Origin and evolution of a placental-specific microRNA family in the human genome

BMC Evolutionary Biology

Volumn 10, Issue 1, 2010, Pages

  Yuan, Zhidong ^a,b   Sun, Xiao ^a   Jiang, Dongke ^a   Ding, Yan ^a   Lu, Zhiyuan ^a   Gong, Lejun ^a   Liu, Hongde ^a   Xie, Jianming ^a  

^a SOUTHEAST UNIVERSITY   (China)

^b HUNAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DIVERGENCE; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; HOMINID; MARSUPIAL; MORTALITY; RECOMBINATION; RNA; TECHNOLOGICAL DEVELOPMENT;

ANIMALIA; DNA VIRUSES; EUTHERIA; MAMMALIA; METATHERIA;

MICRORNA;

ARTICLE; DNA SEQUENCE; FEMALE; GENETICS; HUMAN; HUMAN GENOME; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; PHYLOGENY; PLACENTA; PREGNANCY; SEGMENTAL DUPLICATION; SEQUENCE ALIGNMENT;

BASE SEQUENCE; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; FEMALE; GENOME, HUMAN; HUMANS; MICRORNAS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; PLACENTA; PREGNANCY; SEGMENTAL DUPLICATIONS, GENOMIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 78149243536     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-10-346     Document Type: Article

References (69)

1. MicroRNAs: small RNAs with a big role in gene regulation. L He GJ Hannon, Nat Rev Genet 2004 5 7 522 531 10.1038/nrg1379 15211354
2. MicroRNAs: genomics, biogenesis, mechanism, and function. DP Bartel, Cell 2004 116 2 281 297 10.1016/S0092-8674(04)00045-5 14744438
3. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. RC Lee RL Feinbaum V Ambros, Cell 1993 75 5 843 854 10.1016/0092-8674(93)90529-Y 8252621
4. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. B Wightman I Ha G Ruvkun, Cell 1993 75 5 855 862 10.1016/0092-8674(93)90530-4 8252622
5. MicroRNAs: regulators of gene expression and cell differentiation. RA Shivdasani, Blood 2006 108 12 3646 3653 10.1182/blood-2006-01-030015 16882713
6. Role of microRNAs in plant and animal development. JC Carrington V Ambros, Science 2003 301 5631 336 338 10.1126/science.1085242 12869753
7. Micro RNAs in animal development. RHA Plasterk, Cell 2006 124 5 877 881 10.1016/j.cell.2006.02.030 16530032
8. An Analysis of Human MicroRNA and Disease Associations. M Lu Q Zhang M Deng J Miao Y Guo W Gao Q Cui, PLoS ONE 2008 3 10 3420 10.1371/journal.pone. 0003420 18923704
9. MicroRNA signatures in human cancers. GA Calin CM Croce, Nat Rev Cancer 2006 6 11 857 866 10.1038/nrc1997 17060945
10. Exon shuffling by L1 retrotransposition. JV Moran RJ DeBerardinis HH Kazazian Jr, Science 1999 283 5407 1530 1534 10.1126/science.283.5407.1530 10066175
11. Evolutionary changes in the structures of the cox2 and atp6 loci in the mitochondrial genome of soybean involving recombination across small interspersed sequences. S Kato A Kanazawa T Mikami Y Shimamoto, Curr Genet 1998 34 4 303 312 10.1007/s002940050400 9799364 (Pubitemid 28523787)
12. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. G Bejerano CB Lowe N Ahituv B King A Siepel SR Salama EM Rubin WJ Kent D Haussler, Nature 2006 441 7089 87 90 10.1038/nature04696 16625209
13. DNA sequence insertion and evolutionary variation in gene regulation. RJ Britten, Proc Natl Acad Sci USA 1996 93 18 9374 9377 10.1073/pnas.93.18.9374 8790336
14. Transposable elements are found in a large number of human protein-coding genes. A Nekrutenko WH Li, Trends Genet 2001 17 11 619 621 10.1016/S0168- 9525(01)02445-3 11672845
15. Protein Coding Palindromes Are a Unique but Recurrent Feature in Rickettsia. H Ogata S Audic C Abergel PE Fournier JM Claverie, Genome Res 2002 12 808 816 10.1101/gr.227602 11997347
16. Host genome surveillance for retrotransposons by transposon-derived proteins. HP Cam K ichi Noma H Ebina HL Levin SIS Grewal, Nature 2008 451 431 436 10.1038/nature06499 18094683
17. Mammalian microRNAs derived from genomic repeats. NR Smalheiser VI Torvik, Trends Genet 2005 21 6 322 326 10.1016/j.tig.2005.04.008 15922829
18. Evidence for Co-Evolution between Human MicroRNAs and Alu-Repeats. S Lehnert P Van Loo PJ Thilakarathne P Marynen G Verbeke FC Schuit, PLoS ONE 2009 4 2 4456 10.1371/journal.pone.0004456 19209240
19. A family of human microRNA genes from miniature inverted-repeat transposable elements. J Piriyapongsa IK Jordan, PLoS ONE 2007 2 2 203 10.1371/journal.pone.0000203 17301878
20. Dual coding of siRNAs and miRNAs by plant transposable elements. J Piriyapongsa IK Jordan, RNA 2008 14 5 814 821 10.1261/rna.916708 18367716
21. Origin and Evolution of Human microRNAs From Transposable Elements. J Piriyapongsa L Marino-Ramirez IK Jordan, Genetics 2007 176 2 1323 1337 10.1534/genetics.107.072553 17435244 (Pubitemid 46961124)
22. Molecular Evolution of a Primate-Specific microRNA Family. R Zhang Y-Q Wang B Su, Mol Biol Evol 2008 25 7 1493 1502 10.1093/molbev/msn094 18417486
23. Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. RD Morin MD O'Connor M Griffith F Kuchenbauer A Delaney A-L Prabhu Y Zhao H McDonald T Zeng M Hirst,, et al. Genome Res 2008 18 4 610 621 10.1101/gr.7179508 18285502
24. In silico detection and characteristics of novel microRNA genes in the Equus caballus genome using an integrated ab initio and comparative genomic approach. M Zhou Q Wang J Sun X Li L Xu H Yang H Shi S Ning L Chen Y Li,, et al. Genomics 2009 94 2 125 131 10.1016/j.ygeno.2009.04.006 19406225
25. Computational identification of novel microRNA homologs in the chimpanzee genome. V Baev E Daskalova I Minkov, Comput Biol Chem 2009 33 1 62 70 10.1016/j.compbiolchem.2008.07.024 18760970
26. MER53, a non-autonomous DNA transposon associated with a variety of functionally related defense genes in the human genome. VV Kapitonov J Jurka, DNA Seq 1998 8 5 277 288 10993599
27. miRBase: microRNA sequences, targets and gene nomenclature. S Griffiths-Jones RJ Grocock S van Dongen A Bateman AJ Enright, Nucleic Acids Res 2006 34 Database issue 140 144 10.1093/nar/gkj112 16381832
28. RepeatMasker Open-3.0. AFA Smit R Hubley P Green, Institute for Systems Biology 1996 http://www.repeatmasker.org
29. Identification of hundreds of conserved and nonconserved human microRNAs. I Bentwich A Avniel Y Karov R Aharonov S Gilad O Barad A Barzilai P Einat U Einav E Meiri,, et al. Nat Genet 2005 37 7 766 770 10.1038/ng1590 15965474
30. MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features. P Jiang H Wu W Wang W Ma X Sun Z Lu, Nucleic Acids Res 2007 35 Web Server issue 339 W344 10.1093/nar/gkm368 17553836
31. The evolution of tribospheny and the antiquity of mammalian clades. MO Woodburne TH Rich MS Springer, Mol Phylogenet Evol 2003 28 2 360 385 10.1016/S1055-7903(03)00113-1 12878472
32. Origins and evolution of microRNA genes in Drosophila species. M Nozawa S Miura M Nei, Genome Biology and Evolution 2010 2010 180 189 10.1093/gbe/evq009
33. Evolution of a large ribosomal RNA multigene family in filamentous fungi: birth and death of a concerted evolution paradigm. AP Rooney TJ Ward, Proc Natl Acad Sci USA 2005 102 14 5084 5089 10.1073/pnas.0409689102 15784739
34. Mechanisms underlying the evolution and maintenance of functionally heterogeneous 18S rRNA genes in Apicomplexans. AP Rooney, Mol Biol Evol 2004 21 9 1704 1711 10.1093/molbev/msh178 15175411
35. Genome-wide analysis of the MADS-box gene family in Populus trichocarpa. CH Leseberg A Li H Kang M Duvall L Mao, Gene 2006 378 84 94 10.1016/j.gene.2006. 05.022 16831523
36. A highly conserved segmental duplication in the subtelomeres of Plasmodium falciparum chromosomes varies in copy number. BW Mok U Ribacke E Sherwood M Wahlgren, Malar J 2008 7 46 10.1186/1475-2875-7-46 18325124
37. Complex evolution of 7E olfactory receptor genes in segmental duplications. T Newman BJ Trask, Genome Res 2003 13 5 781 793 10.1101/gr.769003 12727898
38. On the expansion of the pentatricopeptide repeat gene family in plants. N O'Toole M Hattori C Andres K Iida C Lurin C Schmitz-Linneweber M Sugita I Small, Mol Biol Evol 2008 25 6 1120 1128 10.1093/molbev/msn057 18343892
39. Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. X Gu Y Wang J Gu, Nat Genet 2002 31 2 205 209 10.1038/ng902 12032571
40. An Alu transposition model for the origin and expansion of human segmental duplications. JA Bailey G Liu EE Eichler, Am J Hum Genet 2003 73 4 823 834 10.1086/378594 14505274
41. The role of site accessibility in microRNA target recognition. M Kertesz N Iovino U Unnerstall U Gaul E Segal, Nat Genet 2007 39 10 1278 1284 10.1038/ng2135 17893677
42. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. BP Lewis CB Burge DP Bartel, Cell 2005 120 1 15 20 10.1016/j.cell.2004.12.035 15652477
43. MicroRNA targeting specificity in mammals: determinants beyond seed pairing. A Grimson KK Farh WK Johnston P Garrett-Engele LP Lim DP Bartel, Mol Cell 2007 27 1 91 105 10.1016/j.molcel.2007.06.017 17612493
44. WebGestalt: an integrated system for exploring gene sets in various biological contexts. B Zhang S Kirov J Snoddy, Nucleic Acids Res 2005 33 Web Server issue 741 W748 10.1093/nar/gki475 15980575
45. The KEGG resource for deciphering the genome. M Kanehisa S Goto S Kawashima Y Okuno M Hattori, Nucleic Acids Res 2004 32 Database issue 277 280 10.1093/nar/gkh063 14681412
46. Expression of Arabidopsis MIRNA genes. Z Xie E Allen N Fahlgren A Calamar SA Givan JC Carrington, Plant Physiol 2005 138 4 2145 2154 10.1104/pp.105. 062943 16040653
47. Origin and evolution of new exons in rodents. W Wang H Zheng S Yang H Yu J Li H Jiang J Su L Yang J Zhang J McDermott,, et al. Genome Res 2005 15 9 1258 1264 10.1101/gr.3929705 16109974
48. Molecular evolution of a microRNA cluster. A Tanzer PF Stadler, J Mol Biol 2004 339 2 327 335 10.1016/j.jmb.2004.03.065 15136036
49. Evolution of Arabidopsis microRNA families through duplication events. C Maher L Stein D Ware, Genome Res 2006 16 4 510 519 10.1101/gr.4680506 16520461
50. Rapid evolution of an X-linked microRNA cluster in primates. R Zhang Y Peng W Wang B Su, Genome Res 2007 17 5 612 617 10.1101/gr.6146507 17416744
51. The Piwi-piRNA Pathway Provides an Adaptive Defense in the Transposon Arms Race. AA Aravin GJ Hannon J Brennecke, Science 2007 318 5851 761 764 10.1126/science.1146484 17975059
52. The human genome browser at UCSC. WJ Kent CW Sugnet TS Furey KM Roskin TH Pringle AM Zahler D Haussler, Genome Res 2002 12 6 996 1006 12045153
53. The UCSC Table Browser data retrieval tool. D Karolchik AS Hinrichs TS Furey KM Roskin CW Sugnet D Haussler WJ Kent, Nucleic Acids Res 2004 32 suppl1 493 496 10.1093/nar/gkh103 14681465
54. Galaxy: a platform for interactive large-scale genome analysis. B Giardine C Riemer RC Hardison R Burhans L Elnitski P Shah Y Zhang D Blankenberg I Albert J Taylor,, et al. Genome Res 2005 15 10 1451 1455 10.1101/gr.4086505 16169926
55. Discovering microRNAs from deep sequencing data using miRDeep. MR Friedländer W Chen C Adamidi J Maaskola R Einspanier S Knespel N Rajewsky, Nat Biotechnol 2008 26 4 407 415 10.1038/nbt1394 18392026
56. Aligning multiple genomic sequences with the threaded blockset aligner. M Blanchette WJ Kent C Riemer L Elnitski AFA Smit KM Roskin R Baertsch K Rosenbloom H Clawson ED Green,, et al. Genome Res 2004 14 4 708 715 10.1101/gr.1933104 15060014
57. Analysis of copy number variation in the rhesus macaque genome identifies candidate loci for evolutionary and human disease studies. AS Lee M Gutierrez-Arcelus GH Perry EJ Vallender WE Johnson GM Miller JO Korbel C Lee, Hum Mol Genet 2008 17 8 1127 1136 10.1093/hmg/ddn002 18180252
58. Comparative analyses of bidirectional promoters in vertebrates. MQ Yang J Taylor L Elnitski, BMC Bioinformatics 2008 9 6 9 10.1186/1471-2105-9-S6-S9 18541062
59. Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees. DM Toleno G Renaud TG Wolfsberg M Islam DE Wildman KD Siegmund JG Hacia, BMC Bioinformatics 2009 10 77 10.1186/1471-2105- 10-77 19265541
60. Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution. X He X Ling S Sinha, PLoS Comput Biol 2009 5 3 1000299 10.1371/journal.pcbi.1000299 19293946
61. CpG dinucleotides and the mutation rate of non-CpG DNA. JC Walser L Ponger AV Furano, Genome Res 2008 18 9 1403 1414 10.1101/gr.076455.108 18550801
62. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. A Siepel G Bejerano JS Pedersen AS Hinrichs M Hou K Rosenbloom H Clawson J Spieth LW Hillier S Richards,, et al. Genome Res 2005 15 8 1034 1050 10.1101/gr.3715005 16024819
63. R-Coffee: a method for multiple alignment of non-coding RNA. A Wilm DG Higgins C Notredame, Nucleic Acids Res 2008 36 9 52 10.1093/nar/gkn174 18420654
64. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. K Tamura J Dudley M Nei S Kumar, Mol Biol Evol 2007 24 8 1596 1599 10.1093/molbev/msm092 17488738
65. The neighbor-joining method: a new method for reconstructing phylogenetic trees. N Saitou M Nei, Mol Biol Evol 1987 4 4 406 425 3447015
66. Segmental duplications: organization and impact within the current human genome project assembly. JA Bailey AM Yavor HF Massa BJ Trask EE Eichler, Genome Res 2001 11 6 1005 1017 10.1101/gr.GR-1871R 11381028
67. Recent segmental duplications in the human genome. JA Bailey Z Gu RA Clark K Reinert RV Samonte S Schwartz MD Adams EW Myers PW Li EE Eichler, Science 2002 297 5583 1003 1007 10.1126/science.1072047 12169732
68. Circos: an information aesthetic for comparative genomics. M Krzywinski J Schein I Birol J Connors R Gascoyne D Horsman SJ Jones MA Marra, Genome Res 2009 19 9 1639 1645 10.1101/gr.092759.109 19541911
69. R: A Language and Environment for Statistical Computing. R Development Core Team, Vienna, Austria: R Foundation for Statistical Computing 2009