The presence of both negative and positive elements in the 5'-flanking sequence of the rat Na,K-ATPase alpha 3 subunit gene are required for brain expression in transgenic mice

Transcriptional regulators of Na,K-ATPase subunits

The Na,K-ATPase classically serves as an ion pump creating an electrochemical gradient across the plasma membrane that is essential for transepithelial transport, nutrient uptake and membrane potential. In addition, Na,K-ATPase also functions as a receptor, a signal transducer and a cell adhesion molecule. With such diverse roles, it is understandable that the Na,K-ATPase subunits, the catalytic α-subunit, the β-subunit and the FXYD proteins, are controlled extensively during development and to accommodate physiological needs. The spatial and temporal expression of Na,K-ATPase is partially regulated at the transcriptional level. Numerous transcription factors, hormones, growth factors, lipids, and extracellular stimuli modulate the transcription of the Na,K-ATPase subunits. Moreover, epigenetic mechanisms also contribute to the regulation of Na,K-ATPase expression. With the ever growing knowledge about diseases associated with the malfunction of Na,K-ATPase, this review aims at summarizing the best-characterized transcription regulators that modulate Na,K-ATPase subunit levels. As abnormal expression of Na,K-ATPase subunits has been observed in many carcinoma, we will also discuss transcription factors that are associated with epithelial-mesenchymal transition, a crucial step in the progression of many tumors to malignant disease.

The expression of the human neuronal alpha3 Na+,K+-ATPase subunit gene is regulated by the activity of the Sp1 and NF-Y transcription factors

The Na+,K+-ATPase is a ubiquitous protein found in virtually all animal cells which is involved in maintaining the electrochemical gradient across the plasma membrane. It is a multimeric enzyme consisting of alpha, beta and gamma subunits that may be present as different isoforms, each of which has a tissue-specific expression profile. The expression of the Na+,K+-ATPase alpha3 subunit in humans is confined to developing and adult brain and heart, thus suggesting that its catalytic activity is strictly required in excitable tissues. In the present study, we used structural, biochemical and functional criteria to analyse the transcriptional mechanisms controlling the expression of the human gene in neurons, and identified a minimal promoter region of approx. 100 bp upstream of the major transcription start site which is capable of preferentially driving the expression of a reporter gene in human neuronal cell lines. This region contains the cognate DNA sites for the transcription factors Sp1/3/4 (transcription factors 1/3/4 purified from Sephacryl and phosphocellulose columns), NF-Y (nuclear factor-Y) and a half CRE (cAMP-response element)-like element that binds a still unknown protein. Although the expression of these factors is not tissue-specific, co-operative functional interactions among them are required to direct the activity of the promoter predominantly in neuronal cells.

GABAA receptors: building the bridge between subunit mRNAs, their promoters, and cognate transcription factors

The type A gamma-aminobutyric acid (GABA(A)) receptors mediate the majority of fast inhibitory neurotransmission in the CNS, and alterations in GABA(A) receptor function is believed to be involved in the pathology of several neurological and psychiatric illnesses, such as epilepsy, anxiety, Alzheimer's disease, and schizophrenia. GABA(A) receptors can be assembled from eight distinct subunit families defined by sequence similarity: alpha(1-6), beta(1-3), gamma(1-3), delta, pi, theta, and rho(1-3). The regulation of GABA(A) receptor function in the brain is a highly compensating system, influencing both the number and the composition of receptors at the cell surface. While transcriptional and translational points of control operate in parallel, it is becoming increasingly evident that many functional changes in GABA(A) receptors reflect the differential gene regulation of its subunits. The fact that certain GABA(A) receptor subunit genes are transcribed in distinct cell types during specific periods of development strongly suggests that genetic control plays a major role in the choice of subunit variants available for receptor assembly. This review focuses on the physiological conditions that alter subunit mRNA levels, the promoters that may control such levels, and the use of a conceptual framework created by bioinformatics to study coordinate and independent GABA(A) receptor subunit gene regulation. As this exciting field moves closer to identifying the language hidden inside the chromatin of GABA(A) receptor subunit gene clusters, future experiments will be aimed at testing models generated by computational analysis with biologically relevant in vivo and in vitro assays. It is hoped that through this functional genomic approach there will be the identification of new targets for therapeutic intervention.

Analysis of transcriptional regulatory sequences of the N-methyl-D-aspartate receptor 2A subunit gene in cultured cortical neurons and transgenic mice

The postnatal appearance and up-regulation of the NR2A subunit of the N-methyl-d-aspartate receptor contributes to the functional heterogeneity of the receptor during development. To elucidate the molecular mechanisms that regulate the neural and developmental specific expression of NR2A, an upstream approximately 9-kb region of the gene harboring the promoter was isolated and characterized in transgenic mice and transfected cortical neurons. Transgenic mouse lines generated with luciferase reporter constructs driven by either 9 or 1 kb of upstream sequence selectively transcribe the transgene in brain, as compared with other non-neural tissues. Reporter luciferase levels in dissociated cultures made from these mice are over 100-fold greater in neuronal/glial co-cultures than in pure glial cultures. Analysis of NR2A 5'-nested deletions in transfected cultures of cortical neurons and glia indicate that while sequences residing upstream of -1079 bp augment NR2A neuronal expression, sequences between -486 and -447 bp are sufficient to maintain neuronal preference. An RE1/NRSE element is not necessary for NR2A neuron specificity. Furthermore, comparison of the 5'-deletion constructs in cortical neurons grown for 5, 8, 11, or 14 days in vitro indicate that sequences between -1253 and -1180 bp are necessary for maturational up-regulation of NR2A. Thus, different cis-acting sequences control the regional and temporal expression of NR2A, implicating distinct regulatory pathways.

Analysis of human neuropeptide FF gene expression

As an initial step to study the function of the gene encoding the human neuropeptide FF (NPFF), we cloned a 4.7-kb sequence from the promoter region. Primer extension and 5'-rapid amplification of cDNA ends revealed multiple transcription initiation sites. Northern blot analysis of the mRNA expression revealed a specific signal only in poly(A) + RNA from medulla and spinal cord. Chimeric luciferase reporter gene constructs were transiently transfected in A549, U-251 MG, SK-N-SH, SK-N-AS and PC12 cells. The promoter activity was directly comparable with the level of endogenous NPFF mRNA as determined by real-time quantitative RT-PCR. The highest promoter activity was measured when a region from - 552 to - 830 bp of the 5'-flanking region was fused to the constructs, and a potential silencer element was localized between nucleotides -220 and -551. A twofold increase in NPFF mRNA was observed after 72 h of nerve growth factor stimulation of PC12 cells and the region between - 61 and - 214 bp of the 5'-flanking region was found to be responsive to this stimulation. We postulate that control of human NPFF gene expression is the result of both positive and negative regulatory elements and the use of multiple transcription initiation sites.

Structure, promoter analysis, and chromosomal localization of the murine H(+)/K(+)-ATPase alpha 2 subunit gene

The H(+)/K(+)-ATPase alpha2 subunit (HK alpha 2) of distal colon and renal collecting ducts plays a critical role in potassium and acid-base homeostasis. The isolation and complete sequence of the murine HK alpha 2 gene are reported. The HK alpha 2 gene contains 23 exons and spans 23.5 kb of genomic DNA. The exon/intron organization is comparable to that of the human ATP1AL1 gene. Primer extension and 5'-rapid amplification of cDNA ends of distal colon RNA were used to map the transcription initiation site. Fluorescence in situ hybridization analysis localized the HK alpha 2 gene to murine chromosome 14C3. Sequence analysis of 7.2 kb of the 5'-flanking region revealed numerous consensus sites for transcription factors, including two potential glucocorticoid response elements. Transient transfection of promoter-luciferase constructs demonstrated strong basal HK alpha 2 promoter activity in renal collecting duct cells but not in fibroblasts or in a medullary thick ascending limb of Henle's loop cell line. Deletion analysis revealed that the proximal 0.2 kb of the promoter was sufficient to confer activity in collecting duct cells. These data should prove important in elucidation of the mechanisms controlling the differential, tissue-specific expression of the HK alpha 2 gene.

The neuron-restrictive silencer element-neuron-restrictive silencer factor system regulates basal and endothelin 1-inducible atrial natriuretic peptide gene expression in ventricular myocytes

Induction of the atrial natriuretic peptide (ANP) gene is a common feature of ventricular hypertrophy. A number of cis-acting enhancer elements for several transcriptional activators have been shown to play central roles in the regulation of ANP gene expression, but much less is known about contributions made by transcriptional repressors. The neuron-restrictive silencer element (NRSE), also known as repressor element 1, mediates repression of neuronal gene expression in nonneuronal cells. We found that NRSE, which is located in the 3' untranslated region of the ANP gene, mediated repression of ANP promoter activity in ventricular myocytes and was also involved in the endothelin 1-induced increase in ANP gene transcription. The repression was conferred by a repressor protein, neuron-restrictive silencer factor (NRSF). NRSF associated with the transcriptional corepressor mSin3 and formed a complex with histone deacetylase (HDAC) in ventricular myocytes. Trichostatin A (TSA), a specific HDAC inhibitor, relieved NRSE-mediated repression of ANP promoter activity, and chromatin immunoprecipitation assays revealed the involvement of histone deacetylation in NRSE-mediated repression of ANP gene expression. Furthermore, in myocytes infected with recombinant adenovirus expressing a dominant-negative form of NRSF, the basal level of endogenous ANP gene expression was increased and a TSA-induced increase in ANP gene expression was apparently attenuated, compared with those in myocytes infected with control adenovirus. Our findings show that an NRSE-NRSF system plays a key role in the regulation of ANP gene expression by HDAC in ventricular myocytes and provide a new insight into the role of the NRSE-NRSF system outside the nervous system.

Expression of brain-derived neurotrophic factor in cortical neurons is regulated by striatal target area

Changes in BDNF expression after different types of brain insults are related to neuroprotection, stimulation of sprouting, and synaptic reorganization. In the cerebral cortex, an autocrine-paracrine mechanism for BDNF has been proposed because the distribution patterns of BDNF and TrkB expression are almost identical. Moreover, cortical BDNF is anterogradely transported to the striatum, suggesting a role of BDNF in the functional interaction between the two brain regions. Here we have examined the expression of this neurotrophin in the cerebral cortex after various striatal lesions. Intrastriatal injection of quinolinate, kainate, 3-nitropropionic acid, or colchicine increased BDNF mRNA levels in cerebral cortex. In contrast, stimulation of neuronal activity in the striatum did not change cortical BDNF expression. Both excitatory amino acids increased BDNF expression in neurons of cortical layers II/III, V, and VI that project to the striatum. Moreover, grafting a BDNF-secreting cell line prevented both the loss of striatal neurons and the cortical upregulation of BDNF induced by excitotoxins. Because retrograde transport in the corticostriatal pathway was intact after striatal lesions, our results suggest that striatal damage upregulates endogenous BDNF in corticostriatal neurons by a transneuronal mechanism, which may constitute a protective mechanism for striatal and/or cortical cells.

Expression of brain-derived neurotrophic factor in cortical neurons is regulated by striatal target area

Changes in BDNF expression after different types of brain insults are related to neuroprotection, stimulation of sprouting, and synaptic reorganization. In the cerebral cortex, an autocrine-paracrine mechanism for BDNF has been proposed because the distribution patterns of BDNF and TrkB expression are almost identical. Moreover, cortical BDNF is anterogradely transported to the striatum, suggesting a role of BDNF in the functional interaction between the two brain regions. Here we have examined the expression of this neurotrophin in the cerebral cortex after various striatal lesions. Intrastriatal injection of quinolinate, kainate, 3-nitropropionic acid, or colchicine increased BDNF mRNA levels in cerebral cortex. In contrast, stimulation of neuronal activity in the striatum did not change cortical BDNF expression. Both excitatory amino acids increased BDNF expression in neurons of cortical layers II/III, V, and VI that project to the striatum. Moreover, grafting a BDNF-secreting cell line prevented both the loss of striatal neurons and the cortical upregulation of BDNF induced by excitotoxins. Because retrograde transport in the corticostriatal pathway was intact after striatal lesions, our results suggest that striatal damage upregulates endogenous BDNF in corticostriatal neurons by a transneuronal mechanism, which may constitute a protective mechanism for striatal and/or cortical cells.

Is RE1/NRSE a common cis-regulatory sequence for ChAT and VAChT genes?

Choline acetyltransferase (ChAT), the biosynthetic enzyme of acetylcholine, and the vesicular acetylcholine transporter (VAChT) are both required for cholinergic neurotransmission. These proteins are encoded by two embedded genes, the VAChT gene lying within the first intron of the ChAT gene. In the nervous system, both ChAT and VAChT are synthesized only in cholinergic neurons, and it is therefore likely that the cell type-specific expression of their genes is coordinately regulated. It has been suggested that a 2336-base pair genomic region upstream from the ChAT and VAChT coding sequences drives ChAT gene expression in cholinergic structures. We investigated whether this region also regulates VAChT gene transcription. Transfection assays showed that this region strongly represses the activity of the native VAChT promoters in non-neuronal cells, but has no major effect in neuronal cells whether or not they express the endogenous ChAT and VAChT genes. The silencer activity of this region is mediated solely by a repressor element 1 or neuron-restrictive silencer element (RE1/NRSE). Moreover, several proteins, including RE1-silencing transcription factor or neuron-restrictive silencer factor, are recruited by this regulatory sequence. These data suggest that this upstream region and RE1/NRSE co-regulate the expression of the ChAT and VAChT genes.

Transcriptional repression by neuron-restrictive silencer factor is mediated via the Sin3-histone deacetylase complex

A large number of neuron-specific genes characterized to date are under the control of negative transcriptional regulation. Many promoter regions of neuron-specific genes possess the repressor element repressor element 1/neuron-restrictive silencing element (RE1/NRSE). Its cognate binding protein, REST/NRSF, is an essential transcription factor; its null mutations result in embryonic lethality, and its dominant negative mutants produce aberrant expression of neuron-specific genes. REST/NRSF acts as a regulator of neuron-specific gene expression in both nonneuronal tissue and developing neurons. Here, we shown that heterologous expression of REST/NRSF in Saccharomyces cerevisiae is able to repress transcription from yeast promoters engineered to contain RE1/NRSEs. Moreover, we have taken advantage of this observation to show that this repression requires both yeast Sin3p and Rpd3p and that REST/NRSF physically interacts with the product of the yeast SIN3 gene in vivo. Furthermore, we show that REST/NRSF binds mammalian SIN3A and HDAC-2 and requires histone deacetylase activity to repress neuronal gene transcription in both nonneuronal and neuronal cell lines. We show that REST/NRSF binding to RE1/NRSE is accompanied by a decrease in the acetylation of histones around RE1/NRSE and that this decrease requires the N-terminal Sin3p binding domain of REST/NRSF. Taken together, these data suggest that REST/NRSF represses neuronal gene transcription by recruiting the SIN3/HDAC complex.

Tissue-specific enhancement and restriction of galanin gene expression in transgenic mice by 5' flanking sequences

Galanin (GAL) is a 29/30 amino acid residue neuropeptide that regulates a wide variety of neuroendocrine functions. Galanin is expressed in specific populations of neurons in the hypothalamus and other regions of the brain and in numerous peripheral sites. Previous studies in which galanin-reporter genes were transfected into neural crest-derived neuroblastoma and other tumor cells indicated that cell-specific galanin expression is controlled by gene elements on the 5' flanking sequence which enhance and restrict transcriptional activity. To determine how the gene sequences act in vivo, we first determined the distribution of endogenous galanin gene expression in normal mice. Galanin mRNA was detected in several parts of the central nervous system (CNS), and in several peripheral organs, including the pituitary, pancreas, small and large intestine, adrenal gland, lung, tongue, testes, ovary-fallopian tubes, and uterus, but not at detectable levels in the heart, liver, kidney, urinary bladder or skeletal muscle. We then created several lines of transgenic mice which contained either 5 or 0.131 kilobases (kb) of the bovine galanin gene 5' flanking sequence fused to the luciferase (luc) reporter gene (5GAL-luc vs. 0.1GAL-luc mice, respectively) and compared luciferase activity in these and other organs. In some regions of the CNS that expressed high amounts of galanin mRNA, such as the spinal cord, hypothalamus, thalamus, and medulla, transgene expression was significantly higher in 5GAL-luc vs. 0.1GAL-luc mice, whereas in certain other regions of the brain and in all peripheral organs, the ratio was strikingly reversed. It is concluded that 5 kb of flanking sequence contains elements that mediate basal transcriptional activity in certain parts of the CNS, but also contains sequences that restrict expression in many tissues. However, because the larger transgene was expressed at very low levels in some peripheral sites of high galanin expression such as the pituitary, pancreas, adrenal gland, and intestine, it is concluded that sequences on the 5 kb transgene are not sufficient to direct expression to these peripheral tissues in mice.

Transcriptional regulation of the GluR2 gene: neural-specific expression, multiple promoters, and regulatory elements

To understand how neurons control the expression of the AMPA receptor subunit GluR2, we cloned the 5' proximal region of the rat gene and investigated GluR2 promoter activity by transient transfection. RNase protection and primer extension of rat brain mRNA revealed multiple transcription initiation sites from -340 to -481 bases upstream of the GluR2 AUG codon. The relative use of 5' start sites was different in cortex and cerebellum, indicating complexity of GluR2 transcript expression among different sets of neurons. When GluR2 promoter activity was investigated by plasmid transfection into cultured cortical neurons, cortical glia, and C6 glioma cells, the promoter construct with the strongest activity, per transfected cell, was 29.4-fold (+/- 3.7) more active in neurons than in non-neural cells. Immunostaining of cortical cultures showed that >97% of the luciferase-positive cells also expressed the neuronal marker MAP-2. Evaluation of internal deletion and substitution mutations identified a functional repressor element I RE1-like silencer and functional Sp1 and nuclear respiratory factor-1 (NRF-1) elements within a GC-rich proximal GluR2 promoter region. The GluR2 silencer reduced promoter activity in glia and non-neuronal cell lines by two- to threefold, was without effect in cortical neurons, and could bind the RE1-silencing transcription factor (REST) because cotransfection of REST into neurons reduced GluR2 promoter activity in a silencer-dependent manner. Substitution of the GluR2 silencer by the homologous NaII RE1 silencer further reduced GluR2 promoter activity in non-neuronal cells by 30-47%. Maximal positive GluR2 promoter activity required both Sp1 and NRF-1 cis elements and an interelement nucleotide bridge sequence. These results indicate that GluR2 transcription initiates from multiple sites, is highly neuronal selective, and is regulated by three regulatory elements in the 5' proximal promoter region.

Transcriptional regulation of the GluR2 gene: neural-specific expression, multiple promoters, and regulatory elements

To understand how neurons control the expression of the AMPA receptor subunit GluR2, we cloned the 5' proximal region of the rat gene and investigated GluR2 promoter activity by transient transfection. RNase protection and primer extension of rat brain mRNA revealed multiple transcription initiation sites from -340 to -481 bases upstream of the GluR2 AUG codon. The relative use of 5' start sites was different in cortex and cerebellum, indicating complexity of GluR2 transcript expression among different sets of neurons. When GluR2 promoter activity was investigated by plasmid transfection into cultured cortical neurons, cortical glia, and C6 glioma cells, the promoter construct with the strongest activity, per transfected cell, was 29.4-fold (+/- 3.7) more active in neurons than in non-neural cells. Immunostaining of cortical cultures showed that >97% of the luciferase-positive cells also expressed the neuronal marker MAP-2. Evaluation of internal deletion and substitution mutations identified a functional repressor element I RE1-like silencer and functional Sp1 and nuclear respiratory factor-1 (NRF-1) elements within a GC-rich proximal GluR2 promoter region. The GluR2 silencer reduced promoter activity in glia and non-neuronal cell lines by two- to threefold, was without effect in cortical neurons, and could bind the RE1-silencing transcription factor (REST) because cotransfection of REST into neurons reduced GluR2 promoter activity in a silencer-dependent manner. Substitution of the GluR2 silencer by the homologous NaII RE1 silencer further reduced GluR2 promoter activity in non-neuronal cells by 30-47%. Maximal positive GluR2 promoter activity required both Sp1 and NRF-1 cis elements and an interelement nucleotide bridge sequence. These results indicate that GluR2 transcription initiates from multiple sites, is highly neuronal selective, and is regulated by three regulatory elements in the 5' proximal promoter region.

Neuronal expression of zinc finger transcription factor REST/NRSF/XBR gene

The identification of a common cis-acting silencer element, a neuron-restrictive silencer element (NRSE), in multiple neuron-specific genes, together with the finding that zinc finger transcription factor REST/NRSF/XBR could confer NRSE-mediated silencing in non-neuronal cells, suggested that REST/NRSF/XBR is a master negative regulator of neurogenesis. Here we show that, although REST/NRSF/XBR expression decreases during neuronal development, it proceeds in the adult nervous system. In situ hybridization analysis revealed neuronal expression of rat REST/NRSF/XBR mRNA in adult brain, with the highest levels in the neurons of hippocampus, pons/medulla, and midbrain. The glutamate analog kainic acid increased REST/NRSF/XBR mRNA levels in various hippocampal and cortical neurons in vivo, suggesting that REST/NRSF/XBR has a role in neuronal activity-implied processes. Several alternatively spliced REST/NRSF/XBR mRNAs encoding proteins with nine, five, or four zinc finger motifs are transcribed from REST/NRSF/XBR gene. Two of these transcripts are generated by neuron-specific splicing of a 28-bp-long exon. Rat REST/NRSF/XBR protein isoforms differ in their DNA binding specificities; however, all mediate repression in transient expression assays. Our data suggest that REST/NRSF/XBR is a negative regulator rather than a transcriptional silencer of neuronal gene expression and counteracts with positive regulators to modulate target gene expression quantitatively in different cell types, including neurons.

Isolation and characterization of kidney-specific ClC-K1 chloride channel gene promoter

The rat ClC-K1 chloride channel is a kidney-specific member of the ClC chloride channel family found exclusively in the thin ascending limb of Henle's loop in the kidney. To gain insight into the mechanism(s) of kidney-specific expression of ClC-K1, a genomic clone that contains the 5'-flanking region of the rat ClC-K1 gene was isolated. A single transcription start site was located 84 bp upstream of the start codon. The sequence of the proximal 5'-flanking region contained an activator protein (AP)-3 site, a glucocorticoid-responsive element, several AP-2 sites, and several E-boxes, but it lacked a TATA box. To functionally express the promoter, the approximately 2.5-kb pair 5'-flanking region was ligated to a luciferase reporter gene and transfected into inner medullary (IM) cells, a stable ClC-K1-expressing cell line derived from the inner medulla of simian virus 40 transgenic mouse, and ClC-K1-nonexpressing cell lines. Luciferase activity was 7-to 24-fold greater in IM cells than those in nonexpressing cell lines, suggesting that the approximately 2.5-kb fragment contained cis-acting regulatory elements for cell-specific expression of the ClC-K1 gene. Deletion analysis revealed that this cell-specific promoter activity in IM cells was still present in the construct containing 51 bp of the 5'-flanking region but was lost in the -29 construct, clearly demonstrating that the 22 bp from -51 to -30 have a major role in the cell-specific activity of the ClC-K1 promoter. These 22 bp consist of purine-rich sequence (GGGGAGGGG-GAGGGGAG), and gel-retardation analysis demonstrated the existence of a specific protein(s) binding to this element in IM cells. These results suggest that the novel purine-rich element may play a key role in the activity of the ClC-K1 gene promoter.

Neuronal expression of zinc finger transcription factor REST/NRSF/XBR gene

The identification of a common cis-acting silencer element, a neuron-restrictive silencer element (NRSE), in multiple neuron-specific genes, together with the finding that zinc finger transcription factor REST/NRSF/XBR could confer NRSE-mediated silencing in non-neuronal cells, suggested that REST/NRSF/XBR is a master negative regulator of neurogenesis. Here we show that, although REST/NRSF/XBR expression decreases during neuronal development, it proceeds in the adult nervous system. In situ hybridization analysis revealed neuronal expression of rat REST/NRSF/XBR mRNA in adult brain, with the highest levels in the neurons of hippocampus, pons/medulla, and midbrain. The glutamate analog kainic acid increased REST/NRSF/XBR mRNA levels in various hippocampal and cortical neurons in vivo, suggesting that REST/NRSF/XBR has a role in neuronal activity-implied processes. Several alternatively spliced REST/NRSF/XBR mRNAs encoding proteins with nine, five, or four zinc finger motifs are transcribed from REST/NRSF/XBR gene. Two of these transcripts are generated by neuron-specific splicing of a 28-bp-long exon. Rat REST/NRSF/XBR protein isoforms differ in their DNA binding specificities; however, all mediate repression in transient expression assays. Our data suggest that REST/NRSF/XBR is a negative regulator rather than a transcriptional silencer of neuronal gene expression and counteracts with positive regulators to modulate target gene expression quantitatively in different cell types, including neurons.

Na,K-ATPase mRNA levels and plaque load in Alzheimer's disease

The expression of Na,K-ATPase alpha 1- and alpha 3-mRNAs was analyzed by in situ hybridization in the superior frontal cortex and cerebellum of brains from five Alzheimer's disease (AD), five nondemented age-matched, and three young control subjects. Brains with well-preserved RNA, tested by Northern hybridization of immobilized RNA with [32P]-labeled human beta-actin riboprobe, were chosen for analysis. In situ hybridization was performed on formalin-fixed, 5 microns-thick Paraplast sections with [35S]-labeled riboprobes prepared by in vitro transcription of the respective linearized clones: a 537-bp EcoRI-PstI fragment of alpha 1-cDNA and a 342-bp PstI-EcoRI fragment of alpha 3-cDNA. In cortex, grains related to mRNA were measured by density per unit area in five cortical columns separated by 1.0-1.2 cm in each of two adjacent sections. Each cortical column of 180-micron width was divided into four depths orthogonal to the pial surface between the pia and the white matter. Amyloid plaques were counted in the same regions of adjacent sections. In addition, alpha 3-mRNA grain clusters over individual pyramidal neurons within depth 4 were analyzed. We found the following significant changes (p < 0.05): 1. Increases in total alpha 1-mRNA by 13-19% in AD compared to young and by 7-12% in AD compared to age-matched controls. 2. Decrease in total alpha 3-mRNA by 31-38% in AD compared to young and age-matched controls. 3. Decrease in alpha 3-mRNA content over individual pyramidal perikarya by 14% in normal aged brains without plaques compared to young controls, and by 44% in AD relative to young controls and by 35% compared to age-matched controls. No significant difference (p < 0.2) was found with respect to alpha 1- or alpha 3-mRNA in cerebellar cortex or individual Purkinje cells among any of the groups. In addition, there was a trend toward an inverse correlation between the levels of alpha 3-mRNA and of diffuse plaques, but not of neuritic plaques, in AD cases.

IN CONCLUSION

1. The increases in alpha 1-mRNA in AD may be related to an increased reactive gliosis. 2. The declines in alpha 3-mRNA per individual neuron found in normal aging occur prior to the formation of diffuse plaques and are greatly accelerated in AD. 3. The declines in alpha 3-mRNA per neuron found in normal aging may predispose to or potentiate AD pathogenesis.

Tissue-specific expression of the L1 cell adhesion molecule is modulated by the neural restrictive silencer element

The cell adhesion molecule L1 mediates neurite outgrowth and fasciculation during embryogenesis and mutations in its gene have been linked to a number of human congenital syndromes. To identify DNA sequences that restrict expression of L1 to the nervous system, we isolated a previously unidentified segment of the mouse L1 gene containing the promoter, the first exon, and the first intron and examined its activity in vitro and in vivo. We found that a neural restrictive silencer element (NRSE) within the second intron prevented expression of L1 gene constructs in nonneural cells. For optimal silencing of L1 gene expression by the NRSE-binding factor RE-1-silencing transcription factor (REST)/NRSF, both the NRSE and sequences in the first intron were required. In transgenic mice, an L1lacZ gene construct with the NRSE generated a neurally restricted expression pattern consistent with the known pattern of L1 expression in postmitotic neurons and peripheral glia. In contrast, a similar construct lacking the NRSE produced precocious expression in the peripheral nervous system and ectopic expression in mesenchymal derivatives of the neural crest and in mesodermal and ectodermal cells. These experiments show that the NRSE and REST/NRSF are important components in restricting L1 expression to the embryonic nervous system.

Functional organization of the promoter region of the mouse F3 axonal glycoprotein gene

F3 is a developmentally regulated adhesive glycoprotein expressed by subpopulations of central and peripheral neurons which mediates neurite growth and fasciculation via cis- and trans-interactions with cell-surface or matrix components. We previously reported on the characterization of the F3 gene 5' flanking region in which we identified promoter and enhancer elements. Here, we report on the functional organization of the F3 gene regulatory regions. We show that the F3 promoter is built of linearly arranged positive and negative elements scattered through the 5' flanking region of the F3 gene and the 1st exon (exon 0). Neural- and cell type-specific expression of F3 appears to be governed by elements located in the most proximal promoter region which includes a neural-specific enhancer. In retardation assays, all these cis-acting elements bind nuclear proteins, three of which interact with the identified enhancer element while a single species interacts with sequences located within exon 0. Some of these proteins are also specifically expressed within the brain, indicating that they could correspond to neural-specific trans-acting factors. Elements located immediately upstream of the cell type-specific enhancer and within exon 0 are responsible for regulation of F3 expression by cAMP and retinoic acid.

Promoter of the Na,K-ATPase alpha3 subunit gene is composed of cis elements to which NF-Y and Sp1/Sp3 bind in rat cardiocytes

Na,K-ATPase alpha subunit has three isoforms whose expression is regulated developmentally and hormonally. Na,K-ATPase alpha3 subunit gene (Atpla3) is expressed only in brain and neonatal heart in a rat. The purpose of this study is to analyze cis-acting elements and trans-acting factors regulating the transcription of Atpla3 in cultured neonatal rat cardiocytes. Transient transfection assays with Atpla3-luciferase chimeric construct and a series of 5' sequential deletion mutations revealed the existence of positive regulatory elements from -74 to -59 and from -59 to -39. A factor was identified to bind across -59 by gel retardation assay. Methylation interference and DNase I footprinting analyses revealed the binding region from -74 to -53 (positive regulatory element (PRE) 1). The binding factor was identified to be NF-Y by gel retardation assay using specific antibody. Gel retardation and methylation interference analyses revealed that factors bind to two other elements from -54 to -43 (PRE2) and from -25 to -13 (PRE3). The binding factors were identified to be Sp1/Sp3 using specific antibodies. The functions of above-mentioned three elements were examined by transient transfection assay with various combinations of mutations. They all regulated the transcription positively and a synergistic enhancement of it was observed. Roles of NF-Y in the transcriptional activation and synergy are discussed.

The neuron-restrictive silencer element: a dual enhancer/silencer crucial for patterned expression of a nicotinic receptor gene in the brain

The neuron-restrictive silencer element (NRSE) has been identified in several neuronal genes and confers neuron specificity by silencing transcription in nonneuronal cells. NRSE is present in the promoter of the neuronal nicotinic acetylcholine receptor beta2-subunit gene that determines its neuron-specific expression in the nervous system. Using transgenic mice, we show that NRSE may either silence or enhance transcription depending on the cellular context within the nervous system. In vitro in neuronal cells, NRSE activates transcription of synthetic promoters when located downstream in the 5' untranslated region, or at less than 50 bp upstream from the TATA box, but switches to a silencer when located further upstream. In contrast, in nonneuronal cells NRSE always functions as a silencer. Antisense RNA inhibition shows that the NRSE-binding protein REST contributes to the activation of transcription in neuronal cells.

Activity of the osteocalcin promoter in skeletal sites of transgenic mice and during osteoblast differentiation in bone marrow-derived stromal cell cultures: effects of age and sex

The bone-specific osteocalcin gene is a well established marker of osteoblast activity. We have studied osteocalcin transcription in transgenic mice carrying rat osteocalcin promoter-chloramphenicol acetyltransferase (CAT) reporter constructs. Transgenic lines carrying each of the 1.7-, 1.1-, 0.72-, or 0.35-kilobase promoter constructs expressed the reporter gene in a tissue-specific manner. However, each of these constructs was sensitive to site of integration effects, reflected by a high frequency of nonexpressing transgenic lines. High expression of the 1.7-kilobase promoter in osseous tissues was accompanied by low ectopic expression in the brain. Analysis of CAT expression in femurs, calvariae, and lumbar vertebrae of this line indicated considerable variability in promoter activity among individual transgenic animals. Analysis of the variance in CAT activity demonstrated a linkage between promoter activities in these distant skeletal sites. Promoter activity was inversely correlated with age, and females exhibited severalfold higher activity than age-matched males. Bone marrow stromal cells from these animals, cultured under conditions that support osteoblast differentiation, exhibited the expected postproliferative onset of osteocalcin promoter activity, as assessed by CAT assay. The ex vivo CAT activity was not dependent on the sex or the age of the donor transgenic mouse. Taken together, our results are consistent with the hypothesis that a common, probably humoral, factor(s) regulates osteocalcin transcription in distant skeletal sites. We suggest that the abundance of this factor(s) is different between males and females and among individual mice at a given time point, and that ex vivo culturing of osteoblasts reduces the variation in osteocalcin promoter activity by eliminating the physiological contribution of this factor.

Expression of the rat m4 muscarinic acetylcholine receptor gene is regulated by the neuron-restrictive silencer element/repressor element 1

Neuronal cell-specific expression of the rat m4 muscarinic acetylcholine receptor (mAChR) is regulated by a silencer element. A likely mediator of this silencing is the neuron-restrictive silencer element/repressor element 1 (NRSE/RE1), which is present 837 base pairs (bp) upstream from the transcription initiation site of the m4 mAChR gene (Wood, I. C., Roopra, A., Harrington, C., and Buckley, N. J. (1995) J. Biol. Chem. 270, 30933-30940; Mieda, M., Haga, T., and Saffen, D. W. (1996) J. Biol. Chem. 271, 5177-5182). In the present study, we examined whether this putative NRSE/RE1 functions as a silencer. Transient expression assays using m4 mAChR promoter/luciferase expression vectors showed that the m4 NRSE/RE1 is necessary and sufficient to repress m4 promoter activity in non-neuronal L6 cells. m4 promoter activity was only partially repressed, however, in neuronal NG108-15 cells exogenously expressing the neuronal-restrictive silencer factor/RE1-silencing transcription factor (NRSF/REST). By contrast, the promoter activity of the type II sodium channel (NaII) gene was nearly completely repressed in NRSF/REST-expressing NG108-15 cells. Experiments with expression vectors containing chimeric promoters revealed that the NRSE/RE1 elements derived from both the m4 and NaII genes are independently sufficient to silence NaII gene promoter activity, but only partially repress m4 mAChR gene promoter activity in NRSF/REST-expressing NG108-15 cells. Thus, the repression activity of NRSF/REST depends upon the species of promoter to which it is linked. Gel-shift assays showed that the NRSF/REST is the only protein that binds to a 92-bp segment from the m4 mAChR promoter containing NRSE/RE1. This and the fact that m4 promoter activity was completely repressed in L6 cells suggest that the proteins that bind to the m4 constitutive promoter may be different from those in NG108-15 cells. Deletion analysis of the m4 constitutive promoter revealed that a 90-bp segment immediately upstream from the transcription initiation site contains significant promoter activity. Gel-shift assays revealed that several proteins in nuclear extracts prepared from L6 and NG108-15 cells bind to this 90-bp segment and that some of these proteins are L6 or NG108-15 cell-specific. These data support the idea that the repression activity of NRSF/REST depends upon the species of promoter to which it is linked and upon the proteins that bind to those promoters.

Polymorphism and structure of the gene coding for the alpha 1 subunit of the Artemia franciscana Na/K-ATPase

Genomic clones coding for one of the two identified Artemia franciscana Na/K-ATPase alpha subunits, the alpha 1 subunit, have been isolated. Several overlapping clones were obtained, although their restriction maps showed a large heterogeneity. Sequencing of their exons showed that they differ in up to 3.46% of their nucleotides in translated regions and 8.18% in untranslated regions. Southern blot analysis of DNA purified from different lots of A. franciscana cysts and from isolated individuals suggests that the variation is due to the existence of multiple Na/K-ATPase alpha 1 subunit alleles in A. franciscana. The Na/K-ATPase alpha 1 subunit gene is divided into 15 exons. Ten of the 14 introns are located in identical positions in this gene as in the human Na/K-ATPase alpha 3 subunit gene. Analysis of the 5' flanking region of the gene has allowed identification of the transcription-initiation sites. The adjacent upstream region has been shown to have functional promoter activity in cultured mammalian cells, suggesting the evolutionary conservation of some of the promoter regulatory sequences.

Cell type-specific regulation of choline acetyltransferase gene expression. Role of the neuron-restrictive silencer element and cholinergic-specific enhancer sequences

This study demonstrates the presence of positive and negative regulatory elements within a 2336-base pair-long region of the rat choline acetyltransferase (ChAT) gene promoter that cooperate to direct cell type-specific expression in cholinergic cells. A 21-base pair-long neuron-restrictive silencer element (NRSE) was identified in the proximal part of this region. This element was recognized by the neuron-restrictive silencer factor (NRSF), previously shown to regulate expression of other neuron-specific genes. The ChAT NRSE was inactive in both cholinergic and non-cholinergic neuronal cells, but repressed expression from a heterologous promoter in non-neuronal cells. Specific deletion of this element allowed ChAT gene promoter activity in non-neuronal cells, and overexpression of NRSF repressed ChAT gene promoter activity in cholinergic cells. The distal part of the ChAT gene promoter showed cholinergic-specific enhancing activity, which stimulated promoter activity in cholinergic cells, but was inactive in non-cholinergic neuronal and non-neuronal cells. This enhancer region suppressed the activity of the ChAT NRSE in cholinergic cells, even after NRSF overexpression. Thus, at least two kinds of regulatory elements cooperate to direct ChAT gene expression to cholinergic neurons, namely a neuron-restrictive silencer element and a cholinergic-specific enhancer.

Two alternative promoters direct neuron-specific expression of the rat microtubule-associated protein 1B gene

Microtubule-associated protein 1B (MAP1B) is a major constituent of the neuronal cytoskeleton that is expressed at high levels during early brain development and plays a role in axonal growth and neuronal plasticity. Previous studies suggested that the regulation of its gene expression is primarily at the transcriptional level. Thus, the characterization of the promoter region should help to define regulatory elements that control neuron-specific and developmental expression of the MAP1B gene. We have isolated genomic clones containing up to 11 kb of the upstream region of the rat MAP1B gene, sequenced approximately 1.8 kb upstream from the translation start codon, and identified several consensus sequences. These sequences include a consensus element common to several neuronal genes, a TCC repeat, a cAMP response element, and two TATA boxes that were 134 nucleotides apart from each other. S1 nuclease and RNase protection assays identified two corresponding groups of transcription initiation sites that were used selectively in distinct regions of the nervous system and during different stages of development. Transient transfection assays with neuronal and non-neuronal cell lines demonstrated that each TATA sequence and its corresponding adjacent region could independently direct neuron-specific expression of a reporter gene. Furthermore, the transcription of the reporter gene was initiated from the same sites as those of the MAP1B gene in vivo. These results suggest that two alternative and overlapping promoters, one inducible and the other constitutive, regulate the temporal and tissue-specific expression of the rat MAP1B gene.

Negative transcriptional regulation of the chicken Na+/K(+)-ATPase alpha 1-subunit gene

Although the Na+/K(+)-ATPase alpha 1-subunit gene is ubiquitously expressed in vertebrates, its level of expression varies among tissue and cell types. In spite of similar mRNA distribution in tissues of mammals and birds, the 5'-flanking regions of alpha 1-subunit genes exhibit remarkable diversity; i.e., the core promoter activity of the TATA-less chicken alpha 1 gene strongly depends upon multiple Sp1-based regulation (six Sp1 sites), whereas the promoter activity of the TATA-like rat alpha 1-subunit gene relies on the two Sp1 and additional positive regulatory factors. Further analysis of the regulatory regions of the Na+/K(+)-ATPase alpha 1-subunit genes revealed that the vertebrate alpha 1-subunit genes may share common inhibitory mechanisms for subtle transcriptional regulation; the core promoter activities can be either enhanced or repressed depending on the availability of inhibitory factors. Two potential candidates for such inhibitory elements in both avian and mammalian Na+/K(+)-ATPase alpha 1-subunit genes are (1) a newly identified element, GCCCTC, and (2) a GCF-binding sequence, NN[G/c]CG[G/c][G/c][G/c]CN, or its reverse complement. Gel retardation assays using the inhibitory region of the chicken gene and crude nuclear extracts from tissue-cultured chicken and mouse cells showed the existence of a set of proteins that bind to this region. The amounts of individual regulatory proteins in different cell types seem to vary, resulting in differential formation of DNA/protein complexes in different cell types. Thus, the regulation of Na+/K(+)-ATPase alpha 1-subunit gene expression under different cellular environment as well as in different cell types can be achieved by a shared mechanism; modulation of the ratio of the abundance of individual inhibitory factors.

Structure and the promoter region of the mouse gene encoding the 67-kD form of glutamic acid decarboxylase

We have cloned and determined the complete structure of the murine gene encoding the 67-kD form of glutamic acid decarboxylase (GAD67), the gamma-aminobutyric acid synthetic enzyme. Its coding region comprises 18 exons spanning 42 kb of genomic DNA. Exon 1 together with 64 bp of exon 2 defines the 5' untranslated region of GAD67 mRNA. Exon 18 specifies the protein's carboxyl terminal and the entire 3' untranslated region. Exons 7/A and 7/B are solely contained in the coding regions of two alternatively spliced bicistronic embryonic mRNAs, which code for the truncated embryonic GAD forms. The promoter region (P1) corresponding to the main group of transcription initiation sites is devoid of TATA and CAAT boxes but has putative binding sites for the transcription factor SP1 and is embedded in a large G + C-rich domain of a CpG island, features shared by the promoters of constitutively expressed housekeeping genes. Primer extension data suggests the existence of additional transcription start sites at 130 bp and 295 bp upstream from the major initiation site that are utilized less frequently in adult brain. The tentative distal promoters (P2 and P3) that correspond to the minor start sites resemble tissue-specific promoters with TATA and CAAT-like boxes. In 1.3 kb of the 5'-upstream region, we identified several putative transcription factor binding sites such as AP2, Hox, E-box, egr-1, and NF-kappaB and putative neuronal-specific regulatory elements, including the neuronal-restrictive silencer element, which may have functional significance in the developmental and tissue-specific expression of the GAD67 gene.

Identification of cis-acting sequences in the promoter of the herpes simplex virus type 1 latency-associated transcripts required for activation by nerve growth factor and sodium butyrate in PC12 cells

In the absence of detectable viral proteins, expression of the latency-associated transcripts (LATs) is likely regulated by cellular factors during latent infection of neurons with herpes simplex virus type 1. The amounts and activation states of these factors may in turn be regulated by extracellular regulatory factors. Consistent with this hypothesis, we have recently demonstrated that LAT expression is significantly enhanced by nerve growth factor (NGF) and sodium butyrate (NaB) in neurally derived PC12 cells. With the ultimate goal of identifying trans-acting cellular factors involved in regulating LAT expression during latency, we have attempted to identify the cis-acting elements to which these putative cellular factors bind by characterizing the LAT promoter and a series of 5' promoter deletion mutants in PC12 cells following treatment with the LAT-enhancing agents NGF and NaB. Transient expression assays demonstrated that distinct cis-acting sequences mediate basal and induced LAT promoter expression. Basal activity in PC12 cells is mediated by two elements: a negative regulatory element between -435 and -270 and a positive element between -240 and -204. The positive element contains binding sites for the transactivator Sp-1, whereas the negative element bears some resemblance to known neuron-specific silencer elements. In contrast to basal expression, maximum induction of the LAT promoter by NGF and NaB requires sequences between -159 and -81. Using gel mobility shift assays, we have identified three sets of protein-DNA complexes that bind to this 78-bp region and shown by competition analysis that binding is specific. The abundance and mobility of these complexes were altered by treatment with NGF or NaB. The nucleotide sequences to which these complexes bind were fine mapped by competition analysis with oligonucleotide probes containing substitution mutations. The target sequences identified exhibit no homology to binding sites of known transcription factors. These regions were critical for complex formation in vitro and for maximum induction of the LAT promoter by NGF and NaB in transient expression assays. The protein complexes that form with target sequences likely participate in the regulation of LAT expression in response to physiological stimuli in neurons in vivo.

Identification of potential target genes for the neuron-restrictive silencer factor

The neuron-restrictive silencer factor (NRSF) represses transcription of several neuronal genes in nonneuronal cells by binding to a 21-bp element called the neuron-restrictive silencer element (NRSE). We have performed data base searches with a composite NRSE to identify additional candidate NRSF target genes. Twenty-two more genes, 17 of which are expressed mainly in neurons, were found to contain NRSE-like sequences. Many of these putative NRSEs bound NRSF in vitro and repressed transcription in vivo. Most of the neuronal genes identified contribute to the basic structural or functional properties of neurons. However, two neuronal transcription factor genes contain NRSEs, suggesting that NRSF may repress neuronal differentiation both directly and indirectly. Functional NRSEs were also found in several nonneuronal genes, implying that NRSF may play a broader role than originally anticipated.

Distinct N-methyl-D-aspartate receptor 2B subunit gene sequences confer neural and developmental specific expression

Expression of the N-methyl--aspartate (NMDA) receptor 2B (NR2B) subunit is neural-specific and differentially regulated. It is expressed in the forebrain and in cerebellar granule cells at early postnatal stages and selectively repressed in the cerebellum after the second postnatal week, where it is replaced by the NR2C subunit. This switch confers distinct properties to the receptor. In order to understand the molecular mechanisms that differentially regulate the NR2B gene in the forebrain and cerebellum during development, we have isolated and characterized the promoter region of the NR2B gene. Two 5' noncoding exons and multiple transcription start sites were identified. Transcriptional analysis in transgenic mice reveals that an upstream 800-base pair region, which includes the first exon, is sufficient to direct neural-specific transcription. Developmental repression of the gene in the cerebellum requires additional regulatory elements residing in the first intron or second exon. Sequence elements that may participate in the regulation of the NR2B gene were identified by comparison to other neural genes. These studies provide insight into the molecular mechanisms regulating the switch of NMDA receptor subunit expression in the cerebellum, which ultimately account for the physiological changes in receptor function during development.

Two alternative promoters direct neuron-specific expression of the rat microtubule-associated protein 1B gene

Microtubule-associated protein 1B (MAP1B) is a major constituent of the neuronal cytoskeleton that is expressed at high levels during early brain development and plays a role in axonal growth and neuronal plasticity. Previous studies suggested that the regulation of its gene expression is primarily at the transcriptional level. Thus, the characterization of the promoter region should help to define regulatory elements that control neuron-specific and developmental expression of the MAP1B gene. We have isolated genomic clones containing up to 11 kb of the upstream region of the rat MAP1B gene, sequenced approximately 1.8 kb upstream from the translation start codon, and identified several consensus sequences. These sequences include a consensus element common to several neuronal genes, a TCC repeat, a cAMP response element, and two TATA boxes that were 134 nucleotides apart from each other. S1 nuclease and RNase protection assays identified two corresponding groups of transcription initiation sites that were used selectively in distinct regions of the nervous system and during different stages of development. Transient transfection assays with neuronal and non-neuronal cell lines demonstrated that each TATA sequence and its corresponding adjacent region could independently direct neuron-specific expression of a reporter gene. Furthermore, the transcription of the reporter gene was initiated from the same sites as those of the MAP1B gene in vivo. These results suggest that two alternative and overlapping promoters, one inducible and the other constitutive, regulate the temporal and tissue-specific expression of the rat MAP1B gene.

Neural specific expression of the m4 muscarinic acetylcholine receptor gene is mediated by a RE1/NRSE-type silencing element

Muscarinic receptor genes are members of the G-protein receptor superfamily that, with the inclusion of the odorant receptors, is believed to contain over a thousand members. Each member of this superfamily, which has been studied to date, appears to have a distinct pattern of expression, but little work has been done on the regulation of these complex expression patterns. We have recently isolated the rat m4 muscarinic receptor gene and identified a genomic 1520-nucleotide sequence that appeared capable of directing cell-specific expression (Wood, I. C., Roopra. A., Harrington, C., and Buckley, N. J. (1995) J. Biol. Chem. 270, 30933-30940). In the present study we have constructed a set of deletion promoter constructs to more closely define the DNA elements that are responsible for m4 gene expression. We have found that deletion of a RE1/NRSE silencer element between nucleotides -574 and -550, similar to that found in other neural specific genes, results in activation of reporter expression in non-m4-expressing cells. Gel mobility shift analysis has shown that a protein present in nonexpressing cells is capable of binding to this element and is probably the recently identified neural silencer, REST/NRSF. Of the constitutively active proximal promoter only a tandem Sp-1 site appears to recruit DNA binding proteins that are present in all cells tested. This represents the first report documenting the role of this silencer in regulating expression of a member of the G-protein receptor family.

Neuron-specific gene expression of synapsin I. Major role of a negative regulatory mechanism

The synapsins are a family of neuron-specific phosphoproteins that selectively bind to small synaptic vesicles in the presynaptic nerve terminal. The human synapsin I gene was functionally analyzed to identify control elements directing the neuron-specific expression of synapsin I. By directly measuring the mRNA transcripts of a reporter gene, we demonstrate that the proximal region of the synapsin I promoter is sufficient for directing neuron-specific gene expression. This proximal region is highly conserved between mouse and human. Deletion of a putative binding site for the zinc finger protein, neuron-restrictive silencer factor/RE-1 silencing transcription factor (NRSF/REST), abolished neuron-specific expression of the reporter gene almost entirely, allowing constitutively acting elements of the promoter to direct expression in a non-tissue-specific manner. These constitutive transcriptional elements are present as a bipartite enhancer, consisting of the region upstream (nucleotides -422 to -235) and downstream (nucleotides -199 to -143) of the putative NRSF/REST-binding site. The latter contains a motif identical to the cAMP response element. Both regions are not active or are only weakly active in promoting transcription on their own and show no tissue-specific preference. From these data we conclude that neuron-specific expression of synapsin I is accomplished by a negative regulatory mechanism via the NRSF/REST binding motif.

Identification of a negative regulatory element in the 5'-flanking region of the human dopamine beta-hydroxylase gene

Transient transfection experiments indicate that a 5'-flanking upstream domain, residing between -437 and -262 bp of the human dopamine beta-hydroxylase (DBH) gene, has a cell type-specific silencer function. This domain contains a putative silencer motif (which we designate DBH negative regulatory element, DNRE), showing sequence homology with the neural-restrictive silencer element (NRSE or RE-1) recently characterized in type II sodium channel, SCG10 and synapsin I genes. When the DNRE was placed at the proximal 262 bp of the homologous (DBH) promoter, it exhibited strong silencer activity both in DBH-expressing SK-N-BE(2)C as well as in DBH-nonexpressing HeLa cells. In addition, the DNRE also exhibited modest silencer activity upon a heterologous tk (herpes simplex virus thymidine kinase) promoter in both cell lines. Electrophoretic mobility shift assay demonstrated that nuclear extracts from both SK-N-BE(2)C and HeLa cells contain protein(s) that specifically bind to the DNRE. Formation of this DNRE/protein complex was specifically inhibited by an excess of unlabeled DNRE or NRSE. Finally, a similar sequence motif residing in the corresponding upstream area of the rat DBH gene also had a negative regulatory function, indicating that the silencer function of the DNRE is conserved in human and rat DBH genes.

Ubiquitous and neuronal DNA-binding proteins interact with a negative regulatory element of the human hypoxanthine phosphoribosyltransferase gene

The hypoxanthine phosphoribosyltransferase (HPRT) gene is constitutively expressed at low levels in all tissues but at higher levels in the brain; the significance and mechanism of this differential expression are unknown. We previously identified a 182-bp element (hHPRT-NE) within the 5'-flanking region of the human HPRT (hHPRT) gene, which is involved not only in conferring neuronal specificity but also in repressing gene expression in nonneuronal tissues. Here we report that this element interacts with different nuclear proteins, some of which are present specifically in neuronal cells (complex I) and others of which are present in cells showing constitutive expression of the gene (complex II). In addition, we found that complex I factors are expressed in human NT2/D1 cells following induction of neuronal differentiation by retinoic acid. This finding correlates with an increase of HPRT gene transcription following neuronal differentiation. We also mapped the binding sites for both complexes to a 60-bp region (Ff; positions -510 to -451) which, when analyzed in transfection assays, functioned as a repressor element analogous to the full-length hHPRT-NE sequence. Methylation interference footprintings revealed a minimal unique DNA motif, 5'-GGAAGCC-3', as the binding site for nuclear proteins from both neuronal and nonneuronal sources. However, site-directed mutagenesis of the footprinted region indicated that different nucleotides are essential for the associations of these two complexes. Moreover, UV cross-linking experiments showed that both complexes are formed by the association of several different proteins. Taken together, these data suggest that differential interaction of DNA-binding factors with this regulatory element plays a crucial role in the brain-preferential expression of the gene, and they should lead to the isolation of transcriptional regulators important in neuronal expression of the HPRT gene.

Silencing is golden: negative regulation in the control of neuronal gene transcription

Recent work has identified negative-acting DNA regulatory elements that function to prevent the expression of neuronal genes in non-neuronal cell types or in inappropriate neuronal subtypes. In some cases, the protein factors that interact with these silencer elements have been isolated and characterized. For example, the recently cloned silencer-binding factor NRSF/REST is a novel zinc-finger protein that interacts with silencer elements in a number of neuron-specific genes. These data suggest that negative regulation plays a major role in determining the diverse patterns of gene expression within the nervous system.