In silico genetic robustness analysis of secondary structural elements in the miRNA gene

Journal of Molecular Evolution

Volumn 67, Issue 5, 2008, Pages 560-569

  Shu, Wenjie ^a,b   Ni, Ming ^a   Bo, Xiaochen ^a   Zheng, Zhiqiang ^b   Wang, Shengqi ^a  

^a BEIJING INSTITUTE OF RADIATION MEDICINE   (China)

^b NATIONAL UNIVERSITY OF DEFENSE TECHNOLOGY   (China)

Author keywords

Evolution; Genetic robustness; MicroRNA; Secondary structural elements

Indexed keywords

MICRORNA;

ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; GENE EXPRESSION; GENE MUTATION; GENE STRUCTURE; GENETIC ANALYSIS; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; RNA STRUCTURE;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; HUMANS; MARKOV CHAINS; MICE; MICRORNAS; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; RATS;

EID: 55949087147     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-008-9174-5     Document Type: Article

References (64)

1. D Baker 2000 A surprising simplicity to protein folding Nature 405 39 42
2. DP Bartel 2004 MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 281 297
3. DP Bartel CZ Chen 2004 Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs Nat Rev Genet 5 396 400
4. I Bentwich A Avniel Y Karov R Aharonov S Gilad O Barad A Barzilai P Einat U Einav E Meiri E Sharon Y Spector Z Bentwich 2005 Identification of hundreds of conserved and nonconserved human microRNAs Nat Genet 37 766 770
5. E Berezikov V Guryev BJ van de E Wienholds RH Plasterk E Cuppen 2005 Phylogenetic shadowing and computational identification of human microRNA genes Cell 120 21 24
6. E Berezikov E Cuppen RH Plasterk 2006 Approaches to microRNA discovery Nat Genet 38 Suppl S2 S7
7. D Boffelli J McAuliffe D Ovcharenko KD Lewis I Ovcharenko L Pachter EM Rubin 2003 Phylogenetic shadowing of primate sequences to find functional regions of the human genome Science 299 1391 1394
8. E Bonnet J Wuyts P Rouze PY Van de 2004 Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences Bioinformatics 20 2911 2917
9. E Borenstein E Ruppin 2006 Direct evolution of genetic robustness in microRNA Proc Natl Acad Sci USA 103 6593 6598
10. J Brennecke A Stark RB Russell SM Cohen 2005 Principles of microRNA-target recognition PLoS Biol 3 e85
11. P Clote F Ferre E Kranakis D Krizanc 2005 Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency RNA 11 578 591
12. JA de Visser J Hermisson GP Wagner ML Ancel H Bagheri-Chaichian JL Blanchard L Chao JM Cheverud SF Elena W Fontana G Gibson TF Hansen D Krakauer RC Lewontin C Ofria SH Rice G von Dassow A Wagner MC Whitlock 2003 Perspective: evolution and detection of genetic robustness Evol Int J Org Evol 57 1959 1972
13. SF Elena RE Lenski 2001 Epistasis between new mutations and genetic background and a test of genetic canalization Evol Int J Org Evol 55 1746 1752
14. SF Elena P Carrasco JA Daros R Sanjuan 2006 Mechanisms of genetic robustness in RNA viruses EMBO Rep 7 168 173
15. AD Ellington JW Szostak 1990 In vitro selection of RNA molecules that bind specific ligands Nature 346 818 822
16. MA Fares MX Ruiz-Gonzalez A Moya SF Elena E Barrio 2002 Endosymbiotic bacteria: groEL buffers against deleterious mutations Nature 417 398
17. KK Farh 2005 The widespread impact of mammalian microRNAs on mRNA repression and evolution Science 310 1817 1821
18. RA Fisher 1928 The possible modifications of the response of the wild type to recurrent mutations Am Nat 62 115 116
19. RA Fisher 1928 Two further notes on the origin of dominance Am Nat 62 571 574
20. RA Fisher 1931 The evolution of dominance Biol Rev 6 345 368
21. G Gibson G Wagner 2000 Canalization in evolutionary genetics: a stabilizing theory? Bioessays 22 372 380
22. S Griffiths-Jones 2004 The microRNA Registry Nucleic Acids Res 32 D109 D111
23. S Griffiths-Jones RJ Grocock S van Dongen A Bateman AJ Enright 2006 miRBase: microRNA sequences, targets and gene nomenclature Nucleic Acids Res 34 D140 D144
24. D Grun YL Wang D Langenberger KC Gunsalus N Rajewsky 2005 microRNA target predictions across seven Drosophila species and comparison to mammalian targets PLoS Comput Biol 1 e13
25. Hermisson J, Wagner GP (2004) Evolution of phenotypic robustness. In: Jen E (ed) Robust design: a repertoire from biology, ecology, and engineering. Oxford University Press, New York, pp 47-70
26. IL Hofacker W Fontana PF Stadler LS Bonhoeffer M Tacker P Schuster 1994 Fast folding and comparison of RNA secondary structures Monatsh Chem [Chem Month] 125 167 188
27. E Hornstein N Shomron 2006 Canalization of development by microRNAs Nat Genet 38 Suppl S20 S24
28. G Hutvagner J McLachlan AE Pasquinelli E Balint T Tuschl PD Zamore 2001 A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA Science 293 834 838
29. K Kaneko 2007 Evolution of robustness to noise and mutation in gene expression dynamics PLoS ONE 2 e434
30. L Katz CB Burge 2003 Widespread selection for local RNA secondary structure in coding regions of bacterial genes Genome Res 13 2042 2051
31. RF Ketting SE Fischer E Bernstein T Sijen GJ Hannon RH Plasterk 2001 Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans Genes Dev 15 2654 2659
32. VN Kim JW Nam 2006 Genomics of microRNA Trends Genet 22 165 173
33. H Kitano 2004 Biological robustness Nat Rev Genet 5 826 837
34. M Lagos-Quintana R Rauhut W Lendeckel T Tuschl 2001 Identification of novel genes coding for small expressed RNAs Science 294 853 858
35. NC Lau LP Lim EG Weinstein DP Bartel 2001 An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans Science 294 858 862
36. RC Lee V Ambros 2001 An extensive class of small RNAs in Caenorhabditis elegans Science 294 862 864
37. RC Lee RL Feinbaum V Ambros 1993 The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 Cell 75 843 854
38. Y Lee C Ahn J Han H Choi J Kim J Yim J Lee P Provost O Radmark S Kim VN Kim 2003 The nuclear RNase III Drosha initiates microRNA processing Nature 425 415 419
39. BP Lewis CB Burge DP Bartel 2005 Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets Cell 120 15 20
40. LP Lim ME Glasner S Yekta CB Burge DP Bartel 2003 Vertebrate microRNA genes Science 299 1540
41. LP Lim NC Lau EG Weinstein A Abdelhakim S Yekta MW Rhoades CB Burge DP Bartel 2003 The microRNAs of Caenorhabditis elegans Genes Dev 17 991 1008
42. E Lund S Guttinger A Calado JE Dahlberg U Kutay 2004 Nuclear export of microRNA precursors Science 303 95 98
43. CD Meiklejohn DL Hartl 2002 A single mode of canalization Trends Ecol Evol 17 468 473
44. R Montville R Froissart SK Remold O Tenaillon PE Turner 2005 Evolution of mutational robustness in an RNA virus PLoS Biol 3 e381
45. KC Pang MC Frith JS Mattick 2006 Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function Trends Genet 22 1 5
46. S Pfeffer A Sewer M Lagos-Quintana R Sheridan C Sander FA Grasser LF van Dyk CK Ho S Shuman M Chien JJ Russo J Ju G Randall BD Lindenbach CM Rice V Simon DD Ho M Zavolan T Tuschl 2005 Identification of microRNAs of the herpesvirus family Nat Methods 2 269 276
47. R Sanjuan J Forment SF Elena 2006 In silico predicted robustness of viroids RNA secondary structures. I. The effect of single mutations Mol Biol Evol 23 1427 1436
48. R Sanjuan J Forment SF Elena 2006 In silico predicted robustness of viroids RNA secondary structures. II. Interaction between mutation pairs Mol Biol Evol 23 2123 2130
49. W Scharloo 1991 Canalization: genetic and developmental aspects Annu Rev Ecol Syst 22 65 93
50. W Shu X Bo M Ni Z Zheng S Wang 2007 In silico genetic robustness analysis of microRNA secondary structures: potential evidence of congruent evolution in microRNA BMC Evol Biol 7 223
51. W Shu X Bo Z Zheng S Wang 2007 RSRE: RNA structural robustness evaluator Nucleic Acids Res 35 W314 W319
52. A Stark J Brennecke N Bushati RB Russell SM Cohen 2005 Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution Cell 123 1133 1146
53. C Tuerk L Gold 1990 Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science 249 505 510
54. CH Waddington 1953 The genetic assimilation of an acquired charcter Evolution 7 118 126
55. Waddington CH (1957) The strategy of the genes. Macmillan, New York
56. Wagner A (2005) Robustness and evolvability in living systems. Princeton studies in complexity. Princeton University Press, Princeton, NJ
57. A Wagner PF Stadler 1999 Viral RNA and evolved mutational robustness J Exp Zool 285 119 127
58. GP Wagner G Booth H Bagheri-Chaichian 1997 A population genetic theory of canalization Evolution 51 329 347
59. C Workman A Krogh 1999 No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution Nucleic Acids Res 27 4816 4822
60. X Xie 2005 Systematic discovery of regulatory motifs in human promoters and 3′UTRs by comparison of several mammals Nature 434 338 345
61. Y Zeng BR Cullen 2003 Sequence requirements for micro RNA processing and function in human cells RNA 9 112 123
62. Y Zeng BR Cullen 2004 Structural requirements for pre-microRNA binding and nuclear export by Exportin 5 Nucleic Acids Res 32 4776 4785
63. Y Zeng R Yi BR Cullen 2003 MicroRNAs and small interfering RNAs can inhibit mRNA expression by similar mechanisms Proc Natl Acad Sci USA 100 9779 9784
64. M Zuker P Stiegler 1981 Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information Nucleic Acids Res 9 133 148