Control of neuronal gene expression

Autoimmune RNA dysregulation and seizures: therapeutic prospects in neuropsychiatric lupus

Lupus autoimmunity frequently presents with neuropsychiatric manifestations, but underlying etiology remains poorly understood. Human brain cytoplasmic 200 RNA (BC200 RNA) is a translational regulator in neuronal synapto-dendritic domains. Here, we show that a BC200 guanosine-adenosine dendritic transport motif is recognized by autoantibodies from a subset of neuropsychiatric lupus patients. These autoantibodies impact BC200 functionality by quasi irreversibly displacing two RNA transport factors from the guanosine-adenosine transport motif. Such anti-BC autoantibodies, which can gain access to brains of neuropsychiatric lupus patients, give rise to clinical manifestations including seizures. To establish causality, naive mice with a permeabilized blood-brain barrier were injected with anti-BC autoantibodies from lupus patients with seizures. Animals so injected developed seizure susceptibility with high mortality. Seizure activity was entirely precluded when animals were injected with lupus anti-BC autoantibodies together with BC200 decoy autoantigen. Seizures are a common clinical manifestation in neuropsychiatric lupus, and our work identifies anti-BC autoantibody activity as a mechanistic cause. The results demonstrate potential utility of BC200 decoys for autoantibody-specific therapeutic interventions in neuropsychiatric lupus.

Long Noncoding RNAs in Lung Cancer

Despite great progress in research and treatment options, lung cancer remains the leading cause of cancer-related deaths worldwide. Oncogenic driver mutations in protein-encoding genes were defined and allow for personalized therapies based on genetic diagnoses. Nonetheless, diagnosis of lung cancer mostly occurs at late stages, and chronic treatment is followed by a fast onset of chemoresistance. Hence, there is an urgent need for reliable biomarkers and alternative treatment options. With the era of whole genome and transcriptome sequencing technologies, long noncoding RNAs emerged as a novel class of versatile, functional RNA molecules. Although for most of them the mechanism of action remains to be defined, accumulating evidence confirms their involvement in various aspects of lung tumorigenesis. They are functional on the epigenetic, transcriptional, and posttranscriptional level and are regulators of pathophysiological key pathways including cell growth, apoptosis, and metastasis. Long noncoding RNAs are gaining increasing attention as potential biomarkers and a novel class of druggable molecules. It has become clear that we are only beginning to understand the complexity of tumorigenic processes. The clinical integration of long noncoding RNAs in terms of prognostic and predictive biomarker signatures and additional cancer targets could provide a chance to increase the therapeutic benefit. Here, we review the current knowledge about the expression, regulation, biological function, and clinical relevance of long noncoding RNAs in lung cancer.

The persistent contributions of RNA to eukaryotic gen(om)e architecture and cellular function

Currently, the best scenario for earliest forms of life is based on RNA molecules as they have the proven ability to catalyze enzymatic reactions and harbor genetic information. Evolutionary principles valid today become apparent in such models already. Furthermore, many features of eukaryotic genome architecture might have their origins in an RNA or RNA/protein (RNP) world, including the onset of a further transition, when DNA replaced RNA as the genetic bookkeeper of the cell. Chromosome maintenance, splicing, and regulatory function via RNA may be deeply rooted in the RNA/RNP worlds. Mostly in eukaryotes, conversion from RNA to DNA is still ongoing, which greatly impacts the plasticity of extant genomes. Raw material for novel genes encoding protein or RNA, or parts of genes including regulatory elements that selection can act on, continues to enter the evolutionary lottery.

Non coding RNA and brain

Small non coding RNAs are a group of very different RNA molecules, present in virtually all cells, with a wide spectrum of regulatory functions which include RNA modification and regulation of protein synthesis. They have been isolated and characterized in all organisms and tissues, from Archaeobacteria to mammals. In mammalian brain there are a number of these small molecules, which are involved in neuronal differentiation as well as, possibly, in learning and memory. In this manuscript, we analyze the present knowledge about the function of the most important groups of small non-coding RNA present in brain: small nucleolar RNAs, small cytoplasmic RNAs, and microRNAs. The last ones, in particular, appear to be critical for dictating neuronal cell identity during development and to play an important role in neurite growth, synaptic development and neuronal plasticity.

Echoes from the past--are we still in an RNP world?

Availability of the human genome sequence and those of other species is unmeasured in their value for a comprehensive understanding of the architecture, function and evolution of genomes and cells. Various mechanisms keep genomes in flux and generate intra- and interspecies variation. The conversion of RNA modules into DNA and their more or less random integration into chromosomes (retroposition) is in many lineages including our own the most pervasive and perhaps the most enigmatic. The proclivity of such events in extant multicellular eukaryotes, even in more recent evolutionary times, gives the impression that the transition period from the RNP (ribonucleoprotein) world to the emergence of modern cells, where DNA became the predominant carrier of genetic information, has lasted billions of years and is an endlessly drawn-out process rather than the punctuated event one might expect. Apart from the impact of such RNA-mediated processes as retroposition, the role of RNA in a wide variety of cellular functions has only recently become more widely appreciated.

From superior adaptation and function to brain dysfunction--the neglect of epigenetic factors

With optimal pregnancy conditions (natural, enriched diet which includes fish) African (Digo) infants are 3-4 weeks ahead of European/American infants in sensorimotor terms at birth, and during the first year. Infants of semi-aquatic sea-gypsies swim before they walk, and have superior visual acuity compared with us. With adverse pregnancy behaviour (fear of fat, a trend to dieting), neglecting the need for brain fat to secure normal brain development and function, we run a risk of dysfunction--death. Sudden Infant Death Syndrome victims have depressed birth weight, lower levels of marine fat in brainstem than controls, and >80 suffer multiple hypoxic episodes prior to death. Depressed birth weight (more than 10% below mean) is seen in learning and behaviour disorders, and a trend towards weights of less than 3kg is increasing, which supports a rise in antenatal sub optimality. Given marine fat deficiency in pregnancy and infancy, neurons starved for fuel could delay myelination and maturation in the latest developed Frontal Lobes. The phylogenetic oldest Lateral Frontal Lobe System (feed-back mechanism etc.) derived from olfactory bulb-amygdala, which crosses in Anterior Commisure is probably spared, while the Medial Frontal Lobe System derived from Hippocampus-Cingulum and crosses in Corpus Callosum (delayed response task) is most likely affected. The rise in infantile autism (intact vision and hearing) with deficit in delayed response task only, could suggest a deficit in the Medial Frontal Lobe System. The human species is unique; 70% of total energy to the foetus goes to development of the brain, which mainly consists of marine fat. It undergoes pervasive regressive events, before birth, in infancy and at puberty. Minimal retraction of neuronal arborisation is advantageous. Attributable to adverse pregnancy childrearing practice, excessive retraction is likely prenatally and in infancy. Pubertal age affects the fundamental property of nervous tissue, excitability: excessive excitatory drive is seen in early, and a deficiency in late puberty. It is postulated that with adequate marine fat, there is probably no risk of psychopathology at the extremes, whereas a deficiency could lead to paroxysmal (subcortical) dysfunction in early puberty, and breakdown of cortical circuitry and cognitive dysfunctions in late puberty. The post-pubertal psychoses, schizophrenia and manic-depressive psychosis at the extremes of the pubertal age continuum, with contrasting excitability and biological treatment, are probably the result of continuous dietary deficiency, which has inactivated the expression of genes for myelin development and oligodendrocyte-related genes in their production of myelin. The beneficial effect of marine fat in both disorders, in other CNS disorders as well as in developmental dyslexia (DD) and ADHD among others, supports our usual diet is persistently deficient. We have neglected the similarity of our great brain to other mammals, and our marine heritage. Given the amount of marine fat needed to secure normal brain development and function is not known, nor the present dietary level, it seems unduly conjectural to postulate that a dietary deficiency in marine fat is causing brain dysfunction and death. However, all observations point in the same direction: our diet focusing on protein mainly, is deficient, the deficiency is most pronounced in maternal nutrition and in infancy.

Neuronal untranslated BC1 RNA: targeted gene elimination in mice

Despite the potentially important roles of untranslated RNAs in cellular form or function, genes encoding such RNAs have until now received surprisingly little attention. One such gene encodes BC1 RNA, a small non-mRNA that is delivered to dendritic microdomains in neurons. We have now eliminated the BC1 RNA gene in mice. Three independent founder lines were established from separate embryonic stem cells. The mutant mice appeared to be healthy and showed no anatomical or neurological abnormalities. The gross brain morphology was unaltered in such mice, as were the subcellular distributions of two prototypical dendritic mRNAs (encoding MAP2 and CaMKIIalpha). Due to the relatively recent evolutionary origin of the gene, we expected molecular and behavioral consequences to be subtle. Behavioral analyses, to be reported separately, indicate that the lack of BC1 RNA appears to reduce exploratory activity.

Transcriptional involvement in neurotoxicity

Exposure to various chemicals and environmental hazards elicits changes in the expression of a variety of genes. The study of gene expression and transcriptional regulation is an important aspect of understanding the mechanisms associated with neurotoxicity. The availability of whole genome sequences and the development of new tools to identify and monitor transcriptional activity have accelerated the rate of discovery. This review surveys the historical steps taken to study gene expression in the brain and deals with recent advances in our understanding and classification of the roles of transcription factors. Disturbances in the regulation of gene expression associated with the neurotoxic response are also presented. Specific focus and detail is presented on the effects of heavy metals on the integrity and function of zinc finger proteins.

Non-coding ribonucleic acids--a class of their own?

Non-coding ribonucleic acids (RNAs) do not contain a peptide-encoding open reading frame and are therefore not translated into proteins. They are expressed in all phyla, and in eukaryotic cells they are found in the nucleus, cytoplasm, and mitochondria. Non-coding RNAs either can exert structural functions, as do transfer and ribosomal RNAs, or they can regulate gene expression. Non-coding RNAs with regulatory functions differ in size ranging from a few nucleotides to over 100 kb and have diverse cell- or development-specific functions. Some of the non-coding RNAs associate with human diseases. This chapter summarizes the current knowledge about regulatory non-coding RNAs.

Transcriptional analysis in the brain: trophin-induced hippocampal synaptic plasticity

Gene profiling in the central nervous system presents unique challenges due to the unprecedented heterogeneity of cells, systems and functions in time and space. We have employed a multidisciplinary approach using whole cell patch clamp recording and transcriptional analysis to define the genomic basis of trophin-induced hippocampal synaptic plasticity. Transcriptional analysis of single cells by linear amplification of antisense RNA has added a new dimension of sensitivity and selectivity to the study of the complex and heterogeneous population of neurons. We describe different gene expression profiling techniques that offer novel approaches to monitoring thousands of genes in parallel, fostering identification of circuits involved in learning and memory.

Applied neurogenomics

Neurogenomics, the study of the genes of the nervous system, has applications in basic research, in the pharmaceutical industry and in the management of neurological disorders. Basic research applications include molecular neuropathology, the detection of genes for neurological disorders, the study of gene expression in the CNS and creation of transgenic models of neurological disorders. Pharmaceutical applications may be in the areas of molecular neuropharmacology, the discovery of new drugs for neurological disorders, gene therapy and the development of personalised medicines based on pharmacogenomics. Clinical applications in neurology include the redefinition and reclassification of diseases, molecular diagnostics and the integration of diagnostics with therapeutics. Various methods for the study of genes and gene expression are described. Genes have been identified for only a limited number of neurological disorders so far. The discovery of genes defective in neurological disorders would facilitate drug discovery, molecular diagnostics and gene therapy diseases. There is a trend towards the integration of diagnosis, genetic screening, prevention, treatment and monitoring of therapy of neurological disorders, which will be facilitated by neurogenomics. Pharmacogenomics-based personalised medicines are anticipated to be part of medical practice by the end of the first decade of the 21st century, and neurogenomics will contribute to the development of personalised medicines for diseases of the CNS.

Rat adrenoleukodystrophy-related (ALDR) gene: full-length cDNA sequence and new insight in expression

X-linked adrenoleukodystrophy (X-ALD) is an inherited demyelinating disorder due to mutations in the ALD gene, which encodes a peroxisomal ABC half-transporter (ALDP). It has been suggested that ALDP assembles with ALDRP (adrenoleukodystrophy-related protein), a close homologous half-transporter, to form a functional heterodimer. For the first time full-length ALDRP cDNA (5.5 kb) was cloned, and 5' and 3' RACE analysis revealed that alternative usage of polyadenylation sites generates the two transcripts of 3.0 and 5.5 kb observed in the rat in Northern blot analysis. Southern blotting and chromosomal mapping demonstrated one ALDR locus in the rat genome. Characterisation of the 3' flanking region suggested that an ID sequence might be responsible for high expression of the 5.5 kb ALDRP transcript in rat brain. ALDR gene expression was found to be high in the liver of rats before weaning and very low in adult rats; the reverse developmental regulation was observed in the brain. Fenofibrate, which is a potent inducer of the ALDR gene in the liver of adult rats, could not induce the ALDR gene in suckling rats. The exact significance of this result with regard to development of an efficient pharmacological gene therapy for X-ALD is discussed.

Neural BC1 RNA associates with pur alpha, a single-stranded DNA and RNA binding protein, which is involved in the transcription of the BC1 RNA gene

BC1 RNA is preferentially expressed in neural cells by RNA polymerase III (Pol III) and forms ribonucleoprotein particles (RNP) in the somatodendritic domain of neurons. Our previous studies have suggested that, in the nucleus, BC1 RNA forms an RNP containing a nuclear protein(s) that participates in the transcription of the BC1 RNA gene. In this study, we have shown that newly synthesized BC1 RNA in purified brain nuclear extracts is immunoprecipitated by an antibody against Pur alpha. Pur alpha is a protein that binds single-stranded DNA and RNA and is known to regulate transcription of Pol II system. Although BC1 RNA is transcribed by Pol III, the BC1 RNA gene has two putative Pur alpha binding sites, which Pur alpha specifically recognizes. Point mutations within these sites reduced transcriptional activity in vitro. Furthermore, transcription was inhibited by depletion of Pur alpha from the nuclear extracts, either by the coexistence of its binding region of BC1 RNA or by the antibody that was able to precipitate the nuclear BC1 RNP. These observations suggest that BC1 RNA associates with Pur alpha which is involved in the transcription of the BC1 RNA gene.

Upstream flanking sequences and transcription of SINEs

SINEs, short interspersed repeated DNA elements, undergo amplification through retroposition and subsequent integration into a new location in the genome. Each new SINE insertion will be located in a new chromosomal environment, with different flanking sequences. Modulation of transcription by different flanking sequences may play an important role in determining which SINE elements are preferentially active in a genome. We evaluated the ability of upstream flanking sequences to regulate the transcription of three different SINEs (Alu, B2 and ID) by constructing chimeric constructs with known 5' flanking sequences of RNA polymerase III-transcribed genes. Upstream sequences from the 7SL RNA gene, U6 RNA gene, vault RNA gene, and BC1 gene increase transcription of Alu, B2 and BC1 in transient transfections of NIH3T3, HeLa, Neuro2a and C6 glioma cell lines. The 7SL sequence proved most efficient in increasing SINE transcription. The 7SL upstream fused to the BC1 RNA gene (an ID element) was used to create a transgenic mouse line. In contrast to the tissue-specific endogenous BC1 transcription, BC1 transgene transcripts were detected in all tissues tested. However, expression was much higher in those tissues that express the endogenous gene, demonstrating both transcriptional and post-transcriptional regulation. The BC1 RNA was detected in a similar ribonucleoprotein complex in the different tissues.

Identification of a negative regulatory DNA element for neuronal BC1 RNA expression by RNA polymerase III

BC1 RNA is a neuronal cell-specific RNA polymerase III (Pol III) transcript. The BC1 RNA gene has plural types of Pol III promoters, in addition to which an E-box sequence (E2 site) acts as a transcriptional activator, which is recognized by a brain-specific protein(s). Using an in vitro transcription system, we found that the upstream region of the BC1 RNA gene contained a sequence that interfered with the activity of the E-box element in a distance-independent manner. A tandem repeat within this sequence, which was weakly homologous with the neuron-restrictive silencer element (NRSE) found in the Pol II system, was recognized by a brain nuclear protein. Consistently, the transcriptional activity increased by deleting the tandem repeat sequence. We called this BC1 RNA-repressing element BCRE. The DNA-binding specificities of BCRE-binding protein differed from that of NRSE-binding protein (NRSF). A similar protein with an ability to bind to BCRE was also found in liver and kidney. Furthermore, the glutamate analog kainic acid increased the DNA-binding of both E2 site-binding protein and BCRE-binding protein, and then the levels of BC1 RNA also increased transiently. Our results suggested that both positive and negative regulatory elements contribute to neuronal BC1 RNA expression.

Transcriptional and post-transcriptional regulation of a brain growth protein: regional differentiation and regeneration induction of GAP-43

During axonal regeneration synthesis of different growth-associated proteins is increased. As yet there is no clear picture of the specific contribution made by the transcriptional and post-transcriptional machinery that provides the gene products necessary for process outgrowth. Here we focus our study on the transcriptional processes in neurons by using intron-directed in situ hybridization to the primary transcript of a brain growth protein GAP-43. In most brain regions, levels of primary transcript expression of GAP-43 were highly correlated with levels of its mRNA. However, there were notable dissociations: in hippocampal granule cells, high levels of primary transcript were evident yet no GAP-43 mRNA was detected. In locus coeruleus the reverse was true; there were high levels of GAP-43 mRNA but no detectable primary transcript. A primary transcript antitermination mechanism is proposed to explain the first dissociation, and a post-transcriptional mRNA stabilization mechanism to explain the second. Transcriptional activation during nerve regeneration was monitored by assessing primary transcript induction of GAP-43 in mouse facial motor neurons. This induction, as well as its mRNA, was restricted to the side of the facial nerve crush. Increases were first observed at 24 h with a rapid increase in both measures up to 3 days. To our knowledge, this is the first in vivo evidence demonstrating transcriptional activation of a brain growth protein in regenerating neurons. The present study points to the GAP-43 transcriptional mechanism as a key determinant of GAP-43 synthesis. Along with the recruitment of post-transcriptional mechanisms, such synthesis occurs in response to both intrinsic developmental programs and extrinsic environmental signals.

Analysis of mouse intron 7 DNA sequence of the APP gene: comparison with the human homologue

Mutations in the beta-amyloid precursor protein gene (APP) cause Alzheimer disease (AD) in certain families. The mature protein (APP) exists in several different isoforms resulting from alternative splicing of the primary transcript. Several lines of evidence indicate that particular isoform(s) of APP may contribute to the etiology of AD. One of the isoforms, APP695, lacks the Kunitz protease inhibitor (KPI) domain encoded by exon 7. APP695 is expressed predominantly in neurons, whereas the KPI domain containing isoforms, APP751 and APP770, are expressed ubiquitously. The ratio of APP751/APP695 mRNA tends to increase in the brain of AD patients. Furthermore, this ratio in mouse brain is much lower than that in human brain, and mice are resistant to the spontaneous development of beta-amyloidosis. In addition, transgenic mice that develop pathological changes similar to those of AD expressed more KPI-domain containing APP mRNA than transgenic mice without the changes. Previous studies imply that the controlling elements exist in the flanking sequences of the alternatively-spliced exons. Therefore, we have determined the DNA sequences of intron 7 and made a comparison between mouse and human DNA sequences of intron 7. Mouse intron 7 shares about 50% sequence identity with the human homologue, with higher sequence identity (approximately 85%) mainly in the 5' end (approximately 250 bp) of the intron. A palindromic sequence was found in both human and mouse intron 7 and showed subtle differences in their structure between the two species. Whether this sequence plays any roles in regulating alternative splicing of exon 7 remains to be determined. Human intron 7 contains a Alu element, which possesses potential retinoic acid and thyroid hormone responsive elements that might be involved in the regulation of alternative splicing. Mouse intron 7 sequence also contains a few repeat sequences which are specific to the genome of mice and rats. Homologies shared between human and mouse intron 7 sequences may contribute to the common characteristics of neuron-specific splicing of APP in both species. The unique features of the intron may account for differences between human and mouse brain in fine tuning of alternative splicing of the APP transcript, which may lead to their different susceptibilities to beta-amyloidosis.

The novel kinase peptidylglycine alpha-amidating monooxygenase cytosolic interactor protein 2 interacts with the cytosolic routing determinants of the peptide processing enzyme peptidylglycine alpha-amidating monooxygenase

The cytosolic domain of the peptide-processing integral membrane protein peptidylglycine alpha-amidating monooxygenase (PAM; EC 1.14. 17.3) contains multiple signals determining its subcellular localization. Three PAM cytosolic interactor proteins (P-CIPs) were identified using the yeast two hybrid system (Alam, M. R., Caldwel, B. D., Johnson, R. C., Darlington, D. N., Mains, R. E., and Eipper, B. A. (1996) J. Biol. Chem. 271, 28636-28640); the partial amino acid sequence of P-CIP2 suggested that it was a protein kinase. In situ hybridization and immunocytochemistry show that P-CIP2 is expressed widely throughout the brain; PAM and P-CIP2 are expressed in the same neurons. Based on subcellular fractionation, the 47-kDa P-CIP2 protein is mostly cytosolic. P-CIP2 is a highly selective kinase, phosphorylating the cytosolic domain of PAM, but not the corresponding region of furin or carboxypeptidase D. Although P-CIP2 interacts with stathmin, it does not phosphorylate stathmin. Site-directed mutagenesis, phosphoamino acid analysis, and use of synthetic peptides demonstrate that PAM-Ser(949) is the major site phosphorylated by P-CIP2. Based on both in vitro binding experiments and co-immunoprecipitation from cell extracts, P-CIP2 interacts with PAM proteins containing the wild type cytosolic domain, but not with mutant forms of PAM whose trafficking is disrupted. P-CIP2, through its highly selective phosphorylation of a key site in the cytosolic domain of PAM, appears to play a critical role in the trafficking of this protein.

The dendritic translocation of translin protein in the form of BC1 RNA protein particles in developing rat hippocampal neurons in primary culture

Neural BC1 RNA is distributed in neuronal dendrites as ribonucleoprotein particles (RNP). Our previous studies indicated the presence of Translin in BC1 RNPs, which is a translational repressor and links a subset of mRNAs to microtubules. In this study, we confirmed that Translin associates with BC1 RNP and we used immunocytochemical methods to examine the subcellular distribution of Translin in developing hippocampal cells in primary cultures. Translin was detected in both the nuclei and cytoplasm of neurons, whereas in glial cells it was localized in the nuclei. Consistent with the reported developmental time course of BC1 RNA expression and dendritic delivery the translocation of Translin to the neuronal dendrites appeared to correlate with neuronal development and differentiation events such as the onset of synaptogenesis in culture. These observations suggest that BC1 RNP or Translin itself may be relevant to the dendritic translation of mRNAs in response to transsynaptic activity.

Control of genes by mammalian retroposons

Available data on possible genetic impacts of mammalian retroposons are reviewed. Most important is the growing number of established examples showing the involvement of retroposons in modulation of expression of protein-coding genes transcribed by RNA polymerase II (Pol II). Retroposons contain conserved blocks of nucleotide sequence for binding of some important Pol II transcription factors as well as sequences involved in regulation of stability of mRNA. Moreover, these mobile genes provide short regions of sequence homology for illegitimate recombinations, leading to diverse genome rearrangements during evolution. Therefore, mammalian retroposons representing a significant fraction of noncoding DNA cannot be considered at present as junk DNA but as important genetic symbionts driving the evolution of regulatory networks controlling gene expression.

Gene trap expression and mutational analysis for genes involved in the development of the mammalian nervous system

We have used a large-scale gene trap approach for the isolation and mutation of genes that might play roles in the developing nervous system. After in vitro integration of two different gene trap vectors (pGT1.8geo: Skarnes et al. [1995] Proc. Natl. Acad. Sci. USA 92:6592-6596; IRES beta geo: Chowdhury et al. [1997] Nucleic Acids Res. 25:1531-1536) in mouse embryonic stem (ES) cell lines, we created 64 transgenic mouse lines. The expression analysis of the reporter gene during embryogenesis of heterozygous embryos revealed 47 lines with a variety of patterns. Around one-third (36%) of these gene trap lines showed spatiotemporal expression that was either restricted predominantly in the developing nervous system (11 lines; 17%) or widespread but with very high levels of expression in the nervous tissue (12 lines; 19%). In most cases, a correlation was found between the in vitro and the in vivo patterns of the reporter gene expression. Thus far, preliminary mutant analysis of 16 gene trap lines with potentially interesting expression patterns in the developing nervous system showed that mice homozygous for eight (50%) insertions were lethal, whereas the homozygous mice from five gene trap lines (31%) showed a lower than expected Mendelian ratio of live homozygous animals. Analysis of beta-galactosidase reporter gene expression during embryogenesis has shown that four transgenic lines are useful lacZ in situ markers for specific regions of the developing nervous system. Here, we discuss some in vivo and in vitro selection criteria that may increase the number of the trapped genes potentially involved in the control of neural development and some future strategies to improve further the efficiency of the gene trap approach.

Which characteristics of schizophrenia predate psychosis?

Neuropsychological and brain structural abnormalities are present in first onset schizophrenia; the balance of evidence is that in the majority of cases these are developmental in origin. A proportion of first degree relatives also show lateral ventricular enlargement, cortical volume decrease and possibly loss of the normal cerebral asymmetry; these findings suggest that certain families transmit a genetic defect in the control of neurodevelopment. On the contrary, decrement in left hippocampal volume appears to be secondary to perinatal hypoxia. High risk, follow-back and cohort studies all demonstrate that preschizophrenics as a group show deviant development; delayed milestones, lower IQ, solitary play, excessive anxiety, and minor neurological problems are all common. It seems likely, but not proven, that these are a manifestation of underlying neurodevelopmental disorder.

An E-box sequence acts as a transcriptional activator for BC1 RNA expression by RNA polymerase III in the brain

BC1 RNA is a small cytoplasmic RNA that is transcribed by RNA polymerase III (Pol III) in the rodent nervous system. In addition to essential intragenic promoter elements for Pol III, the BC1 RNA gene has five E-box sequences (CANNTG) in its 5' flanking region. Deletion analysis using an in vitro transcription system revealed that the region containing the E2 site (CAATTG) was necessary for effective transcription of BC1 RNA. A construct with point mutations within the E2 site showed reduced transcriptional activity. Furthermore, DNaseT I protection and gel retardation assays demonstrated that the E2 site was recognized specifically by a brain nuclear protein(s). These results suggest that the upstream E-box sequence and its binding protein may be involved in the regulation by Pol III of preferential BC1 RNA expression in the brain.

Mutational analysis reveals that an array of GCAAG/CTTGC motifs between sprit promoter sequences for RNA polymerase III is essential for neural BC1 RNA transcription

BC1 RNA is expressed from an identifier (ID) sequence by RNA polymerase III (Pol III) and occurs in neural cells as a ribonucleoprotein particle (BC1 RNP). On the BC1 RNA gene, between the Pol III promoter A and B boxes, there is a region which contains short inverted repeats, including three GCAAG/CTTGC motifs. We found that a nuclear protein binds specifically to this region and, using an in vitro transcription system, demonstrated that point mutations within these motifs markedly inhibit BC1 RNA transcription. These results suggest that the GCAAG/CTTGC motif region and its binding protein may play a role in the transcription of BC1 RNA. Moreover, we demonstrated that transcription is repressed by a concomitant molar excess of BC1 RNA and that the BC1 RNA transcribed by this system forms an RNP with nuclear protein(s), suggesting some interaction of BC1 RNA with transcription factor(s).

Identification and characterization of BC1 RNP particles

Rodent brain-specific small cytoplasmic BC1 RNA is an unusual RNA in several respects. It is an RNA polymerase III transcript expressed specifically in neurons, with regional and developmental regulation. Moreover, it is one of a few RNAs actively transported into dendrites. Three findings indicate that BC1 RNA exists as a ribonucleoprotein complex in vivo. First, the buoyant density of fractions containing BC1 RNA from brain extract on CsCI and Cs2SO4 gradients is 1.45 g/ml and 1.55 g/ml, respectively; this is consistent with the density of RNA-protein complexes. Second, in sucrose gradients, the BC1 particle has a larger S value (8.7S) than naked RNA (6.1S). Third, BC1 RNA from brain extracts migrates with retarded mobility compared to naked BC1 RNA during agarose gel electrophoresis. Additionally, in comparison to the signal recognition particle (SRP), the BC1 RNP is more heat resistant and less Mg(2+)-dependent. The buoyant density of the BC1 RNP suggests the presence of protein(s) with a total mass of about 138kD.

An Alu element in the myeloperoxidase promoter contains a composite SP1-thyroid hormone-retinoic acid response element

An Alu element preceding the myeloperoxidase gene (MPO) contains four hexamer motifs related to the consensus recognition sequence for nuclear hormone receptors (AGGTCA), arranged as direct repeats with spacing of 2, 4, and 2 nucleotides (DR-2-4-2). Gel shift experiments and transient transfection assays demonstrate that these sequences include binding sites for retinoic acid and thyroid hormone receptors and function in vivo to activate transcription of a chloramphenicol acetyltransferase reporter gene. The first DR-2 elements of the series do not bind known receptors but do bind the SP1 transcription factor. Two alleles of the MPO gene exist that differ at one position within this element, resulting in one allele with and one without a strong SP1 binding site. The element with the SP1 site activates transcription by 25-fold in transient transfection assays, while the alternative allele confers severalfold less transcriptional activity. Most cases of acute myelocytic leukemia are homozygous for the allele with the SP1 binding site, suggesting this element plays an important role in regulating the MPO gene in myeloid leukemias. This MPO-Alu is a representative of an Alu subclass numbering approximately 400,000 copies, suggesting many genes may be regulated by such elements.

Association of repeat sequences with integrated retroviruses in a murine leukaemia cell line

An analysis was made of the retroviral integration sites for retroviruses in a murine lymphoid precursor cell line, C1-V13D, derived following in vitro infection with RadLV, an ecotropic murine retrovirus. A genomic library was constructed and lambda clones were selected for their capacity to hybridize with the specific RadLV gp70 ecotropic env probe. Analysis of these clones by a combination of approaches, including subcloning, partial restriction mapping and sequencing, has confirmed the existence of multiple recombinant and defective viruses in C1-V13D. To check for the presence of coding sequences in flanking genomic DNA, 32P-labelled cDNA from C1-V13D was used to probe HindIII- and Psti-digested virus-positive lambda clones by Southern analysis. Regions hybridizing specifically with 32P-labelled C1-V13D cDNA were subcloned and analysed. A notable feature of these cDNA+ regions was the frequent presence of B1, B2 and simple repeats. These repeat elements were found to be present in high frequency in the genomic regions flanking the proviruses, in numbers higher than expected for the genome as a whole. All full-length viruses isolated appeared to represent integration events into regions rich in repeat elements. Some B1 and B2 repeats have been shown to code for functional proteins and to play regulatory roles. Viral integration in the vicinity of these genetic elements could contribute to oncogenesis if the integration event were to disrupt normal gene function.

Promoter region of the rat phosphoribosylpyrophosphate synthetase-associated protein 39

The 5' region of the 39-kDa rat phosphoribosylpyrophosphate synthetase-associated protein (PAP39) gene was isolated and sequenced. The promoter region of the rat PAP39 is GC-rich and contains potential binding sites for regulatory factors. Its promoter activity was demonstrated by transfection of the promoter region in fusion with the chloramphenicol acetyltransferase gene into rat pheochromocytoma PC12 cell.

BC1 RNA and vasopressin mRNA in rat neurohypophysis: axonal compartmentalization and differential regulation during dehydration and rehydration

Brain cytoplasmic 1 (BC1) RNA is a small non-translated RNA polymerase III transcript. Because this RNA can be detected in the rat posterior pituitary with 35S in situ hybridization autoradiography, it has been hypothesized that this RNA might be transported in the axons of hypothalamo-neurohypophyseal neurons. In the present study, we aimed to determine the cellular localization of BC1 more precisely by using non-radioactive in situ hybridization of BC1 RNA at both the light and electron microscopic levels. Our studies revealed that BC1 RNA was indeed located intra-axonally. Furthermore, BC1 RNA was abundant within a subset of axonal swellings and/or terminals, and was also found in discrete cytoplasmic domains of undilated axonal segments. Using a semiquantitative in situ hybridization approach, we have measured and compared the changes in BC1 RNA and arginine vasopressin (AVP) mRNA during dehydration (chronic salt-loading) and rehydration. Chronic salt-loading significantly increased both BC1 RNA and AVP mRNA. The increase in BC1 RNA labelling (2.5-fold), however, was modest and somewhat less enduring than the increase in AVP mRNA labelling (13-fold). Upon rehydration, both the BC1 and vasopressin transcripts in the posterior pituitary rapidly returned to control values. In conclusion, like vasopressin mRNA, BC1 RNA is transported in axons of the hypothalamo-neurohypophyseal system where it aggregates in a subset of axonal swellings, and its axonal transport is similarly regulated. Therefore, we propose that BC1 RNA might be involved in the axonal targeting, docking and/or transport of AVP or other axonal mRNAs.

The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element

Alu repeats are interspersed repetitive DNA elements specific to primates that are present in 500,000 to 1 million copies. We show here that an Alu sequence encodes functional binding sites for retinoic acid receptors, which are members of the nuclear receptor family of transcription factors. The consensus sequences for the evolutionarily recent Alu subclasses contain three hexamer half sites, related to the consensus AGGTCA, arranged as direct repeats with a spacing of 2 bp, which is consistent with the binding specificities of retinoic acid receptors. An analysis was made of the DNA binding and transactivation potential of these sites from an Alu sequence that has been previously implicated in the regulation of the keratin K18 gene. These Alu double half sites are shown to bind bacterially synthesized retinoic acid receptors as assayed by electrophoretic mobility shift assays. These sites are further shown to function as a retinoic acid response element in transiently transfected CV-1 cells, increasing transcription of a reporter gene by a factor of approximately 35-fold. This transactivation requires cotransfection with vectors expressing retinoic acid receptors, as well as the presence of all-trans-retinoic acid, which is consistent with the known function of retinoic acid receptors as ligand-inducible transcription factors. The random insertion of potentially thousands of Alu repeats containing retinoic acid response elements throughout the primate genome is likely to have altered the expression of numerous genes, thereby contributing to evolutionary potential.

Identification of a nuclear receptor that is activated by farnesol metabolites

Nuclear hormone receptors comprise a superfamily of ligand-modulated transcription factors that mediate the transcriptional activities of steroids, retinoids, and thyroid hormones. A growing number of related proteins have been identified that possess the structural features of hormone receptors, but that lack known ligands. Known as orphan receptors, these proteins represent targets for novel signaling molecules. We have isolated a mammalian orphan receptor that forms a heterodimeric complex with the retinoid X receptor. A screen of candidate ligands identified farnesol and related metabolites as effective activators of this complex. Farnesol metabolites are generated intracellularly and are required for the synthesis of cholesterol, bile acids, steroids, retinoids, and farnesylated proteins. Intermediary metabolites have been recognized as transcriptional regulators in bacteria and yeast. Our results now suggest that metabolite-controlled intracellular signaling systems are utilized by higher organisms.

Reverse transcriptase: mediator of genomic plasticity

Reverse transcription has been an important mediator of genomic change. This influence dates back more than three billion years, when the RNA genome was converted into the DNA genome. While the current cellular role(s) of reverse transcriptase are not yet completely understood, it has become clear over the last few years that this enzyme is still responsible for generating significant genomic change and that its activities are one of the driving forces of evolution. Reverse transcriptase generates, for example, extra gene copies (retrogenes), using as a template mature messenger RNAs. Such retrogenes do not always end up as nonfunctional pseudogenes but form, after reinsertion into the genome, new unions with resident promoter elements that may alter the gene's temporal and/or spatial expression levels. More frequently, reverse transcriptase produces copies of nonmessenger RNAs, such as small nuclear or cytoplasmic RNAs. Extremely high copy numbers can be generated by this process. The resulting reinserted DNA copies are therefore referred to as short interspersed repetitive elements (SINEs). SINEs have long been considered selfish DNA, littering the genome via exponential propagation but not contributing to the host's fitness. Many SINEs, however, can give rise to novel genes encoding small RNAs, and are the migrant carriers of numerous control elements and sequence motifs that can equip resident genes with novel regulatory elements [Brosius J. and Gould S.J., Proc Natl Acad Sci USA 89, 10706-10710, 1992]. Retrosequences, such as SINEs and portions of retroelements (e.g., long terminal repeats, LTRs), are capable of donating sequence motifs for nucleosome positioning, DNA methylation, transcriptional enhancers and silencers, poly(A) addition sequences, determinants of RNA stability or transport, splice sites, and even amino acid codons for incorporation into open reading frames as novel protein domains. Retroposition can therefore be considered as a major pacemaker for evolution (including speciation). Retroposons, with their unique properties and actions, form the molecular basis of important evolutionary concepts, such as exaptation [Gould S.J. and Vrba E., Paleobiology 8, 4-15, 1982] and punctuated equilibrium [Elredge N. and Gould S.J. in Schopf T.J.M. (ed). Models in Paleobiology. Freeman, Cooper, San Francisco, 1972, pp. 82-115].

BC1 RNA: transcriptional analysis of a neural cell-specific RNA polymerase III transcript

Rodent BC1 RNA represents the first example of a neural cell-specific RNA polymerase III (Pol III) transcription product. By developing a rat brain in vitro system capable of supporting Pol III-directed transcription, we showed that the rat BC1 RNA intragenic promoter elements, comprising an A box element and a variant B box element, as well as its upstream region, containing octamer-binding consensus sequences and functional TATA and proximal sequence element sites, are necessary for transcription. The BC1 B box, lacking the invariant A residue found in the consensus B boxes of tRNAs, represents a functionally related and possibly distinct promoter element. The transcriptional activity of the BC1 B box element is greatly increased, in both a BC1 RNA and a chimeric tRNA(Leu) gene construct, when the BC1 5' flanking region is present and is appropriately spaced. Moreover, a tRNA consensus B-box sequence can efficiently replace the BC1 B box only if the BC1 upstream region is removed. These interactions, identified only in a homologous in vitro system, between upstream Pol II and intragenic Pol III promoters suggest a mechanism by which the tissue-specific BC1 RNA gene and possibly other Pol III-transcribed genes can be regulated.

Neural BC1 RNA as an evolutionary marker: guinea pig remains a rodent

The traditional morphologically grounded placement of South American guinea pig-like rodents (Caviomorpha) within one of the two rodent suborders, Hystricognathi, has been disputed by recent analysis of protein and nucleic acid sequence data. The Caviomorpha and possibly all Hystricognathi would be considered a separate order, distinct from the other rodent suborder, Sciurognathi, and thus of the order Rodentia, and would be placed closer phylogenetically to other mammals [Graur, D., Hide, W. A. & Li, W.-H. (1991) Nature (London) 351, 649-652]. To address the discrepancy between morphological comparisons and sequence analyses, we have applied an alternative form of molecular analysis. We demonstrate that BC1 RNA, a neural-specific small cytoplasmic RNA that is the product of a retropositionally generated gene (a gene derived by reverse transcription of RNA followed by insertion of the DNA copy into the genome), is present in Sciurognathi and guinea pig but not in other mammalian orders including Lagomorpha, Artiodactyla, and Primates. The species-confined, tissue-specific expression of a retroposed sequence therefore supports the morphological evidence for monophyly of Rodentia inclusive of guinea pig and demonstrates the usefulness of such molecular genetic markers. Furthermore, the conservation and tissue-specific expression of the BC1 RNA gene in the two divergent rodent suborders suggests that this macromolecule has been exapted into a functional role (i.e., coopted into a variant or novel function) in the rodent nervous system.

Coordinated posttranscriptional control of gene expression by modular elements including Alu-like repetitive sequences

We previously reported that in rat fibroblasts, accumulation of a set of mRNAs ("pIL genes") was modulated as a function of cell growth and transformation, at a posttranscriptional stage, and by a mechanism that depends on a short nucleotide sequence containing an ID repetitive element. In mouse fibroblasts, hybridization with rat pIL probes identified mRNAs with the same pattern of expression, which did not contain ID sequences but contained a different regulatory element, encompassing a repetitive sequence of the B1 family. Expression in mouse cells of a reporter beta-globin gene carrying this element inserted in its 3' noncoding region was growth- and transformation-dependent. The nucleotide sequences of two murine and of three rat pIL cDNAs showed clear similarities in the region immediately adjacent to the ID and B1 repeats. Both the repeat and the flanking sequence were required to confer on beta-globin constructs the pattern of expression characteristic of the pIL genes. The hypothesis is presented that repetitive sequences in the eukaryotic genome might be modular parts of complex regulatory elements ensuring the coordinated expression of various mRNA species.

Genes, viruses and neurodevelopmental schizophrenia

Recent neuroimaging and neuropathological studies suggest a developmental origin for schizophrenia. Some cases may, therefore, be caused by a genetic defect in the specification of brain development. Early environmental hazards such as obstetric complications, and maternal exposure during pregnancy to influenza epidemics, have also been found to increase the risk of later schizophrenia. The relationship between the prevalence of influenza and birth date has been found more consistently for female than male schizophrenics. Female schizophrenia is also associated with a higher risk of schizophrenia in first degree relatives. This raises the question of whether part of the genetic predisposition to schizophrenia may comprise an abnormal reaction to maternal influenza.

Murine BC1 RNA in dendritic fields of the retinal inner plexiform layer

Rodent BC1 RNA is a non-messenger RNA polymerase III transcript that is almost exclusively expressed in nerve cells. BC1 RNA has been localised in somatic and dendritic domains of neurons, and its location has been interpreted to indicate a functional role in extrasomatic postsynaptic protein synthesis. In previous in situ hybridisation experiments, it has been demonstrated that in the retina most of the BC1 labelling signal was confined to the ganglion cell layer and the inner plexiform layer. Dendritic processes of several types of neurons form the neuritic plexus of the inner plexiform layer, and in order to determine the contribution of ganglion cells to the BC1 labelling signal, we eliminated this cell type by transecting the optic nerve unilaterally in newborn mice. Deletion of the ganglion cells resulted in a significant reduction although not a complete elimination of the BC1 signal in the inner plexiform layer. These data indicate that dendritic processes of both ganglion cells and amacrine cells contain BC1 RNA.

Characterization of the rat pulmonary surfactant protein A promoter

The expression of the pulmonary surfactant protein A (SP-A) is developmentally regulated and controlled by several hormones. In an attempt to characterize cis-acting elements involved in the regulation of SP-A expression, we have cloned the 5' flanking sequence of the rat SP-A gene. The promoter region contains a TATA box but no CAAT box. The transcription start site has been identified by anchored polymerase chain reaction and S1 nuclease mapping of the mature and precursor transcripts. S1 mapping of precursor transcripts has confirmed the stimulating effect of glucocorticoids on SP-A rat gene transcription in vivo. This hormonal effect may be mediated by a putative glucocorticoid responsive element located 140 bp upstream from the initiation site and protected against DNase 1 digestion in footprinting experiments. In vitro transcription of a G-free reporter cassette linked to the 212-bp 5' flanking DNA fragment has established that this putative promoter region is functional. Efficient transcription of the G-free reporter cassette was obtained with cell-free fetal lung extracts, whereas no transcript was detectable with cell-free liver extracts. Comparative analysis of the human and rat 5' flanking sequences shows the presence of strongly conserved motifs, unrelated to previously known consensus sequences. Some of these motifs, specifically protected in DNase 1 footprinting studies, could therefore be involved in the regulation of SP-A gene expression.

Getting the message from the gene to the synapse: sorting and intracellular transport of RNA in neurons

A key question in cellular neurobiology is how neurons target molecules to cellular microdomains at a distance from the nucleus. Of special importance are the thousands of postsynaptic sites that form the basis for synaptic communication. Recent evidence suggests that an important aspect of molecular trafficking involves differential sorting, selective intracellular transport, and docking of particular mRNA molecules and associated protein synthetic machinery at postsynaptic sites. This offers the potential for local regulation of the production of key proteins in response to conditions at individual synapses. This article reviews what is known about the mechanisms of mRNA trafficking in neurons and in other cells ranging from oocytes to oligodendrocytes, and considers the possible role that mRNA trafficking and the resulting local synthesis of particular proteins may play in cellular function.

Presence of low amounts of "neuronal" antigens in cultured human skin fibroblasts

To explore the utility of cultured skin fibroblasts in investigating diseases of the nervous system in which constituents characteristic of neurons are involved, sensitive immunochemical methods were used to test for the presence in skin fibroblasts of low amounts of proteins normally used as neuronal markers. The presence of each of the neurofilament triplet proteins and of neuron-specific enolase was demonstrated by immunoblotting and by immunocytochemistry, and of an 86-kDa synapsin-like material by immunoblotting. These observations agree with previous suggestions that readily available cultured fibroblasts may be useful in investigations of disorders in which molecules are involved which are typically associated with neurons in vivo, such as Alzheimer's disease.

Modular transposition and the dynamical structure of eukaryote regulatory evolution

This paper examines a model in which transposable elements provide a modular architecture for the cellular genome, complemented by cellular recombinational transformations, arising in turn as a dynamical consequence of this modular structure. It is proposed that the ecology of transposable elements in a given organism is a function of recombinational protocols of the evolving cellular genome. In mammals this is proposed to involve coordinated meiosis-phased activation of LINEs, SINEs and retrogenes complemented by endogenous retroviral transfer between cells.

The genetics of schizophrenia is the genetics of neurodevelopment

Genes are now accepted as being important in the aetiology of schizophrenia (Gottesman & Shields, 1982; McGuffinet al,1987), and over the past decade the emphasis in genetic research has shifted away from genetic epidemiology to searching the chromosomal DNA for the genes themselves. Despite this increasing technical sophistication, the application of linkage analysis to families multiply affected by schizophrenia has been accompanied by the familiar controversy over the exact borders of the adult clinical phenotype (Sherringtonet al,1988; St Clairet al,1989). Indeed, the preoccupation of researchers with the vagaries of the clinical definition has resulted in repeated attempts to use genetic studies to determine the relative validity of different operational definitions of schizophrenia (McGuffinet al,1984; Farmeret al,1987). To us, such studies beg the question of how precisely genes are involved in the aetiology of schizophrenia; after all, genes code for proteins, not for auditory hallucinations in the third person.

Dendritic location of neural BC1 RNA

In nerve cells, a specialized protein synthetic machinery is thought to operate in local compartments of dendrites, in particular beneath synaptic junctions, and thereby to facilitate swift adjustments of the postsynaptic protein repertoire in situ. This notion has been supported by the identification of polyribosomes and selected mRNAs in those compartments. In this study, we report the discovery of a specific RNA polymerase III transcript in dendrites. This RNA, a noncoding, 152-nucleotide-long, single-gene transcript known as BC1 RNA, is expressed almost exclusively in the nervous system. In adult rats as well as in immature rats in late developmental stages, BC1 RNA has been located in the dendrites and somata of a subset of neurons in the central and peripheral nervous system. The colocalization of BC1 RNA with dendritic mRNAs and polyribosomes may indicate a role--possibly within the functional unit of a high molecular mass ribonucleoprotein particle--in specific pre- or posttranslational processes in postsynaptic compartments of neurons.