A novel 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR) splice variant with an alternative exon 1 potentially encoding an extended N-terminus
© Stormo et al.; licensee BioMed Central Ltd. 2012
Received: 3 January 2012
Accepted: 11 July 2012
Published: 18 September 2012
The major rate-limiting enzyme for de novo cholesterol synthesis is 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR). HMGCR is sterically inhibited by statins, the most commonly prescribed drugs for the prevention of cardiovascular events. Alternative splicing of HMGCR has been implicated in the control of cholesterol homeostasis. The aim of this study was to identify novel alternatively spliced variants of HMGCR with potential physiological importance.
Bioinformatic analyses predicted three novel HMGCR transcripts containing an alternative exon 1 (HMGCR-1b, -1c, -1d) compared with the canonical transcript (HMGCR-1a). The open reading frame of the HMGCR-1b transcript potentially encodes 20 additional amino acids at the N-terminus, compared with HMGCR-1a. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to examine the mRNA levels of HMGCR in different tissues; HMGCR-1a was the most highly expressed variant in most tissues, with the exception of the skin, esophagus, and uterine cervix, in which HMGCR-1b was the most highly expressed transcript. Atorvastatin treatment of HepG2 cells resulted in increased HMGCR-1b mRNA levels, but unaltered proximal promoter activity compared to untreated cells. In contrast, HMGCR-1c showed a more restricted transcription pattern, but was also induced by atorvastatin treatment.
The gene encoding HMGCR uses alternative, mutually exclusive exon 1 sequences. This contributes to an increased complexity of HMGCR transcripts. Further studies are needed to investigate whether HMGCR splice variants identified in this study are physiologically functional.
Keywords3-hydroxy-3-methylglutaryl-coenzyme A reductase HMG-CoA Transcription Alternative splicing Statin Cholesterol
Human 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase (HMGCR) is the rate-limiting enzyme in the isoprenoid/cholesterol biosynthesis pathway. The enzyme converts HMG-CoA to mevalonate and is the main target of commonly used lipid-lowering drugs (i.e., statins). Some of the major intermediates in the pathway are used to synthesise ubiquinone, dolichol, heme A and isoprenoid lipids. The end-product, cholesterol, is the precursor for the synthesis of crucial compounds, such as steroid hormones, bile acid and vitamin D.
HMGCR is encoded by a single gene on chromosome 5 (5q13.3-q14). Two transcript variants are annotated in the National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database; the canonical full-length transcript composed of 20 exons (NM_000859.2) and an alternatively spliced variant lacking exon 13 (NM_001130996.1). Additionally, exon junction microarray experiments suggest the presence of at least three more HMGCR splice variants lacking exon 8 (AY429542), exon 18 (AY429543) and exons 17 and 18 (AY429544).
Expression of HMGCR is strictly regulated at the transcriptional and post-transcriptional level. Cholesterol homeostasis is maintained by HMGCR transcriptional inhibition and enzyme modifications via negative feedback mechanisms (reviewed in). Under sterol-depleted conditions, such as statin treatment, HMGCR transcription is co-ordinately activated with transcription of the low density lipoprotein receptor and other genes in the cholesterol biosynthetic pathway.
Genomic diversity is greatly expanded by the process of alternative splicing, by which introns are removed and exons are ligated together to form various mature mRNA transcripts. Alternative splicing has been suggested as another mechanism underlying HMGCR regulation and cholesterol homeostasis. An HMGCR splice variant lacking exon 13 (denoted here as HMGCRΔexon13) was reported to have decreased enzymatic activity and to be less sensitive to statin inhibition[3, 7, 8]. Exon 13 encodes parts of the catalytic domain and the statin binding site of HMGCR[9, 10]. Recently, the major A allele of a single-nucleotide polymorphism (SNP, rs3846662, A > G) located within intron 13 of HMGCR was found to be associated with skipping of exon 13. The relative abundance of HMGCRΔexon13 mRNA has also been reported to be associated with interindividual variation in statin-mediated lipid-lowering responses[8, 11]. In the present study, nucleotide sequence database queries identified several novel HMGCR splice variants. One of these, HMGCR-1b, shows alternative exon 1 usage, with a novel HMGCR N-terminus predicted. We report the mRNA levels of novel HMGCR splice variants in a variety of healthy human tissues. Furthermore, we present the regulatory responses of these variants in HepG2 cells upon statin treatment.
Inspection of displayed mRNA, expressed sequence tag (EST) and RNA sequencing (RNA-seq) tracks at the HMGCR gene locus was performed using the Genome Browser Database provided by the University of California, Santa Cruz (UCSC) on human genome assembly GRCh37/hg19. The other bioinformatic tools used were Primer3 software, Finch TV1.4.0 (Geospiza, Seattle, USA), DNASTAR Lasergene 7.2 (Madison, WI, USA) and the NCBI database of SNPs.
Cell culture and statin treatment
The HepG2 cell line (American Type Culture Collection, Manassas, VA, USA) was grown in modified Eagle’s minimal essential medium (MEM; ATCC) supplemented with 10% heat inactivated fetal bovine serum (FBS) and and 1× penicillin-streptomycin-glutamine (P/S/G) mixture (Sigma-Aldrich, St Louis, MO, USA) in collagen I-coated tissue culture flasks (BD Biosciences, San Jose, CA, USA). Cells were seeded at 2 × 105 cells/mL in 12-well collagen I-coated plates (BD Biosciences), and the statin treatment was carried out in triplicate on the following day. HepG2 cells were cultivated for 24 hrs in MEM with 1× P/S/G containing 3 mg/mL of human lipoprotein deficient serum (LPDS; Millipore, Billerica, MA, USA), with or without 10 μM of (3 S, 5 S)-Atorvastatin Sodium Salt (Toronto Research Chemicals North York, Ontario, Canada) dissolved in water in a total volume of 1 mL. Two lymphoblastoid cell lines (GM17752 and GM20518; Coriell Institute for Medical Research, Camden, NJ, USA) were cultured according to the manufacturer’s instructions. Sequencing confirmed the CC and AA genotypes of the rs3761740 polymorphism in GM17752 and GM20518 cell lines, respectively. Statin treatment was carried out as described above, except that 5 × 105 cells/mL of each cell line were seeded into 24-well plates and treated the same day. Cell cultures were maintained at 37°C/5% CO2.
Purification of total RNA from cells
Total RNA from HepG2 cells was isolated using an RNeasy Mini Kit (Qiagen, Venlo, The Netherlands) by following the protocol provided by the manufacturer. DNase digestion with an RNase-Free DNase Set (Qiagen) was used to ensure DNA-free RNA samples. The RNA was eluted in 30 μL of RNase/DNase-free water and stored at −80°C until required. RNA samples were quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). RNA quality was assessed by microfluidic capillary electrophoresis using an Agilent 2100 Bioanalyzer and the RNA 6000 Nano Chip kit (Agilent Technologies, Santa Clara, CA, USA). RNA samples were denatured for 2 min at 70°C prior to cDNA synthesis.
Total RNA from human tissues
High-quality pooled RNA samples from the Human Total Master panel II and the Human Adult Normal Tissue panel were purchased from Clontech (Mountain View, CA, USA) and BioCat GmbH (Heidelberg, Germany), respectively. Ten random RNA samples were assessed for concentration and integrity as described above. All samples were from anonymous donors and commercially available.
Synthesis of cDNA
The levels of mRNA expression were analysed using total RNA from tissues (1000 ng) and cells (200 ng) in a 20 μL cDNA synthesis reaction using an Omniscript RT Kit (Qiagen) and a mixture of 2.5 μM oligo-dT and 6.25 μM random hexamers (Applied Biosystems, Foster City, CA, USA). Reverse transcription (RT) was performed at 37°C for 60 min, followed by 95°C for 5 min. The cDNA samples were diluted 1:5 in RNase/DNase-free water and stored at −20°C prior to use as templates for PCR amplification. A pooled cDNA sample was obtained by mixing an aliquot of each of the 44 undiluted cDNA samples and a 1:10 dilution in RNase/DNase-free water.
Polymerase chain reaction (PCR) amplification of the different first exons of HMGCR in a cDNA pool derived from 44 human tissues (as described above) was performed with HotStarTaq DNA Polymerase (Qiagen) following the manufacturer’s instructions Forward primers (exon1a, 5′-GAG CGT GCG TAA GGT GAG G-3′; exon1b, 5′-GAG AGC AGA AGG AAC GCA CA-3′; exon1c, 5′-GAC ATG GTC CTG CAG AGT CG-3′; and exon1d, 5′-GCA GCA TTG CAT AAA TAC TGT CA-3′) were used in combination with a reverse primer in exon 3 (exon3, 5′-TGT CAG AAT TAT AAT GTC ACT GCT CAA-3′). The cycling conditions were 15 min at 95°C, followed by 37 cycles of 30 s at 94°C, 30 s at 55°C, 1 min at 72°C and a final extension step at 72°C for 10 min. PCR products were separated on 1–3% (w/v) agarose gels. Images were captured using a Kodak Image Station 440CF and visualised using Kodak Molecular Imaging Software, version 4.5 (Eastman Kodak Co., New Haven, CT, USA). The PCR products of interest were excised and purified using the QIAquick Gel Extraction Kit (Qiagen) and confirmed by sequencing.
The full-length HMGCR-1b transcript was PCR amplified using a ProofStart DNA polymerase kit (Qiagen) and a cDNA template synthesised from skin (BioCat GmbH). The PCR mix contained 1× proof start buffer, 1× Q-solution, 0.25 U ProofStart, 5 U HotStarTaq plus DNA polymerase, 350 mM dNTP mix, 2 μL of cDNA and 0.4 μM forward primer (exon1b, 5′-CGC AGG AGA GGC ACA TTT CAG-3′) and reverse primer (exon20, 5′-GGG CTG TCT TCT TGG TGC AAG C-3′) in a total volume of 50 μL. The cycling conditions were 5 min at 95°C, followed by 37 cycles of 30 s at 94°C, 1 min at 55°C, 3 min at 72°C and a final extension step at 72°C for 30 min. Purified PCR products were cloned using the CT-GFP Fusion TOPO TA Expression Kit (Invitrogen Corporation, Carlsbad, CA, USA) according to the manufacturer’s instructions. Positive clones were confirmed by sequencing.
Quantitative PCR (qPCR)
All qPCRs were performed on an ABI 7900HT Real-Time PCR System in a standard 96-well format. TaqMan hydrolysis probes (Custom TaqMan Gene Expression Assay from Applied Biosystems) were designed for specific gene quantification of HMGCR-1a, HMGCR-1b and HMGCR-1c. The following TaqMan primer and probe sets were used: 5′-CCA TGC ATT CGA AAA AGT CTT GAC A-3′ (forward primer), 5′-GGT TCG GTG GCC TCT AGT G-3′ (reverse primer) and the FAM-reporter probe 5′-TCC TTG GAT CCT CCA GAT CT-3′ for targeting the HMGCR exon 1a-exon 2 boundary; 5′-AAT GGA TGT CGC ACA CAA GAG A-3′ (forward primer), 5′-CCA TGC ATT CGA AAA AGT CTT GAC A-3′ (reverse primer), and the FAM-reporter probe 5′-CTT GGA TCC TGC GTC TCT-3′ for targeting the HMGCR exon 1b-exon 2 boundary; and 5′-TTT CTG GGC TAT ACT AAA TGT GCA TGA-3′ (forward primer), 5′-CCA TGC ATT CGA AAA AGT CTT GAC A-3′ (reverse primer) and the FAM-reporter probe 5′-ACA AGG ATC CAA GGA TTC-3′ for targeting the HMGCR exon 1c-exon 2 boundary. Each qPCR mix comprised 10 μL of TaqMan Universal PCR Master Mix, 7 μL of RNase-free water, 1 μL of TaqMan hydrolysis probe and 2 μL of cDNA. The cycling steps were 10 min at 95°C followed by 40 cycles of 95°C for 15 s and 60°C for 1 min. Non-template controls were included in each run. All qPCR experiments were performed at least in duplicate. Samples exhibiting more than a 0.5 quantification cycle (Cq) difference between the duplicates were excluded from the relative quantification analysis. Samples showing Cq > 35 or undetermined were set to Cq = 38 and were considered not detectable.
Reference gene selection
Reporter vector construction
Different regions of the human HMGCR promoter covering −1626 to +12 (relative to the annotated HMGCR transcription start) were amplified by PCR. Genomic DNA from the Human Variation Panels (NA07055; Coriell Institute for Medical Research) heterozygous for the HMGCR promoter SNP C > A (rs3761740) were used as PCR templates. The PCR primers were: 5′-AGC GGT ACC GCC ATT TAC ACT AAT GGG TAA AT-3′ (forward primer) and 5′-AGT AAG CTT GAC CAA TAA GAG AGG ATC GTT CG-3′ (reverse primer) for construction of the reporter vector 1 (−559 to +12); 5′-AGC GGT ACC AAT GGG TAG GCA TAT CCA AGG-3′ (forward primer) and 5′-AGT AAG CTT CTG CGT CTT CTG TGC GTT C-3′ (reverse primer) for construction of reporter vectors 2 and 3 (−1009 to −615); and 5′-AGC GGT ACC TTG ACA AGG CTG CTA AGA GAA CA-3′ (forward primer) for construction of reporter vectors 4 and 5 (−1626 to −615) in combination with the same reverse primer used for reporter vectors 2 and 3. Restriction sites for KpnI and HindIII are underlined in the forward and reverse primer sequences, respectively. The PCR was performed using a Phusion High-Fidelity PCR kit (Finnzymes Oy, Espoo, Finland) according to the manufacturer’s instructions. Cycling conditions were as follows: 30 s at 98°C, followed by 35 cycles of 10 s at 98°C, 30 s at 63°C, 1 min at 72°C and a final extension step of 10 min at 72°C. The PCR-amplified promoter regions were cloned into the KpnI and HindIII restriction sites of the promoterless firefly luciferase vector pGL.4.10 (Promega, Madison, WI, USA).
Transfection and reporter gene assay
Identification of HMGCR splice variants
Tissue distribution of HMGCR-1a, -1b and -1c
Expression analysis before and after atorvastatin treatment in HepG2 cells
HMGCR promoter analysis
HMGCR is the key enzyme in the cholesterol biosynthesis pathway and is the major target of cholesterol-lowering statin drugs. Here, we demonstrate the existence of alternative exon 1 usage in human HMGCR, resulting in several novel transcript variants. One of these, HMGCR-1b, encodes a novel N-terminus which potentially extends the membrane domain by 20 amino acids compared with the canonical sequence. The canonical HMGCR protein is composed of 888 amino acids with a regulatory, sterol-sensing transmembrane domain (residues 10 – 339), a flexible linker (residues 340 – 449) and a C-terminal catalytic region (residues 450 – 888). We studied HMGCR-1b at the genomic and transcriptional levels. Whether the translation machinery actually recognises the first AUG as a start codon to produce a protein with 20 additional amino acids in the membrane domain remains to be determined. Unfortunately, initial experiments using rabbit antibodies raised against the novel N-terminus of the predicted HMGCR-1b polypeptide exhibited non-specific binding (data not shown).
In mammalian genomes, only one gene encodes the HMGCR enzyme, which mainly resides in the membrane of the endoplasmic reticulum[19, 20]. A minor fraction (approximately 5%) of the reductase activity has been demonstrated in rat liver[21–23] and mouse brain to be localised in the matrix of peroxisomes. The signal that targets HMGCR to peroxisomes has not yet been determined. The HMGCR-1b transcript identified in this study is remarkably less abundant than the canonical HMGCR-1a in most of the tissues analysed, and it is tempting to speculate that exon 1b might encode the missing HMGCR peroxisomal targeting information. However, bioinformatic analysis of the N-terminus of the hypothetical HMGCR-1b protein did not reveal any peroxisomal targeting signals (data not shown).
Our finding that HMGCR generates multiple 5′ end transcripts is not unusual in the human genome. There are numerous other examples in the literature. The gene locus encoding the uridine diphosphate–glucuronosyltransferase 1 family contains several different coding first exons, which generate at least nine different transcripts encoding various isozymes with unique N-termini and substrate specificities. Another example is the CYP19A1 gene encoding aromatase, the rate-limiting enzyme of estrogen biosynthesis, which contains alternative non-coding first exons affecting RNA stability and aromatase levels in tissues. Differential use of non-coding first exons is suggested to be an important mechanism of post-transcriptional regulation of aromatase gene expression.
Whether an alternatively spliced variant is functional is considered in the context of tissue-specific expression and conservation in most studies. The mRNA levels for the alternative HMGCR-1b splice variant were more abundant than the canonical HMGCR-1a levels in epithelial tissues, such as skin. Skin is one of the major sites for cholesterol production in the body, where HMGCR activity and cholesterol synthesis are crucial for hindering fluid loss from the body by maintaining the permeability barrier. In addition, the production of non-cholesterol isoprenoid intermediates by HMGCR has been reported to be important during acute wound healing. Sequence alignment of HMGCR-1b did not show conservation of the open reading frame in all terrestrial animals. Therefore, it remains to be determined whether the HMGCR-1b splice variant exerts an epithelial or skin-specific role in sustaining the epithelial barrier function in certain primates.
Tissue-specific gene expression may be regulated via differential gene promoter activity. The weak promoter activity of the genomic region upstream of exon 1b is in accordance with the rather low, basal mRNA expression level of exon 1b found in HepG2 cells. Unexpectedly, the alternative promoter activity in the reporter assay was not induced by sterol depletion, although there was an increase in the HMGCR-1b mRNA level in HepG2 cells. Based on these results, the increased HMGCR-1b mRNA level due to sterol depletion in HepG2 cells most likely results from post-transcriptional regulation and/or regulatory promoter DNA sequences not captured in our reporter vector constructs. Moreover, previous studies have identified a functional C > A SNP (rs3761740) in the HMGCR promoter[23, 33]. Keller et al. identified a sterol regulatory element (SRE) in this position. They found that the minor A allele was more responsive to the overexpression of sterol regulatory element-binding protein 2, compared with the major C allele. In our experiments, this promoter SNP, which is close to the transcription start of exon 1b, did not contribute significantly to the proximal promoter activity or mRNA level of HMGCR-1b or to the transcription of the canonical HMGCR-1a variant upon sterol depletion.
Approximately half of human genes are predicted to have alternative promoters. A comparative study of different promoter features in human and mouse genes reported a distinct class of “non-conserved” promoters in humans. Alternative promoters differ from the major promoter in their responsiveness to a specific condition, resulting in different expression levels in tissues or developmental stages and thereby increasing the flexibility of gene expression. Given that the putative HMGCR-1b promoter identified in our study (i) exhibits a different response to statin treatment compared with the canonical HMGCR promoter, (ii) is of minor usage, (iii) is lacking CpG islands, and (iv) that the HMGCR-1b transcript shows an expression pattern distinct from that of HMGCR-1a, it seems likely that the HMGCR-1b promoter represents an alternative, non-conserved HMGCR promoter that contributes to the expressional diversity of this gene.
With respect to HMGCR-1a, we also found that exon 13, which encodes amino acids in the catalytic region, is a cassette exon in the HMGCR-1b transcript, meaning that this exon is either included (HMGCR-1b) or skipped (HMGCR-1bΔ13). The catalytically active HMGCR is formed as a tetramer with two dimers. Medina et al. have proposed that the inactive HMGCR lacking exon 13 modulates the HMGCR enzyme activity by being part of the catalytically active tetramer and thereby reducing its total enzyme activity. Further studies are needed to clarify whether the delta-exon 13 variant of the HMGCR-1b transcript also contributes to HMGCR enzyme activity modulation and statin response.
We have shown that human HMGCR uses different first exons to produce multiple alternatively spliced variants, thereby contributing to increased transcriptional complexity. We have designated these splice variants HMGCR-1a, HMGCR-1b and HMGCR-1c. The novel HMGCR exon 1 (HMGCR-1b) we identified contains an in-frame ATG translational start codon predicting an extended N-terminus of HMGCR. Moreover, we showed that this transcript variant is differentially expressed in a wide variety of healthy human tissues, and that its mRNA levels are regulated upon statin treatment. Further studies are needed to elucidate potential physiological roles of differential first exon usage in HMGCR.
3-Hydroxy-3-Methylglutaryl-Coenzyme A reductase
Expressed Sequence Tag
Modified Eagle’s Minimal essential medium
Fetal Bovine Serum
Lipoprotein Deficient Serum
Polymerase Chain Reaction
Quantitative Polymerase Chain Reaction
We give special thanks to Daniel Sachse for technical assistance with figure illustrations and statistical analysis. We thank Dr. Bernd Thiede for help with protein bioinformatics. This work was funded by the Division of Diagnostics and Intervention, Oslo University Hospital, Norway and South-Eastern Norway Regional Health Authority.
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