MicroRNA-499 expression distinctively correlates to target genes sox6 and rod1 profiles to resolve the skeletal muscle phenotype in nile tilapia profiles to resolve the skeletal muscle phenotype in nile tilapia

PLoS ONE

Volumn 10, Issue 3, 2015, Pages

  Nachtigall, Pedro G ^a   Dias, Marcos C ^a,b   Carvalho, Robson F ^a   Martins, Cesar ^a   Pinhal, Danillo ^a  

^a SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^b Universidade Federal Do Mato Grosso (UFMT)   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MICRORNA 499; REGULATOR OF DIFFERENTIATION 1 PROTEIN; REGULATOR PROTEIN; TRANSCRIPTION FACTOR SOX6; UNCLASSIFIED DRUG; 3' UNTRANSLATED REGION; MESSENGER RNA;

ADULT; ANIMAL TISSUE; ARTICLE; CELLS BY BODY ANATOMY; CONTROLLED STUDY; FEMALE; FLUORESCENCE IN SITU HYBRIDIZATION; GENE EXPRESSION; GENE REGULATORY NETWORK; IMMUNOFLUORESCENCE; MALE; MUSCLE CELL; NONHUMAN; OREOCHROMIS NILOTICUS; PHENOTYPE; PROTEIN EXPRESSION; PROTEIN PROCESSING; QUANTITATIVE ANALYSIS; REGULATOR OF DIFFERENTIATION 1 GENE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SKELETAL MUSCLE; TRANSCRIPTION FACTOR SOX6 GENE; 3' UNTRANSLATED REGION; ANIMAL; CHEMISTRY; CICHLID; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; PROTEIN ANALYSIS; RNA INTERFERENCE;

OREOCHROMIS NILOTICUS; VERTEBRATA;

3' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; CICHLIDS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; MICRORNAS; MUSCLE, SKELETAL; PHENOTYPE; PROTEIN INTERACTION MAPPING; RNA INTERFERENCE; RNA, MESSENGER;

EID: 84925864954     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0119804     Document Type: Article

References (49)

1. Driedzic WR, Hochachka PW. Control of energy metabolism in fish white muscle. Am J Phisiol. 1976; 230: 579-582. PMID: 131493
2. Schiaffino S, Reggiani C. Fiber types in mammalian skeletal muscles. Physiol Rev. 2011; 91(4): 1447-1531. doi: 10.1152/physrev.00031.2010 PMID: 22013216
3. Pette D, Staron RS. Myosin isoforms, muscle fiber types, and transitions. Microsc Res Tech. 2000; 50 (6): 500-509. PMID: 10998639
4. Berezikov E. Evolution of microRNA diversity and regulation in animals. Nat Reviews. 2012; 12: 846-860.
5. Sood P, Krek A, Zavolan M, Macino G, Rajewsky N. Cell-type-specific signatures of microRNAs on target mRNA expression. Proc Natl Acad Sci USA. 2006; 103: 2746-2751. PMID: 16477010
6. van Rooij E, Quiat D, Johnson BA, Sutherland LB, Qi X, Richardson JA, et al. A family of microRNAs encoded by myosin genes governs myosin expression and muscle performance. Dev Cell. 2009; 17(5): 662-673. doi: 10.1016/j.devcel.2009.10.013 PMID: 19922871
7. Small EM, O'Rourke JR, Moresi V, Sutherland LB, McAnally J, Gerard RD, et al. Regulation of PI3-kinase/ Akt signaling by muscle-enriched microRNA-486. Proc Natl Acad Sci USA. 2010; 107(9): 4218-4223. doi: 10.1073/pnas.1000300107 PMID: 20142475
8. Ge Y, Chen J. MicroRNAs in skeletal myogenesis. Cell Cycle. 2011; 10(3): 441-448. PMID: 21270519
9. Kwon C, Han Z, Olson EN, Srivastava D. MicroRNA1 influences cardiac differentiation in Drosophila and regulates Notch signaling. Proc Natl Acad Sci USA. 2005; 102:18986-18991. PMID: 16357195
10. Flynt AS, Li N, Thatcher EJ, Solnica-Krezel L, Patton JG. Zebrafish miR-214 modulates Hedgehog signaling to specify muscle cell fate. Nat Genet. 2007; 39(2): 259-263. PMID: 17220889
11. Mishima Y, Abreu-Goodger C, Staton AA, Stahlhut C, Shou C, Cheng C, et al. Zebrafish miR-1 and miR-133 shape muscle gene expression and regulate sarcomeric actin organization. Genes Dev. 2009; 23: 619-632. doi: 10.1101/gad.1760209 PMID: 19240126
12. Ketley A, Warren A, Holmes E, Gering M, Aboobaker AA, Brook JD. The miR-30 microRNA family targets smoothened to regulate hedgehog signalling in zebrafish early muscle development. PLoS One. 2013; 8(6): e65170. doi: 10.1371/journal.pone.0065170 PMID: 23755189
13. Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature. 2010; 466(7308): 835-840. doi: 10.1038/nature09267 PMID: 20703300
14. Pase L, Lieschke GJ. Discerning different in vivo roles of microRNAs by experimental approaches in zebrafish. In: Detrich HW, Westerfield M, Zon LI, editors. The Zebrafish: Genetics, Genomics and Informatics. Waltham: Academic Press; 2011. pp. 353-378.
15. Ebert M, Sharp P. Roles for microRNAs in conferring robustness to biological processes. Cell. 2012; 149: 515-524. doi: 10.1016/j.cell.2012.04.005 PMID: 22541426
16. Bartel DP, Chen CZ. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nature. 2004; 5: 396-400.
17. Hosoda T, Zheng H, Cabral-da-Silva M, Sanada F, Ide-Iwata N, Ogórek B, et al. Human cardiac stem cell differentiation is regulated by a mircrine mechanism. Circulation. 2011; 123: 1287-1296. doi: 10. 1161/CIRCULATIONAHA.110.982918 PMID: 21403094
18. Wang XG, Ono Y, Tan SC, Chai RJF, Parkin C, Ingham PW. Prdm1a and miR-499 act sequentially to restrict Sox6 activity to the fast-twitch muscle lineage in the zebrafish embryo. Development. 2011; 138: 4399-4404. doi: 10.1242/dev.070516 PMID: 21880783
19. Bhuiyan SS, Kinoshita S, Wongwarangkana C, Asaduzzaman M, Asakawa S, Watabe S. Evolution of the myosin heavy chain gene MYH14 and its intronic microRNA miR-499: muscle-specific miR-499 expression persists in the absence of the ancestral host gene.BMC Evolutionary Biology 13(1), 2013
20. Hagiwara N, Yeh M, Liu A. Sox6 is required for normal fiber type differentiation of fetal skeletal muscle in mice.Developmental Dynamics 236(8),2007,pp:2062-2076.
21. Sadvakassova G, Dobocan MC, Difalco MR, Congote LF. Regulator of differentiation 1 (ROD1) binds to the amphipathic C-terminal peptide of thrombospondin-4 and is involved in its mitogenic activity.Journal of Cellular Physiology 220(3),2009,pp:672-679.
22. Kruger J, Rehmsmeier M. RNAhybrid: microRNA target prediction easy, fast and flexible.Nucleic Acids Research 34,2006.
23. Cohen-Barak O, Yi Z, Hagiwara N, Monzen K, Komuro I, Brilliant MH. Sox6 regulation of cardiac myocyte development.Nucleic Acids Research 2003; 31(10),pp: 5941–5948
24. An C, Dong Y, Hagiwara N. Genome-wide mapping of Sox6 binding sites in skeletal muscle reveals both direct and indirect regulation of muscle terminal differentiation by Sox6.BMC Developmental Biology 11(1),2011
25. Quiat D, Voelker KA, Pei J, Grishinc NV, Grange RW, Bassel-Duby R. Concerted regulation of myofiber-specific gene expression and muscle performance by the transcriptional repressor Sox6.Proceedings of the National Academy of Sciences. 2011;108(25),pp: 10196–10201.
26. Bell ML, Buvoli M, Leinwand LA. Uncoupling of expression of an intronic microRNA and its myosin host gene by exon skipping.Molecular and Cellular Biology 2010;30 (8): 1937–1945.
27. Vogel C, Bashton M, Kerrison N, Chothia C, Teichmann SA. Structure, function and evolution of multi-domain proteins.Current Opinion in Structural Biology . 2004;14(2): 208–216.
28. McCarthy JJ. The MyomiR network in skeletal muscle plasticity. Exerc Sport Sci Rev. 2011; 39(3):150–154
29. Chen JF, Mandel EM, Thomson JM, Wu Q, Callis TE, Hammond SM,Conlon F.L.,Wang D.-Z. The role of microRNA-1 and microRNA-133 in skeletal muscle proliferation and differentiation.Nature Genetics 2006,38(2),pp: 228–233
30. Gagan J, Dey BK, Dutta A. MicroRNAs regulate and provide robustness to the myogenic transcriptional network.Current Opinion in Pharmacology 2012,12(3),pp: 1–6.
31. McCarthy JJ. MicroRNA-206: the skeletal muscle-specific myomiR.Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 2008;1779(11),pp: 682–691
32. Williams AH, Valdez G, Moresi V, Qi X, McAnally J, Elliott JL, Bassel-Duby R.,Sanes J.R.,Olso E.N. MicroRNA-206 delays ALS progression and promotes regeneration of neuromuscular synapses in mice. Science. 2009,326(5959),pp: 1549–1554
33. Sweetman D, Goljanek K, Rathjen T, Oustanina S, Braun T, Dalmay T,Münsterberg A.Specific requirements of MRFs for the expression of muscle specific microRNAs,miR-1, miR-206 and miR-133. Dev Biol. 2008;321(5),pp: 491–499
34. Chu WY, Du S, Li HH, Li YL, Liu LS, Wang KZ, et al. Systematic identification and differential expression profiling of MicroRNAs from white and red muscles of Siniperca chuatsi. Curr Mol Med 2013;13(8): 1397–1407.
35. von Hofsten J, Elworthy S, Gilchrist MJ, Smith JC, Wardle FC, Ingham PW. Prdm1- and Sox6-mediated transcriptional repression specifies muscle fiber type in the zebrafish embryo.EMBO Reports. 2008,9(7),pp:683–689
36. Stadler M, Artiles K, Pak J, Fire A. Contributions of mRNA abundance, ribosome loading, and post- or peri-translational effects to temporal repression of C. elegans heterochronic miRNA targets.Genome Research 2012,22(12),pp: 2418–2426
37. Filipowicz W, Bhattacharyya SN, Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat Rev Genet. 2008; 9: 102–114.
38. Yamamoto H, Tsukahara K, Kanaoka Y, Jinno S, Okayama H. Isolation of a mammalian homologue of a fission yeast differentiation regulator.Molecular and Cellular Biology. 1999,19(5),pp: 3829–3841
39. Bearzi C, Leri A, Lo Monaco F, Rota M, Gonzalez A, Hosoda T, et al. Identification of a coronary vascular progenitor cell in the human heart. Proc Natl Acad Sci USA. 2009;106: 15885–15890
40. Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM. Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3UTR evolution. Cell. 2005; 123: 1133-1146. PMID: 16337999
41. Levine E, McHale P, Levine H. Small regulatory RNAs may sharpen spatial expression patterns. PLoS Comput Biol, 3, p. e233.Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2007; 32(5): 1792-1797.
42. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Mol Biol Evol. 2011; 28: 2731-2739. doi: 10.1093/molbev/msr121 PMID: 21546353
43. Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, et al. Ensembl 2014. Nucleic Acids Res. 2014; 42: D749-755. doi: 10.1093/nar/gkt1196 PMID: 24316576
44. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009; 55(4): 611-622. doi: 10.1373/clinchem.2008.112797 PMID: 19246619
45. Ramakers C, Ruijter JM, Deprez RHL, Moorman AFM. Assumption-free analysis of quantitative realtime polymerase chain reaction (PCR) data. Neurosci Lett. 2003; 339: 62-66. PMID: 12618301
46. Pfaffl MW, Horgan GW, Dempfle L. Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Ac Res. 2002; 30(9): e36 PMID: 11972351
47. Obernosterer G, Martinez J, Alenius M. Locked nucleic acid based in situ detection of microRNAs in mouse tissue sections. Nat Protoc. 2007; 2: 1508-1514. PMID: 17571058
48. Tani S, Kuraku S, Sakamoto H, Inoue K, Kusakabe R. Developmental expression and evolution of mus-cle-specific microRNAs conserved in vertebrates. Evol Dev 2013; 15(4): 293-304. doi: 10.1111/ede.12039 PMID: 23809703
49. Nakajima RT, Cabral-de-Mello DC, Valente GT, Venere PC, Martins C. Evolutionary dynamics of rRNA gene clusters in cichlid fish. BMC Evol Biol. 2012; 12: 198. doi: 10.1186/1471-2148-12-198 PMID: 23035959