.8+/-3.3% level exhibited ataxia severer than the 28.4+/-3.4% level mutants, absence-like seizures and additionally paroxysmal dyskinesia, and died premature around 3 weeks of age. These results indicate that knock down of Ca(v)2.1 quantity to 13.8+/-3.3% of the wild-type level are sufficient to induce the all neurological disorders observed in natural occurring Cacna1a mutants. These knockdown animals with Ca(v)2.1 calcium channels intact can contribute to functional studies of the molecule in the disease.

Functional analysis of 5' untranslated region of a TIR-NBS-encoding gene from triploid white poplar

Genome-wide analyses have identified a set of TIR-NBS-encoding genes in plants. However, the molecular mechanism underlying the expression of these genes is still unknown. In this study, we presented a TIR-NBS-encoding gene, PtDrl02, that displayed a low level of tissue-specific expression in a triploid white poplar [(Populus tomentosa x P. bolleana) x P. tomentosa], and analyzed the effects of the 5' untranslated region (UTR) on gene expression. The 5' UTR sequence repressed the reporter activity of beta-glucuronidase (GUS) gene under PtDrl02 promoter by 113.5-fold with a staining ratio of 2.97% in the transgenic tobacco plants. Quantitative RT-PCR assays revealed that the 5' UTR sequence decreased the transcript level of the GUS reporter gene by 13.3-fold, implying a regulatory role of 5' UTR in transcription and/or mRNA destabilization. The comparison of GUS activity with the transcript abundance indicated that the 5' UTR sequence decreased the translation efficiency of target gene by 88.3%. Additionally, the analysis of the transgenic P-985/UTRDelta/GUS plants showed that both the exon1 sequence and the leading intron within the 5' UTR region were responsible for the regulation of gene expression. Our results suggested a negative effect of the 5' UTR of PtDrl02 gene on gene expression.

Translational regulation of GluR2 mRNAs in rat hippocampus by alternative 3' untranslated regions

The glutamate receptor 2 (GluR2) subunit determines many of the functional properties of the alpha-amino-3-hydroxy-5-methylisoxazole-4-propionate subtype of glutamate receptor. The roles of untranslated regions (UTRs) in mRNA stability, transport, or translation are increasingly recognized. The 3' end of the GluR2 transcripts are alternatively processed to form a short and long 3'UTR, giving rise to two pools of GluR2 mRNA of 4 and 6 kb in length, respectively, in the mammalian brain. However, the role of these alternative 3'UTRs in GluR2 expression has not been reported. We demonstrate that in the cytoplasm of rat hippocampus, native GluR2 mRNAs bearing the long 3'UTR are mostly retained in translationally dormant complexes of ribosome-free messenger ribonucleoprotein (mRNP), whereas GluR2 transcripts bearing the short 3'UTR are predominantly associated with actively translating ribosomes. One day after pilocarpine-induced status epilepticus (SE), the levels of both long and short GluR2 transcripts were markedly decreased in rat hippocampus. However, GluR2 mRNAs bearing the long 3'-UTRs were shifted from untranslating mRNP complexes to ribosome-containing complexes after SE, pointing to a selective translational derepression of GluR2 mRNA mediated by the long 3'UTR. In Xenopus oocytes, expression of firefly luciferase reporters bearing alternative GluR2 3'UTRs confirmed that the long 3'UTR is sufficient to suppress translation. The stability of reporter mRNAs in oocytes was not significantly influenced by alternative 5' or 3'UTRs of GluR2 over the time period examined. Overall, our findings that the long 3'UTR of GluR2 mRNA alone is sufficient to suppress translation, and the evidence for seizure-induced derepression of translation of GluR2 via the long 3'UTR strongly suggests that a regulatory signaling mechanism exists that differentially targets GluR2 transcripts with alternative 3'UTRs.

Novel markers for enterochromaffin cells and gastrointestinal neuroendocrine carcinomas

The gene expression profile of metastasizing serotonin-producing neuroendocrine carcinomas, which arise from enterochromaffin cells in the jejunum and ileum, is still largely unknown. The aim of this study was to identify genes and proteins, which are preferentially expressed by neuroendocrine carcinoma and enterochromaffin cells and therefore potential novel biomarkers and/or therapeutic targets. Six carcinoma specimens and six normal ileal mucosas were profiled by Affymetrix microarrays. Advanced bioinformatics identified differentially and specifically expressed genes, which were validated by quantitative real-time-PCR on tumor cells extracted by laser capture microdissection and normal enterochromaffin cells extracted by immunolaser capture microdissection. We identified six novel marker genes for neuroendocrine carcinoma cells: paraneoplastic antigen Ma2 (PNMA2), testican-1 precursor (SPOCK1), serpin A10 (SERPINA10), glutamate receptor ionotropic AMPA 2 (GRIA2), G protein-coupled receptor 112 (GPR112) and olfactory receptor family 51 subfamily E member 1 (OR51E1). GRIA2 is specifically expressed by neuroendocrine carcinoma cells whereas the others are also expressed by normal enterochromaffin cells. GPR112 and OR51E1 encode proteins associated with the plasma membrane and may therefore become targets for antibody-based diagnosis and therapy. Hierarchical clustering shows high similarity between primary lesions and liver metastases. However, chemokine C-X-C motif ligand 14 (CXCL14) and NK2 transcription factor related locus 3 Drosophila (NKX2-3) are expressed to a lower level in liver metastases than in primary tumors and normal enterochromaffin cells, which implies a role in neuroendocrine carcinoma differentiation. In conclusion, this study provides a list of genes, which possess relatively specific expression to enterochromaffin and neuroendocrine carcinoma cells and genes with differential expression between primary tumors and metastases. We verified six novel marker genes that may be developed as biomarkers and/or therapeutic targets.

MODULATOR OF PIN genes control steady-state levels of Arabidopsis PIN proteins

Polar transport of the phytohormone auxin controls numerous growth responses in plants. Molecular characterization of auxin transport in Arabidopsis thaliana has provided important insights into the mechanisms underlying the regulation of auxin distribution. In particular, the control of subcellular localization and expression of PIN-type auxin efflux components appears to be fundamental for orchestrated distribution of the growth regulator throughout the entire plant body. Here we describe the identification of two Arabidopsis loci, MOP2 and MOP3 (for MODULATOR OF PIN), that are involved in control of the steady-state levels of PIN protein. Mutations in both loci result in defects in auxin distribution and polar auxin transport, and cause phenotypes consistent with a reduction of PIN protein levels. Genetic interaction between PIN2 and both MOP loci is suggestive of functional cross-talk, which is further substantiated by findings demonstrating that ectopic PIN up-regulation is compensated in the mop background. Thus, in addition to pathways that control PIN localization and transcription, MOP2 and MOP3 appear to be involved in fine-tuning of auxin distribution via post-transcriptional regulation of PIN expression.

Activity-dependent regulation of NR2B translation contributes to metaplasticity in mouse visual cortex

Visual experience and deprivation bidirectionally modify the NR2A and NR2B subunit composition of NMDARs, and these changes in turn modify the properties of synaptic plasticity in the visual cortex. Deprivation-induced lowering of the NR2A/2B ratio can occur by altering either NR2A or NR2B protein levels, but how a reduction in synaptic activity regulates these changes in a subunit-specific manner is poorly understood. Here, we find that visual deprivation in juvenile mice by dark-rearing or monocular lid suture reduces the NR2A/2B ratio in the deprived cortex in temporally distinct phases--initially by increasing NR2B protein levels, and later by decreasing NR2A protein levels. Brief dark-exposure of juvenile rats likewise produces an increase in NR2B expression. Furthermore, we are able to model the early increase in NR2B by blocking NMDARs in vitro, and we find that translation of NR2B is likely a major point of regulation. Translation of NR2A is not regulated in this manner. Therefore, the differential translational regulation of NR2A and NR2B may contribute to experience-dependent modification of NMDAR subunit composition.

Identification and regulation of novel PPAR-gamma splice variants in human THP-1 macrophages

We have previously identified four novel isoforms of PPAR-gamma transcripts in monkey macrophages (J. Zhou, K.M. Wilson, J.D. Medh, Genetic analysis of four novel peroxisome proliferator receptor-gamma splice variants in monkey macrophages. Biochem. Biophys. Res. Commun., 293 (2002) 274-283). The purpose of this study was to ascertain that these isoforms are also present in humans. Specific primers were designed to amplify individual isoform transcripts. The presence of PPAR-gamma4, PPAR-gamma5, and PPAR-gamma7 transcripts in human THP-1 macrophages was confirmed by RT-PCR and sequencing. A transcript corresponding to PPAR-gamma6 was not detected. The presence of novel full-length transcripts and protein was also ascertained by Northern and Western blot analysis. Treatment of THP-1 cells with 15-deoxy-Delta12,14-prostaglandin J2 (15d-PGJ2) resulted in more than 20% induction in the expression of PPAR-gamma5 and PPAR-gamma7 transcripts by both Northern blot analysis and RT-PCR. Another PPAR-gamma ligand, troglitazone, induced expression of only PPAR-gamma5. Both ligands inhibited the expression of PPAR-gamma1 and PPAR-gamma2. Additionally, 15d-PGJ2 and troglitazone increased the level of apolipoprotein E transcript by 60% but decreased lipoprotein lipase expression by 15% in THP-1 cells. The differential regulation of PPAR-gamma transcripts suggests that each transcript isoform may contribute to macrophage function.

Transcriptional regulation of the mouse gene encoding the alpha-4 subunit of the GABAA receptor

The gamma-aminobutyric acid type A receptors (GABAA-Rs) mediate fast inhibitory synaptic transmission in the brain. The alpha4 subunit of the GABAA-R confers distinct pharmacological properties on the receptor and its expression pattern exhibits plasticity in response to physiological and pharmacological stimuli, including withdrawal from progesterone and alcohol. We have analyzed the promoter region of the mouse GABRA4 gene that encodes the alpha4 subunit and found that the promoter has multiple transcriptional initiation sites and lacks a TATA box. The minimal promoter for GABRA4 spans the region between -444 to -19 bp relative to the coding ATG and shows high activity in cultured mouse cortical neurons. Both Sp3 and Sp4 transcription factors can interact with the two Sp1 binding sites within the minimal promoter and are critical for maximal activity of the promoter in neurons.