In silico identification of conserved microRNAs and their targets in bovine fat tissue

Gene

Volumn 559, Issue 2, 2015, Pages 119-128

  Wang, HaiYang ^a,b   Xiao, ShenHua ^a   Wang, Min ^a   Kim, Nam Hyung ^b   Li, HuiXia ^a   Wang, GenLin ^a  

^a NANJING AGRICULTURAL UNIVERSITY   (China)

^b Chungbuk National University   (South Korea)

Author keywords

Bioinformatics; Fat tissue; Homology search; Microarray

Indexed keywords

MESSENGER RNA; MICRORNA; MICRORNA 143; MICRORNA 145; MICRORNA 2325C; MICRORNA 2361; TRANSCRIPTOME; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

ADIPOSE TISSUE; ANIMAL TISSUE; ARTICLE; BEEF CATTLE; BIOINFORMATICS; BOS TAURUS; BOVINAE; COMPUTER MODEL; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENETIC CONSERVATION; MICROARRAY ANALYSIS; MULTIGENE FAMILY; NONHUMAN; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA CONFORMATION; RNA EXTRACTION; RNA HYBRIDIZATION; RNA TRANSLATION; SUBCUTANEOUS FAT; ANIMAL; BIOLOGICAL MODEL; COMPUTER SIMULATION; DNA MICROARRAY; GENETICS; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; RNA INTERFERENCE; SEQUENCE ANALYSIS;

BOS; BOS TAURUS; BOVINAE;

ANIMALS; BASE SEQUENCE; CATTLE; COMPUTER SIMULATION; CONSERVED SEQUENCE; MODELS, GENETIC; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA INTERFERENCE; SEQUENCE ANALYSIS, RNA; SUBCUTANEOUS FAT;

EID: 84922380637     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2015.01.021     Document Type: Article

References (55)

1. Adams N.J., Smith G.C., Carpenter Z.L. Performance, carcass and palatability characteristics of Longhorn and other types of cattle. Meat Sci. 1982, 7:67-79.
2. Ambros V. The functions of animal microRNAs. Nature 2004, 431:350-355.
3. Ambros V., Bartel B., Bartel D.P., Burge C.B., Carrington J.C., et al. A uniform system for microRNA annotation. RNA 2003, 9:277-279.
4. Baker M. MicroRNA profiling: separating signal from noise. Nat. Methods 2010, 7:687-692.
5. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
6. Bentwich I., Avniel A., Karov Y., Aharonov R., Gilad S., et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 2005, 37:766-770.
7. Bolstad B.M., Irizarry R.A., Astrand M., Speed T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193.
8. Bowers R.R., Lane M.D. Wnt signaling and adipocyte lineage commitment. Cell Cycle 2008, 7:1191-1196.
9. Brown J.R., Sanseau P. A computational view of microRNAs and their targets. Drug Discov. Today 2005, 10:595-601.
10. Chung S.S., Lee J.S., Kim M., Ahn B.Y., Jung H.S., et al. Regulation of Wnt/beta-catenin signaling by CCAAT/enhancer binding protein beta during adipogenesis. Obesity (Silver Spring) 2012, 20:482-487.
11. Creighton C.J., Reid J.G., Gunaratne P.H. Expression profiling of microRNAs by deep sequencing. Brief. Bioinform. 2009, 10:490-497.
12. Dennis G.J., Sherman B.T., Hosack D.A., Yang J., Gao W., et al. DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol. 2003, 4:P3.
13. Esau C., Kang X., Peralta E., Hanson E., Marcusson E.G., et al. MicroRNA-143 regulates adipocyte differentiation. J. Biol. Chem. 2004, 279:52361-52365.
14. Flynt A.S., Lai E.C. Biological principles of microRNA-mediated regulation: shared themes amid diversity. Nat. Rev. Genet. 2008, 9:831-842.
15. Git A., Dvinge H., Salmon-Divon M., Osborne M., Kutter C., et al. Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 2010, 16:991-1006.
16. Glazov E.A., Kongsuwan K., Assavalapsakul W., Horwood P.F., Mitter N., Mahony T.J. Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection. PLoS One 2009, 4:e6349.
17. Griffiths-Jones S. The microRNA Registry. Nucleic Acids Res. 2004, 32:D109-D111.
18. Griffiths-Jones S., Grocock R.J., van Dongen S., Bateman A., Enright A.J. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006, 34:D140-D144.
19. Guo Y., Chen Y., Zhang Y., Zhang Y., Chen L., Mo D. Up-regulated miR-145 expression inhibits porcine preadipocytes differentiation by targeting IRS1. Int. J. Biol. Sci. 2012, 8:1408-1417.
20. Hackl H., Burkard T.R., Sturn A., Rubio R., Schleiffer A., et al. Molecular processes during fat cell development revealed by gene expression profiling and functional annotation. Genome Biol. 2005, 6:R108.
21. He Z., Yu J., Zhou C., Ren G., Cong P., et al. MiR-143 is not essential for adipose development as revealed by in vivo antisense targeting. Biotechnol. Lett. 2013, 35:499-507.
22. Huang J., Ju Z., Li Q., Hou Q., Wang C., et al. Solexa sequencing of novel and differentially expressed microRNAs in testicular and ovarian tissues in Holstein cattle. Int. J. Biol. Sci. 2011, 7:1016-1026.
23. Ivanovska I., Cleary M.A. Combinatorial microRNAs: working together to make a difference. Cell Cycle 2008, 7:3137-3142.
24. Kennell J.A., MacDougald O.A. Wnt signaling inhibits adipogenesis through beta-catenin-dependent and -independent mechanisms. J. Biol. Chem. 2005, 280:24004-24010.
25. Kim V.N. MicroRNA biogenesis: coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 2005, 6:376-385.
26. Kim Y.J., Hwang S.J., Bae Y.C., Jung J.S. MiR-21 regulates adipogenic differentiation through the modulation of TGF-beta signaling in mesenchymal stem cells derived from human adipose tissue. Stem Cells 2009, 27:3093-3102.
27. Kloting N., Berthold S., Kovacs P., Schon M.R., Fasshauer M., et al. MicroRNA expression in human omental and subcutaneous adipose tissue. PLoS One 2009, 4:e4699.
28. Lai E.C., Tomancak P., Williams R.W., Rubin G.M. Computational identification of Drosophila microRNA genes. Genome Biol. 2003, 4:R42.
29. Lewis B.P., Shih I.H., Jones-Rhoades M.W., Bartel D.P., Burge C.B. Prediction of mammalian microRNA targets. Cell 2003, 115:787-798.
30. Lewis B.P., Burge C.B., Bartel D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20.
31. Li H.X., Luo X., Liu R.X., Yang Y.J., Yang G.S. Roles of Wnt/beta-catenin signaling in adipogenic differentiation potential of adipose-derived mesenchymal stem cells. Mol. Cell. Endocrinol. 2008, 291:116-124.
32. Li H., Zhang Z., Zhou X., Wang Z., Wang G., Han Z. Effects of microRNA-143 in the differentiation and proliferation of bovine intramuscular preadipocytes. Mol. Biol. Rep. 2011, 38:4273-4280.
33. Linsen S.E., de Wit E., Janssens G., Heater S., Chapman L., et al. Limitations and possibilities of small RNA digital gene expression profiling. Nat. Methods 2009, 6:474-476.
34. Livak K.J., Schmittgen T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25:402-408.
35. Luo X., Li H., Yang G. Sequential expression of Wnt/beta-catenin signal pathway related genes and adipocyte transcription factors during porcine adipose tissue development. Sheng Wu Gong Cheng Xue Bao 2008, 24:746-753.
36. Nakamura Y., Hinoi E., Iezaki T., Takada S., Hashizume S., et al. Repression of adipogenesis through promotion of Wnt/beta-catenin signaling by TIS7 up-regulated in adipocytes under hypoxia. Biochim. Biophys. Acta 2013, 1832:1117-1128.
37. Ng K.L.S., Mishra S.K. Unique folding of precursor microRNAs: quantitative evidence and implications for de novo identification. RNA 2007, 13:170-187.
38. Romao J.M., Jin W., He M., McAllister T., Guan L.L. Altered microRNA expression in bovine subcutaneous and visceral adipose tissues from cattle under different diet. PLoS One 2012, 7:e40605.
39. Ruby J.G., Jan C., Player C., Axtell M.J., Lee W., et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 2006, 127:1193-1207.
40. Sheng X., Song X., Yu Y., Niu L., Li S., et al. Characterization of microRNAs from sheep (Ovis aries) using computational and experimental analyses. Mol. Biol. Rep. 2011, 38:3161-3171.
41. Sun T., Fu M., Bookout A.L., Kliewer S.A., Mangelsdorf D.J. MicroRNA let-7 regulates 3T3-L1 adipogenesis. Mol. Endocrinol. 2009, 23:925-931.
42. Takanabe R., Ono K., Abe Y., Takaya T., Horie T., et al. Up-regulated expression of microRNA-143 in association with obesity in adipose tissue of mice fed high-fat diet. Biochem. Biophys. Res. Commun. 2008, 376:728-732.
43. Wang Y., Blelloch R. Cell cycle regulation by microRNAs in embryonic stem cells. Cancer Res. 2009, 69:4093-4096.
44. Wang Q., Li Y.C., Wang J., Kong J., Qi Y., et al. miR-17-92 cluster accelerates adipocyte differentiation by negatively regulating tumor-suppressor Rb2/p130. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:2889-2894.
45. Wang M., Wang J.J., Li J., Park K., Qian X., et al. Pigment epithelium-derived factor suppresses adipogenesis via inhibition of the MAPK/ERK pathway in 3T3-L1 preadipocytes. Am. J. Physiol. Endocrinol. Metab. 2009, 297:E1378-E1387.
46. Wang H., Zheng Y., Wang G., Li H. Identification of microRNA and bioinformatics target gene analysis in beef cattle intramuscular fat and subcutaneous fat. Mol. Biosyst. 2013, 9:2154-2162.
47. Weber M.J. New human and mouse microRNA genes found by homology search. FEBS J. 2005, 272:59-73.
48. Xie H., Lim B., Lodish H.F. MicroRNAs induced during adipogenesis that accelerate fat cell development are downregulated in obesity. Diabetes 2009, 58:1050-1057.
49. Xu P., Vernooy S.Y., Guo M., Hay B.A. The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism. Curr. Biol. 2003, 13:790-795.
50. Yang H., Zhang H., Zhu L., Zhang C., Li D. Identification and characterization of microRNAs in Macaca fascicularis by EST analysis. Comp. Funct. Genomics 2012, 2012:957607.
51. Zhang B., Pan X., Anderson T.A. Identification of 188 conserved maize microRNAs and their targets. FEBS Lett. 2006, 580:3753-3762.
52. Zhang B.H., Pan X.P., Cox S.B., Cobb G.P., Anderson T.A. Evidence that miRNAs are different from other RNAs. Cell. Mol. Life Sci. 2006, 63(2):246-254.
53. Zhang J., Zeng R., Chen J., Liu X., Liao Q. Identification of conserved microRNAs and their targets from Solanum lycopersicum Mill. Gene 2008, 423:1-7.
54. Zhou B., Liu H.L. Computational identification of new porcine microRNAs and their targets. Anim. Sci. J. 2010, 81:290-296.
55. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.