Diversity and evolution of MicroRNA gene clusters

Science in China, Series C: Life Sciences

Volumn 52, Issue 3, 2009, Pages 261-266

  Zhang, YanFeng ^a   Zhang, Rui ^a   Su, Bing ^a  

^a KUNMING INSTITUTE OF ZOOLOGY   (China)

Author keywords

Adaptive evolution; Gene duplication; MicroRNA gene clusters; Transposition

Indexed keywords

MICRORNA;

BIOLOGICAL MODEL; GENETICS; MOLECULAR EVOLUTION; MULTIGENE FAMILY; REVIEW;

EVOLUTION, MOLECULAR; MICRORNAS; MODELS, GENETIC; MULTIGENE FAMILY;

ANIMALIA;

EID: 63049110327     PISSN: 10069305     EISSN: 18622798     Source Type: Journal    
DOI: 10.1007/s11427-009-0032-5     Document Type: Review

References (54)

1. C. Dennis 2002 The brave new world of RNA Nature 418 122 124
2. Y. Lee Y. Lee M. Kim 2004 MicroRNA genes are transcribed by RNA polymerase II EMBO 23 4051 4060
3. G. M. Borchert W. Lanier B. L. Davidson 2006 RNA polymerase III transcribes human microRNAs Nat Struct Mol Biol 13 1097 1101
4. D. P. Bartel 2004 MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 281 297
5. J. Han Y. Lee K. H. Yeom 2006 Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex Cell 125 887 901
6. M. T. Bohnsack K. Czaplinski D. Gorlich 2004 Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs RNA 10 185 191
7. J. Brennecke A. Stark R. B. Russell 2005 Principles of microRNA-target recognition PLoS Biol 3 3 e85
8. E. C. Lai 2002 Micro RNAs are complementary to 3′ UTR sequence motifs that mediate negative post-transcriptional regulation Nat Genet 30 363 364
9. M. Selbach B. Schwanhausser N. Thierfelder 2008 Widespread changes in protein synthesis induced by microRNAs Nature 455 7209 58 63
10. A. Krek D. Grun M. N. Poy 2005 Combinatorial microRNA target predictions Nat Genet 37 495 500
11. B. J. Reinhart F. J. Slack M. Basson 2000 The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans Nature 403 901 906
12. R. C. Lee R. L. Feinbaum V. Ambros 1993 The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 Cell 75 843 854
13. N. Felli L. Fontana E. Pelosi 2005 MicroRNAs 221 and 222 inhibit normal erythropoiesis and erythroleukemic cell growth via kit receptor down-modulation Proc Natl Acad Sci USA 102 18081 18086
14. V. Ambros 2004 The functions of animal microRNAs Nature 431 350 355
15. + T lymphocytes Nat Med 13 1241 1247
16. R. E. Van L. B. Sutherland X. Qi 2007 Control of stress-dependent cardiac growth and gene expression by a microRNA Science 316 575 579
17. A. Esquela-Kerscher F. J. Slack 2006 Oncomirs - microRNAs with a role in cancer Nat Rev Cancer 6 259 269
18. T. C. Chang J. T. Mendell 2007 microRNAs in vertebrate physiology and human disease Annu Rev Genom Human Genet 8 215 239
19. S. S. Hébert B. De Strooper 2007 miRNAs in neurodegeneration Science 31317 1179 1180
20. B. Yang H. Lin J. Xiao 2007 The muscle-specific microRNA miR-1 regulates cardiac arrhythmogenic potential by targeting GJA1 and KCNJ2 Nat Med 13 486 491
21. M. Lagos-Quintana R. Rauhut J. Meyer 2003 New microRNAs from mouse and human RNA 9 175 179
22. E. C. Lai P. Tomancak R. W. Williams 2003 Computational identification of Drosophila microRNA genes Genome Biol 4 R42
23. Lewin B. Genes VIII. New Jersey: Pearson Education Inc, 2004
24. Y. Altuvia P. Landgraf G. Lithwick 2005 Clustering and conservation patterns of human microRNAs Nucleic Acids Res 33 2697 2706
25. M. Megraw P. Sethupathy B. Corda 2007 miRGen: A database for the study of animal microRNA genomic organization and function Nucleic Acids Res 35 D149 D155
26. G. Q. Tang E. S. Maxwell 2008 Xenopus microRNA genes are predominantly located within introns and are differentially expressed in adult frog tissues via post-transcriptional regulation Genome Res 18 104 112
27. J. T. Mendell 2008 miRiad roles for the miR-17-92 cluster in development and disease Cell 133 217 222
28. N. Lau L. Lim E. Weinstein 2001 An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans Science 294 858 862
29. A. Pasquinelli B. Reinhart F. Slack 2000 Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA Nature 408 86 89
30. B. John A. J. Enright A. Aravin 2004 Human MicroRNA targets PLoS Biol 2 11 e363
31. M. N. Poy L. Eliasson J. Krutzfeldt 2004 A pancreatic islet-specific microRNA regulates insulin secretion Nature 432 226 230
32. B. R. Cullen 2004 Transcription and processing of human microRNA precursors Mol Cell 16 861 865
33. S. Baskerville D. P. Bartel 2005 Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes RNA 11 241 247
34. J. Lu Y. Fu S. Kumar 2008 Adaptive evolution of newly emerged microRNA genes in Drosophila Mol Biol Evol 25 929 938
35. J. Yu F. Wang G. H. Yang 2006 Human microRNA clusters: Genomic organization and expression profile in leukemia cell lines Biochem Biophys Res Commun 349 59 68
36. J. Z. Xu C. W. Wong 2008 A computational screen for mouse signaling pathways targeted by microRNA clusters RNA 14 1276 1283
37. Q. Liu H. Fu F. Sun 2008 miR-16 family induces cell cycle arrest by regulating multiple cell cycle genes Nucleic Acids Res 36 5391 5404
38. F. Friggi-Grelin L. Lavenant-Staccini P. Therond 2008 Control of antagonistic components of the hedgehog signaling pathway by microRNAs in Drosophila Genetics 179 429 439
39. D. Leaman P. Y. Chen J. Fak 2005 Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development Cell 121 1097 1108
40. U. Ohler S. Yekta L. P. Lim 2004 Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification RNA 10 1309 1322
41. E. Berezikov V. Guryev J. van de Belt 2005 Phylogenetic shadowing and computational identification of human microRNA genes Cell 120 21 24
42. X. Li S. Yang L. X. Peng 2004 Origin and evolution of new genes Chinese Science Bulletin 49 13 1219 1225
43. R. Zhang Y. Peng W. Wang 2007 Rapid evolution of an X-linked microRNA cluster in primates Genome Res 17 612 617
44. Su B, Zhang R. MicroRNA evolution in the human genome. Encyclopedia of Life Sciences, 2008, DOI: 10.1002/9780470015902. a0020788
45. A. Tanzer P. F. Stadler 2004 Molecular evolution of a microRNA cluster Mol Biol 339 327 335
46. J. Hertel M. Lindemeyer K. Missal 2006 The expansion of the metazoan microRNA repertoire BMC Genomics 7 25
47. A. Li L. Mao 2006 Evolution of plant microRNA gene families Cell Res 17 212 218
48. C. Maher L. Stein D. Ware 2006 Evolution of Arabidopsis microRNA families through duplication events Genome Res 16 510 519
49. J. Piriyapongsa L. Marino-Ramirez I. K. Jordan 2007 Origin and evolution of human microRNAs from transposable elements Genetics 176 1323 1337
50. R. Zhang Y. Q. Wang B. Su 2008 Molecular evolution of a primate-specific microRNA family Mol Biol Evol 25 1493 1502
51. J. Lu Y. Shen Q. Wu 2008 The birth and death of microRNA genes in Drosophila Nat Genet 40 351 355
52. E. Richly D. Leister 2004 NUMTs in sequenced eukaryotic genomes Mol Biol Evol 21 1081 1084
53. M. J. Lercher C. Pál 2008 Integration of horizontally transferred genes into regulatory interaction networks takes many million years Mol Biol Evol 25 559 567
54. D. P. Bartel C. Z. Chen 2004 Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs Nat Rev Genet 5 396 400