[en] The callipyge phenotype is a monogenic muscular hypertrophy that is only expressed in heterozygous sheep receiving the CLPG mutation from their sire. The wild-type phenotype of CLPG/CLPG animals is thought to result from translational inhibition of paternally expressed DLK1 transcripts by maternally expressed miRNAs. To identify the miRNA responsible for this trans effect, we used high-throughput sequencing to exhaustively catalog miRNAs expressed in skeletal muscle of sheep of the four CLPG genotypes. We have identified 747 miRNA species of which 110 map to the DLK1-GTL2 or callipyge domain. We demonstrate that the latter are imprinted and preferentially expressed from the maternal allele. We show that the CLPG mutation affects their level of expression in cis ( approximately 3.2-fold increase) as well as in trans ( approximately 1.8-fold increase). In CLPG/CLPG animals, miRNAs from the DLK1-GTL2 domain account for approximately 20% of miRNAs in skeletal muscle. We show that the CLPG genotype affects the levels of A-to-I editing of at least five pri-miRNAs of the DLK1-GTL2 domain, but that levels of editing of mature miRNAs are always minor. We present suggestive evidence that the miRNAs from the domain target the ORF of DLK1, thereby causing the trans inhibition underlying polar overdominance. We highlight the limitations of high-throughput sequencing for digital gene expression profiling as a result of biased and inconsistent amplification of specific miRNAs.
Disciplines :
Genetics & genetic processes Veterinary medicine & animal health Biochemistry, biophysics & molecular biology
Author, co-author :
Caiment, Florian ; Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
Charlier, Carole ; Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
Hadfield, Tracy; Utah State University > Department of Animal, Dairy and Veterinary Sciences
Cockett, Noelle; Utah State University > Department of Animal, Dairy and Veterinary Sciences
Georges, Michel ✱; Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
Baurain, Denis ✱; Université de Liège - ULiège > Département de productions animales > GIGA-R : Génomique animale
✱ These authors have contributed equally to this work.
Language :
English
Title :
Assessing the effect of the CLPG mutation on the microRNA catalog of skeletal muscle using high-throughput sequencing.
Publication date :
2010
Journal title :
Genome Research
ISSN :
1088-9051
eISSN :
1549-5469
Publisher :
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, United States - New York
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. 2000. Gene Ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
Baek D, Villen J, Shin C, Camargo FD, Gygi SP, Bartel DP. 2008. The impact of microRNAs on protein output. Nature 455: 64-71.
Byrne K, Colgrave ML, Vuocolo T, Pearson R, Bidwell CA, Cockett NE, Lynn DJ, Fleming-Waddell JN, Tellam RL. 2010. The imprinted retrotransposon-like gene PEG11 (RTL1) is expressed as a full-length protein in skeletal muscle from Callipyge sheep. PLoS ONE 5: e8638. doi: 10.1371/journal.pone.0008638.
Cavaille J, Seitz H, Paulsen M, Ferguson-Smith AC, Bachellerie JP. 2002. Identification of tandemly-repeated C/D snoRNA genes at the imprinted human 14q32 domain reminiscent of those at the Prader-Willi/Angelman syndrome region. Hum Mol Genet 11: 1527-1538.
Charlier C, Segers K, Karim L, Shay T, Gyapay G, Cockett N, Georges M. 2001a. The callipyge mutation enhances the expression of coregulated imprinted genes in cis without affecting their imprinting status. Nat Genet 27: 367-369.
Charlier C, Segers K, Wagenaar D, Karim L, Berghmans S, Jaillon O, Shay T, Weissenbach J, Cockett N, Gyapay G, et al. 2001b. Human-ovine comparative sequencing of a 250-kb imprinted domain encompassing the callipyge (clpg) locus and identification of six imprinted transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8. Genome Res 11: 850-862.
Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, et al. 2005. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33: e179. doi: 10.1093/nar/gni178.
Chi SW, Zang JB, Mele A, Darnell RB. 2009. Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460: 479-486.
Cockett NE, Jackson SP, Shay TL, Farnir F, Berghmans S, Snowder GD, Nielsen DM, Georges M. 1996. Polar overdominance at the ovine callipyge locus. Science 273: 236-238.
Davis E, Jensen CH, Schroder HD, Farnir F, Shay-Hadfield T, Kliem A, Cockett N, Georges M, Charlier C. 2004. Ectopic expression of DLK1 protein in skeletal muscle of padumnal heterozygotes causes the callipyge phenotype. Curr Biol 14: 1858-1862.
Davis E, Caiment F, Tordoir X, Cavaille J, Ferguson-Smith A, Cockett N, Georges M, Charlier C. 2005. RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus. Curr Biol 15: 743-749.
Durbin R, Eddy SR, Krogh A, Mitchison G. 1998. Biological sequence analysis: Probabilistic models of proteins and nucleic acids. Cambridge University Press, Cambridge, UK.
Ender C, Krek A, Friedlander MR, Beitzinger M, Weinmann L, Chen W, Pfeffer S, Rajewsky N, Meister G. 2008. A human snoRNA with microRNA-like functions. Mol Cell 32: 519-528.
Enright AJ, Van Dongen S, Ouzounis CA. 2002. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30: 1575-1584.
Freking BA, Murphy SK, Wylie AA, Rhodes SJ, Keele JW, Leymaster KA, Jirtle RL, Smith TP. 2002. Identification of the single base change causing the callipygemuscle hypertrophy phenotype, the only known example of polar overdominance in mammals. Genome Res 12: 1496-1506.
Friedlander MR, Chen W, Adamidi C, Maaskola J, Einspanier R, Knespel S, Rajewsky N. 2008. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26: 407-415.
Friedman RC, Farh KK, Burge CB, Bartel DP. 2009. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19: 92-105.
Ge B, Gurd S, Gaudin T, Dore C, Lepage P, Harmsen E, Hudson TJ, Pastinen T. 2005. Survey of allelic expression using EST mining. Genome Res 15: 1584-1591.
Georges M, Charlier C, Cockett N. 2003. The callipyge locus: Evidence for the trans interaction of reciprocally imprinted genes. Trends Genet 19: 248-252.
Georges M, Charlier C, Smit M, Davis E, Shay T, Tordoir X, Takeda H, Caiment F, Cockett N. 2004. Toward molecular understanding of polar overdominance at the ovine callipyge locus. Cold Spring Harb Symp Quant Biol 69: 477-483.
Glazov EA, Kongsuwan K, Assavalapsakul W, Horwood PF, Mitter N, Mahony TJ. 2009. Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection. PLoS ONE 4: e6349. doi: 10.1371/journal.pone. 0006349.
Griffiths-Jones S. 2006. miRBase: The microRNA sequence database. Methods Mol Biol 342: 129-138.
John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS. 2004. Human microRNA targets. PLoS Biol 2: e363. doi: 10.1371/journal.pbio.0020363.
Kagami M, Yamazawa K, Matsubara K, Matsuo N, Ogata T. 2008. Placentomegaly in paternal uniparental disomy for human chromosome 14. Placenta 29: 760-761.
Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG, Nishikura K. 2007. Redirection of silencing targets by adenosine-toinosine editing of miRNAs. Science 315: 1137-1140.
Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, et al. 2007. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129: 1401-1414.
Li R, Li Y, Kristiansen K, Wang J. 2008. SOAP: Short oligonucleotide alignment program. Bioinformatics 24: 713-714.
Lin SP, Youngson N, Takada S, Seitz H, Reik W, Paulsen M, Cavaille J, Ferguson-Smith AC. 2003. Asymmetric regulation of imprinting on the maternal and paternal chromosomes at the Dlk1-Gtl2 imprinted cluster on mouse chromosome 12. Nat Genet 35: 97-102.
Linsen SE, de Wit E, Janssens G, Heater S, Chapman L, Parkin RK, Fritz B, Wyman SK, de Bruijn E, Voest EE, et al. 2009. Limitations and possibilities of small RNA digital gene expression profiling. Nat Methods 6: 474-476.
Morin RD, O'Connor MD, Griffith M, Kuchenbauer F, Delaney A, Prabhu AL, Zhao Y, McDonald H, Zeng T, Hirst M, et al. 2008. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res 18: 610-621.
Ozsolak F, Poling LL, Wang Z, Liu H, Liu XS, Roeder RG, Zhang X, Song JS, Fisher DE. 2008. Chromatin structure analyses identify miRNA promoters. Genes Dev 22: 3172-3183.
Seitz H, Youngson N, Lin SP, Dalbert S, Paulsen M, Bachellerie JP, Ferguson- Smith AC, Cavaille J. 2003. Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene. Nat Genet 34: 261-262.
Seitz H, Royo H, Bortolin ML, Lin SP, Ferguson-Smith AC, Cavaille J. 2004. A large imprinted microRNA gene cluster at the mouse Dlk1-Gtl2 domain. Genome Res 14: 1741-1748.
Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. 2008. Widespread changes in protein synthesis induced by microRNAs. Nature 455: 58-63.
Smit M, Segers K, Carrascosa LG, Shay T, Baraldi F, Gyapay G, Snowder G, Georges M, Cockett N, Charlier C. 2003. Mosaicism of Solid Gold supports the causality of a noncoding A-to-G transition in the determinism of the callipyge phenotype. Genetics 163: 453-456.
Song G, Wang L. 2008. MiR-433 and miR-127 arise from independent overlapping primary transcripts encoded by the miR-433-127 locus. PLoS ONE 3: e3574. doi: 10.1371/journal.pone.0003574.
Takeda H, Charlier C, Farnir F, Georges M. 2010. Demonstrating polymoprhic miRNA-mediated gene regulation in vivo: Application to the g+6223G→A mutation of Texel sheep. RNA 16: 1854-1863.
Tay Y, Zhang J, Thomson AM, Lim B, Rigoutsos I. 2008. MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 455: 1124-1128.
Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. 2002. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 3: research0034-research0034.11.
Vuocolo T, Byrne K, White J, McWilliam S, Reverter A, Cockett NE, Tellam RL. 2007. Identification of a gene network contributing to hypertrophy in callipyge skeletal muscle. Physiol Genomics 28: 253-272. (Pubitemid 46711003)
