Comparative genomic analysis reveals evolutionary characteristics and patterns of microRNA clusters in vertebrates

Gene

Volumn 512, Issue 2, 2013, Pages 383-391

  Sun, Jie ^a   Gao, Bo ^a   Zhou, Meng ^a   Wang, Zhen zhen ^a   Zhang, Fan ^a   Deng, Jia en ^a   Li, Xia ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

Comparative genomics; Evolution; Genomic duplication events; MiRNA clusters; Vertebrates

Indexed keywords

MICRORNA;

ARTICLE; EVOLUTIONARY HOMOLOGY; GENE; GENE CLUSTER; GENE CONSTRUCT; GENE DUPLICATION; GENOME ANALYSIS; HUMAN; MOLECULAR DYNAMICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; VERTEBRATE;

ANIMALS; EVOLUTION, MOLECULAR; GENOME, HUMAN; GENOMICS; HUMANS; MICRORNAS; MULTIGENE FAMILY; SEQUENCE ANALYSIS, RNA;

ANIMALIA; VERTEBRATA;

EID: 84870364819     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.09.102     Document Type: Article

References (44)

1. Altuvia Y., et al. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res. 2005, 33:2697-2706.
2. Baev V., Daskalova E., Minkov I. Computational identification of novel microRNA homologs in the chimpanzee genome. Comput. Biol. Chem. 2009, 33:62-70.
3. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
4. Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233.
5. Baskerville S., Bartel D.P. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA 2005, 11:241-247.
6. Brameier M. Genome-wide comparative analysis of microRNA in three non-human primates. BMC Res. Notes 2010, 3:64.
7. Carthew R.W., Sontheimer E.J. Origins and mechanisms of miRNAs and siRNAs. Cell 2009, 136:642-655.
8. Chhabra R., Dubey R., Saini N. Cooperative and individualistic functions of the microRNAs in the miR-23a 27a 24-2 cluster and its implication in human diseases. Mol. Cancer 2010, 9:232.
9. Cullen B.R. Transcription and processing of human microRNA precursors. Mol. Cell 2004, 16:861-865.
10. Glazov E.A., McWilliam S., Barris W.C., Dalrymple B.P. Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals. Mol. Biol. Evol. 2008, 25:939-948.
11. Griffiths-Jones S., Saini H.K., van Dongen S., Enright A.J. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008, 36:D154-D158.
12. Grimson A., et al. Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 2008, 455:1193-1197.
13. He P.A., et al. Identification and characteristics of microRNAs from Bombyx mori. BMC Genomics 2008, 9:248.
14. Heimberg A.M., Sempere L.F., Moy V.N., Donoghue P.C., Peterson K.J. MicroRNAs and the advent of vertebrate morphological complexity. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:2946-2950.
15. Hertel J., et al. The expansion of the metazoan microRNA repertoire. BMC Genomics 2006, 7:25.
16. Kaczkowski B., Torarinsson E., Reiche K., Havgaard J.H., Stadler P.F., Gorodkin J. Structural profiles of human miRNA families from pairwise clustering. Bioinformatics 2009, 25:291-294.
17. Lagos-Quintana M., Rauhut R., Meyer J., Borkhardt A., Tuschl T. New microRNAs from mouse and human. RNA 2003, 9:175-179.
18. Li J., Liu Y., Dong D., Zhang Z. Evolution of an X-linked primate-specific micro RNA cluster. Mol. Biol. Evol. 2010, 27:671-683.
19. Lu M., et al. An analysis of human microRNA and disease associations. PLoS One 2008, 3:e3420.
20. Mendes N.D., Freitas A.T., Sagot M.F. Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res. 2009, 37:2419-2433.
21. Mu P., et al. Genetic dissection of the miR-17 92 cluster of microRNAs in Myc-induced B-cell lymphomas. Genes Dev. 2009, 23:2806-2811.
22. Niwa R., Slack F.J. The evolution of animal microRNA function. Curr. Opin. Genet. Dev. 2007, 17:145-150.
23. Nozawa M., Miura S., Nei M. Origins and evolution of microRNA genes in Drosophila species. Genome Biol. Evol. 2010, 2:180-189.
24. Prochnik S.E., Rokhsar D.S., Aboobaker A.A. Evidence for a microRNA expansion in the bilaterian ancestor. Dev. Genes Evol. 2007, 217:73-77.
25. Retief J.D. Phylogenetic analysis using PHYLIP. Methods Mol. Biol. 2000, 132:243-258.
26. Ruepp A., et al. PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes. Genome Biol. 2010, 11:R6.
27. Sempere L.F., Cole C.N., McPeek M.A., Peterson K.J. The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint. J. Exp. Zool. B Mol. Dev. Evol. 2006, 306:575-588.
28. Shabalina S.A., Koonin E.V. Origins and evolution of eukaryotic RNA interference. Trends Ecol. Evol. 2008, 23:578-587.
29. Streicher K.L., et al. A novel oncogenic role for the miRNA-506-514 cluster in initiating melanocyte transformation and promoting melanoma growth. Oncogene 2012, 31:1558-1570.
30. Sun Z., Wei Q., Zhang Y., He X., Ji W., Su B. MicroRNA profiling of rhesus macaque embryonic stem cells. BMC Genomics 2011, 12:276.
31. Sun J., Liu H.P., Deng J.E., Zhou M. Systematic analysis of genomic organization and heterogeneities of miRNA cluster in vertebrates. Mol. Biol. Rep. 2012, 39:5143-5149.
32. Tanzer A., Stadler P.F. Molecular evolution of a microRNA cluster. J. Mol. Biol. 2004, 339:327-335.
33. Wang J., et al. Regulatory coordination of clustered microRNAs based on microRNA-transcription factor regulatory network. BMC Syst. Biol. 2011, 5:199.
34. Wang Q.H., et al. Systematic analysis of human microRNA divergence based on evolutionary emergence. FEBS Lett. 2011, 585:240-248.
35. Wheeler B.M., et al. The deep evolution of metazoan microRNAs. Evol. Dev. 2009, 11:50-68.
36. Yosef N., Kupiec M., Ruppin E., Sharan R. A complex-centric view of protein network evolution. Nucleic Acids Res. 2009, 37:e88.
37. Yu J., et al. Human microRNA clusters: genomic organization and expression profile in leukemia cell lines. Biochem. Biophys. Res. Commun. 2006, 349:59-68.
38. Yuan X., et al. Clustered microRNAs' coordination in regulating protein-protein interaction network. BMC Syst. Biol. 2009, 3:65.
39. Yuan Z., Sun X., Liu H., Xie J. MicroRNA genes derived from repetitive elements and expanded by segmental duplication events in mammalian genomes. PLoS One 2011, 6:e17666.
40. Yue J., Sheng Y., Orwig K.E. Identification of novel homologous microRNA genes in the rhesus macaque genome. BMC Genomics 2008, 9:8.
41. Zhang R., Peng Y., Wang W., Su B. Rapid evolution of an X-linked microRNA cluster in primates. Genome Res. 2007, 17:612-617.
42. Zhang L., et al. A genome-wide characterization of microRNA genes in maize. PLoS Genet. 2009, 5:e1000716.
43. Zhang Y., Zhang R., Su B. Diversity and evolution of MicroRNA gene clusters. Sci. China C Life Sci. 2009, 52:261-266.
44. Zhou M., et al. In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and comparative genomic approach. Genomics 2009, 94:125-131.