Systematic analysis of human microRNA divergence based on evolutionary emergence

FEBS Letters

Volumn 585, Issue 1, 2011, Pages 240-248

  Li, Xia ^a   Wang, Qiang Hu ^a   Zhou, Meng ^a   Sun, Jie ^a   Ning, Shang Wei ^a   Li, Yan ^a   Chen, Li ^a   Zheng, Yan ^a   Li, Xiang ^a   Lv, Sa Li ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

Divergence; Evolutionary emergence; microRNAs

Indexed keywords

MICRORNA;

ARTICLE; GENETIC VARIABILITY; HUMAN GENETICS; MAMMAL; MOLECULAR EVOLUTION; PHYLOGENY; PRIMATE; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE HOMOLOGY; SYSTEMATIC REVIEW; VERTEBRATE;

ANIMALS; BASE COMPOSITION; CHROMOSOME MAPPING; DATABASES, GENETIC; EVOLUTION, MOLECULAR; GENETIC PREDISPOSITION TO DISEASE; GENETIC VARIATION; GENOME, HUMAN; HUMANS; MICRORNAS; TIME FACTORS;

MAMMALIA; PRIMATES; VERTEBRATA;

EID: 78650860741     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2010.11.053     Document Type: Article

References (46)

1. Y. Zhao, and D. Srivastava A developmental view of microRNA function Trends Biochem. Sci. 32 2007 189 197
2. R. Niwa, and F.J. Slack The evolution of animal microRNA function Curr. Opin. Genet. Dev. 17 2007 145 150
3. M.J. Axtell, and D.P. Bartel Antiquity of microRNAs and their targets in land plants Plant Cell 17 2005 1658 1673
4. B.H. Zhang, X.P. Pan, Q.L. Wang, G.P. Cobb, and T.A. Anderson Identification and characterization of new plant microRNAs using EST analysis Cell Res. 15 2005 336 360
5. J. Hertel, M. Lindemeyer, K. Missal, C. Fried, A. Tanzer, C. Flamm, I.L. Hofacker, and P.F. Stadler The expansion of the metazoan microRNA repertoire BMC Genomics 7 2006 25
6. L.F. Sempere, C.N. Cole, M.A. McPeek, and K.J. Peterson The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint J. Exp. Zool. B: Mol. Dev. Evol. 306 2006 575 588
7. B. Zhang, X. Pan, C.H. Cannon, G.P. Cobb, and T.A. Anderson Conservation and divergence of plant microRNA genes Plant J. 46 2006 243 259
8. A.M. Heimberg, L.F. Sempere, V.N. Moy, P.C. Donoghue, and K.J. Peterson MicroRNAs and the advent of vertebrate morphological complexity Proc. Natl. Acad. Sci. USA 105 2008 2946 2950
9. N. Liu, K. Okamura, D.M. Tyler, M.D. Phillips, W.J. Chung, and E.C. Lai The evolution and functional diversification of animal microRNA genes Cell Res. 18 2008 985 996
10. J. Lu The birth and death of microRNA genes in Drosophila Nat. Genet. 40 2008 351 355
11. M. Nozawa, S. Miura, and M. Nei Origins and evolution of microRNA genes in Drosophila species Genome Biol. Evol. 2010 180 189
12. A.M. Heimberg, R. Cowper-Sal Lari, M. Semon, P.C. Donoghue, and K.J. Peterson From the Cover: microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate Proc. Natl. Acad. Sci. USA 107 2010 19379 19383
13. R. Zhang, Y.Q. Wang, and B. Su Molecular evolution of a primate-specific microRNA family Mol. Biol. Evol. 25 2008 1493 1502
14. A. Tanzer, and P.F. Stadler Molecular evolution of a microRNA cluster J. Mol. Biol. 339 2004 327 335
15. C. Ibanez-Ventoso, M. Vora, and M. Driscoll Sequence relationships among C. elegans, D. melanogaster and human microRNAs highlight the extensive conservation of microRNAs in biology PLoS One 3 2008 e2818
16. H. Liang, and W.H. Li Lowly expressed human microRNA genes evolve rapidly Mol. Biol. Evol. 26 2009 1195 1198
17. S. Griffiths-Jones, H.K. Saini, S. van Dongen, and A.J. Enright MiRBase: tools for microRNA genomics Nucleic Acids Res. 36 2008 D154 D158
18. M. Megraw, P. Sethupathy, B. Corda, and A.G. Hatzigeorgiou MiRGen: a database for the study of animal microRNA genomic organization and function Nucleic Acids Res. 35 2007 D149 D155
19. S.D. Hsu MiRNAMap 2.0: genomic maps of microRNAs in metazoan genomes Nucleic Acids Res. 36 2008 D165 D169
20. P. Sethupathy, M. Megraw, and A.G. Hatzigeorgiou A guide through present computational approaches for the identification of mammalian microRNA targets Nat. Meth. 3 2006 881 886
21. Brameier, M. (2010) Genome-wide comparative analysis of microRNAs in three non-human primates. BMC Res. Notes 3, 64.
22. B.M. Wheeler, A.M. Heimberg, V.N. Moy, E.A. Sperling, T.W. Holstein, S. Heber, and K.J. Peterson The deep evolution of metazoan microRNAs Evol. Dev. 11 2009 50 68
23. B. Rhead The UCSC Genome Browser database: update 2010 Nucleic Acids Res 38 2010 D613 D619
24. Q. Jiang MiR2Disease: a manually curated database for microRNA deregulation in human disease Nucleic Acids Res. 37 2009 D98 D104
25. T.S. Keshava Prasad Human Protein Reference Database - 2009 update Nucleic Acids Res. 37 2009 D767 D772
26. A. Grimson Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals Nature 455 2008 1193 1197
27. S.E. Prochnik, D.S. Rokhsar, and A.A. Aboobaker Evidence for a microRNA expansion in the bilaterian ancestor Dev. Genes Evol. 217 2007 73 77
28. I. Bentwich Identification of hundreds of conserved and nonconserved human microRNAs Nat. Genet. 37 2005 766 770
29. E. Berezikov, V. Guryev, J. van de Belt, E. Wienholds, R.H. Plasterk, and E. Cuppen Phylogenetic shadowing and computational identification of human microRNA genes Cell 120 2005 21 24
30. B. Zhang, X. Pan, and E.J. Stellwag Identification of soybean microRNAs and their targets Planta 229 2008 161 182
31. M. Zhou In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and comparative genomic approach Genomics 94 2009 125 131
32. B.H. Zhang, X.P. Pan, S.B. Cox, G.P. Cobb, and T.A. Anderson Evidence that miRNAs are different from other RNAs Cell Mol. Life Sci. 63 2006 246 254
33. P.A. He Identification and characteristics of microRNAs from Bombyx mori BMC Genomics 9 2008 248
34. J. Yue, Y. Sheng, and K.E. Orwig Identification of novel homologous microRNA genes in the rhesus macaque genome BMC Genomics 9 2008 8
35. G.A. Calin, and C.M. Croce MicroRNAs and chromosomal abnormalities in cancer cells Oncogene 25 2006 6202 6210
36. G.A. Calin Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers Proc. Natl. Acad. Sci. USA 101 2004 2999 3004
37. X. Guo, B. Su, Z. Zhou, and J. Sha Rapid evolution of mammalian X-linked testis microRNAs BMC Genomics 10 2009 97
38. H. Cao, C.S. Yang, and T.M. Rana Evolutionary emergence of microRNAs in human embryonic stem cells PLoS One 3 2008 e2820
39. A. Rodriguez, S. Griffiths-Jones, J.L. Ashurst, and A. Bradley Identification of mammalian microRNA host genes and transcription units Genome Res. 14 2004 1902 1910
40. S. Baskerville, and D.P. Bartel Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes RNA 11 2005 241 247
41. S.C. Janga, J. Collado-Vides, and M.M. Babu Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes Proc. Natl. Acad. Sci. USA 105 2008 15761 15766
42. N. Fahlgren High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes PLoS One 2 2007 e219
43. I.K. Jordan, L. Marino-Ramirez, Y.I. Wolf, and E.V. Koonin Conservation and coevolution in the scale-free human gene coexpression network Mol. Biol. Evol. 21 2004 2058 2070
44. M. Lu, Q. Zhang, M. Deng, J. Miao, Y. Guo, W. Gao, and Q. Cui An analysis of human microRNA and disease associations PLoS One 3 2008 e3420
45. C.W. Hsu, H.F. Juan, and H.C. Huang Characterization of microRNA-regulated protein-protein interaction network Proteomics 8 2008 1975 1979
46. H. Liang, and W.H. Li MicroRNA regulation of human protein protein interaction network RNA 13 2007 1402 1408