Nerve growth factor-induced derepression of peripherin gene expression is associated with alterations in proteins binding to a negative regulatory element

α-Internexin and Peripherin: Expression, Assembly, Functions, and Roles in Disease

α-Internexin and peripherin are neuronal-specific intermediate filament (IF) proteins. α-Internexin is a type IV IF protein like the neurofilament triplet proteins (NFTPs, which include neurofilament light chain, neurofilament medium chain, and neurofilament high chain) that are generally considered to be the primary components of the neuronal IFs. However, α-internexin is often expressed together with the NFTPs and has been proposed as the fourth subunit of the neurofilaments in the central nervous system. α-Internexin is also expressed earlier in the development than the NFTPs and is a maker for neuronal IF inclusion disease. α-Internexin can self-polymerize in vitro and in transfected cells and it is present in the absence of the NFTP in development and in granule cells in the cerebellum. In contrast, peripherin is a type III IF protein. Like α-internexin, peripherin is specific to the nervous system, but it is expressed predominantly in the peripheral nervous system (PNS). Peripherin can also self-assemble both in vitro and in transfected cells. It is as abundant as the NFTPs in the sciatic nerve and can be considered a fourth subunit of the neurofilaments in the PNS. Peripherin has multiple isoforms that arise from intron retention, cryptic intron receptor site or alternative translation initiation. The functional significance of these isoforms is not clear. Peripherin is a major component found in inclusions of patients with amyotrophic lateral sclerosis (ALS) and peripherin expression is upregulated in ALS patients.

A silencer element in the cartilage oligomeric matrix protein gene regulates chondrocyte-specific expression

The molecular mechanisms by which mesenchymal cells differentiate into chondrocytes are poorly understood. The cartilage oligomeric matrix protein gene (COMP) encodes a noncollagenous extracellular matrix protein whose expression pattern correlates with chondrocyte differentiation and arthritis. We have used the COMP promoter as a model to identify regulatory sequences necessary for chondrocyte-specific expression and to identify cell type-specific proteins that bind these sequences. We have previously cloned 1.9 kilobases of the 5(') flanking promoter sequence of the murine COMP gene and by deletion analysis have identified two spatially distant chondrocyte-specific regulatory regions. One element is situated proximally (-125 to -75), and a second region is located distally (-1925 to -592) relative to the transcription start site. In the present study, we performed a finer deletion analysis of the region of the COMP promoter from -1925 to -592 and identified a silencer region situated between -1775 and -1725. This silencer binds sequence-specific protein complexes; the intensity of these complexes is greater in two different fibroblast cell lines (NIH3T3 and 10T1/2) than in chondrocytic RCS cells. Competition experiments localized the binding site of these protein complexes from -1775 to -1746; deletion of this 30-bp site results in a selective increase in COMP promoter activity in fibroblasts. Four tandem repeats of this 30-bp site are sufficient to confer negative transcriptional regulation on a heterologous promoter (SV40) in NIH3T3 fibroblasts. These results suggest that negative regulation of transcription is an important mechanism for chondrocyte-specific expression of the COMP gene.

An intact intermediate filament network is required for collateral sprouting of small diameter nerve fibers

Expression of the intermediate filament (IF) protein peripherin is initiated during development at the time of axonal extension and increases during regeneration of nerve fibers. To test whether the IF network is essential for neuron process outgrowth in the mature organism in vivo, we disrupted endogenous peripherin IF in small-sized dorsal root ganglion (DRG) neurons in transgenic mice via expression of a mutant peripherin transgene under control of peripherin gene regulatory sequences. Anatomical and functional analyses showed that these neurons send peripheral and central axonal projections to correct targets, express correct neuropeptides, and mediate acute pain responses normally. However, disruption of IF significantly impaired the ability of uninjured small-sized DRG neurons to sprout collateral axons into adjacent denervated skin, indicating a critical role for intact IF in plasticity, specifically in compensatory nociceptive nerve sprouting.

Intron 1 is required for cell type-specific, but not injury-responsive, peripherin gene expression

The "primitive" neurons of the peripheral nervous system (PNS) have the remarkable ability to regenerate new fibers. This regenerative process requires a sequence of gene activation and repression that is poorly understood. One gene that is almost exclusively expressed in neurons of the PNS and is activated after nerve injury is the peripherin intermediate filament gene, but little is known about the genomic elements that control either its restricted expression or its response to nerve injury in adult mice. Previous studies suggested that both 5' flanking sequence and intragenic regions were required for cell type-specific and injury-specific expression. To determine which intragenic regions were critical, mice were generated that expressed peripherin transgenes lacking different introns. Analyses of these mice revealed that deletion of introns 2-8 had no effect on either the cell type-specific or injury-specific expression of the peripherin gene; however, the remaining intron, intron 1, differentially bound Sp1 transcription-related proteins/protein complexes in extracts from peripherin-expressing and nonexpressing tissues. Furthermore, a transgene that lacked intron 1 was not expressed in many neurons that contain endogenous peripherin but was activated after injury. Thus, accurate cell type-specific peripherin gene expression in the PNS depends on elements within intron 1, but other sequences, most likely in the 5'flanking region, are required for activating the peripherin gene in response to nerve injury.

In vivo expression of the intermediate filament peripherin in rat motoneurons: modulation by inhibitory and stimulatory signals

Peripherin is a type III intermediate filament which, in contrast to the neurofilaments, is strongly up-regulated after nerve injury. Although peripherin expression is stimulated in vitro by neurotrophins and cytokines, little is known about its in vivo regulation. In this report, we show that the in vivo down-regulation of peripherin expression to normal levels during regeneration closely correlates with target reconnection in rat facial motoneurons. Prevention of reconnection, by transection and suture, results in the persistence of strong peripherin expression for prolonged periods of up to 11months. This contrasts with the modulation of the p75 low-affinity neurotrophin receptor, whose expression returns to normal even in the absence of reconnection. We further demonstrate that blockade of the axonal transport in non-injured motoneurons increases the expression of peripherin. Blockade of the axonal transport simultaneously to, or after injury of, facial motoneurons does not abolish the axotomy-induced peripherin up-regulation. These data demonstrate that the in vivo expression of peripherin is normally restrained by a distal retrogradely transported inhibitory signal. Thus, peripherin up-regulation results primarily from a lack of supply in this factor. Our results show that stimulatory factors released at the injury site are not required for the initial up-regulation and maintenance of high peripherin expression. However, they appear to enhance this increase during the acute post-lesion phase. Peripherin expression is thus finely tuned by both glial cell-derived stimulatory and distal inhibitory signals that reflect neuron-target interactions.

The 5'2 promoter of the neuronal nitric oxide synthase dual promoter complex mediates inducibility by nerve growth factor

Neuronal nitric oxide synthase (nNOS) is induced by nerve growth factor (NGF) in pheochromocytoma PC12 cells. Previous studies from our laboratory identified two closely linked promoters (designated 5'1 and 5'2) that mediate transcription of the human nNOS gene in the brain [J. Xie, P. Roddy, T.K. Rife, F. Murad, A.P. Young, Two closely linked but separable promoters for human neuronal nitric oxide synthase gene transcription, Proc. Natl. Acad. Sci. U. S. A. 92 (1995) 1242-1246]. In this report, we demonstrate that luciferase fusion genes under transcriptional control by the 5'1 and 5'2 dual promoter complex are inducible by NGF in stably transformed PC12 cells. In sharp contrast, neither epidermal growth factor (EGF) nor fibroblast growth factor 2 (FGF2) are able to significantly enhance the expression of NOS-luciferase fusion genes. Deletion studies indicate that the 5'2 promoter plays a major role in mediating NGF inducibility. The 5'2 promoter contains six potential Ets binding sites as well as four potential AP1 binding sites. Thus, it is possible that activation of Ets and/or AP1 transcription factors by the Ras-Raf-MAP kinase cascade contributes to the NGF-mediated induction of nNOS.

Regulation of the neural-specific gene VGF in PC12 cells. Identification of transcription factors interacting with NGF-responsive elements

Nerve growth factor (NGF) is an important regulator of differentiation and survival in both the peripheral and central nervous systems. We have begun to analyze the mechanism by which NGF induces the expression of a neural specific gene, VGF, in PC12 cells. Using DNase I footprinting and transient transfection analysis, we identified two VGF promoter regions, V1 and V2, that are required for basal promoter expression as well as gene induction by NGF, epidermal growth factor (EGF), and cAMP. The V1 element is essential for VGF promoter function, but it is not sufficient to confer NGF responsiveness to a heterologous promoter. In contrast, the V2 element can independently stimulate the expression of a linked herpes simplex virus (HSV) thymidine kinase promoter in response to NGF. We showed that the V2 region also contains a sequence that acts as a promoter-specific negative regulator of basal VGF gene expression. As determined by gel mobility shift and Southwestern analysis, the V1 sequence is recognized by a novel PC12 nuclear protein of about 110-kDa molecular mass. Using oligonucleotide competition and antibody supershift assays, we demonstrated that the cAMP-response element (CRE) motif within the V2 element interacted specifically with proteins related to cAMP-response element binding (CREB), JunB, and JunD transcription factors. The JunB-related binding activities were transiently induced by NGF, suggesting that part of the mechanism utilized by NGF to activate VGF transcription includes increased synthesis of a V2 binding protein. Taken together, our analysis suggests that the VGF promoter is regulated by a complex mechanism, and its activation requires combinatorial action of several transcription factors interacting with multiple promoter elements.

The molecular biology of preprotachykinin-A gene expression

The expression of neuropeptides is largely tissue-specific and under strictly regulated and complex control. In view of the diversity of neuronal phenotypes, with concomitant plasticity of gene expression within any phenotype, it is obvious that there is coordinated activation and repression of genes. One of the central observations from these studies is that neuropeptide gene expression is dependent upon the combinatorial interaction of multiple transcription factors with the regulatory elements which determine mRNA synthesis. These factors mediate both tissue specific and stimulus inducible gene expression. We will illustrate some of the mechanisms that regulate neuropeptide gene expression utilizing our own studies on the rat preprotachykinin-A gene (rPPT) and, where appropriate, expand on the generality of these findings to other neuropeptide genes.

Neuronal-specific gene expression--the interaction of both positive and negative transcriptional regulators

Gene expression patterns in neurons are complex and are modulated in response to multiple extracellular stimuli. In addition, during development and as neurons differentiate into distinct neuronal phenotypes, there is a co-ordinated activation and repression of a variety of genes. It is becoming increasingly evident that negative regulatory elements are present in neuronal-specific promoters. These elements have been shown, in part, to restrict promoter activity to the correct physiological cell type, both in transient transfection and in transgenic mouse models. Repression can be effected by different mechanisms depending on location within the promoter of silencer complexes and their relationship to other bound transcription factors. This review will discuss the molecular mechanisms regulating promoter function, in particular: (1) the combinatorial interaction between transcription factors which generate regulated promoter function; and (2) the restriction of promoter function to the correct cell type by bound repressor molecules. Determination of the mechanism of regulated gene expression will allow advances in gene therapy and definition of novel targets for pharmaceutical intervention. At the more basic level, functional dissection of the promoters of specific neuronal expressed genes will provide information of importance in two key areas of neurobiology: (1) the mechanism by which extracellular factors, such as neurotrophins and cytokines, regulate gene expression; (2) the events which lead to the tissue-specific expression of genes in subpopulations of neurons, both in the adult and during development.

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.

The TATA motif is a target for efficient transcriptional activation and nerve growth factor induction of the peripherin gene

Three proximal elements, PER1, PER2, and PER3, have been implicated in the regulation of peripherin gene expression. PER1 contains the TATA motif and was identified as the principal mediator of neuronal specificity. Here, we demonstrate by transfection of constructs mutated in PER1 that the in vitro protein binding activity of PER1 is irrelevant to its function. However, mutations or substitutions in the TATA box decreased promoter activity by up to 80%. We have investigated this unusual preference for a particular TATA sequence in PC12 cells. In these cells, nerve growth factor induces neuronal differentiation, increasing peripherin gene expression 3-4-fold, while dexamethasone elicits chromaffin differentiation and a 3-fold decrease in peripherin mRNA. Experiments with stably transfected PC12 cells revealed that the specific TATA box of the peripherin gene was crucial for nerve growth factor response. However, it did not affect dexamethasone down-regulation. Therefore, nerve growth factor acts through an element essential for neuronal peripherin gene expression. The results predict that proteins interacting in the vicinity of the TATA box, by inference factors associated with the preinitiation complex, are important for peripherin gene regulation and provide new insights into the mechanisms underlying neuronal differentiation.

Three different states of the chromatin structure of the mouse peripherin gene

The chromatin structure of the mouse peripherin gene domain was analyzed in peripherin-positive and -negative cell lines. At least nine DNase I hypersensitive sites (HSS) are present within the 20-kb peripherin domain in the mouse neuroblastoma cell lines which express peripherin. Three of them are situated in intron I and intron III, the others being distributed within the 5' flanking region up to -5.5 kb. The presence of these sites was also investigated in the peripherin chromatin domain of peripherin-negative cell lines. Two other types of HSS distribution were observed along the peripherin gene according to the category of cell considered: constantly peripherin-negative cells, or negative cells arising from transiently peripherin-expressing precursors. From comparison of HSS patterns in these cell lines with those of neuroblastoma cells, it can be predicted that HSS located in the region -1500/+800 bp participate in cell-specific expression of the mouse peripherin gene.

The 66-kDa neurofilament protein (NF-66): sequence analysis and evolution

A 2.5 kb cDNA clone encoding the mouse 66 kd neurofilament protein (NF-66) was isolated and sequenced. The deduced protein sequence contains 501 amino acid residues. Comparison of the mouse, rat and human NF-66 indicated > 90% homology in protein sequence and 85% homology in coding nucleotide sequence. A high degree of homology was observed between NF-66 and other intermediate filament proteins especially in the alpha-helical domain. Zooblot analyses suggested that the putative ancestral gene for vimentin and NF-66 was detectable in the avian. By comparison, the ancestral sequence for GFAP appeared after that for vimentin.

Cell type-specific expression of the mouse peripherin gene requires both upstream and intragenic sequences in transgenic mouse embryos

Peripherin is a neuron-specific type III intermediate filament protein expressed in well-defined populations of neurons projecting towards peripheral targets. To investigate the molecular mechanisms by which a gene is expressed in a specific subset of neurons, we used a transgenic approach in order to define peripherin gene sequences that are necessary for cell-type specific expression. Transgenic mice carrying different various genomic regions of the mouse peripherin gene fused to the Escherichia coli lacZ reporter gene were generated. We used three different peripherin/lacZ constructs containing either 5.8 kb upstream sequences, or both 5.8 kb upstream and 1.1 kb intragenic sequences, or 1.1 kb intragenic sequences associated with an heterologous promoter. Analysis of lacZ gene expression in transgenic mouse embryos showed that cell type-specific expression of the mouse peripherin gene requires both upstream and intragenic sequences. Analysis of transgenic mouse lines expressing the construct containing both upstream and intragenic sequences showed that this transgene contains all regulatory elements essential for both spatial and temporal expression of the mouse peripherin gene during embryogenesis. Furthermore, lacZ+ positive cells isolated from these transgenic lines by fluorescence-activated cell sorting (FACS) can be stained with a peripherin antibody, demonstrating that the transgene containing both upstream and intragenic sequences is expressed in peripherin neurons. These mouse peripherin upstream and intragenic sequences can now be used to identify cis-acting regulatory elements and transcription factors involved in peripherin gene regulation.

Activity of the distal positive element of the peripherin gene is dependent on proteins binding to an Ets-like recognition site and a novel inverted repeat site

The peripherin gene, encoding a neuron-specific intermediate filament protein, is transcriptionally induced when PC12 cells begin to terminally differentiate into neurons in response to nerve growth factor. Previously we identified two regulatory sequences of the peripherin gene: a proximal negative element (centered at -173), which prevents peripherin expression in undifferentiated PC12 cells, and a distal positive region (-2660 to -2308) necessary for full induction of peripherin in differentiated PC12 cells (Thompson, M., Lee, E. Lawe, D., Gizang-Ginsberg, E., and Ziff, E. (1992) Mol. Cell. Biol. 12,2501-2513). Here we define a distal positive element (DPE, -2445 to -2337) within the distal positive region. Methylation interference footprinting of the DPE identified DNA-protein contact points at a novel inverted repeat sequence (AACCACTGGTT) and an Ets-like recognition sequence (CAGGAG). Functional analysis using site-directed mutagenesis demonstrates that both sites are necessary for the activity of the DPE. In addition, ternary complex formation at the DPE is dependent on both sites. Antibody competition assays confirm that an Ets family member participates in the DNA-protein complex. We have indirect evidence that the inverted repeat binding protein and the Ets-related protein interact directly with each other. Finally, we demonstrate that the DPE is constitutively active and that neuron-specific regulation of peripherin expression may be due to interaction with distal and proximal negative regulatory elements.

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.

A novel nerve growth factor-responsive element in the stromelysin-1 (transin) gene that is necessary and sufficient for gene expression in PC12 cells

Stromelysin-1 (ST-1) is an extracellular matrix metalloproteinase whose expression is transcriptionally regulated by nerve growth factor (NGF) in the PC12 rat pheochromocytoma cell line. In this paper, we define sequences in the proximal ST-1 promoter that contain a novel NGF-responsive element(s). We show that this cis-acting promoter element can bind nuclear proteins from both untreated and NGF-treated PC12 cells in a specific and saturable manner and is sufficient to confer NGF-inducibility to a heterologous promoter. At least a portion of this NGF-responsive element lies within a 12-base pair region between positions -241 and -229 of the ST-1 promoter and bears no sequence homology to other known transcriptional elements. In contrast to what has been reported for fibroblasts, an AP1 site centered around position -68 does not seem to be involved in the growth factor regulation of ST-1 in PC12 cells. These results suggest that the NGF regulation of ST-1 gene expression involves different promoter elements, and possibly different transcription factors, from that described for ST-1 induction by other growth factors.

NF1-L is the DNA-binding component of the protein complex at the peripherin negative regulatory element

The peripherin gene, which encodes a neuronal-specific intermediate filament protein, is transcriptionally induced with a late time course when nerve growth factor stimulates PC12 cells to differentiate into neurons. We have defined a negative regulatory element (NRE) that has a functional role in repressing peripherin expression in undifferentiate and nonneuronal cells. Nerve growth factor-induced derepression of peripherin gene expression is associated with alterations in proteins binding to a GC-rich DNA sequence in the NRE as detected by the DNA electrophoretic mobility shift assay (EMSA). We have utilized DNA affinity chromatography to purify from rat liver a 33-kDa DNA-binding protein that specifically recognizes the NRE. Microsequencing reveals identity with NF1-L, a member of the CTF/NF-1 transcription factor family. This protein forms a single complex when incubated with the NRE probe using EMSA analysis. The more slowly migrating complexes characteristic of crude undifferentiated PC12 cell extract are reconstituted by mixing the purified protein with the flow-through from the DNA affinity column, thereby demonstrating that protein-protein interactions are involved in complex formation. Supershift experiments incubating anti-CTF-1 antibody with undifferentiated PC12 cell extract prior to EMSA analysis confirm that NF1-L, or a closely related family member, is the DNA-binding protein component of the multiprotein complex at the NRE.

Characterization of the proximal promoter and two silencer elements in the CYP2C11 gene expressed in rat liver

The cytochrome P450 gene CYP2C11, expressed in the liver of male rats, is transcriptionally regulated in a dual fashion by the sexually dimorphic secretion pattern of growth hormone. To enable analysis of transcriptional regulatory DNA elements, rat genomic sequences were cloned. DNase I hypersensitivity analysis of rat liver nuclei revealed the existence of two hypersensitive sites whose presence in the vicinity of the transcription start site correlates to high transcriptional activity of the gene. Deletion mutants of the 5' flank were fused to reporter genes and transiently transfected into HepG2 cells or into primary adult rat hypatocytes. Transfection experiments in combination with DNase I footprinting analysis in vitro led to the identification of two negative regulatory regions spanning nucleotides -1,230 to -1,188 and -409 to -368 and designated (SIL1200) and (SIL400), respectively. When placed in front of the heterologous thymidine kinase promoter, SIL1200 and SIL400 reduced the activity of the chloramphenicol acetyl transferase reporter gene to 13% and 23% of the control value, respectively. No sex-dependent binding of liver nuclear extracts to the two silencers could be detected by in vitro footprinting or gel retardation assays. However, a sex-dependent footprint consistently stronger with male liver nuclear extracts than with female extracts was observed in the -320 to -294 region. A significant level of identity was found between the DNA sequence corresponding to this footprint and that of orphan steroid receptor elements as well as with that of a basal transcription element common to several CYP2C genes. However, the identity of a potential trans-acting factor binding between -320 and -294 or response of this element to growth hormone is as yet unknown. A sex- and GH secretory profile-dependent protein-DNA interaction in vitro was observed in the -107 to -95 region. In spite of the sequence similarity that exists between this region and the consensus binding site for HNF-1, this region does not bind HNF-1 alpha. This element acted as a repressor on the heterologous thymidine kinase promoter. To date, the two silencer elements and possibly also the HNF-1-like element are the only functional elements defined in the CYP2C11 gene, and it is conceivable that induction of the gene involves derepression of the silencer elements.

Molecular biology of neuronal intermediate filaments

In the past few years, several neuronal intermediate filament proteins have been characterized. While ongoing investigations have continued to shed light on their developmental expression, the importance of different domains of the proteins for assembly, the elements in their genes necessary for tissue-specific expression, and the role of phosphorylation of neurofilaments, the function(s) of these structures remain a matter of speculation.