The proximal first exon architecture of the murine ghrelin gene is highly similar to its human orthologue
© Chopin et al; licensee BioMed Central Ltd. 2009
Received: 12 January 2009
Accepted: 09 May 2009
Published: 09 May 2009
The murine ghrelin gene (Ghrl), originally sequenced from stomach tissue, contains five exons and a single transcription start site in a short, 19 bp first exon (exon 0). We recently isolated several novel first exons of the human ghrelin gene and found evidence of a complex transcriptional repertoire. In this report, we examined the 5' exons of the murine ghrelin orthologue in a range of tissues using 5' RACE.
5' RACE revealed two transcription start sites (TSSs) in exon 0 and four TSSs in intron 0, which correspond to 5' extensions of exon 1. Using quantitative, real-time RT-PCR (qRT-PCR), we demonstrated that extended exon 1 containing Ghrl transcripts are largely confined to the spleen, adrenal gland, stomach, and skin.
We demonstrate that multiple transcription start sites are present in exon 0 and an extended exon 1 of the murine ghrelin gene, similar to the proximal first exon organisation of its human orthologue. The identification of several transcription start sites in intron 0 of mouse ghrelin (resulting in an extension of exon 1) raises the possibility that developmental-, cell- and tissue-specific Ghrl mRNA species are created by employing alternative promoters and further studies of the murine ghrelin gene are warranted.
Ghrelin is a 28 amino acid peptide, predominantly expressed in the stomach, and is cleaved from a 117 amino acid preprohormone, preproghrelin . Our previously published comparative genomics analysis suggested that the mouse and human first exon architecture is conserved  and we demonstrated that the human ghrelin gene (GHRL) contains several untranslated first exons that may play a role in regulating ghrelin gene translation . In this study we investigate the existence of novel exons of the murine ghrelin orthologue (Ghrl).
Identification of a novel first exon and transcription start sites of the murine ghrelin gene
It has previously been reported that the mouse ghrelin gene consists of four coding exons (exons 1 to 4) and a short, non-coding 19 bp first exon , which we have termed exon 0. To determine if additional first exon and transcription start sites are present, 5' RACE (rapid amplification of 5' complementary DNA ends) was performed with exon 1-specific reverse primers and a RACE-ready panel of anchored cDNA libraries derived from 24 mouse tissues (OriGene, Rockville, MD). A list of exons and exon-intron boundaries of the ghrelin locus derived-transcripts identified in this and previous studies is given in [Additional file 1].
In a recent study we also identified a human ghrelin exon (exon -1) 2.6 kb upstream of the preproghrelin translation start site in exon 1 . These human exon 1-derived ghrelin transcripts contain a putative secretion signal peptide, which is not present in the rodent sequence, and may give rise to novel peptides . Mouse ghrelin appears to lack exon -1, as we have been unable to identify murine exon -1 ghrelin sequence using 5' RACE and RT-PCR (data not shown). Promoter sequences are known to evolve rapidly and show a high rate of sequence turnover [6, 7]; thus, it is not surprising that the region corresponding to murine exon -1 is not a functional ghrelin gene exon in the mouse.
The extended exon 1 of Ghrl is transcribed and gives rise to full-length preproghrelin transcripts
Ghrelin transcripts with an extended exon 1 are highly expressed in a limited number of tissues
A possible role for 5' variant exons of preproghrelin transcripts in translational control
As observed previously for exon 0 of the human ghrelin gene , several very short upstream open reading frames (uORFs) are present in the extended exon 1 and exon 0 sequence (data not shown). Upstream open reading frames, mRNA secondary structure and other motifs in 5' untranslated exons have been shown to regulate the translation of developmental genes . Interestingly, it has been reported that ghrelin mRNA and protein levels do not directly correlate in the rat . We hypothesise that this may be caused by the transcription of different first Ghrl exons with different preproghrelin translation efficiencies. This mechanism is exemplified in the chicken embryo where transcripts harbouring uORFs allow low-level translation of proinsulin, whereas a higher level of proinsulin expression is achieved in the adult pancreas by transcription of mRNAs from a downstream first exon devoid of uORFs . Moreover, alternative 5' untranslated exons can have an mRNA secondary structure that restrains translation, particularly if a hairpin occurs close to the 5' cap, which is the ribosomal entry site . The short 19 bp exon 0, which we and others  have described, is devoid of upstream open reading frames or stable secondary structure. This transcript, therefore, could be more efficiently translated than the 233 bp 5' extended exon 1 (exon 1e) that contains a 266 bp 5' untranslated region, for example (see [Additional file 2]).
In this report, we demonstrate that transcription start sites in exon 0 an extended exon 1 are present in the murine ghrelin gene, suggesting that there are similarities in the proximal first exon organisation of the murine ghrelin gene and its human orthologue. A novel, extended exon 1 is expressed at high levels in the spleen, adrenal gland, stomach, and skin, indicating that the murine ghrelin gene harbours a cell-type, development-stage and/or tissue-specific, proximal promoter in intron 0. Little is known about the promoters of the murine ghrelin gene. Only the role of rat ghrelin sequence, which is upstream of the 19 bp exon 0, has been investigated in promoter constructs in murine cell-lines, and this demonstrated minimal promoter activity . The upstream, proximal promoter region of the murine ghrelin gene, therefore, warrants further studies.
The murine ghrelin gene (Ghrl) architecture was examined using the RIKEN Genomic Element Viewer provided by the FANTOM (Functional Annotation of Mouse) consortium . This database includes transcripts within the mouse genome as well as CAGE (Cap Analysis of Gene Expression) tags corresponding to the 5' ends of transcripts . The location of ghrelin locus-derived ESTs and mRNA entries, as well as sequenced PCR amplicons obtained in this study, were identified by BLAST searches against GenBank databases . The minimum free energies (ΔG) of the 5' untranslated regions (5' UTRs) were calculated using the RNAfold web server .
Designations and sequences of primers used in RT-PCR
Verification of extended exon 1 and cloning of full-length preproghrelin with an extended exon 1
2 μg DNase-treated total RNA from the liver, brain and spleen of Swiss Webster mice (Ambion) was reverse transcribed with 200 units of SuperScript III (Invitrogen) using oligo(dT)20 primers in a final volume of 20 μl according to the manufacturer's instructions. The resulting single-stranded cDNA was treated with ribonuclease H (Invitrogen). PCRs were performed with a forward primer in the extended exon 1 (Ext1-F, Table 1) and a reverse primer in exon 1 (Ex1-R, Table 1) in a total reaction volume of 50 μl using 1 unit Platinum Taq Polymerase (Invitrogen) according to the manufacturer's instructions. RNA samples that were not reverse transcribed were run to control for genomic DNA and a no template control (water) was included to control for exogenous contamination. Cloning of full-length (exon 1 to 4) Ghrl transcripts containing the extended exon 1 was achieved by PCRs using the same extended exon 1 primer (Ext1-F, Table 1) and a primer in exon 4 (ex4-R, Table 1). PCR products were purified and sequenced as described above.
Transcript Profiling in Mouse Tissues
Transcript profiling of murine Ghrl transcripts that contain an extended exon 1 was performed by using a TissueScan Mouse Normal Tissue qPCR array (OriGene) derived from both male and female NIH Swiss mice. The samples in this array are generated by reverse transcription of mouse poly(A)+ RNAs, which are free of genomic DNA, using oligo(dT) primers. The array plates are loaded with equal amounts of cDNA per well, as described by the manufacturer (OriGene). Extended exon 1 transcript expression levels were examined using 2× SYBR Green PCR Master Mix (AB) and the primers Ext1-F/R (Table 1). The amount of mRNA was determined by normalising the levels of expression with the glyceraldehyde 3-phosphate dehydrogenase (Gapdh) (Gapdh-F/R, Table 1) expression in the tissues. Primers were designed using Primer Express v.2.0 (AB) to yield a single amplicon, and were verified by dissociation curve analysis. The quantitative real-time RT-PCR conditions were optimised using purified PCR products. Real-time RT-PCR was performed using the 2× SYBR green PCR master mix on the AB 7000 sequence detection system and data analysed using the absolute standard curve method (User Bulletin #2, AB) to determine expression levels.
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).
- Kojima M, Hosoda H, Date Y, Nakazato M, Matsuo H, Kangawa K: Ghrelin is a growth-hormone-releasing acylated peptide from stomach. Nature. 1999, 402 (6762): 656-660. 10.1038/45230.View ArticlePubMedGoogle Scholar
- Seim I, Collet C, Herington AC, Chopin LK: Revised genomic structure of the human ghrelin gene and identification of novel exons, alternative splice variants and natural antisense transcripts. BMC Genomics. 2007, 8: 298-10.1186/1471-2164-8-298.PubMed CentralView ArticlePubMedGoogle Scholar
- Tanaka M, Hayashida Y, Iguchi T, Nakao N, Nakai N, Nakashima K: Organization of the mouse ghrelin gene and promoter: occurrence of a short noncoding first exon. Endocrinology. 2001, 142 (8): 3697-3700. 10.1210/en.142.8.3697.View ArticlePubMedGoogle Scholar
- Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, Kodzius R, Watahiki A, Nakamura M, Arakawa T, et al: Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci USA. 2003, 100 (26): 15776-15781. 10.1073/pnas.2136655100.PubMed CentralView ArticlePubMedGoogle Scholar
- Kanamoto N, Akamizu T, Tagami T, Hataya Y, Moriyama K, Takaya K, Hosoda H, Kojima M, Kangawa K, Nakao K: Genomic structure and characterization of the 5'-flanking region of the human ghrelin gene. Endocrinology. 2004, 145 (9): 4144-4153. 10.1210/en.2003-1718.View ArticlePubMedGoogle Scholar
- Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin A: Evolutionary turnover of mammalian transcription start sites. Genome Res. 2006, 16 (6): 713-722. 10.1101/gr.5031006.PubMed CentralView ArticlePubMedGoogle Scholar
- Tsuritani K, Irie T, Yamashita R, Sakakibara Y, Wakaguri H, Kanai A, Mizushima-Sugano J, Sugano S, Nakai K, Suzuki Y: Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes. Genome Res. 2007, 17 (7): 1005-1014. 10.1101/gr.6030107.PubMed CentralView 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 (6): 424-436. 10.1038/nrg2026.View ArticlePubMedGoogle Scholar
- Jeffery PL, Duncan RP, Yeh AH, Jaskolski RA, Hammond DS, Herington AC, Chopin LK: Expression of the ghrelin axis in the mouse: an exon 4-deleted mouse proghrelin variant encodes a novel C terminal peptide. Endocrinology. 2005, 146 (1): 432-440. 10.1210/en.2003-1466.View ArticlePubMedGoogle Scholar
- Gnanapavan S, Kola B, Bustin SA, Morris DG, McGee P, Fairclough P, Bhattacharya S, Carpenter R, Grossman AB, Korbonits M: The tissue distribution of the mRNA of ghrelin and subtypes of its receptor, GHS-R, in humans. J Clin Endocrinol Metab. 2002, 87 (6): 2988-10.1210/jc.87.6.2988.View ArticlePubMedGoogle Scholar
- Hughes TA: Regulation of gene expression by alternative untranslated regions. Trends Genet. 2006, 22 (3): 119-122. 10.1016/j.tig.2006.01.001.View ArticlePubMedGoogle Scholar
- Ghelardoni S, Carnicelli V, Frascarelli S, Ronca-Testoni S, Zucchi R: Ghrelin tissue distribution: comparison between gene and protein expression. J Endocrinol Invest. 2006, 29 (2): 115-121.View ArticlePubMedGoogle Scholar
- Hernandez-Sanchez C, Mansilla A, de la Rosa EJ, Pollerberg GE, Martinez-Salas E, de Pablo F: Upstream AUGs in embryonic proinsulin mRNA control its low translation level. EMBO J. 2003, 22 (20): 5582-5592. 10.1093/emboj/cdg515.PubMed CentralView ArticlePubMedGoogle Scholar
- Kozak M: Regulation of translation via mRNA structure in prokaryotes and eukaryotes. Gene. 2005, 361: 13-37. 10.1016/j.gene.2005.06.037.View ArticlePubMedGoogle Scholar
- Wei W, Wang G, Qi X, Englander EW, Greeley GH: Characterization and regulation of the rat and human ghrelin promoters. Endocrinology. 2005, 146 (3): 1611-1625. 10.1210/en.2004-1306.View ArticlePubMedGoogle Scholar
- Kawaji H, Kasukawa T, Fukuda S, Katayama S, Kai C, Kawai J, Carninci P, Hayashizaki Y: CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Nucleic Acids Res. 2006, D632-636. 10.1093/nar/gkj034. 34 DatabaseGoogle Scholar
- Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL: NCBI BLAST: a better web interface. Nucleic Acids Res. 2008, W5-9. 10.1093/nar/gkn201. 36 Web ServerGoogle Scholar
- Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL: The Vienna RNA websuite. Nucleic Acids Res. 2008, W70-74. 10.1093/nar/gkn188. 36 Web ServerGoogle Scholar
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