Large-scale analysis of microRNA evolution

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Guerra Assunção, José A ^a,b   Enright, Anton J ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ANIMAL GENETICS; ARTICLE; BIRTH; CONTROLLED STUDY; DEATH; GENETIC ASSOCIATION; GENOMICS; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; RNA ANALYSIS; SPECIES DIFFERENTIATION; SYNTENY;

ANIMALS; BIOLOGICAL EVOLUTION; DATABASES, GENETIC; MICRORNAS; PHYLOGENY; SPECIES SPECIFICITY;

ANIMALIA; BILATERIA;

EID: 84861815513     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-218     Document Type: Article

References (53)

1. Kim VN. MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 2005, 6:376-385.
2. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM. Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 2005, 433:769-773. 10.1038/nature03315, 15685193.
3. Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 2010, 466:835-840. 10.1038/nature09267, 2990499, 20703300.
4. Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, Enright AJ, Schier AF. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 2006, 312:75-79. 10.1126/science.1122689, 16484454.
5. Baek D, Villén J, Shin C, Camargo FD, Gygi SP, Bartel DP. The impact of microRNAs on protein output. Nature 2008, 455:64-71. 10.1038/nature07242, 2745094, 18668037.
6. Van Dongen S, Abreu-Goodger C, Enright AJ. Detecting microRNA binding and siRNA off-target effects from expression data. Nat Methods 2008, 5:1023-1025. 10.1038/nmeth.1267, 2635553, 18978784.
7. Kosik KS. MicroRNAs and cellular phenotypy. Cell 2010, 143:21-26. 10.1016/j.cell.2010.09.008, 20887887.
8. Shabalina SA, Koonin EV. Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol (Amst) 2008, 23:578-587.
9. Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell 2009, 136:669-687. 10.1016/j.cell.2009.01.046, 19239888.
10. Heimberg A, Sempere L, Moy V, Donoghue P, Peterson K. MicroRNAs and the advent of vertebrate morphological complexity. Proceedings of the National Academy of Sciences 2008, 105:2946-2950.
11. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Müller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 2000, 408:86-89. 10.1038/35040556, 11081512.
12. Krol J, Loedige I, Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 2010, 11:597-610.
13. Griffiths-Jones S, Saini HK, Van Dongen S, Enright AJ. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008, 36:D154-8. 10.1093/nar/gkn221, 2238936, 17991681.
14. Lewis BP, Burge CB, Bartel DP. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 2005, 120:15-20. 10.1016/j.cell.2004.12.035, 15652477.
15. Guerra-Assunção JA, Enright AJ. MapMi: automated mapping of microRNA loci. BMC Bioinformatics 2010, 11:133. 10.1186/1471-2105-11-133, 2858034, 20233390.
16. Olena AF, Patton JG. Genomic organization of microRNAs. Journal of cellular physiology 2009, 222:540-545.
17. van Rooij E, Quiat D, Johnson BA, Sutherland LB, Qi X, Richardson JA, Kelm RJ, Olson EN. A family of microRNAs encoded by myosin genes governs myosin expression and muscle performance. Dev Cell 2009, 17:662-673. 10.1016/j.devcel.2009.10.013, 2796371, 19922871.
18. Rayner KJ, Esau CC, Hussain FN, McDaniel AL, Marshall SM, van Gils JM, Ray TD, Sheedy FJ, Goedeke L, Liu X, Khatsenko OG, Kaimal V, Lees CJ, Fernández-Hernando C, Fisher EA, Temel RE, Moore KJ. Inhibition of miR-33a/b in non-human primates raises plasma HDL and lowers VLDL triglycerides. Nature 2011, 478:404-407. 10.1038/nature10486, 3235584, 22012398.
19. Pellegrini M, Marcotte E, Thompson M, Eisenberg D, Yeates T. Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc Natl Acad Sci USA 1999, 96:4285-4288. 10.1073/pnas.96.8.4285, 16324, 10200254.
20. Farris J. Phylogenetic analysis under Dollo's Law. Syst Biol 1977, 26:77-88.
21. Milinkovitch M, Helaers R, Depiereux E, Tzika A, Gabaldon T. 2X genomes - depth does matter. Genome Biol 2010, 11:R16. 10.1186/gb-2010-11-2-r16, 2872876, 20144222.
22. Vilella AJ, Birney E, Flicek P, Herrero J. Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses. Genome Biol 2011, 12:401. 3188792, 21320298.
23. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GRS, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJP, Parker A, Proctor G, Vogel J, Searle SMJ. Ensembl 2011. Nucleic Acids Res 2011, 39:D800-6. 10.1093/nar/gkq1064, 3013672, 21045057.
24. Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kähäri A, Kinsella RJ, Kulesha E, Maheswari U, Megy K, Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A. Ensembl Genomes: Extending Ensembl across the taxonomic space. Nucleic Acids Res 2009, 38:D563-D569. 2808935, 19884133.
25. Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A, Flamm C, Hofacker IL, Stadler PF. Students of Bioinformatics Computer Labs 2004 and 2005: The expansion of the metazoan microRNA repertoire. BMC Genomics 2006, 7:25. 10.1186/1471-2164-7-25, 1388199, 16480513.
26. De Bie T, Cristianini N, Demuth JP, Hahn MW. CAFE: a computational tool for the study of gene family evolution. Bioinformatics 2006, 22:1269-1271. 10.1093/bioinformatics/btl097, 16543274.
27. Houbaviy HB, Murray MF, Sharp PA. Embryonic stem cell-specific MicroRNAs. Dev Cell 2003, 5:351-358. 10.1016/S1534-5807(03)00227-2, 12919684.
28. Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foà R, Schliwka J, Fuchs U, Novosel A, Müller R-U, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter H-I, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 2007, 129:1401-1414. 10.1016/j.cell.2007.04.040, 2681231, 17604727.
29. Tang F, Kaneda M, O'Carroll D, Hajkova P, Barton SC, Sun YA, Lee C, Tarakhovsky A, Lao K, Surani MA. Maternal microRNAs are essential for mouse zygotic development. Genes Dev 2007, 21:644-648. 10.1101/gad.418707, 1820938, 17369397.
30. Roccanova L, Ramphal P. The role of stem cells in the evolution of longevity and its application to tissue therapy. Tissue Cell 2003, 35:79-81. 10.1016/S0040-8166(02)00104-0, 12589732.
31. Enard W, Pääbo S. Comparative primate genomics. Annu Rev Genomics Hum Genet 2004, 5:351-378. 10.1146/annurev.genom.5.061903.180040, 15485353.
32. Zhang R, Wang Y-Q, Su B. Molecular evolution of a primate-specific microRNA family. Mol Biol Evol 2008, 25:1493-1502. 10.1093/molbev/msn094, 18417486.
33. 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. 10.1371/journal.pone.0017666, 3059204, 21436881.
34. Paten B, Herrero J, Beal K, Fitzgerald S, Birney E. Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res 2008, 18:1814-1828. 10.1101/gr.076554.108, 2577869, 18849524.
35. Nadeau JH, Taylor BA. Lengths of chromosomal segments conserved since divergence of man and mouse. Proc Natl Acad Sci USA 1984, 81:814-818. 10.1073/pnas.81.3.814, 344928, 6583681.
36. Ehrlich J, Sankoff D, Nadeau JH. Synteny conservation and chromosome rearrangements during mammalian evolution. Genetics 1997, 147:289-296. 1208112, 9286688.
37. Bhaskaran M, Wang Y, Zhang H, Weng T, Baviskar P, Guo Y, Gou D, Liu L. MicroRNA-127 modulates fetal lung development. Physiological genomics 2009, 37:268-278. 10.1152/physiolgenomics.90268.2008, 2685501, 19439715.
38. Barroso-delJesus A, Lucena-Aguilar G, Sanchez L, Ligero G, Gutierrez-Aranda I, Menendez P. The Nodal inhibitor Lefty is negatively modulated by the microRNA miR-302 in human embryonic stem cells. FASEB J 2011, 25:1497-1508. 10.1096/fj.10-172221, 21266536.
39. Nadeau JH, Sankoff D. Counting on comparative maps. Trends Genet 1998, 14:495-501. 10.1016/S0168-9525(98)01607-2, 9865155.
40. Altuvia Y, Landgraf P, Lithwick G, Elefant N, Pfeffer S, Aravin A, Brownstein MJ, Tuschl T, Margalit H. Clustering and conservation patterns of human microRNAs. Nucleic Acids Res 2005, 33:2697-2706. 10.1093/nar/gki567, 1110742, 15891114.
41. Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA. Protein interaction maps for complete genomes based on gene fusion events. Nature News 1999, 402:86-90.
42. Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. A combined algorithm for genome-wide prediction of protein function. Nature News 1999, 402:83-86.
43. Dandekar T, Snel B, Huynen M, Bork P. Conservation of gene order: a fingerprint of proteins that physically interact. Trends in biochemical sciences 1998, 23:324-328. 10.1016/S0968-0004(98)01274-2, 9787636.
44. Barker D, Meade A, Pagel M. Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes. Bioinformatics 2007, 23:14-20. 10.1093/bioinformatics/btl558, 17090580.
45. Hsu S-D, Lin F-M, Wu W-Y, Liang C, Huang W-C, Chan W-L, Tsai W-T, Chen G-Z, Lee C-J, Chiu C-M, Chien C-H, Wu M-C, Huang C-Y, Tsou A-P, Huang H-D. miRTarBase: a database curates experimentally validated microRNA-target interactions. Nucleic Acids Res 2011, 39:D163-9. 10.1093/nar/gkq1107, 3013699, 21071411.
46. Friedman RC, Farh KK-H, Burge CB, Bartel DP. Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009, 19:92-105. 2612969, 18955434.
47. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011, 39:D152-7. 10.1093/nar/gkq1027, 3013655, 21037258.
48. Maddison WP, Maddison DR. Mesquite: A modular system for evolutionary analysis. Evolution 2008, 62:1103-1118. 10.1111/j.1558-5646.2008.00349.x, 18298648.
49. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988, 85:2444-2448. 10.1073/pnas.85.8.2444, 280013, 3162770.
50. Van Dongen S. Graph clustering by flow simulation. University of Utrecht May 2000,
51. Barker D, Pagel M. Predicting functional gene links from phylogenetic-statistical analyses of whole genomes. PLoS Comput Biol 2005, 1:e3. 10.1371/journal.pcbi.0010003, 1183509, 16103904.
52. Felsenstein J. Parsimony in systematics: biological and statistical issues. Annual review of ecology and systematics 1983, 14:313-333.
53. Felsenstein J. PHYLIP (phylogeny inference package), version 3.5 c. Distributed by the author 1993,