Next-generation sequencing of the porcine skeletal muscle transcriptome for computational prediction of microRNA gene targets

PLoS ONE

Volumn 7, Issue 7, 2012, Pages

  McDaneld, Tara G ^a   Smith, Tim P L ^a   Harhay, Gregory P ^a   Wiedmann, Ralph T ^a  

^a U S MEAT ANIMAL RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; MICRORNA; TRANSCRIPTOME;

3' UNTRANSLATED REGION; ANIMAL TISSUE; ARTICLE; CONTIG MAPPING; DATA ANALYSIS SOFTWARE; DNA LIBRARY; DNA SEQUENCE; DNA TRANSCRIPTION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE IDENTIFICATION; GENE TARGETING; GENETIC DATABASE; MATHEMATICAL COMPUTING; MUSCLE DEVELOPMENT; MUSCLE GROWTH; NONHUMAN; PREDICTION; PYROSEQUENCING; RNA SEQUENCE; SKELETAL MUSCLE; SWINE; TRANSCRIPTOMICS;

3' UNTRANSLATED REGIONS; ANIMALS; COMPUTATIONAL BIOLOGY; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICRORNAS; MOLECULAR SEQUENCE ANNOTATION; MUSCLE, SKELETAL; SEQUENCE ANALYSIS, DNA; SWINE; TRANSCRIPTOME;

SUS;

EID: 84864406821     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0042039     Document Type: Article

References (47)

1. Hutvagner G, ((2005)) Small RNA asymmetry in RNAi: function in RISC assembly and gene regulation. FEBS Lett 579 (26):: 5850--5857.
2. Lai EC, ((2005)) miRNAs: whys and wherefores of miRNA-mediated regulation. Curr Biol 15 (12):: R458--R460.
3. Chan SP, Slack FJ, ((2006)) microRNA-mediated silencing inside P-bodies. RNA Biol 3 (3):: 97--100.
4. Aleman LM, Doench J, Sharp PA, ((2007)) Comparison of siRNA-induced off-target RNA and protein effects. RNA 13:: 385--395.
5. Bagga S, Bracht J, Hunter S, Massirer K, Holtz J, et al. ((2005)) Regulation by let-7 and lin-4 miRNA results in target mRNA degradation. Cell 122:: 553--563.
6. Carthew RW, ((2006)) Gene regulation by microRNAs. Curr Opin Genet Dev 16 (2):: 203--208.
7. Garzon R, Fabbri M, Cimmino A, Calin GA, Croce CM, ((2006)) MicroRNA expression and function in cancer. Trends Mol Med 12 (12):: 580--587.
8. Brennecke J, Stark A, Cohen SM, ((2005)) Not miR-ly muscular: microRNAs and muscle development. Genes Dev 19 (19):: 2261--2264.
9. Kajimoto K, Naraba H, Iwai N, ((2006)) MicroRNA and 3T3-L1 pre-adipocyte differentiation. RNA 12 (9):: 1626--1632.
10. Anderson C, Catoe H, Werner R, ((2006)) MIR-206 regulates connexin43 expression during skeletal muscle development. Nucleic Acids Res 34 (20):: 5863--5871.
11. Nakajima N, Takahashi T, Kitamura R, Isodono K, Asada S, et al. ((2006)) MicroRNA-1 facilitates skeletal myogenic differentiation without affecting osteoblastic and adipogenic differentiation. Biochem Biophys Res Commun 350 (4):: 1006--1012.
12. Callis TE, Chen JF, Wang DZ, ((2007)) MicroRNAs in skeletal and cardiac muscle development. DNA Cell Biol 26 (4):: 219--225.
13. McCarthy JJ, Esser KA, ((2007)) MicroRNA-1 and microRNA-133a expression are decreased during skeletal muscle hypertrophy. J Appl Physiol 102 (1):: 306--313.
14. Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X, et al. ((2006)) A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet 38 (7):: 813--818.
15. McDaneld TG, Smith TPL, Doumit ME, Miles JR, Coutinho LL, et al. ((2009)) MicroRNA expression profiles during swine skeletal muscle development. BMC Genomics 10:: 77.
16. Xie SS, Huang TH, Shen Y, Li XY, Zhang XX, et al. ((2010)) Identification and characterization of microRNAs from porcine skeletal muscle. Anim Genet 41 (2):: 179--190.
17. Nielsen M, Hansen JH, Hedegaard J, Nielsen RO, Panitz F, et al. ((2010)) MicroRNA identity and abundance in porcine skeletal muscles determined by deep sequencing. Anim Genet 41 (2):: 159--168.
18. Reddy AM, Zheng Y, Jagadeeswaren G, Macmil SL, Graham WB, et al. ((2009)) Cloning, characterization and expression analysis of porcine microRNAs. BMC Genomics 10:: 65.
19. Huang TH, Zhu MJ, Li XY, Zhao SH, ((2008)) Discovery of porcine microRNAs and profiling from skeletal muscle tissues during development. PLoS One 3 (9):: e3225.
20. Cheveruex B, Wetter T, Suhai S, ((1999)) Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99,: 45--56.
21. Drummond AJ, Ashton B, Cheung M, Heled J, Kearse Kearse,et al. (2010) Geneious v5.0. Geneious website. Available: http://www.geneious.com. Accessed 2011 May 5.
22. Enright AJ, Arvin A, Tuschl T, Sander C, Marks DS, ((2004)) Human MicroRNA targets. PLoS Biology 3 (7):: e264.
23. Enright AJ, John B, Gaul U, Tuschl T, Sander C, et al. ((2003)) MicroRNA targets in Drosophila. Genome Biology 5:: R1.
24. Lewis BP, Burge CB, Bartel DP, ((2005)) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:: 15--20.
25. Friedman RC, Fahr KK, Burge CB, Bartel DP, ((2009)) Most mammalian mRNA are conserved targets of microRNAs. Genome Research 19:: 92--105.
26. Grimson A, Farh KK, Johnston WK, Garrett-Engele P, et al. ((2007)) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Molecular Cell 27:: 91--105.
27. Goto S, Bono H, Ogata H, Fujibuchi W, Nishioka T, et al. ((1997)) Organizing and computing metabolic pathway data in terms of binary relations. Pac Symp Biocomput pp. 175--86.
28. Denne SC, Kalhan SC, ((1987)) Leucine metabolism in human newborns. Am J Physiol P 253 (61):: E608--E615.
29. Davis TA, Fiorotto ML, Nguyen HV, Reeds PJ, ((1989)) Protein turnover in skeletal muscle of suckling rats. Am J Physiol 257 (5 Pt2):: R1141--R1146.
30. Clemmons DR, ((2009)) Role of IGF-I in skeletal muscle mass maintenance. Trends Endocrinol Metab 20 (7):: 349--356.
31. Perrini S, Laviola L, Carreira MC, Cignarelli A, Natalicchio A, et al. ((2010)) The GH/IGF1 axis and signaling pathways in the muscle and bone: mechanisms underlying age-related skeletal muscle wasting and osteoporosis. J Endocrinol 205 (3):: 201--210.
32. Buckingham M, Bajard L, Chang T, Daubas P, Hadchouel J, et al. ((2003)) The formation of skeletal muscle: from somite to limb. J Anat 202 (1):: 59--68.
33. Trenerry MK, Gatta PA, Cameron-Smith D, ((2011)) JAK/STAT signaling and human in vitro myogenesis. BMC Physiol 11:: 6.
34. Keren A, Tamir Y, Bengal E, ((2006)) The p38 MAPK signaling pathway: a major regulator of skeletal muscle development. Mol Cell Endocrinol 252 (1-2):: 224--230.
35. Miyazaki M, Esser KA, ((2009)) Cellular mechanisms regulating protein synthesis and skeletal muscle hypertrophy in animals. J Appl Physiol 106 (4):: 1367--1373.
36. Yoon MS, Chen J, ((2008)) PLD regulates myoblast differentiation through the mTOR-IGF2 pathway. J Cell Sci 121 (Pt3):: 282--9.
37. Han XH, Jin YR, Seto M, Yoon JK, ((2011)) A WNT/beta-catenin signaling activator, R-spondin, plays positive regulatory roles during skeletal myogenesis. J Biol Chem 286 (12):: 10649--10659.
38. Ehrenborg E, Krook A, ((2009)) Regulation of skeletal muscle physiology and metabolism by peroxisome proliferator-activated receptor delta. Pharmacol Rev 61 (3):: 373--393.
39. Kollias HD, McDermott JC, ((2008)) Transforming growth factor-beta and myostatin signaling in skeletal muscle. J Appl Physiol 104 (3):: 579--587.
40. Khaitlina SY, ((2001)) Functional specificity of actin isoforms. Int Rev Cytol 202:: 35--98.
41. Kee AJ, Gunning PW, Hardeman EC, ((2009)) Diverse roles of the actin cytoskeleton in striated muscle. J Muscle Res Cell Motil 30 (5-6):: 187--197.
42. Potter JD, Gergely J, ((1974)) Troponin, tropomyosin, and actin interactions in the Ca2+ regulation of muscle contraction. Biochemistry 13 (13):: 2697--2703.
43. Chalovich JM, ((1992)) Actin mediated regulation of muscle contraction. Pharmacol Ther 55 (2):: 95--148.
44. Berchtold MW, Brinkmeier H, Müntener M, ((2000)) Calcium ion in skeletal muscle: its crucial role for muscle function, plasticity, and disease. Physiol Rev 80 (3):: 1215--1265.
45. Beam KG, Knudson CM, ((1998)) Effect of postnatal development on calcium currents and slow charge movement in mammalian skeletal muscle. J Gen Physiol 91 (6):: 799--815.
46. Schatz MC, Phillippy AM, Shneiderman B, Salzberg SL, ((2007)) Hawkeye: a visual analytics tool for genome assemblies. Genome Biology 8:: R34.
47. Harhay GP, Keele JW, ((2003)) Positional candidate gene selection from livestock EST databases using Gene Ontology. Bioinformatics 19 (2):: 249--255.