Human Brain mRNA Research Articles

Large-scale identification of novel transcripts in the human genome

Although the sequencing of the human genome has been completed, the number and identity of genes contained within it remains to be fully determined. We used LongSAGE to analyze 660,357 human transcripts from human brain mRNA and identified expression of 17,409 known genes and >15,000 different transcripts that were not annotated in genome databases. Analysis of a subset of these unannotated transcripts suggests that 85% were differentially expressed in various tissue types and that fewer than 20% would have been detected by ab initio gene predictions. These studies suggest that the human genome contains on the order of twice as many transcribed regions as are currently annotated and that experimental approaches will be required to fully elucidate the novel genes corresponding to these transcripts.

Characterization of the human PRIP-1 gene structure and transcriptional regulation

The PRIP [phospholipase C related, but catalytically inactive protein] family has been isolated as a novel inositol 1,4,5-trisphosphate binding protein with a domain organization similar to phospholipase C-δ but lacking the enzyme activity, comprising PRIP-1 and PRIP-2. The PRIP-1 gene is expressed predominantly in the brain, while PRIP-2 exhibits a relatively ubiquitous expression in rats and mice. We also found that PRIP-1 plays an important role in type A receptor signaling for γ-aminobutyric acid in the brain. In this study, we investigated PRIP-1 gene structure and the possible mechanisms involved in the expression. The tissue distribution pattern of PRIP gene expression in humans was similar to that in rodents. 5′RACE (rapid amplification of cDNA ends) analysis using PRIP-1 gene specific primers with human brain mRNA revealed the presence of three new exons, indicating that the PRIP-1 gene is organized into 8 exons intervened by 7 introns. Although three transcripts resulting from the alternative splicing of exon 2 and/or 3 were detected, a transcript lacking exons 2 and 3 was predominantly expressed in humans, suggesting that the translation start codon of human PRIP-1 exists in exon 1. To characterize the human PRIP-1 promoter, transient luciferase assay was carried out with luciferase constructs including various lengths of the 5′ flanking region of the PRIP-1 gene. The results indicated that the positive regulatory region is located − 237 to − 108 bp upstream from the transcription start site. Gel shift assay revealed the specific binding of some nuclear proteins to this region, suggesting that the existence of transcription factors contributes to the positive regulation of PRIP-1 gene expression. Mutation analyses revealed that the binding of a transcription factor, MAZ to the regulatory site leads to the promoter activity, indicating that MAZ is involved in the expression regulation of the human PRIP-1 gene.

Structural organization of the human complexin 2 gene ( CPLX2) and aspects of its functional activity

We report here on the in vitro and in silico characterization of the organization of the human complexin 2 ( CPLX2) gene. This encodes for a protein of 134 amino acid residues, contains five exons, is localized on human chromosome 5q35.3, and spans more than 87 kb. We performed in silico analysis of the CPLX2 5′ untranslated region (UTR) and propose an alternative variant of the gene transcript. Compared to the mRNA reported earlier [McMahon, H.T., Missler, M., Li, C., Sudhof, T.C., 1995. Complexins: cytosolic proteins that regulate SNAP receptor function. Cell 83, 111–119.], this transcript bears a partly altered 5′-UTR associated with the same open reading frame. Both CPLX2 transcripts share exons III–V; the alternative transcript is devoid of exons I and II, and includes exon A instead. Exon A is localized within CPLX2 intron 2 about 7 kb upstream to exon III. Using reverse transcription polymerase chain reaction (RT-PCR) we detected both types of transcripts in human brain mRNA. In silico data suggest that two putative alternative TATA-less promoter regions separated by 74 kb govern the expression of two CPLX2 transcripts. Several potential transcription start sites were detected by primer extension for each of two alternative CPLX2 transcripts. The relative abundance of the alternative transcripts was investigated in human and rat forebrain, cerebellum, and hippocampus. Whereas both transcripts were detected in human and rat brain, their expression levels were found to vary significantly among the regions investigated. The organization of CPLX2 transcripts is conserved in humans and rodents.

Letter from the editor: adenosine‐to‐inosine RNA editing in Alu repeats in the human genome

Adenosine-to-inosine (A-to-I) RNA editing increases the complexity of the human transcriptome and is essential for maintenance of normal life in mammals. Most A-to-I substitutions occur within repetitive elements in the genome, mainly in Alu repeats. The phenomenon of A-to-I editing is far less abundant in mice, rats, chickens and flies than in humans, which correlates with the relative under-representation of Alu repeats in these non-primate genomes. Here, we review the recent results of bioinformatic and laboratory approaches that have estimated the extent of the editing phenomenon. We discuss the possible biological relevance of the editing pathway, its possible interaction with other cellular pathways that respond to double-stranded RNA and its possible contribution to the accelerated evolution of primates.

R1, a Novel Repressor of the Human Monoamine Oxidase A

Monoamine oxidase catalyzes the oxidative deamination of a number of neurotransmitters. A deficiency in monoamine oxidase A results in aggressive behavior in both humans and mice. Studies on the regulation of monoamine oxidase A gene expression have shown that the Sp1 family is important for monoamine oxidase A expression. To search for novel transcription factors, the sequences of three Sp1 sites in the monoamine oxidase A core promoter were used in the yeast one-hybrid system to screen a human cDNA library. A novel repressor, R1 (RAM2), has been cloned. The R1 cDNA encodes a protein with 454 amino acids and an open reading frame at the 5'-end. The transfection of R1 in a human neuroblastoma cell line, SK-N-BE (2)-C, inhibited the monoamine oxidase A promoter and enzymatic activity. The degree of inhibition of monoamine oxidase A by R1 correlated with the level of R1 protein expression. R1 was also found to repress monoamine oxidase A promoter activity within a natural chromatin environment. A gel-shift assay indicated that the endogenous R1 protein in SK-N-BE (2)-C cells interacted with the R1 binding sequence. R1 also bound directly to the natural monoamine oxidase A promoter in vivo as shown by chromatin immunoprecipitation assay. Immunocytochemical analysis showed that R1 was expressed in both cytosol and nucleus, which suggested a role for R1 in transcriptional regulation. Northern blot analysis revealed the presence of endogenous R1 mRNA in human brain and peripheral tissues. Taken together, this study shows that R1 is a novel repressor that inhibits monoamine oxidase A gene expression.

Functional Analysis of Genetic Variation in Catechol-O-Methyltransferase ( COMT): Effects on mRNA, Protein, and Enzyme Activity in Postmortem Human Brain

Catechol-O-methyltransferase (COMT) is a key enzyme in the elimination of dopamine in the prefrontal cortex of the human brain. Genetic variation in the COMT gene (MIM 116790) has been associated with altered prefrontal cortex function and higher risk for schizophrenia, but the specific alleles and their functional implications have been controversial. We analyzed the effects of several single-nucleotide polymorphisms (SNPs) within COMT on mRNA expression levels (using reverse-transcriptase polymerase chain reaction analysis), protein levels (using Western blot analysis), and enzyme activity (using catechol methylation) in a large sample (n = 108) of postmortem human prefrontal cortex tissue, which predominantly expresses the -membrane-bound isoform. A common coding SNP, Val158Met (rs4680), significantly affected protein abundance and enzyme activity but not mRNA expression levels, suggesting that differences in protein integrity account for the difference in enzyme activity between alleles. A SNP in intron 1 (rs737865) and a SNP in the 3' flanking region (rs165599)--both of which have been reported to contribute to allelic expression differences and to be associated with schizophrenia as part of a haplotype with Val--had no effect on mRNA expression levels, protein immunoreactivity, or enzyme activity. In lymphocytes from 47 subjects, we confirmed a similar effect on enzyme activity in samples with the Val/Met genotype but no effect in samples with the intron 1 or 3' SNPs. Separate analyses revealed that the subject's sex, as well as the presence of a SNP in the P2 promoter region (rs2097603), had small effects on COMT enzyme activity. Using site-directed mutagenesis of mouse COMT cDNA, followed by in vitro translation, we found that the conversion of Leu at the homologous position into Met or Val progressively and significantly diminished enzyme activity. Thus, although we cannot exclude a more complex genetic basis for functional effects of COMT, Val is a predominant factor that determines higher COMT activity in the prefrontal cortex, which presumably leads to lower synaptic dopamine levels and relatively deleterious prefrontal function.

The major form of MeCP2 has a novel N-terminus generated by alternative splicing.

MeCP2 is a methyl-CpG binding protein that can repress transcription of nearby genes. In humans, mutations in the MECP2 gene are the major cause of Rett syndrome. By searching expressed sequence tag (EST) databases we have found a novel MeCP2 splice isoform (MeCP2alpha) which encodes a distinct N-terminus. We demonstrate that the MeCP2alpha mRNA splice variant is more abundant than the previously annotated MeCP2 mRNA (MeCP2beta) in mouse tissues and human brain. Furthermore, MeCP2beta mRNA has an upstream open reading frame that inhibits its translation. As a result of these differences, >90% of MeCP2 in mouse brain is MeCP2alpha. Both protein isoforms are nuclear and colocalize with densely methylated heterochromatic foci in mouse cells. The presence of a previously unknown MeCP2 isoform has implications for the genetic screening of Rett syndrome patients and for studies of the functional significance of MeCP2.

Alteration in alpha-synuclein mRNA expression in Parkinson's disease.

The presynaptic protein alpha-synuclein is considered to play an important role in the pathophysiology of Parkinson's disease (PD). Point mutations in the alpha-synuclein gene have been demonstrated in familial PD and alpha-synuclein is a major component of Lewy bodies, the pathological hallmark of the sporadic disease. It is not clear whether abnormal accumulation of alpha-synuclein is the result of abnormal levels of expression of the gene in neurodegenerative conditions. Expression of alpha-synuclein mRNA was therefore studied in control and PD brain using semiquantitative in situ hybridization. alpha-synuclein was expressed widely and hybridization signal was seen in most cortical regions, hippocampus, cerebellum, and brain stem. There was little mRNA in the striatum and no hybridization signal was detected in glia. High levels of alpha-synuclein mRNA expression in neurons did not seem to be a marker for Lewy body formation. Abundant signal was seen both in regions in which Lewy body deposition occurs commonly in idiopathic PD (PD), such as substantia nigra and frontal and temporal cortex, as well as in less susceptible regions, e.g. visual cortex. Quantitative comparison of mRNA expression in regions of predilection for Lewy body formation showed that mRNA expression was reduced significantly in melanized substantia nigra neurons and frontal cortex neurons in Parkinson's disease. In substantia nigra neurons there seemed to be a negative correlation between cellular mRNA expression and disease duration. These findings are in broad agreement with other studies of the expression of alpha-synuclein mRNA in human brain and suggest that Lewy body formation is unlikely to be the result of overexpression of alpha-synuclein.

Quantifying mRNA in postmortem human brain: influence of gender, age at death, postmortem interval, brain pH, agonal state and inter-lobe mRNA variance

The quantification of mRNA in postmortem human brain is often made complicated by confounding factors. To assess the importance of potential confounders TaqMan™ real-time RT-PCR was used to measure seven mRNAs (β-actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), cyclophilin, microtubule-associated protein (MAP) 2, neuron-specific enolase (NSE), glial fibrillary acidic protein (GFAP), amyloid precursor protein (APP) isoform 770) in cortical samples taken from 90 Alzheimer's disease (AD) and 81 control brains. Demographic data for the brain samples were assessed for interaction between factors and amounts of mRNA. Gender was found to play a role in that females had lower levels of mRNA relative to males; this was consistent in both the AD and control brains. Age at death had inconsistent but significant correlations to amounts of mRNA; male and female controls both had negative correlations, female AD a positive correlation and male AD no correlation. Positive correlations were found between brain pH and amount of mRNA in all genes except glial fibrillary acidic protein (GFAP); correlations were consistent across all groupings of pathology and gender. Mean brain pH was significantly lower in AD (6.4) than in control subjects (6.5, ANOVA, p<0.01), though there was no difference between male and females of either group. No correlation was found between brain pH and age at death. Postmortem interval was correlated with brain pH in Alzheimer's disease brains but not controls. Agonal state was generally a poor predictor of mRNA levels whilst inter-lobe variance of mRNA was found to be non-significant in control brains. Given that gender, age at death and brain pH all have significant effects upon mRNA levels it is recommended that these factors be taken into account when quantifying gene expression in postmortem human brain.

An optimistic view for quantifying mRNA in post-mortem human brain

Quantitative human mRNA data are derived from post-mortem or biopsied tissue. RNA degradation, poor replication, a large mRNA variance and confounding factors such as brain pH and age of death are often cited, however, as objections to the data’s reliability. A central question is whether post-mortem human mRNA can be treated as a statistically ordered system. TaqMan™ real-time RT-PCR was used to measure seven mRNAs in 513 cortical samples taken from 90 Alzheimer’s disease and 81 control brains. Despite a high mRNA variance strong correlations were found between the mRNA transcripts in a single brain. Where a brain has a high/low level of one mRNA, the same brain invariably has a high/low level of other mRNAs; correlated order is present and allows removal of that source of variation common to all genes. Although levels of mRNA are highly variable between subjects (>1000-fold), quantitative order is present in post-mortem human mRNA, allowing effects due to pathology or gender to be isolated and tested for significance.

Low editing efficiency of GluR2 mRNA is associated with a low relative abundance of ADAR2 mRNA in white matter of normal human brain.

The ionotropic glutamate receptor (GluR) subunits GluR2, GluR5 and GluR6 are subject to RNA editing at their Q/R sites, resulting in significant alterations in the channel properties of the receptors. RNA editing at the Q/R site of GluRs is both developmentally and regionally regulated. Here we provide the first quantitative measurements of both mRNAs of the GluR subunits and mRNAs of the RNA editing enzymes ADAR1-ADAR3 in a comparison of the efficiency of editing at the Q/R site with the expression levels of ADAR mRNA in human brain. We demonstrate that the Q/R site of GluRs in white matter is edited significantly less than in grey matter. In addition, by means of quantitative reverse transcription-polymerase chain reaction methods, we demonstrate that the relative abundance of ADAR2 mRNA to GluR2 mRNA is significantly lower in white matter than in grey matter and that the GluR2 Q/R site editing decreased only when the ratio of ADAR2 mRNA (not that of ADAR1 mRNA) to GluR2 mRNA dropped below a threshold (20 x 10(-3)). These results suggest that Q/R site of GluRs editing is regulated in a regional, and hence presumably cell-specific, manner and that the GluR2 Q/R site editing is critically regulated by ADAR2 in human brain.

Expression patterns of epidermal growth factor receptor and fibroblast growth factor receptor 1 mRNA in fetal human brain.

Factors that interact with the epidermal growth factor and fibroblast growth factor receptors have numerous effects in the central nervous system (CNS), inducing the proliferation of CNS stem cells and astrocytes and the survival and differentiation of neurons. Both receptors are expressed in the embryonic rodent brain in proliferative and nonproliferative regions, suggesting roles in numerous developmental processes. However, the roles of these factors in human brain development are not known. In the current study, we examined the expression of human epidermal growth factor receptor (HEGFR) and human fibroblast growth factor receptor 1 (HFGFR1) mRNAs in the human fetal brain. The expression of both receptors is strikingly conserved relative to previously reported patterns in the rodent. In the germinal zones, the sites of cellular proliferation, HFGFR1 was expressed primarily in the ventricular zone, whereas HEGFR was expressed in the subventricular zone, suggesting different roles in CNS progenitor proliferation. Differential expression was also observed in other brain areas examined, including the hippocampus and the cerebellum. The current study suggests that HEGFR and HFGFR1 are likely to play different roles during human brain development, but that these roles will be similar to those observed in the rodent brain.

Hmob3 brain-specific sequence is a part of phylogenetically conserved human MAP1B gene 3′-untranslated region

Using in vitro and in silico approaches, we demonstrate that the Hmob3 brain-specific sequence is a part of the extended human MAP1B gene 3′UTR encoded by the portion of the exon 7. Previously we had isolated the 1.4 kb Hmob3 clone (Acc. No Y09836) from the human medulla oblongata cDNA library. In the present paper, we report the RT-PCR detection of extended transcripts containing the Hmob3 sequence as well as a fragment of MAP1B mRNA in the human brain mRNA samples. The existence of such transcripts confirms that Hmob3 is transcribed from the MAP1B gene. Thus we report a previously unknown region of the human MAP1B gene which encodes the MAP1B mRNA 3′UTR. The length of the 3′UTR was estimated of 4330 nucleotides. Comparative sequence analysis shows high phylogenetic conservation of MAP1B 3′UTR in mammals. Using Hmob3 as a probe in the Northern blot analysis, we have revealed two different types of transcripts for brain and kidney mRNA samples; in the skeletal muscle sample we detected both transcripts.

The regional pattern of μ-opioid receptor (MOR1) mRNA in human brain: a real-time PCR assay

In this study, a reverse transcription/real-time PCR assay was established to semi-quantify the mRNA levels of the human μ-opioid receptor (MOR1) relative to the housekeeping gene β-2-microglobulin in human autopsy brain tissue. Nine selected regions (thalamus, caudate putamen, hypothalamus, ventral tegmentum, hippocampus, amygdala, frontal cortex, nucleus accumbens, putamen) of five human brains were analysed. The observed expression pattern of μ-opioid receptor mRNA correlates with results obtained by in situ hybridisation. The method described here will be useful in further studies on steady-state mRNA levels in the brains of addicts who died due to opiate overdose, in order to elucidate whether chronic opioid abuse is followed by a regulation of μ-opioid receptor expression.

Six Genes Expressed in Bones and Teeth Encode the Current Members of the SIBLING Family of Proteins

Bone sialoprotein (BSP), dentin matrix protein 1 (DMP1), dentin sialophosphoprotein (DSPP), enamelin (ENAM), matrix extracellular phosphoglycoprotein (MEPE), and osteopontin (OPN) are glycophosphoproteins expressed in bones and/or teeth. Direct comparison of their amino acid sequences do not suggest that they belong to a single genetic family, but a detailed analysis of their chromosomal location and gene structure does. Analysis of human brain mRNA by RT-PCR has led to the discovery of two additional exons thereby making it more convincing that MEPE is a member of the SIBLING (Small Integrin-Binding LIgand, N-linked Glycoprotein) family. We propose that the members of this SIBLING family are extended, flexible proteins in solution that can facilitate the formation of a number of different complexes. For example, OPN can bridge complement Factor H to either an RGD-dependent integrin or to CD44 forming a membrane-bound complex that actively suppresses the alternate complement pathway. Two possible mechanisms for inhibiting the lytic pathway of alternate complement are presented.

Six Genes Expressed in Bones and Teeth Encode the Current Members of the SIBLING Family of Proteins

Bone sialoprotein (BSP), dentin matrix protein 1 (DMP1), dentin sialophosphoprotein (DSPP), enamelin (ENAM), matrix extracellular phosphoglycoprotein (MEPE), and osteopontin (OPN) are glycophosphoproteins expressed in bones and/or teeth. Direct comparison of their amino acid sequences do not suggest that they belong to a single genetic family, but a detailed analysis of their chromosomal location and gene structure does. Analysis of human brain mRNA by RT-PCR has led to the discovery of two additional exons thereby making it more convincing that MEPE is a member of the SIBLING (Small Integrin-Binding LIgand, N-linked Glycoprotein) family. We propose that the members of this SIBLING family are extended, flexible proteins in solution that can facilitate the formation of a number of different complexes. For example, OPN can bridge complement Factor H to either an RGD-dependent integrin or to CD44 forming a membrane-bound complex that actively suppresses the alternate complement pathway. Two possible mechanisms for inhibiting the lytic pathway of alternate complement are presented.

Downregulation of putative tumor suppressor gene TSC-22 in human brain tumors.

Our objective was to identify differentially expressed genes involved in the pathogenesis of glioblastoma multiforme (GBM). Screening of arrayed human fetal brain and human postnatal brain cDNA libraries was performed by differential hybridization with glioblastoma multiforme and human normal brain cDNAs. Repeated differential hybridization of more than 100 cDNA clones selected by primary screening and analysis of RNA from adult normal brain and glial tumors showed 16 nucleotide sequences differentially expressed between normal brain and brain tumors. Among others, decreased content in astrocytic tumors was determined for TSC-22 mRNA corresponding to cDNA in the ICRFp507J1041 clone from human fetal brain cDNA library. Northern blot hybridization of RNA from different human brain tumors showed very low amounts of TSC-22 mRNA in most investigated samples of GBM, anaplastic astrocytoma, and some other tumors. Complete lack of expression of TSC-22 occurred in one sample of anaplastic astrocytoma, as well as in meningioma, brain sarcoma, sarcomatous meningioma, and oligodendroglioma. The differential expression of TSC-22 gene was confirmed by semiquantitative RT-PCR in 15 samples of astrocytomas WHO grade II-IV and three samples of normal brain. Significantly decreased levels of TSC-22 mRNA in human brain and salivary gland tumors and antiproliferative role of TSC-22 strongly suggest a tumor suppressor role for TSC-22. J.

Nuclear Localization of L-type Glutaminase in Mammalian Brain

In mammals, there are two different genes encoding for glutaminase isoforms, named liver (LGA) and kidney (KGA) types. LGA has long been believed to be present only in liver mitochondria from adult animals. However, we have recently reported the presence of LGA mRNA in human brain. We now describe the expression of LGA mRNA in the brain of other mammals (cow, mouse, rabbit, and rat) and in different areas of human brain as assessed by Northern blot analysis. The presence of mRNA encoding for this isoform in rat brain was further confirmed by reverse transcriptase-PCR cloning and sequencing. Although it has been well accepted that glutaminase is a mitochondrial enzyme, using newly generated isoform-specific antibodies, we have found a differential intracellular immunolocalization of both glutaminase isoforms in rat and monkey brain. In both species, KGA protein was present in mitochondria, whereas LGA protein was localized in nuclei. Furthermore, subcellular fractionation and Western blot analysis revealed that brain LGA was enriched in nuclei where it was catalytically active. Nuclear glutaminase exhibited a kinetic behavior that resembles that of the liver-type enzyme with regard to the low phosphate concentration requirement; however, nuclear glutaminase was susceptible to glutamate inhibition, a property that is absent in the rat liver enzyme.

Cellular and subcellular distribution of D-aspartate oxidase in human and rat brain.

The unusual amino acid D-aspartate is present in significant amounts in brain and endocrine glands and is supposed to be involved in neurotransmission and neurosecretion (Wolosker et al. [2000] Neuroscience 100:183-189). D-aspartate oxidase is the only enzyme known to metabolize D-aspartate and could regulate its level in different regions of the brain. We examined the cellular and subcellular distribution of this enzyme and its mRNA in human and rat brain by immunohistochemistry, in situ hybridization, and immunoelectron microscopy. D-aspartate oxidase protein and mRNA are ubiquitous. The protein shows a granular pattern, particularly within neurons and to a significantly lesser extent in astrocytes and oligodendrocytes. No evidence for a synaptic association was observed. Whereas between most positive neurons only gradual differences were observed, in the hypothalamic paraventricular nucleus, neurons with high enzyme content were found next to others with no labeling. cDNA cloning of D-aspartate oxidase corroborates an inherent targeting signal sequence for protein import into peroxisomes. Immunoelectron microscopy showed that the protein is localized in single membrane-bound organelles, apparently peroxisomes.

Molecular Characterization of a Specific Thiamine Triphosphatase Widely Expressed in Mammalian Tissues

Thiamine triphosphate (ThTP) is found at low concentrations in most animal tissues, and recent data suggest that it may act as a phosphate donor for the phosphorylation of some proteins. In the mammalian brain, ThTP synthesis is rapid, but its steady-state concentration remains low, presumably because of rapid hydrolysis. In this report we purified a soluble thiamine triphosphatase (ThTPase; EC ) from calf brain. The bovine ThTPase is a 24-kDa monomer, hydrolyzing ThTP with virtually absolute specificity. Partial sequence data obtained from the purified bovine enzyme by tandem mass spectrometry were used to search the GenBank data base. A significant identity was found with only one human sequence, the hypothetical 230-amino acid protein MGC2652. The coding regions from human and bovine brain mRNA were amplified by reverse transcription-PCR, cloned in Escherichia coli, and sequenced. The human open reading frame was expressed in E. coli as a GST fusion protein. Transformed bacteria had a high isopropyl-beta-d-thiogalactopyranoside-inducible ThTPase activity. The recombinant ThTPase had properties similar to those of human brain ThTPase, and it was specific for ThTP. The mRNA was expressed in most human tissues but at relatively low levels. This is the first report of a molecular characterization of a specific ThTPase.