A cryptic promoter in the first exon of the SPG4gene directs the synthesis of the 60-kDa spastin isoform
© Mancuso and Rugarli; licensee BioMed Central Ltd. 2008
Received: 10 June 2008
Accepted: 09 July 2008
Published: 09 July 2008
Mutations in SPG4 cause the most common form of autosomal dominant hereditary spastic paraplegia, a neurodegenerative disease characterized by weakness and spasticity of the lower limbs due to degeneration of the corticospinal tract. SPG4 encodes spastin, a microtubule-severing ATPase belonging to the AAA family. Two isoforms of spastin, 68 and 60 kDa, respectively, are variably abundant in tissues, show different subcellular localizations and interact with distinct molecules. The isoforms arise through alternative initiation of translation from two AUG codons in exon 1; however, it is unclear how regulation of their expression may be achieved.
We present data that rule out the hypothesis that a cap-independent mechanism may be involved in the translation of the 60-kDa spastin isoform. Instead, we provide evidence for a complex transcriptional regulation of SPG4 that involves both a TATA-less ubiquitous promoter and a cryptic promoter in exon 1. The cryptic promoter covers the 5'-UTR and overlaps with the coding region of the gene. By using promoter-less constructs in various experimental settings, we found that the cryptic promoter is active in HeLa, HEK293 and motoneuronal NSC34 cells but not in SH-SY-5Y neuroblastoma cells. We showed that the cryptic promoter directs the synthesis of a SPG4 transcript that contains a shorter 5'-UTR and translates the 60-kDa spastin isoform selectively. Two polymorphisms (S44L and P45Q), leading to an early onset severe form of hereditary spastic paraplegia when present in heterozygosity with a mutant allele, fall a few nucleotides downstream of the novel transcriptional start site, opening up the possibility that they may exert their modifier effect at the transcriptional level. We provide evidence that at least one of them decreases the activity of the cryptic promoter in luciferase assays.
We identified a cryptic promoter in exon 1 of the SPG4 gene that selectively drives the expression of the 60-kDa spastin isoform in a tissue-regulated manner. These data may have implications for the understanding of the biology of spastin and the pathogenic basis of hereditary spastic paraplegia.
Hereditary spastic paraplegia (HSP) is a genetically heterogeneous disorder characterized by progressive weakness and spasticity of the lower limbs owing to retrograde degeneration of the corticospinal axons . SPG4, the gene most commonly involved in autosomal dominant HSP, encodes spastin, an ATPase belonging to the AAA family . Spastin acts as a microtubule-severing protein, suggesting that axonal degeneration in HSP may depend on defective regulation of cytoskeleton dynamics in long axonal tracts [3–5]. The identification of several spastin molecular interactors involved in cell trafficking led to the proposal that the microtubule-severing activity of spastin may be coupled to specific processes and therefore, occur in a regulated manner .
Spastin has a complex subcellular localization. It is enriched in the centrosome in interphase and during mitosis, similarly to p60 katanin, another microtubule-severing protein [7, 8]. Low levels of spastin are present in the nucleus of proliferating cells, while neurons show a prevalent cytoplasmic localization [7, 9, 10]. We previously found that one mechanism to regulate targeting of spastin to specific cell compartments is the alternative initiation of translation from two AUGs present in exon 1 of the SPG4 gene . Both spastin isoforms contain a nuclear localization signal, however, the long 68-kDa spastin isoform also bears a nuclear export signal and is efficiently exported to the cytoplasm in an exportin-dependent fashion. Conversely, the shorter 60-kDa spastin isoform localizes to both the nucleus and cytoplasm upon over-expression in eukaryotic cells.
Although both spastin isoforms efficiently sever microtubules [4, 5], they display several functional differences. First, the shorter isoform is the most abundant in all tissues examined, while the longer form is efficiently detectable only in brain and spinal cord [11, 12]. Second, two proteins, atlastin and NA14, have been shown to interact specifically to the N-terminal region of spastin present in the long isoform but absent in the short isoform [7, 13, 14]. Since atlastin is in turn implicated in HSP, this observation may be of direct relevance to the pathogenesis of the disease. Third, two polymorphisms (S44L and P45Q) acting as phenotype modifiers have been identified in the long-isoform-specific region. Patients carrying a mutated allele of spastin and one of these two polymorphisms on the other allele are affected by a severe disease with an early age of onset [15–17]. Furthermore, a family has been described in which one patient with a late onset mild spastic paraplegia was homozygous for the S44L polymorphism .
Although the scanning mechanism for initiation of translation can satisfactorily explain our previous data, there might still be the possibility that translation of the short abundant 60-kDa spastin isoform occurs via direct entry of the ribosomes at the downstream AUG codon. Albeit this mechanism is well documented for certain viral genes, it is still quite controversial as to whether it occurs in mammalian genes [21, 22].
While testing for the presence of an internal ribosome entry site (IRES) in the SPG4 mRNA, we found evidence for a cryptic promoter in exon 1, responsible for the production of a shorter mRNA specific for the 60-kDa spastin isoform. This promoter shows some degree of tissue-specificity, providing a way to regulate the production of the different spastin isoforms.
Translation of the 60-kDa spastin isoform does not depend on an IRES
Although the dicistronic test has been considered the gold standard for testing the existence of functional IRES elements, a major drawback of this approach is that it cannot distinguish between IRES activity and the presence of a cryptic promoter . To exclude this possibility, we cloned the same SPG4 sequence into a promoter-less pRF vector (pRFΔP), in which the SV40 promoter has been removed (Figure 2b). Both Renilla and firefly luciferase activities were almost undetectable when the empty pRFΔP vector was transfected, whereas a dramatic increase of firefly activity was observed for the pRFΔP +4/+258 construct in HeLa cells, strongly suggesting the presence of a promoter activity in the first exon of SPG4 (Figure 2b). Again, the fold of activation was lower in SH-SY-5Y cells (Figure 2b).
The presence of a strong promoter in the region under analysis could mask the presence of the IRES, hampering the detection of its functionality. To circumvent this problem, an effective method is direct transfection of the dicistronic RNAs . To this end, in vitro-transcribed capped dicistronic mRNAs were transfected into HeLa cells and the activities of both Renilla and firefly luciferases were measured. The firefly activities of both the empty vector and the pRF +4/+258 were barely detectable, while the Renilla luciferase activities were comparable, indicating that the first exon of SPG4 does not contain an IRES element (Figure 2c).
A minimal ubiquitous SPG4promoter
To define the minimal genomic region that confers basic expression of the SPG4 gene, we tested the ability of different fragments of the genomic region upstream of the first ATG of the SPG4 gene to drive the expression of the luciferase gene in transiently transfected HeLa, HEK293 and SH-SY-5Y cells (Figure 3b). The activities of these promoters were measured by a luciferase assay and considered as fold of induction in respect to the activity of the empty vector. We did not find any cell-specific difference in the activities of the different fragments in the three cell lines (Figure 3c). The construct that showed higher promoter activity was S -621/-1, which contained the highly conserved, 400 bp-genomic region and the 5'-UTR. Inclusion of an additional 669 bp upstream of this region led to a certain decrease of promoter activity, while removal of a sequence of approximately 220 bp containing the CAAT box (S -400/+3) did not reduce significantly the promoter activity. Deletion of the 5'-UTR and approximately 200 bp upstream of the transcription initiation site (construct S -1290/-424) completely abolished promoter activity, while the removal of only the 5'-UTR (S -400/-206) reduced the basal transcriptional activity (Figure 3c). These experiments identified a region of 400 bp upstream of the first ATG as a minimal promoter region active in all cell lines tested and point to a role of the 5'-UTR to sustain basic ubiquitous SPG4 expression.
A tissue-specific cryptic promoter in the first exon of SPG4
We used the TRANSFAC program to identify binding sites for known transcription factors in the cryptic promoter region. This allowed us to identify two putative Sp1 binding sites that were conserved in the human and mouse genomes (Figure 4a). Site-directed mutagenesis was employed to insert mutations into the upstream, the downstream, or both Sp1 sites in the construct S -207/+259. Transfection of the mutated constructs showed a significant reduction of the cryptic promoter activity in HeLa cells only when both Sp1 sites are mutagenized (Figure 4c).
In conclusion, both reporter and expression studies with promoter-less constructs strongly indicate that the first SPG4 exon contains a cryptic promoter that may contribute to produce the 60-kDa isoform in several cell types in vivo.
Two phenotype-modifier polymorphisms lie within the cryptic promoter
Identification of an endogenous SPG4transcript specific for the short spastin isoform
The previous experiments strongly suggest the existence of a cryptic promoter in the first exon of the SPG4 gene. Differentially regulated, alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N-termini . Genome-wide analyses, using short tags derived from the 5'-ends of capped RNAs (CAGE), oligocapping methods and full-length cDNA collections, can be publicly accessed in the CAGE analysis website and in the database of transcriptional start sites (DBTSS). We searched these databases for TSSs within the human SPG4 gene. Remarkably, we found that both databases identify an alternative promoter located within exon 1, downstream of the first ATG, defined by a clustering of TSSs separated by fewer than 500 bp. The tags derive from HEK293 cells, as well as from different tissues, including brain tissue. A summary of these data is represented in Additional file 1 and additional file 2.
Haplo-insufficiency of spastin causes HSP, suggesting that tight control of the protein levels is required for axonal integrity. We previously showed that the SPG4 gene synthesizes two isoforms of spastin (68 kDa and 60 kDa, respectively), depending on the alternative initiation of translation from two AUGs in the first exon . Regulation of the expression of protein isoforms simply based on inefficient translation or leaky scanning is, however, hard to achieve. Here, we report a transcriptional mechanism of SPG4 regulation that may contribute to the production of a different ratio of long and short spastin isoforms in tissues.
We identified a ubiquitous spastin minimal promoter and found evidence for a tissue-specific cryptic promoter in the first exon of the gene. An evolutionary highly conserved region of 400 bp upstream of the first in-frame AUG of the SPG4 gene was sufficient to provide basal expression in HeLa, HEK293 and SH-SY-5Y cells. This region does not contain a TATA box, but includes several cis-acting, GC-rich elements, suggesting that the SPG4 promoter belongs to the vast category of TATA-less promoters common to mammalian housekeeping genes . Inclusion in the reporter constructs of upstream genomic regions did not significantly increase transcriptional activity. Furthermore, deletion of a putative CAAT box, not conserved in the mouse, did not decrease substantially promoter activity. In contrast, a certain drop in activity was found when the majority of the 5'-UTR of the gene was removed from all the constructs tested. A possible explanation is that the 5'-UTR itself may contain additional TSS or regulatory elements that cooperate with upstream sequences to allow basal transcription of the SPG4 gene. Consistently high levels of sequence conservation are observed in the 5'-UTR among different species from human to chicken.
The latter hypothesis is supported by the finding of a cryptic promoter in the first exon of the SPG4 gene. The region between the most upstream TSS (corresponding to position -221) and the first ATG, and the region between the first and the second in-frame ATGs, both, alone and even stronger in combination, are able to drive the expression of a reporter gene in promoter-less vectors. Collectively, we define these regions in SPG4 exon 1 as a cryptic promoter. Furthermore, promoter-less constructs containing only the coding sequence of spastin drove the expression of the shorter spastin isoform in Hela, HEK293 and NSC34 cells. These are murine immortalized spinal motoneurons that express both long and short spastin isoforms . This result suggests that the cryptic promoter may also be active in neurons implicated in human pathology. Remarkably, the cryptic promoter shows some degree of tissue-specificity, as shown by low activity in the neuroblastoma-derived SH-SY-5Y cells.
The presence of shorter capped SPG4 mRNAs is supported by the successful identification of a novel SPG4 transcript that starts downstream of the first AUG in HeLa cells by 5'-end RACE experiments. Moreover, our experimental data are consistent with high-throughput, genome-wide studies, which identified a cluster of TSSs within both the human and murine SPG4 genes located in close proximity to the TSS of the novel transcript identified in our study. The previous results strongly suggest that the SPG4 gene has multiple core promoters containing multiple TSSs, the use of which generates diversity, not only in the transcripts, but most importantly, in the proteins produced. A similar scenario is emerging with more and more frequency from studies of mammalian core promoters . As expected for a broad promoter with multiple TSSs, several CpG islands boxes and multiple binding sites for the transcription factor Sp1 are present in the cryptic promoter. It has been suggested that Sp1 may direct the basal machinery to form a pre-initiation complex within a loosely defined window . Mutagenesis of two evolutionary conserved Sp1 sites decreased the activity of the cryptic promoter, suggesting that Sp1 or Sp family member transcription factors may bind to the cryptic promoter. Sp1 elements are required for the expression of many ubiquitous, tissue-specific and viral genes . Interestingly, Sp1 levels decrease with cellular aging . Further studies however, are required to define the transcription factors involved in SPG4 expression.
Western blot analysis strongly indicates that the 60-kDa spastin isoform is predominant in many tissues and cells [11, 12]. Based on our data, we propose that a combination of transcriptional and translational mechanisms is employed in concert to modulate the levels of spastin isoforms in cells. At the transcriptional level, cells may synthesize the 60-kDa isoform simply through the production of a shorter transcript that possesses as first in-frame AUG, the one in position 259–261. However, an additional mechanism to ensure preferential synthesis of the 60-kDa spastin isoform likely arises during translation, due to several constraints imposed on translation from the first in-frame AUG, such as the presence of a 73% GC-rich 5'-UTR, an overlapping uORF and a poor Kozak's context . Indeed, in our experiments with spastin expression constructs, it is clear that the short spastin isoform is expressed at high levels when the SPG4 coding sequence is under the control of the CMV promoter, suggesting that translation of this isoform occurs even when the synthesis of a longer mRNA is favored.
Our study tends to exclude a role for a cap-independent mechanism through recognition of an IRES in the translation of the spastin 60-kDa short isoform. This latter mechanism has been extensively demonstrated in viral transcripts, and more recently has also been found in a number of eukaryotic transcripts, whose translation needs to occur also in circumstances in which cap-dependent translation is inhibited. Functional IRES elements have been proposed in several eukaryotic genes, but subsequent studies using more sensitive procedures have questioned the validity of several of them [29–31]. Similarly, we showed by direct RNA transfection of a dicistronic transcript that the predicted IRES in the SPG4 exon 1 is not functional, further confirming the imprecision of bioinformatic approaches to predict IRES sequences and stressing the importance of adequate functional validation.
It remains to be established why several mechanisms have evolved to maintain the low levels of the long 68-kDa spastin isoform in most cells and tissues. This apparently seems to contrast with the evolutionary conservation of the first AUG and even of the uORF in several organisms, and may point to the need for a regulated expression of this isoform, or a possible toxic effect if expressed at a high level.
The identification of the cryptic SPG4 promoter and a shorter SPG4 transcript may have implications in human pathology. We found that a previously reported polymorphism (c.131C>T) that acts as a disease modifier falls into the cryptic promoter region and decreases its activity significantly. Notably, this polymorphism is a few base pairs downstream of the TSS of the novel transcript described here and therefore, within a bona fide SPG4 core promoter. However, a second polymorphism, c.134C>A, did not affect cryptic promoter activity, casting doubts on whether these polymorphisms actually act transcriptionally. Further studies on cell lines derived from HSP families in which both a mutant SPG4 allele and the polymorphism segregate are needed to address this issue.
Our study describes alternative promoter usage and heterogeneity of transcription initiation for the SPG4 gene. A canonical promoter has features typical of housekeeping genes, while a cryptic promoter in the 5'-UTR and coding region of spastin seems to provide tissue-specificity. Use of these alternative promoters generates SPG4 mRNAs with 5'-UTRs of different length and with different AUGs driving the production of different spastin isoforms. Our study emphasizes the need to take into account SPG4 complex transcriptional regulation to achieve a better understanding of the biology of spastin and the pathogenic effect of mutations or polymorphisms located in the first exon of the gene.
In all numeric references in this study, nucleotide +1 corresponds to the A of the first ATG codon according to den Dunnen and Antonarakis .
Dicistronic constructs (pRF)
The +4/+258 region of SPG4 was amplified by polymerase chain reaction (PCR) from human genomic DNA using Pfu Ultra (Stratagene) and cloned SpeI/NcoI into pRF and pRFΔP (Fw: 5'-GCAGTACTTAATTCTCCGGGTGGACGA-3', Rev: 5'-ATCCATGGGAGGGCGCGGGAGAAGCG-3', SpeI and NcoI sites in bold, respectively). Both dicistronic vectors were a kind gift from Dr J-T Zhang . For RNA transfection experiments, the dicistronic cassette was excised from pRF +4/+258 using a BamHI/NheI digestion and then cloned BamHI/EcoRV into the multiple cloning site of pBluescript KS (Stratagene).
Spastin promoter constructs (S)
All of these constructs were obtained by cloning different portions of the human genomic sequence upstream of the SPG4 start codon into the pGL3 vector (Promega). The S -1290/-1 insert was amplified by PCR using Pfu Ultra (Stratagene) from human genomic DNA and cloned in the XhoI/HindIII sites of pGL3 vector (Fw: 5'-ATCTCGAGAACCCAGCAGCTCTGGGGGA-3', Rev: 5'-ATAAGCTTTCACAGCTCTCACTGCCGCC-3', XhoI and HindIII sites in bold, respectively). S -621/-1 was obtained from S -1290/-1 by SmaI/EcoRV excision and self-ligation. S -207/-1 was obtained from S -1290/-1 by KpnI/PstI excision and self-ligation. S -1290/-424 was obtained from S -1290/-1 by HindIII/PstI excision and self-ligation. The S -400/+259 insert was amplified by PCR using Pfu Ultra (Stratagene) from human genomic DNA and cloned XhoI/HindIII (Fw: 5'-ATCTCGAGTGGGAACTGTAGTTGAGT-3', Rev: 5'-ATAAGCTTCGGAGCTCCTCCTGGCTG-3', XhoI and HindIII sites in bold, respectively). S -207/+259 was obtained from S -400/+259 by SmaI/PstI excision and self-ligation. S +4/+259 was obtained from S -400/+259 by SmaI/EcoRI excision and self-ligation. S -400/+3 was obtained from S -400/+259 by EcoRI/HindIII excision and self-ligation. S -400/-206 was obtained from S -400/+259 by PstI/HindIII excision and self-ligation.
Spastin-GFP-ΔCMV was obtained from CMV-spastin-GFP vector  by digestion with NruI/KpnI and self-ligation. Spastin-GFP-ΔM1 was obtained from spastin-GFP vector by digestion with EcoRI/KpnI and self-ligation. To obtain the CMV-EGFP-STOP-spastin construct, the SPG4 coding region was cloned blunt in the NotI site of pEGFP N°2 (Clontech).
Site-directed mutagenesis was performed by PCR reactions using Pfu Ultra (Stratagene). After amplification, 10 U of DpnI were added to the PCR product and incubated for 1 hour at 37°C. The mutagenized DNA was transformed into E. coli XL1Blue super-competent cells. The c.131C>T polymorphism was introduced into S -400/+259, S -207/+259 and S +4/+259 vectors using the following set of oligos: Fw: 5'-GCCCCTCCGCCCGAGTTGCCGCATAAGCGGAAC-3', Rev: 5'-GTTCCGCTTATGCGGCAACTCGGGCGGAGGGGC-3' (mismatches reported in bold). The c.134C>A polymorphism was introduced into S -400/+259, S -207/+259 and S +4/+259 vectors using the following set of oligos: Fw: 5'-CCTCCGCCCGAGTCGCAGCATAAGCGGAACCTG-3', Rev: 5'-CAGGTTCCGCTTATGCTGCGACTCGGGCGGAGG-3' (mismatches reported in bold). Mutagenesis of Sp1 sites was introduced in the S-207/+259 construct. The upstream Sp1 site was mutated using this set of oligos: Fw: 5'-AGGAAGGAGAAAGGGGAAGGGCAAGCGGGCAGCGTGCGG-3', Rev: 5'-CCGCACGCTGCCCGCTTGCCCTTCCCCTTTCTCCTTCCT-3' (mismatches reported in bold). The downstream Sp1 site was mutated using the following set of oligos: Fw: 5'-CCCTTGCCTGGCCCCAACCCCAACCGCCGCCGGGCCGGC-3', Rev: 5'-GCCGGCCCGGCGGCGGTTGGGGTTGGGGCCAGGCAAGGG-3' (mismatches reported in bold). All mutagenized vectors were controlled by DNA sequencing.
DNA sequencing was performed by using a 3100 Genetic Analyzer (Applied Biosystems) and BigDye Terminator v1.1 Cycle Sequencing kit (Applied Biosystems) according to the manufacturer's specifications.
Renilla (RL) and firefly luciferase (FL) activities were measured using the Dual-Luciferase Reporter System (Promega) and a Victor2 1420 Multilabel Counter (Perkin Elmer). At 24 hours post-transfection, 20 μl of cell lysate was combined sequentially with FL- and RL-specific substrates according to the protocol supplied by the manufacturer. Light emission was measured 2 seconds after addition of each of the substrates and integrated over a 10-second interval. All experiments were performed in duplicates and were repeated at least three times using different DNA preparations.
pRF and pBS-pRF +4/+258 plasmids were linearized prior to transcription by BamHI restriction, purified by incubation at 50°C for 30 minutes with 10 μg proteinase K and 0.5% sodium dodecyl sulfate (SDS), and precipitated with 25 mM ethylene diamine tetraacetic acid (EDTA) and 300 mM sodium acetate pH 5.2. Capped RNA transcripts were synthesized by using MAXIscript in vitro transcription kit (Ambion) according to the manufacturer's specifications. Briefly, recombinant T7 or T3 polymerases were used to synthesize mRNA from 2.5 μg linearized DNA and 0.5 mM Ribo m7 G Cap Analog (Promega) was added to the reaction mix. In vitro transcription was performed by incubation at 37°C for 1 hour in 40 U of RNAsin RNAse inhibitor (Promega). Following transcription, reactions were treated with DNAse I for 15 minutes at 37°C.
Cell culture, DNA and mRNA transfection and immunofluorescence
HeLa, HEK293 and NSC34 cells were cultured in Dulbecco's Modified Eagle's Media (Euroclone) supplemented with 10% or 5% fetal bovine serum, 200 U/ml penicillin, 200 μg/ml streptomycin and 2 mM glutamine. SH-SY-5Y cells were cultured in Minimum Essential Media (Euroclone) supplemented with 10% Fetalclone III (Hyclone), 200 U/ml penicillin, 200 μg/ml streptomycin and 2 mM glutamine. All cultures were grown as a monolayer in a humidified incubator at 37°C in an atmosphere of 5% CO2.
Transient DNA transfections were performed by using Lipofectamine 2000 (Invitrogen) according to the manufacturer's specifications. Briefly, 8 × 104 cells per well of a 24-well plate were seeded the day prior to transfection. Cells were transfected with DNA (500 ng) and cultured for an additional 24 or 48 hours. In cotransfection experiments, pRL-CMV DNA was added in 1:100 ratio.
mRNA transfections were performed by using Transmessenger Transfection Reagent (Qiagen) according to the manufacturer's specifications. Briefly, 8 × 104 cells per well of a 24-well plate were seeded the day prior to transfection. Cells were transfected with mRNA (2 μg) and cultured for an additional 8 hours.
Immunofluorescences were performed as described previously .
Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblotting
Cells were scraped in phosphate-buffered saline and lysed for 30 minutes in RIPA buffer (50 mM Tris-HCl, 1% NP-40, 0.25% Na-deoxycholate, 150 mM NaCl, 1 mM EDTA, pH 7.4) and protease inhibitor cocktail (Sigma-Aldrich) in ice. Protein samples were resuspended in SDS sample buffer and subjected to standard sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) followed by protein transfer to a polyvinylidene difluoride membrane (Amersham). Spastin was revealed by immunoblotting with S51 polyclonal antibody .
Total RNA was extracted from cells using TRIzol (Invitrogen) according to the manufacturer's specifications. Rapid amplification of 5'-ends cDNA was carried out using a FirstChoice RLM-RACE kit (Ambion) according to the manufacturer's instructions with the following exceptions. The outer PCR reaction was carried out with 10 pmol gene-specific outer primer (5'-ACCATTCCACAGCTTGCTCCTTCT-3'), 1.25 units of Pfu Ultra (Stratagene) and 1.5 ng first-strand cDNA reaction. The PCR conditions were as follows: (1×) 94°C, 3 minutes; (35×) 94°C, 30 seconds; 55°C, 30 seconds; 72°C, 90 seconds; (1×) 72°C, 10 minutes. The inner PCR reaction was carried out with 10 pmol gene-specific inner primer (5'-CGCAAGCTTAGGCCTGTTTGTGGAAGACTCGGACG-3', BamHI site in bold), using the same conditions as for the outer PCR. PCR products were separated on 2% agarose gel, cloned BamHI into a pBluescript KS-vector (Stratagene) and sequenced.
Conservation studies were performed using the human BLAT search database . Alignments between human and mouse sequences were performed by using mVISTA  with the following parameters: min_Y (minimum Y value on the mVISTA plot) 40%, min_id (minimum conservation identity) 50%, min_length (minimum length for a CNS) 50 bp. IRES prediction was performed by using UTRScan . Transcription factors binding sites were predicted using two different matrixes. MATCH™  parameters: profile, vertebrates; cut-off selection, minimize the sum of both error rates. PATCH™  parameters: sites selection, vertebrate sites; minimum length of site, 10 bp; maximum number of mismatches, 0; mismatch penalty, 100; lower score boundary, 87.5. Bio-informatic analysis of 5'-end full-length SPG4 cDNas was performed using the CAGE analysis website  and the DBTSS .
Data are expressed as the mean ± standard error of the mean. Statistical analysis was performed using a two-way unpaired Student's t test.
List of abbreviations
database of transcriptional start sites
ethylene diamine tetraacetic acid
hereditary spastic paraplegia
internal ribosome entry site
open reading frame
polymerase chain reaction
tobacco acid pyrophosphatase
sodium dodecyl sulfate
transcriptional start sites.
The authors wish to thank Dr J-T Zhang for kindly providing the pRF vectors and Elena Riano and Germana Meroni for critical discussions and helpful suggestions. This work was supported by grants from the European Union (LSHM-CT-2003-503382 to EIR) and Italian Telethon Foundation (GGP05057 to EIR).
- Fink JK: Hereditary spastic paraplegia. Curr Neurol Neurosci Rep. 2006, 6: 65-76. 10.1007/s11910-996-0011-1.View ArticlePubMedGoogle Scholar
- Hazan J, Fonknechten N, Mavel D, Paternotte C, Samson D, Artiguenave F, Davoine CS, Cruaud C, Durr A, Wincker P, Brottier P, Cattolico L, Barbe V, Burgunder JM, Prud'homme JF, Brice A, Fontaine B, Heilig R, Weissenbach J: Spastin, a new AAA protein, is altered in the most frequent form of autosomal dominant spastic paraplegia. Nat Genet. 1999, 23: 296-303. 10.1038/15472.View ArticlePubMedGoogle Scholar
- Errico A, Ballabio A, Rugarli EI: Spastin, the protein mutated in autosomal dominant hereditary spastic paraplegia, is involved in microtubule dynamics. Hum Mol Genet. 2002, 11: 153-163. 10.1093/hmg/11.2.153.View ArticlePubMedGoogle Scholar
- Evans KJ, Gomes ER, Reisenweber SM, Gundersen GG, Lauring BP: Linking axonal degeneration to microtubule remodeling by spastin-mediated microtubule severing. J Cell Biol. 2005, 168: 599-606. 10.1083/jcb.200409058.PubMed CentralView ArticlePubMedGoogle Scholar
- Salinas S, Carazo-Salas RE, Proukakis C, Cooper JM, Weston AE, Schiavo G, Warner TT: Human spastin has multiple microtubule-related functions. J Neurochem. 2005, 95: 1411-1420. 10.1111/j.1471-4159.2005.03472.x.View ArticlePubMedGoogle Scholar
- Salinas S, Carazo-Salas RE, Proukakis C, Schiavo G, Warner TT: Spastin and microtubules: Functions in health and disease. J Neurosci Res. 2007, 85: 2778-2782. 10.1002/jnr.21238.View ArticlePubMedGoogle Scholar
- Errico A, Claudiani P, D'Addio M, Rugarli EI: Spastin interacts with the centrosomal protein NA14, and is enriched in the spindle pole, the midbody and the distal axon. Hum Mol Genet. 2004, 13: 2121-2132. 10.1093/hmg/ddh223.View ArticlePubMedGoogle Scholar
- McNally FJ, Okawa K, Iwamatsu A, Vale RD: Katanin, the microtubule-severing ATPase, is concentrated at centrosomes. J Cell Sci. 1996, 109: 561-567.PubMedGoogle Scholar
- Wharton SB, McDermott CJ, Grierson AJ, Wood JD, Gelsthorpe C, Ince PG, Shaw PJ: The cellular and molecular pathology of the motor system in hereditary spastic paraparesis due to mutation of the spastin gene. J Neuropathol Exp Neurol. 2003, 62: 1166-1177.PubMedGoogle Scholar
- Yu W, Qiang L, Solowska JM, Karabay A, Korulu S, Baas PW: The microtubule-severing proteins spastin and katanin participate differently in the formation of axonal branches. Mol Biol Cell. 2008, 19: 1485-1498. 10.1091/mbc.E07-09-0878.PubMed CentralView ArticlePubMedGoogle Scholar
- Claudiani P, Riano E, Errico A, Andolfi G, Rugarli EI: Spastin subcellular localization is regulated through usage of different translation start sites and active export from the nucleus. Exp Cell Res. 2005, 309: 358-369. 10.1016/j.yexcr.2005.06.009.View ArticlePubMedGoogle Scholar
- Solowska JM, Morfini G, Falnikar A, Himes BT, Brady ST, Huang D, Baas PW: Quantitative and functional analyses of spastin in the nervous system: implications for hereditary spastic paraplegia. J Neurosci. 2008, 28: 2147-2157. 10.1523/JNEUROSCI.3159-07.2008.PubMed CentralView ArticlePubMedGoogle Scholar
- Sanderson CM, Connell JW, Edwards TL, Bright NA, Duley S, Thompson A, Luzio JP, Reid E: Spastin and atlastin, two proteins mutated in autosomal-dominant hereditary spastic paraplegia, are binding partners. Hum Mol Genet. 2006, 15: 307-318. 10.1093/hmg/ddi447.PubMed CentralView ArticlePubMedGoogle Scholar
- Evans K, Keller C, Pavur K, Glasgow K, Conn B, Lauring B: Interaction of two hereditary spastic paraplegia gene products, spastin and atlastin, suggests a common pathway for axonal maintenance. Proc Natl Acad Sci USA. 2006, 103: 10666-10671. 10.1073/pnas.0510863103.PubMed CentralView ArticlePubMedGoogle Scholar
- Chinnery PF, Keers SM, Holden MJ, Ramesh V, Dalton A: Infantile hereditary spastic paraparesis due to codominant mutations in the spastin gene. Neurology. 2004, 63: 710-712.View ArticlePubMedGoogle Scholar
- Svenson IK, Kloos MT, Gaskell PC, Nance MA, Garbern JY, Hisanaga S, Pericak-Vance MA, Ashley-Koch AE, Marchuk DA: Intragenic modifiers of hereditary spastic paraplegia due to spastin gene mutations. Neurogenetics. 2004, 5: 157-164. 10.1007/s10048-004-0186-z.View ArticlePubMedGoogle Scholar
- McDermott CJ, Burness CE, Kirby J, Cox LE, Rao DG, Hewamadduma C, Sharrack B, Hadjivassiliou M, Chinnery PF, Dalton A, Shaw PJ, UK and Irish HSP Consortium: Clinical features of hereditary spastic paraplegia due to spastin mutation. Neurology. 2006, 67: 45-51. 10.1212/01.wnl.0000223315.62404.00.View ArticlePubMedGoogle Scholar
- Lindsey JC, Lusher ME, McDermott CJ, White KD, Reid E, Rubinsztein DC, Bashir R, Hazan J, Shaw PJ, Bushby KMD: Mutation analysis of the spastin gene (SPG4) in patients with hereditary spastic paraparesis. J Med Genet. 2000, 37: 759-765. 10.1136/jmg.37.10.759.PubMed CentralView ArticlePubMedGoogle Scholar
- Kozak M: Pushing the limits of the scanning mechanism for initiation of translation. Gene. 2002, 299: 1-34. 10.1016/S0378-1119(02)01056-9.View ArticlePubMedGoogle Scholar
- Morris DR, Geballe AP: Upstream open reading frames as regulators of mRNA translation. Mol Cell Biol. 2000, 20: 8635-8642. 10.1128/MCB.20.23.8635-8642.2000.PubMed CentralView ArticlePubMedGoogle Scholar
- Kozak M: A second look at cellular mRNA sequences said to function as internal ribosome entry sites. Nucleic Acids Res. 2005, 33: 6593-6602. 10.1093/nar/gki958.PubMed CentralView ArticlePubMedGoogle Scholar
- Komar AA, Hatzoglou M: Internal ribosome entry sites in cellular mRNAs: mystery of their existence. J Biol Chem. 2005, 280: 23425-23428. 10.1074/jbc.R400041200.View ArticlePubMedGoogle Scholar
- Van Eden ME, Byrd MP, Sherrill KW, Lloyd RE: Demonstrating internal ribosome entry sites in eukaryotic mRNAs using stringent RNA test procedures. RNA. 2004, 10: 720-730. 10.1261/rna.5225204.PubMed CentralView ArticlePubMedGoogle Scholar
- Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC, Forrest ARR, Alkema W, Tan SL, Plessy C, Kodzius R, Ravasi T, Kasukawa T, Fukuda S, Kanamori-Katayama M, Kitazume Y, Kawaji H, Kai C, Nakamura M, Konno H, Nakano K, Mottagui-Tabar S, Arner P, Chesi A, Gustincich S, Persichetti F, Suzuki H, Grimmond SM, Wells CA, Orlando V, Wahlestedt C, Liu ET, Harbers M, Kawai J, Bajic VB, Hume DA, Hayashizaki Y: Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet. 2006, 38: 626-635. 10.1038/ng1789.View ArticlePubMedGoogle Scholar
- Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume DA: Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet. 2007, 8: 424-436. 10.1038/nrg2026.View ArticlePubMedGoogle Scholar
- Smale ST, Kadonaga JT: The RNA polymerase II core promoter. Annu Rev Biochem. 2003, 72: 449-479. 10.1146/annurev.biochem.72.121801.161520.View ArticlePubMedGoogle Scholar
- Suske G: The Sp-family of transcription factors. Gene. 1999, 238: 291-300. 10.1016/S0378-1119(99)00357-1.View ArticlePubMedGoogle Scholar
- Oh JE, Han JA, Hwang ES: Downregulation of transcription factor, Sp1, during cellular senescence. Biochem Biophys Res Commun. 2007, 353: 86-91. 10.1016/j.bbrc.2006.11.118.View ArticlePubMedGoogle Scholar
- Bert AG, Grepin R, Vadas MA, Goodall GJ: Assessing IRES activity in the HIF-1alpha and other cellular 5' UTRs. RNA. 2006, 12: 1074-1083. 10.1261/rna.2320506.PubMed CentralView ArticlePubMedGoogle Scholar
- Han B, Zhang JT: Regulation of gene expression by internal ribosome entry sites or cryptic promoters: the eIF4G story. Mol Cell Biol. 2002, 22: 7372-7384. 10.1128/MCB.22.21.7372-7384.2002.PubMed CentralView ArticlePubMedGoogle Scholar
- Wang Z, Weaver M, Magnuson NS: Cryptic promoter activity in the DNA sequence corresponding to the pim-1 5'-UTR. Nucleic Acids Res. 2005, 33: 2248-2258. 10.1093/nar/gki523.PubMed CentralView ArticlePubMedGoogle Scholar
- den Dunnen JT, Antonarakis SE: Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat. 2000, 15: 7-12. 10.1002/(SICI)1098-1004(200001)15:1<7::AID-HUMU4>3.0.CO;2-N.View ArticlePubMedGoogle Scholar
- BLAT Search Genome. [http://genome.ucsc.edu/cgi-bin/hgBlat]
- Vista: Tools for Comparative Genomics. [http://genome.lbl.gov/vista/mvista/submit.shtml]
- UTRScan. [http://www.ba.itb.cnr.it/BIG/UTRScan]
- Match and Patch . [http://www.biobase-international.com/pages/index.php?id=transfac]
- Fantom 3: Database. [http://fantom3.gsc.riken.jp]
- Database of Transcriptional Start Sites. [http://dbtss.hgc.jp]
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.