Haplotype distribution and evolutionary pattern of miR-17 and miR-124 families based on population analysis

PLoS ONE

Volumn 4, Issue 11, 2009, Pages

  Guo, Li ^a   Sun, Beili ^a   Sang, Fei ^b   Wang, Wei ^a   Lu, Zuhong ^a,b  

^a SOUTHEAST UNIVERSITY   (China)

^b Southeast University   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; MICRORNA 124; MICRORNA 17; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; MIRN124 MICRORNA, HUMAN; MIRN17 MICRORNA, HUMAN;

ARTICLE; CHROMOSOME 8; EVOLUTION; FAMILY STUDY; GENE IDENTIFICATION; GENE LOCATION; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; MULTIGENE FAMILY; NONHUMAN; PHYLOGENY; RNA SEQUENCE; ANIMAL; BIOLOGICAL MODEL; CAENORHABDITIS ELEGANS; CLUSTER ANALYSIS; COMPUTER PROGRAM; GENETICS; METABOLISM; MOLECULAR EVOLUTION; SPECIES DIFFERENCE;

ANIMALIA; CAENORHABDITIS; VERTEBRATA;

ANIMALS; CAENORHABDITIS ELEGANS; CLUSTER ANALYSIS; EVOLUTION, MOLECULAR; HAPLOTYPES; HUMANS; MICRORNAS; MODELS, GENETIC; PHYLOGENY; SOFTWARE; SPECIES SPECIFICITY;

EID: 71049188566     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0007944     Document Type: Article

References (40)

1. Carrington JC, Ambros V (2003) Role of microRNAs in plant and animal development. Science 301: 336-338.
2. Bartel DP (2004) MicroRNAs: Genomics, biogenesis, mechanism, and function. Cell 116: 281-297.
3. Bartel DP, Chen CZ (2004) Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nature Reviews Genetics 5: 396-400.
4. Miranda KC, Huynh T, Tay Y, Ang YS, Tam WL, et al. (2006) A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 126: 1203-1217.
5. Plasterk RHA (2006) Micro RNAs in animal development. Cell 124: 877-881.
6. Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294: 853-858.
7. Lau NC, Lim LP, Weinstein EG, Bartel DP (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294: 858-862.
8. Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294: 862-864.
9. Chen K, Rajewsky N (2007) The evolution of gene regulation by transcription factors and microRNAs. Nature Reviews Genetics 8: 93-103.
10. Sempere LF, Cole CN, McPeek MA, Peterson KJ (2006) The phylogenetic distribution of metazoan microRNAs: Insights into evolutionary complexity and constraint. Journal of Experimental Zoology Part B-Molecular and Developmental Evolution 306B: 575-588.
11. Niwa R, Slack FJ (2007) The evolution of animal microRNA function. Current Opinion in Genetics & Development 17: 145-150.
12. Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, et al. (2008) Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455: 1193-U1115.
13. Liu N, Okamura K, Tyler DM, Phillips MD, Chung WJ, et al. (2008) The evolution and functional diversification of animal microRNA genes. Cell Research 18: 985-996.
14. Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A, et al. (2006) The expansion of the metazoan microRNA repertoire. Bmc Genomics 7: 75.
15. Prochnik SE, Rokhsar DS, Aboobaker AA (2007) Evidence for a microRNA expansion in the bilaterian ancestor. Development Genes and Evolution 217: 73-77.
16. Heimberg AM, Sempere LF, Moy VN, Donoghue PCJ, Peterson KJ (2008) MicroRNAs and the advent of vertebrate morphological complexity. Proceedings of the National Academy of Sciences of the United States of America 105: 2946-2950.
17. Wheeler BM, Heimberg AM, Moy VN, Sperling EA, Holstein TW, et al. (2009) The deep evolution of metazoan microRNAs. Evolution & Development 11: 50-68.
18. Fu XH, Adamski M, Thompson EM (2008) Altered miRNA repertoire in the simplified chordate, Oikopleura dioica. Molecular Biology and Evolution 25: 1067-1080.
19. Allen E, Xie ZX, Gustafson AM, Sung GH, Spatafora JW, et al. (2004) Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nature Genetics 36: 1282-1290.
20. Tanzer A, Stadler PF (2004) Molecular evolution of a microRNA cluster. Journal of Molecular Biology 339: 327-335.
21. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, et al. (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408: 86-89.
22. Zhang BH, Pan XP, Wang QL, Cobb GP, Anderson TA (2006) Computational identification of microRNAs and their targets. Computational Biology and Chemistry 30: 395-407.
23. Smirnova L, Grafe A, Seiler A, Schumacher S, Nitsch R, et al. (2005) Regulation of miRNA expression during neural cell specification. European Journal of Neuroscience 21: 1469-1477.
24. Nelson PT, Baldwin DA, Kloosterman WP, Kauppinen S, Plasterk RHA, et al. (2006) RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. Rna-a Publication of the Rna Society 12: 187-191.
25. Cheng LC, Pastrana E, Tavazoie M, Doetsch F (2009) miR-124 regulates adult neurogenesis in the subventricular zone stem cell niche. Nature Neuroscience 12: 399-408.
26. Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM (2005) Animal microRNAs confer robustness to gene expression and have a significant impact on 3′UTR evolution. Cell 123: 1133-1146.
27. Visvanathan J, Lee S, Lee B, Lee JW, Lee SK (2007) The microRNA miR-124 antagonizes the anti-neural REST/SCP1 pathway during embryonic CNS development. Genes & Development 21: 744-749.
28. Ehrenreich IM, Purugganan MD (2008) Sequence variation of microRNAs and their binding sites in Arabidopsis. Plant Physiology 146: 1974-1982.
29. Wittkopp PJ (2005) Genomic sources of regulatory variation in cis and in trans. Cmls-Cellular and Molecular Life Sciences 62: 1779-1783.
30. Davidson EH, Erwin DH (2006) Gene regulatory networks and the evolution of animal body plans. Science 311: 796-800.
31. Erwin DH, Davidson EH (2009) The evolution of hierarchical gene regulatory networks. Nature Reviews Genetics 10: 141-148.
32. Ambros V (2004) The functions of animal microRNAs. Nature 431: 350-355.
33. He L, Hannon GJ (2004) MicroRNAs: Small RNAs with a big role in gene regulation (vol 5, pg 522 2004). Nature Reviews Genetics 5: 522.
34. Chapman EJ, Carrington JC (2007) Specialization and evolution of endogenous small RNA pathways. Nature Reviews Genetics 8: 884-896.
35. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and clustal X version 2.0. Bioinformatics 23: 2947-2948.
36. Librado P, Rozas J (2009) A software for comprehensive analysis of DNA polymorphism data. Bioinformatics doi: 10.1093/bioinformatics/btp187.
37. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.
38. Bandelt HJ, Forster P, Rohl A (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37-48.
39. Polzin T, Daneshmand SV (2003) On Steiner trees and minimum spanning trees in hypergraphs. Operations Research Letters 31: 12-20.
40. Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, et al. (2009) The UCSC Genome Browser Database: update 2009. Nucleic Acids Research 37: D755-D761.