Revised genomic structure of the human ghrelin gene and identification of novel exons, alternative splice variants and natural antisense transcripts
© Seim et al; licensee BioMed Central Ltd. 2007
Received: 24 May 2007
Accepted: 30 August 2007
Published: 30 August 2007
Ghrelin is a multifunctional peptide hormone expressed in a range of normal tissues and pathologies. It has been reported that the human ghrelin gene consists of five exons which span 5 kb of genomic DNA on chromosome 3 and includes a 20 bp non-coding first exon (20 bp exon 0). The availability of bioinformatic tools enabling comparative analysis and the finalisation of the human genome prompted us to re-examine the genomic structure of the ghrelin locus.
We have demonstrated the presence of an additional novel exon (exon -1) and 5' extensions to exon 0 and 1 using comparative in silico analysis and have demonstrated their existence experimentally using RT-PCR and 5' RACE. A revised exon-intron structure demonstrates that the human ghrelin gene spans 7.2 kb and consists of six rather than five exons. Several ghrelin gene-derived splice forms were detected in a range of human tissues and cell lines. We have demonstrated ghrelin gene-derived mRNA transcripts that do not code for ghrelin, but instead may encode the C-terminal region of full-length preproghrelin (C-ghrelin, which contains the coding region for obestatin) and a transcript encoding obestatin-only. Splice variants that differed in their 5' untranslated regions were also found, suggesting a role of these regions in the post-transcriptional regulation of preproghrelin translation. Finally, several natural antisense transcripts, termed ghrelinOS (ghrelin opposite strand) transcripts, were demonstrated via orientation-specific RT-PCR, 5' RACE and in silico analysis of ESTs and cloned amplicons.
The sense and antisense alternative transcripts demonstrated in this study may function as non-coding regulatory RNA, or code for novel protein isoforms. This is the first demonstration of putative obestatin and C-ghrelin specific transcripts and these findings suggest that these ghrelin gene-derived peptides may also be produced independently of preproghrelin. This study reveals several novel aspects of the ghrelin gene and suggests that the ghrelin locus is far more complex than previously recognised.
Ghrelin is a 28 amino acid peptide hormone originally isolated from the stomach (where it is highly expressed) and it is the endogenous ligand for the growth hormone secretagogue receptor (GSH-R 1a) . It is well established that ghrelin is a multifunctional peptide with roles in growth hormone release, appetite regulation and gut motility  and we have demonstrated that it plays a role in cancer cell proliferation [3–5]. Despite its widespread and important physiological actions, its precise regulatory mechanisms remain ambiguous. Compared to other preprohormones, the genomic structure of ghrelin is thought to be relatively simple, consisting of four coding exons and a short, 20 bp first exon [6, 7], hereafter termed exon 0. The ghrelin gene (GHRL) spans 5 kb on chromosome 3 [6–8] and exons 1 to 4 encode an 117 amino acid preprohormone, preproghrelin. The preproghrelin signal peptide is encoded in exon 1, and the coding sequence of the 28 amino acid ghrelin peptide hormone is encoded by parts of exons 1 and 2. Exon 3 codes for obestatin, a recently identified 23 amino acid ghrelin gene-derived peptide hormone . The physiological relevance of obestatin is somewhat controversial, as it does not circulate in human serum, although the C terminal peptide of ghrelin, C-ghrelin does . C-ghrelin, encoded by exons 2, 3 and 4, is a 66 amino acid peptide that contains the 23 amino acid obestatin peptide within its sequence [10, 11]. It is currently not known if obestatin is cleaved from the large preproghrelin peptide, or whether distinct human obestatin-only and C-ghrelin-only transcripts exist. We have previously reported an obestatin-deleted transcript . Interestingly, a murine intron 1 retained variant lacking exon 0, 3 and 4 has recently been reported . The transcript therefore lacks the coding sequence of obestatin, but contains a putative peptide containing the first five amino acids of ghrelin and a novel 19 amino acid sequence.
Re-examination of the ghrelin locus is required for a number of reasons. First, the ghrelin gene structure has not been examined since the finalisation of the human chromosome 3 sequence in 2006  and the release of orthologous sequencing data. Second, newly developed bioinformatic tools now enable comparative genomics analyses. The aim of this study was, therefore, to re-examine the organisation of the human ghrelin gene with the aid of recently available genomic sequence information from multiple species, including the continuously updated draft mouse  and chicken  genomes. Using in silico approaches we predicted the existence of a novel, distal ghrelin exon (exon -1) and this was confirmed experimentally using 5' RACE and RT-PCR. We have also identified the expression of extended exon 0 species and re-annotated a 5' extended exon 1 not previously recognised in the literature . Multiple alternative mRNA transcripts were also identified experimentally from normal tissues and from prostate cell lines and a chondrosarcoma cell line, indicating that the ghrelin gene has a complex transcriptional pattern. In addition, we report a gene on the antisense strand of the ghrelin gene, ghrelinOS (ghrelin opposite strand), and have demonstrated the expression of endogenous natural antisense transcripts (NATs) that partially overlap the recognised sense ghrelin gene exons.
Results and discussion
Conserved regions identified using comparative genomic analysis of the ghrelin gene are transcribed
The conserved regions upstream of exon 1 are ghrelin exons
To examine whether the conserved regions identified using Mulan were transcribed, PCRs from human stomach (using cDNA reverse transcribed with oligo(dT)18 primers) were performed with antisense primers in exon 1 of ghrelin and sense primers in the conserved regions. Agarose gel electrophoresis of these PCRs showed that both of the conserved regions were transcribed (Fig. 1B) and their identity was confirmed by sequencing. The putative exon regions appeared to be mutually exclusive in the human stomach and the putative exon-intron junctions conform to the GT/AG rule. Therefore, initial analysis indicated that the conserved regions are true exons and not artefacts. The two conserved regions have been termed exon -1 [GenBank:EF549566] and exon 0 [GenBank:EF549567]. In addition to these two regions, a sequence immediately upstream of exon 1 of the human ghrelin gene is conserved in comparison to mouse sequence (Fig. 1A). This conserved sequence matches the first 50 base pairs of a 188 bp exon 1 sequence previously reported in mRNAs isolated from human stomach and thyroid medullary carcinoma TT cells . The previous study, however, did not annotate this sequence as a 5' extended exon 1 (and we have termed it exon 1b). We have, therefore, identified a novel, distal exon and 5' extensions to two previously reported exons (20 bp exon 0 and exon 1).
Exon 0 and -1 are novel first exons
Several transcripts initiating in the 5' extended exon 0 were obtained in many of the tissues examined [GenBank:EF549565, EF549562, and EF549563] including normal human testis, stomach, adipose tissue, leukocytes and ovary (TSS 3–5, Fig. 2). While it is possible that the transcription start sites identified in exon 0 via 5' RACE represent truncated cDNA, the sites are likely to be genuine, as we found multiple CAGE tag starting sites in the putative, extended exon 0 of mouse ghrelin (Fig. 3B). While the transcription start site of the short 20 bp human exon 0 aligns with the murine start site, the TSSs of the human extended exon 0 and the putative extended murine exon 0 are quite different (Fig. 3B). This suggests that these exons have diverged significantly over time, resulting in considerable variation in their start sites, termed TSS turnover . TSS turnover, with the translocation of mouse start sites compared to human start sites, occurs in a number of genes .
Recent studies indicate that many genes have broad transcriptional regulation with a wide distribution of proximal start sites, and not all genes are regulated by distinct start sites controlled by a TATA box [19, 20]. While a putative TATA box flanks the originally described 20 bp exon 0, it appears to be a very weak start site [21, 22]. The cluster of transcription start sites (TSSs) in the extended exon 0 sequence upstream of the short 20 bp exon 0 (Fig. 3B) contains no apparent TATA boxes (data not shown). Our study indicates that the ghrelin gene is broadly regulated and has many potential transcription start sites. This may allow the transcription of numerous tissue-specific and developmental stage-specific transcripts. Using in silico analysis coupled with RT-PCR and 5' RACE analysis, we have demonstrated that the conserved regions upstream of exon 1 (exon -1 and extended exon 0) are transcribed and correspond to novel first exons of the human ghrelin gene.
Multiple transcripts arise from alternative splicing from exons upstream of exon 1
Expression of exon -1-containing and extended exon 0-containing transcripts were examined using RT-PCR with exon-specific sense primers (for exons -1 and extended exon 0) and with an antisense primer in the 3' terminal exon 4 of the ghrelin gene. A list of exons and exon-intron boundaries of ghrelin locus derived-transcripts identified in this and previous studies, as well as ESTs, is given in [Additional file 1].
In the first group (I), all amplicons include exon 1 to 4 which code for preproghrelin, and vary only in the length of the sequence upstream of exon 1 (the preproghrelin 5' UTR). The amplicons obtained from the human stomach [GenBank:EF549571, EF549572, and EF549573] are depicted in Fig. 4B. The 855 bp amplicon, demonstrated in the human stomach, was also observed in all cell lines examined (DU145, RWPE-1, RWPE-2, LNCaP, PC3 and SW1353, data not shown), as well as in the heart, brain, spleen, testis, salivary gland, leukocytes and bone marrow (see [Additional file 2]). As depicted in Fig. 5, sequencing of the Rapid-Scan human tissue cDNA panel also revealed a 1316 bp amplicon with a 736 bp exon 0b in the placenta [GenBank:EU072083]. Furthermore, splice variants with an alternative exon 2 splice site (hereafter termed exon 2b), which results in loss of a glutamine residue at position 14 of the mature ghrelin peptide (termed des-Gln14-ghrelin or ghrelin-27) , were also sequenced and correspond to a 1313 bp [GenBank:EU072084] amplicon from the kidney and a 852 amplicon from heart tissue [GenBank:EU072085] (Fig. 5). Interestingly, a 1067 bp amplicon with a 212 bp exon 0h initiating at the start of the 736 bp exon 0, followed by the 275 bp exon 0d (separated by a 294 bp novel intron), was found in the kidney [GenBank:EU072087]. A single nucleotide polymorphism (SNP) g.-1062G > C (nucleotide number -1 corresponds to the first nucleotide upstream of the translation start site of preproghrelin in exon 1 of the ghrelin gene) [dbSNP:rs26311] is present in base 209 of the 736 bp exon 0 (exon 0b), creating a 3' splice-site consensus sequence (CAG) . This polymorphism has recently been linked to obesity and metabolic syndrome in the Korean population and is thought to influence the ghrelin promoter, ultimately increasing preproghrelin transcription efficiency . Our findings raise the possibility that this SNP effects mRNA splicing, resulting in allele-specific transcription of a 736 bp (exon 0b) or a 487 bp exon 0 (the latter resulting from g.-1062C induced splicing of a 212 bp exon 0h into a 275 bp exon 0d).
The large, extended 736 bp exon 0 is extensively spliced and contains numerous non-conserved uORFs (upstream open reading frames), while exon -1 contains a single translation start site in the human sequence only (data not shown). Approximately 12% of human genes are alternatively spliced within their 5' untranslated regions . Upstream open reading frames, as well as mRNA secondary structure and other motifs in 5' UTRs are known to regulate the translation of downstream major ORFs and particularly those which translate developmental genes . We suggest that the alternative transcripts identified which splice into exon 1 may be a part of such a regulatory mechanism. The 20 bp exon 0 found in human stomach and thyroid medullary carcinoma TT cells [6, 7] is devoid of upstream open reading frames and stable secondary structure (data not shown). As a consequence, this transcript may be more efficiently translated than the group I transcripts with exon -1 and extended exon 0 which have more extensive 5' untranslated regions.
Natural antisense transcripts are transcribed from a gene on the opposite strand of ghrelin (ghrelinOS)
The third (III) group of alternative transcripts containing exon -1 and 4 that we identified in the human stomach (a 1176 bp amplicon [GenBank:EF549568] and a 921 bp amplicon [GenBank:EF549570], Fig. 4B) result from splicing of transcripts with exon -1 sequences of ~880 bp, termed exon -1*a, and ~625 bp, termed exon -1*b. These exons extend into intron -1 and are considerably larger than the 106 bp and 92 bp exon -1 sequences obtained in this study. Moreover, these splice variants also contain two novel intron 2-derived exons (exon 2* and 2**) and an alternative exon 4 (exon 4*) (Fig. 4B). As is the case in the stomach, the fragments corresponding to these unusual transcripts were observed in all cell lines examined (DU145, RWPE-1, RWPE-2, LNCaP, PC3 and SW1353, data not shown). The 1176 bp amplicon expressed in the stomach is also expressed in the heart and fetal liver (data not shown). Furthermore, an mRNA variant with a ~880 bp exon -1*a and exon 2*, but lacking exon 2** (the 1108 bp amplicon in Fig. 5) was sequenced from the spleen [GenBank:EU072081], while a 950 bp amplicon [GenBank:EU072082] harbouring exon -1*a and exon 4* only was obtained from the kidney (Fig. 5). We then determined the direction of transcription of these transcripts. GMAP  and manual analyses were performed using sequenced PCR products obtained in this study, as well as expressed sequence tags (ESTs) spanning at least one intron. This analysis showed that while there are no canonical GT/AG splice junctions if the variants are transcribed from the sense (ghrelin gene) DNA strand, the reverse strand contains GT/AG intron junctions. All exons demonstrated this pattern with the exception of the intron flanking exon 2* of these fragments and -1*a/b, where the splice junction is GC/AG. GC/AG is relatively rare, but the most common non-canonical splice site pair .
In order to firmly establish the origin of the antisense ghrelinOS mRNA transcripts, and to determine how far they extend relative to the ghrelin gene, 5' RLM-RACE using human stomach cDNA was performed. Sequencing of RACE products identified two transcription start sites (TSSs) corresponding to a 63 bp and an 86 bp exon 4* [GenBank:EF549559, and EF549560]. Furthermore, a CAGE tag starting site was identified (T03F009D342E) in the antisense direction corresponding to a 28 base pair exon 4*. The three TSSs of ghrelinOS transcripts are summarised in Fig. 7B. We did not identify any potential TATA-boxes, therefore, these findings suggest that exon 4* contains multiple TSSs, which is typical of TATA-less promoters .
The ghrelin NATs that we have described span the non-coding 3' UTR region of exon 4 and exon -1 of mature, sense ghrelin gene-derived transcripts and overlap intron 2 sequence of ghrelin pre-mRNAs (Fig. 8A). Sense exons -1 and 4 are conserved when compared to mouse genomic sequence, while the degree of sequence similarity to exon -1* (the region not overlapping the sense exon -1), exon 2* and exon 2** appears to be very low (data not shown). Interestingly, most previously reported cis-NATs overlap with the sense transcript in their untranslated regions . This appears to be the case for ghrelinOS transcript as exon -1 and 4 corresponds to 5' and 3' UTRs of sense ghrelin transcripts encoding preproghrelin.
It has been demonstrated that the mammalian genome is often transcribed from both the sense and antisense DNA strands . Although the understanding of the mechanisms of action of natural antisense transcripts remains in its infancy, these transcripts have been shown to be involved in transcriptional and post-transcriptional regulation. NATs have been associated with a range of regulatory mechanisms, including transcriptional interference, RNA masking and dsRNA mediated gene-silencing via direct interaction between the sense and antisense transcripts [39, 41]. Intriguingly, in a very recent study, rats were administered a short, 22 base pair ghrelin antisense oligonucleotide into the cerebrospinal fluid . The antisense oligonucleotide is complementary to sequence in the rat preproghrelin 3' UTR in exon 4 (exon 4* of putative rat ghrelinOS transcripts). The study found that the antisense oligonucleotide decreased anxiety in rats (the opposite effect to ghrelin) and may act as an antidepressant . We suggest that this preliminary evidence may provide a first glimpse of the function of endogenous ghrelin natural antisense transcripts.
It has been reported that ghrelin mRNA and protein levels are dissociated [43–45]. We hypothesise that this may be due to either the presence of upstream open reading frames in exons 5' to exon 1 (exon 1 harbours the preproghrelin start codon); expression of ghrelin locus derived transcripts lacking coding potential for ghrelin; or non-coding sense and/or antisense regulatory transcripts. The transcripts identified in this study may be examples of at least one of these factors. Therefore the physiological significance of each transcript species, in particular mRNA variants encoding preproghrelin, cannot be determined based on mRNA expression data alone.
In the present study, we have shown that two newly identified exon regions of the ghrelin gene have the potential to generate a broad and complex transcriptional repertoire. Furthermore, a gene on the antisense strand of ghrelin, ghrelinOS, generates antisense transcripts that overlap conventional, sense ghrelin gene-derived transcripts. It would now seem imperative to perform a large-scale, thorough re-examination of the ghrelin locus in order to identify and characterise novel transcripts and peptides, as well as their function in various physiological and pathophysiological states, including obesity, depression and cancer. Such efforts may result in a reconceptualisation of the regulation and mechanisms of action of the multifunctional ghrelin peptide.
The identification of conserved regions in the ghrelin locus was facilitated by comparisons of the chromosomal regions spanning the human [GenBank:NT_022517], mouse [GenBank:NC_000072] and chicken (Contig12.626 of WASHUC2 draft release 2.1) ghrelin loci using Mulan (MUltiple sequence Local AligNment and conservation visualization tool) . The Evolutionary Conserved Region (ECR) Browser within Mulan was used to visualise phylogenetically conserved regions of 100 bp with greater than 70% sequence identity between the ghrelin genes and 20 kb upstream of their preproghrelin translation start sites. The human ghrelin gene sequence [GenBank:NM_016362] and the 20 bp exon 0 sequence [6, 7] was used as the reference sequence for annotation in Mulan. The CAGE (Cap Analysis of Gene Expression) basic viewer provided by the FANTOM (Functional Annotation of Mouse) consortium  was employed to locate transcription start sites in the putative first exons of the human and murine ghrelin loci. The exon-intron-structure of ghrelin locus-derived ESTs and mRNA entries identified from BLAST searches, as well as sequenced PCR amplicons obtained in this study, were analysed against the human genome (NCBI release 35) using GMAP . The location of putative signal peptides of deduced amino acid sequences were predicted using the SignalP 3.0 Server with default parameters . The HapMap genome browser  was employed to locate single nucleotide polymorphisms (SNPs) in novel ghrelin exons.
The chondrosarcoma cell line SW1353 (ATCC HTB 94; a kind gift from Shea Carter, IHBI, Brisbane, Australia) was cultured in DMEM/F12 media (Invitrogen, Mount Waverley, Australia). Cultured SW1353 cells were grown in T80 or T175 flasks (Nagle Nunc International, Roskilde, Denmark) in 95% CO2 in a Sanyo incubator at 37°C. Prostate and/or prostate cancer derived cell lines DU145, RWPE-1, RWPE-2, LNCaP and PC3 cell lines were obtained from the American Type Culture Collection (ATCC, Rockville, MD) and cultured in RPMI1640 media (Invitrogen) as described previously .
RNA extraction and reverse transcription
RNA was harvested from cultured cells at 70% confluence using RNeasy kits and on-column DNase treatment (QIAGEN, Doncaster, Australia). cDNA was synthesised in a final volume of 20 μl from 3 μg total RNA, from human stomach (FirstChoice, Ambion, Austin, TX) and cell lines, using Transcriptor reverse transcriptase (Roche, Castle Hill, Australia), 20 U RNasin Plus RNase Inhibitor (Promega, Annandale, Australia) and, unless otherwise indicated, oligo(dT)18 primers (Proligo, Armidale, Australia) according to the manufacturer's instructions.
RT-PCR verification of putative ghrelin exons identified by comparative genomics
Designations and sequences of primers used in RT-PCR
Primer sequence (5'-3')
59 → 57
25 (10 → 15)
30, 35, 40
5' RACE validation of novel first ghrelin exons
5' RACE was performed with primers specific to extended exon 0 using a Sure-RACE kit (OriGene, Rockville, MD) according to the manufacturer's instructions. Samples of cDNAs from 22 adult human tissues (brain, heart, kidney, spleen, liver, colon, lung, small intestine, muscle, stomach, testis, placenta, pituitary, thyroid gland, adrenal gland, pancreas, ovary, uterus, prostate, leukocytes (PBL), adipose tissue, and mammary gland) and two fetal tissues (brain and liver) were challenged. First round PCR was performed with an adapter-specific sense primer and an exon 0-specific antisense primer (Sure-F and Outer-R, Table 1). PCR products were diluted and used in a secondary, hemi-nested PCR with a gene-specific antisense primer (Inner-R, Table 1).
Isolation of alternatively spliced mRNAs
In order to investigate the patterns of alternative splicing of the putative first exons, RT-PCRs were performed employing an antisense primer in the 3' terminal exon 4 and sense primers in exon -1 or extended exon 0 (Exon-1-Full-F/R and V-long-ex0-F/R in Table 1, respectively). The integrity of the cDNA was confirmed by RT-PCR for β2 microglobulin using intron-spanning primers (B2MG-F/R, Table 1). Human stomach and the SW1353 chondrosarcoma cell line were examined to investigate alternative splicing of extended exon 0 transcripts. RT-PCR of exon -1 was performed using mRNA from the SW1353 chondrosarcoma cell line and from five prostate and prostate cancer cell lines (DU145, RWPE-1, RWPE-2, LNCaP and PC3). To verify their identity, exon -1 to 4 specific RT-PCR products amplified from the cell lines were transferred to a positively charged nylon membrane (Roche) for Southern analysis. The membrane was hybridised at 48°C with an antisense digoxigenin (DIG) labelled cRNA probe specific to exon -1 synthesised from a 5' RACE PCR product (cRNA-exon-1-F/R, Table 1) and detected as described by the manufacturer (Roche). PCR reagents, purification, cloning and sequencing were performed as described above.
To further investigate the expression profiles of exon -1 to 4 containing transcripts in various normal adult and fetal human tissues, RT-PCR was employed using Rapid-Scan gene expression panels (OriGene) according to the manufacturer's instructions. Rapid-Scan panels include duplicate 96-well PCR plates containing first-strand cDNA synthesised from poly(A)+ RNA from 24 human tissues (brain, heart, kidney, spleen, liver, colon, lung, small intestine, muscle, stomach, testis, placenta, salivary gland, thyroid gland, adrenal gland, pancreas, ovary, uterus, prostate, skin, leukocytes (PBL), bone marrow, fetal brain, fetal liver) serially diluted over a 4-log range (1000X-1X), where the lowest concentration (1X) is approximately 1 pg cDNA. The panels are normalised to β-actin allowing an assessment of the relative abundance of exon -1 to 4 splice variants by limiting the number of PCR cycles. PCR, cloning and sequencing was performed as above, except that the samples were subjected to 35 cycles of PCR in a total reaction volume of 25 μl.
To verify the orientation of putative antisense transcripts, total stomach RNA was reverse transcribed using primers specific for sense or antisense transcripts (CF264800-F/R in Table 1) and subjected to PCR combining both reverse transcription primers. To verify the identity of the transcripts, a nested DIG-labelled (Roche) PCR probe (ex2*-nested-South-F/R, Table 1) was synthesised from cloned sequence and employed in Southern hybridisation at 42°C, as described previously . In addition, a PCR product at the expected size of an amplicon corresponding to a putative antisense EST [GenBank:CF264800] was eluted from agarose gels, reamplified and subsequently purified and sequenced as described above.
5' RACE analysis of antisense transcription start sites
To characterise the 5' end of the putative antisense RNAs, 5' RACE was undertaken using FirstChoice RLM-RACE-Ready human stomach cDNA (Ambion) according to the manufacturer's instructions. The first round PCR was performed with an adapter-specific sense primer and an exon 4* specific antisense primer (5'adapter-out-F and 5'OS-out-R in Table 1, respectively). PCR product (1 μl) was used in a secondary, nested PCR with a gene specific primer in exon 4* (5'adapter-in-F and 5'OS-in-R, Table 1). PCRs were performed in a total reaction volume of 50 μl using Platinum Taq Polymerase High Fidelity (Invitrogen) according to the manufacturer's instructions.
This work was supported by grants from the Cancer Council Queensland (to LKC and ACH), the Faculty of Science, Queensland University of Technology, and a QUT International Doctoral Scholarship (to IS). We thank Shea Carter (IHBI, Brisbane, Australia) for the chondrosarcoma cell line SW1353 (ATCC HTB 94).
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