Molecular cloning and functional analysis of the promoter of rat skeletal muscle voltage-sensitive sodium channel subtype 2 (rSkM2): evidence for muscle-specific nuclear protein binding to the core promoter

Epigenetic Changes Governing Scn5a Expression in Denervated Skeletal Muscle

The SCN5A gene encodes the α-subunit of the voltage-gated cardiac sodium channel (Na_V1.5), a key player in cardiac action potential depolarization. Genetic variants in protein-coding regions of the human SCN5A have been largely associated with inherited cardiac arrhythmias. Increasing evidence also suggests that aberrant expression of the SCN5A gene could increase susceptibility to arrhythmogenic diseases, but the mechanisms governing SCN5A expression are not yet well understood. To gain insights into the molecular basis of SCN5A gene regulation, we used rat gastrocnemius muscle four days following denervation, a process well known to stimulate Scn5a expression. Our results show that denervation of rat skeletal muscle induces the expression of the adult cardiac Scn5a isoform. RNA-seq experiments reveal that denervation leads to significant changes in the transcriptome, with Scn5a amongst the fifty top upregulated genes. Consistent with this increase in expression, ChIP-qPCR assays show enrichment of H3K27ac and H3K4me3 and binding of the transcription factor Gata4 near the Scn5a promoter region. Also, Gata4 mRNA levels are significantly induced upon denervation. Genome-wide analysis of H3K27ac by ChIP-seq suggest that a super enhancer recently described to regulate Scn5a in cardiac tissue is activated in response to denervation. Altogether, our experiments reveal that similar mechanisms regulate the expression of Scn5a in denervated muscle and cardiac tissue, suggesting a conserved pathway for SCN5A expression among striated muscles.

Identifying potential functional impact of mutations and polymorphisms: linking heart failure, increased risk of arrhythmias and sudden cardiac death

Researchers and clinicians have discovered several important concepts regarding the mechanisms responsible for increased risk of arrhythmias, heart failure, and sudden cardiac death. One major step in defining the molecular basis of normal and abnormal cardiac electrical behavior has been the identification of single mutations that greatly increase the risk for arrhythmias and sudden cardiac death by changing channel-gating characteristics. Indeed, mutations in several genes encoding ion channels, such as SCN5A, which encodes the major cardiac Na⁺ channel, have emerged as the basis for a variety of inherited cardiac arrhythmias such as long QT syndrome, Brugada syndrome, progressive cardiac conduction disorder, sinus node dysfunction, or sudden infant death syndrome. In addition, genes encoding ion channel accessory proteins, like anchoring or chaperone proteins, which modify the expression, the regulation of endocytosis, and the degradation of ion channel a-subunits have also been reported as susceptibility genes for arrhythmic syndromes. The regulation of ion channel protein expression also depends on a fine-tuned balance among different other mechanisms, such as gene transcription, RNA processing, post-transcriptional control of gene expression by miRNA, protein synthesis, assembly and post-translational modification and trafficking. The aim of this review is to inventory, through the description of few representative examples, the role of these different biogenic mechanisms in arrhythmogenesis, HF and SCD in order to help the researcher to identify all the processes that could lead to arrhythmias. Identification of novel targets for drug intervention should result from further understanding of these fundamental mechanisms.

The effect of plasma from muscle-specific tyrosine kinase myasthenia patients on regenerating endplates

Muscle-specific tyrosine kinase (MuSK) is essential for clustering of acetylcholine receptors (AChRs) at embryogenesis and likely also important for maintaining synaptic structure in adult muscle. In 5 to 7% of myasthenia gravis (MG) cases, the patients' blood contains antibodies to MuSK. To investigate the effect of MuSK-MG antibody on synapse regeneration, notexin was used to induce damage to the flexor digitorum brevis muscle. We administered aliquots of MuSK-MG patients' plasma to the flexor digitorum brevis twice daily for a period up to 21 days, and muscles were investigated ex vivo in contraction experiments. AChR levels were measured with (125)I-alpha-bungarotoxin, and endplates were studied with quantitative immunohistochemistry. In normal muscles and in 14-day regenerated muscles, MuSK plasma caused impairment of nerve stimulus-induced contraction in the presence of 0.35 and 0.5 mmol/L Ca(2+) with or without 100 to 400 nmol/L tubocurarine. Endplate size was decreased in regenerated muscles relative to controls; however, we did not observe such differences in muscle not treated with notexin. MuSK plasma had no effect on the amount and turnover rate of AChRs. Our results suggest that anti-MuSK antibodies influence the activity of MuSK molecules without reducing their number, thereby diminishing the size of the endplate and affecting the functioning of AChRs.

Identification of the sensory neuron specific regulatory region for the mouse gene encoding the voltage-gated sodium channel NaV1.8

Voltage-gated sodium channels (VGSC) are critical membrane components that participate in the electrical activity of excitable cells. The type one VGSC family includes the tetrodotoxin insensitive sodium channel, Na(V)1.8, encoded by the Scn10a gene. Na(V)1.8 expression is restricted to small and medium diameter nociceptive sensory neurons of the dorsal root ganglia and cranial sensory ganglia. To understand the stringent transcriptional regulation of the Scn10a gene, the sensory neuron specific promoter was functionally identified. While identifying the mRNA 5'-end, alternative splicing within the 5'-UTR was observed to create heterogeneity in the RNA transcript. Four kilobases of upstream genomic DNA was cloned and the presence of tissue specific promoter activity was tested by microinjection and adenoviral infection of fluorescent protein reporter constructs into primary mouse and rat neurons, and cell lines. The region contained many putative transcription factor-binding sites and strong homology with the predicted rat ortholog. Homology to the predicted human ortholog was limited to the proximal end and several conserved cis elements were noted. Two regulatory modules were identified by microinjection of reporter constructs into dorsal root ganglia and superior cervical ganglia neurons: a neuron specific proximal promoter region between -1.6 and -0.2 kb of the transcription start site cluster, and a distal sensory neuron switch region beyond -1.6 kb that restricted fluorescent protein expression to a subset of primary sensory neurons.

Polymorphisms in the cardiac sodium channel promoter displaying variant in vitro expression activity

Variable transcription of the cardiac sodium channel gene is a candidate mechanism determining arrhythmia susceptibility. We have previously cloned and characterized the core promoter and flanking region of SCN5A, encoding the cardiac sodium channel. Loss-of-function mutations in this gene have been reported in approximately 20% of patients with Brugada syndrome, an inherited cardiac electrical disorder associated with a high incidence of life-threatening arrhythmias. In this study, we identified DNA variants in the proximal 2.8 kb promoter region of SCN5A and determined their frequency in 1,121 subjects. This population consisted of 88 Brugada syndrome patients with no SCN5A coding region mutation, and 1,033 anonymized subjects from various ethnicities. Variant promoter activity was assayed in CHO cells and neonatal cardiomyocytes by transient transfection of promoter-reporter constructs. Single-nucleotide polymorphisms (SNPs) were identified at approximately 1/200 base pairs which are: 11 in the 5'-flanking region, 1 in exon 1, and 5 in intron 1. In addition, a haplotype consisting of two SNPs in complete linkage disequilibrium was identified. Minor allele frequencies were >5% in at least one ethnic panel at 5/19 polymorphic sites. In vitro functional analysis in cardiomyocytes identified four variants with significantly (P<0.05) reduced reporter activity (up to 63% reduction). The largest changes were seen with c.-225-1790 G>A, which reduced reporter activity by 62.8% in CHO cells and 55% in cardiomyocytes. From these results, we can conclude that the SCN5A core promoter includes multiple DNA polymorphisms with altered in vitro activity, further supporting the concept of interindividual variability in transcription of this cardiac ion channel gene.

Brn-3a neuronal transcription factor functional expression in human prostate cancer

Neuroendocrine differentiation has been associated with prostate cancer (CaP). Brn-3a (short isoform) and Brn-3c, transcriptional controllers of neuronal differentiation, were readily detectable in human CaP both in vitro and in vivo. Brn-3a expression, but not Brn-3c, was significantly upregulated in >50% of tumours. Furthermore, overexpression of this transcription factor in vitro (i) potentiated CaP cell growth and (ii) regulated the expression of a neuronal gene, the Nav1.7 sodium channel, concomitantly upregulated in human CaP, in an isoform-specific manner. It is concluded that targeting Brn-3a could be a useful strategy for controlling the expression of multiple genes that promote CaP.

Tandem Promoters and Developmentally Regulated 5′- and 3′-mRNA Untranslated Regions of the Mouse Scn5a Cardiac Sodium Channel

The SCN5A gene encodes a voltage-sensitive sodium channel expressed in cardiac and skeletal muscle. Coding region mutations cause cardiac sudden death syndromes and conduction system failure. Polymorphisms in the 5'-sequence adjacent to the SCN5A gene have been linked to cardiac arrhythmias. We identified three alternative 5'-splice variants (1A, 1B, and 1C) of the untranslated exon 1 and two 3'-variants in the murine Scn5a mRNA. Two of the exon 1 isoforms (1B and 1C) were novel when compared with the published human and rat SCN5A sequences. Quantitative real time PCR results showed that the abundance of the isoforms varied during cardiac development. The 1A, 1B, and 1C mRNA splice variants increased 7.8 +/- 1.7-fold (E1A), 6.0 +/- 1.0-fold (E1B), and 20.6 +/- 3.7-fold (E1C) from fetal to adult heart, respectively. Promoter deletion and luciferase reporter gene analysis using cardiac and skeletal muscle cell lines demonstrated a pattern of distinct cardiac-specific enhancer elements associated with exons 1A and 1C. In the case of exon 1C, the enhancer element appeared to be within the exon. A 5'-repressor preceded each cardiac enhancer element. We concluded that the murine Na(+) channel has both 5'- and 3'-untranslated region mRNA variants that are developmentally regulated and that the promoter region contains two distinct cardiac-specific enhancer regions. The presence of homologous human splicing suggests that that these regions may be fruitful new areas of study in understanding cardiac sodium channel regulation and the genetic susceptibility to sudden death.

Molecular cloning and functional characterization of a unique mammalian cardiac Na(v) channel isoform with low sensitivity to the synthetic inactivation inhibitor (-)-(S)-6-amino-alpha-[(4-diphenylmethyl-1-piperazinyl)-methyl]-9H-purine-9-ethanol (SDZ 211-939)

Cardiac voltage-dependent sodium channels (Na(v)) are drug targets for synthetic inactivation inhibitors typified by (+/-)-4- [3-(4-diphenylmethyl-1-piperazinyl)-2-hydroxy propoxy]-1H-indole-2-carbonitrile (DPI 201-106), of which the molecular mode of action is not yet defined. The previous observation by Mevissen and coworkers in 2001 of the electrophysiological ineffectiveness of DPI 201-106 in the bovine heart, in contrast to other species, offers the opportunity for investigating these open questions. We now report about the molecular cloning, expression in Xenopus laevis oocytes, and electrophysiological characterization of a unique bovine heart sodium channel. Although the predicted 2022-amino acid bovine heart sodium channel (bH1) shares 92% identity with the rat and human isoforms and normal gating properties, it displays drastically reduced sensitivity to (-)-(S)-6-amino-alpha-[(4-diphenylmethyl-1-piperazinyl)-methyl]-9H-purine-9-ethanol (SDZ 211-939). Experimental results with Anemonia sulcata toxin II (0.1-2.5 microM) exclude the possibility of an overall insensitivity of this isoform to various sodium channel modulators. The binding of SDZ 211-939 seems to be largely unaffected (EC(50) of 10.3 and 10.6 microM for bovine and rat isoforms, respectively) but the corresponding efficacy in bovine (V(m) of 0.15) is approximately 5 times smaller compared with the rat heart isoform (V(m) of 0.69). The comparison of the primary structure of bH1 to other sodium channels and the gating properties obtained in presence or absence of SDZ 211-939 revealed a high degree of similarity. Whether the mechanism of channel modulation depends on the interaction of synthetic modulators with some possibly voltage-independent part of the inactivation machinery needs to be determined.

Sodium channel mRNAs at the neuromuscular junction: distinct patterns of accumulation and effects of muscle activity

Voltage-gated sodium channels (VGSCs) are highly concentrated at the neuromuscular junction (NMJ) in mammalian skeletal muscle. Here we test the hypothesis that local upregulation of mRNA contributes to this accumulation. We designed radiolabeled antisense RNA probes, specific for the "adult" Na(V)1.4 and "fetal" Na(V)1.5 isoforms of VGSC in mammalian skeletal muscle, and used them in in situ hybridization studies of rat soleus muscles. Na(V)1.4 mRNA is present throughout normal adult muscles but is highly concentrated at the NMJ, in which the amount per myonucleus is more than eightfold greater than away from the NMJ. Na(V)1.5 mRNA is undetectable in innervated muscles but is dramatically upregulated by denervation. In muscles denervated for 1 week, both Na(V)1.4 and Na(V)1.5 mRNAs are present throughout the muscle, and both are concentrated at the NMJ. No Na(V)1.5 mRNA was detectable in denervated muscles stimulated electrically for 1 week in vivo. Neither denervation nor stimulation had any significant effect on the level or distribution of Na(V)1.4 mRNA. We conclude that factors, probably derived from the nerve, lead to the increased concentration of VGSC mRNAs at the NMJ. In addition, the expression of Na(V)1.5 mRNA is downregulated by muscle activity, both at the NMJ and away from it.

Identifying the promoter region of the human brain sodium channel subtype II gene (SCN2A)

Sodium channel genes are highly regulated. To begin analyzing the human brain sodium channel subtype II gene, SCN2A, at the transcriptional level, we mapped multiple transcriptional start sites within a 397 bp stretch of the 5'-UTR and -flanking region. When inserted into a basic luciferase reporter vector, this 397 bp region can promote luciferase expression in transiently transfected neuroblastoma cells, but not in non-neuronal cells. Thus, this study provides the initial description of a functional promoter in a human voltage-gated sodium channel gene.

The Na-G ion channel is transcribed from a single promoter controlled by distinct neuron- and Schwann cell-specific DNA elements

Na-G is a putative sodium (or cationic) channel expressed in neurons and glia of the PNS, in restricted neuronal subpopulations of the brain, and in several tissues outside the nervous system, like lung and adrenal medulla. To analyze the mechanisms underlying tissue-specific expression of this channel, we isolated the 5' region of the corresponding gene and show that Na-G mRNA transcription proceeds from a single promoter with multiple initiation sites. By transgenic mice studies, we demonstrate that 600 bp containing the Na-G proximal promoter region and the first exon are sufficient to drive the expression of a beta-galactosidase reporter gene in neurons of both CNS and PNS, whereas expression in Schwann cells depends on more remote DNA elements lying in the region between -6,500 and -1,050 bp upstream of the main transcription initiation sites. Crucial elements for lung-specific expression seem to be located in the region between -1,050 and -375 bp upstream of the promoter. Using in vivo footprint experiments, we demonstrate that several sites of the Na-G proximal promoter region are bound specifically by nuclear proteins in dorsal root ganglion neurons, as compared with nonexpressing hepatoma cells.

Coding sequence, genomic organization, and conserved chromosomal localization of the mouse gene Scn11a encoding the sodium channel NaN

Previous studies have shown that sodium channel alpha-subunit NaN is preferentially expressed in small-diameter sensory neurons of dorsal root ganglia and trigeminal ganglia. These neurons include high-threshold nociceptors that are involved in transduction of pain associated with tissue and nerve injury. In this study, we show that mouse NaN is a 1765-amino-acid peptide that is predicted to produce a current that is resistant to tetrodotoxin (TTX-R). Mouse and rat NaN are 80 and 89% identical at the nucleotide and amino acid levels, respectively. The Scn11a gene encoding this cDNA is organized into 24 exons. Unlike some alpha-subunits, Scn11a does not have an alternative exon 5 in domain I. Introns of the U2 and U12 spliceosome types are present at conserved positions relative to other members of this family. Scn11a is located on mouse chromosome 9, close to the two other TTX-R sodium channel genes, Scn5a and Scn10a. The human gene, SCN11A, was mapped to the conserved linkage group on chromosome 3p21-p24, close to human SCN5A and SCN10A. The colocalization of the three sodium channel genes supports a common lineage of the TTX-R sodium channels.

Multiple promoter elements interact to control the transcription of the potassium channel gene, KCNJ2

Potassium channels play important roles in shaping the electrical properties of excitable cells. Toward understanding the transcriptional regulation of a member of the inwardly rectifying potassium channel family, we have characterized the genomic structure and 5'-proximal promoter of the murine Kcnj2 gene (also referred to as IRK1 and Kir2.1). The Kcnj2 transcription unit is composed of two exons separated by a 5.5-kilobase pair intron. Deletion analysis of 5'-flanking sequences identified a promiscuously active 172-base pair minimal promoter, whereas expression from a construct containing additional upstream sequences was cell type-restricted. The minimal promoter contained an E box, a Y box, and three GC box consensus elements but lacked both TATA and CCAAT box elements. The activity of the minimal promoter was found to be controlled by a combination of the activities of the transcription factors Sp1, Sp3, and NF-Y. The interplay between Sp1, Sp3, and NF-Y within the architecture of the Kcnj2 promoter, the ubiquitous nature of these trans-acting factors, and the action of tissue-selective repressor element(s) may combine to enable a wide variety of cell types to differentially regulate Kcnj2 expression through transcriptional control.

Two E-boxes are the focal point of muscle-specific skeletal muscle type 1 Na+ channel gene expression

We have characterized a group of cis-regulatory elements that control muscle-specific expression of the rat skeletal muscle type 1 sodium channel (SkM1) gene. These elements are located within a 3. 1-kilobase fragment that encompasses the 5'-flanking region, first exon, and part of the first intron of SkM1. We sequenced the region between -1062 and +311 and determined the start sites of transcription; multiple sites were identified between +1 and +30. The basal promoter (-65/+11) lacks cell-type specificity, while an upstream repressor (-174/-65) confers muscle-specific expression. A positive element (+49/+254) increases muscle-specific expression. Within these broad elements, two E boxes play a pivotal role. One E box at -31/-26 within the promoter, acting in part through its ability to bind the myogenic basic helix-loop-helix proteins, recruits additional factor(s) that bind elsewhere within the SkM1 sequence to control positive expression of the gene. A second E box at -90/-85 within the repressor controls negative regulation of the gene and acts through a different complex of proteins. Several of these cis-regulatory elements share both sequence and functional similarities with cis-regulatory elements of the acetylcholine receptor delta-subunit; the different arrangement of these elements may contribute to unique expression patterns for the two genes.

Characterization of the transcription unit of mouse Kv1.4, a voltage-gated potassium channel gene

The mouse voltage-gated K+ channel gene, Kv1.4, is expressed in brain and heart as approximately 4.5- and approximately 3.5-kilobase (kb) transcripts. Both mRNAs begin at a common site 1338 bp upstream of the initiation codon, contain 3477 and 4411 nucleotides, respectively, and are encoded by two exons; exon 1 contains 0.5 kb of the 5'-noncoding region (NCR), while exon 2 encodes the remaining 0.8 kb of the 5'-NCR, the entire coding region (2 kb), and all of the 3'-NCR. The 3.5-kb transcript terminates at a polyadenylation signal 177 bp 3' of the stop codon, while the 4.5-kb mRNA utilizes a signal 94 bp farther downstream. Although the proteins generated from either transcript are identical, the two mRNAs are functionally different, the 3.5-kb transcript producing approximately 4-5-fold larger currents when expressed in Xenopus oocytes compared to the 4. 5-kb mRNA. The decreased expression of the longer transcript is due to the presence of five ATTTA repeats in the 3'-NCR which inhibit translation; such motifs have also been reported to destabilize the messages of many other genes and might therefore shorten the life of the 4.5-kb transcript during its natural expression. The Kv1.4 basal promoter is GC-rich, contains three SP1 repeats (CCGCCC, -65 to -35), lacks canonical TATAAA and GGCAATCT motifs, and has no apparent tissue specificity. One region enhances activity of this promoter. Thus, transcriptional and post-transcriptional regulation of mKv1.4, coupled with selective usage of the two alternate Kv1.4 mRNAs, may modulate the levels of functional Kv1.4 channels.

Expression of the rat S100A1 gene in neurons, glia, and skeletal muscle

Using a rat S100A1 cDNA probe, S100A1 expression has been documented in rat C6 glioma cells, a cell line previously thought to express only the S100B protein. To identify the molecular mechanisms which target S100A1 gene expression to specific cell types, the rat S100A1 gene was cloned, and functional analysis of the 5' flanking region of the gene was performed. The rat S100A1 gene was located in an 8.5 kb BamHI genomic fragment which contained 3 exons plus 1.6 kb of 5'-upstream and 0.37 kb of 3'-downstream flanking sequence. A single transcription initiation start site and a single polyadenylation signal were identified in this gene. A number of potential regulatory consensus sequences were identified in the rat S100A1 gene including general transcription factor binding sequences (TATA box, GC box and CCAAT box), cAMP regulated sequences (CRE), skeletal muscle specific sequences (E-box and M-CAT), an S100 protein element, and a (GCT) trinucleotide repeat. Analysis of an S100A1 promoter-CAT construct by ribonuclease protection assay demonstrated that this gene is functional in three S100A1 expressing cell lines, C6 cells, PC12 cells and L6 cells. CAT constructs containing progressive deletions of the S100A1 promoter region revealed a positive regulatory element in skeletal muscle (L6) cells between -1600/-1081. The fact that these same sequences were negative in glial (C6) cells and neutral in neuronal (PC12) cells suggests that this region plays a major role in targeting S100A1 expression to specific cell types. The -1081/+10 region contained both positive and negative elements, some of which were cell-type specific. Thus, S100A1 expression is under complex transcriptional control which involves positive and negative elements as well as cell type specific elements.