Signatures of Purifying and Local Positive Selection in Human miRNAs

American Journal of Human Genetics

Volumn 84, Issue 3, 2009, Pages 316-327

  Quach, Hélène ^a   Barreiro, Luis B ^a   Laval, Guillaume ^a   Zidane, Nora ^a   Patin, Etienne ^a   Kidd, Kenneth K ^b   Kidd, Judith R ^b   Bouchier, Christiane ^a   Veuille, Michel ^c   Antoniewski, Christophe ^a   Quintana Murci, Lluís ^a  

^a INSTITUT PASTEUR   (France)

^b YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c MUSÉUM NATIONAL D'HISTOIRE NATURELLE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA;

ARTICLE; CHROMOSOME 14; CONTROLLED STUDY; GENE CONTROL; GENE DELETION; GENE EXPRESSION; GENE MUTATION; GENETIC DISORDER; GENETIC VARIABILITY; HUMAN; MOLECULAR MODEL; NATURAL SELECTION; PHENOTYPE; POPULATION GENETICS; PRIORITY JOURNAL; RNA ANALYSIS; RNA PURIFICATION; RNA SEQUENCE;

BASE SEQUENCE; CHROMOSOMES, HUMAN, PAIR 14; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENETICS, POPULATION; HUMANS; MICRORNAS; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; RNA, UNTRANSLATED; SELECTION (GENETICS);

EID: 61849140663     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ajhg.2009.01.022     Document Type: Article

References (58)

1. Ambros V. The functions of animal microRNAs. Nature 431 (2004) 350-355
2. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116 (2004) 281-297
3. Bartel D.P., and Chen C.Z. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat. Rev. Genet. 5 (2004) 396-400
4. Lim L.P., Glasner M.E., Yekta S., Burge C.B., and Bartel D.P. Vertebrate microRNA genes. Science 299 (2003) 1540
5. Lagos-Quintana M., Rauhut R., Lendeckel W., and Tuschl T. Identification of novel genes coding for small expressed RNAs. Science 294 (2001) 853-858
6. Du T., and Zamore P.D. microPrimer: the biogenesis and function of microRNA. Development 132 (2005) 4645-4652
7. Han J., Lee Y., Yeom K.H., Nam J.W., Heo I., Rhee J.K., Sohn S.Y., Cho Y., Zhang B.T., and Kim V.N. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125 (2006) 887-901
8. Lee Y., Ahn C., Han J., Choi H., Kim J., Yim J., Lee J., Provost P., Radmark O., Kim S., et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 425 (2003) 415-419
9. Hutvagner G., McLachlan J., Pasquinelli A.E., Balint E., Tuschl T., and Zamore P.D. A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293 (2001) 834-838
10. Ketting R.F., Fischer S.E., Bernstein E., Sijen T., Hannon G.J., and Plasterk R.H. Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans. Genes Dev. 15 (2001) 2654-2659
11. Lau N.C., Lim L.P., Weinstein E.G., and Bartel D.P. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science 294 (2001) 858-862
12. Meister G., Landthaler M., Patkaniowska A., Dorsett Y., Teng G., and Tuschl T. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. Mol. Cell 15 (2004) 185-197
13. Liu J., Carmell M.A., Rivas F.V., Marsden C.G., Thomson J.M., Song J.J., Hammond S.M., Joshua-Tor L., and Hannon G.J. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305 (2004) 1437-1441
14. Plasterk R.H. Micro RNAs in animal development. Cell 124 (2006) 877-881
15. Valencia-Sanchez M.A., Liu J., Hannon G.J., and Parker R. Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev. 20 (2006) 515-524
16. Croce C.M., and Calin G.A. miRNAs, cancer, and stem cell division. Cell 122 (2005) 6-7
17. Esquela-Kerscher A., and Slack F.J. Oncomirs - microRNAs with a role in cancer. Nat. Rev. Cancer 6 (2006) 259-269
18. Zhang B., Pan X., Cobb G.P., and Anderson T.A. microRNAs as oncogenes and tumor suppressors. Dev. Biol. 302 (2007) 1-12
19. Couzin J. MicroRNAs make big impression in disease after disease. Science 319 (2008) 1782-1784
20. Lu M., Zhang Q., Deng M., Miao J., Guo Y., Gao W., and Cui Q. An analysis of human microRNA and disease associations. PLoS ONE 3 (2008) e3420
21. Sethupathy P., and Collins F.S. MicroRNA target site polymorphisms and human disease. Trends Genet. 24 (2008) 489-497
22. Bentwich I., Avniel A., Karov Y., Aharonov R., Gilad S., Barad O., Barzilai A., Einat P., Einav U., Meiri E., et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat. Genet. 37 (2005) 766-770
23. Berezikov E., Guryev V., van de Belt J., Wienholds E., Plasterk R.H., and Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120 (2005) 21-24
24. Rigoutsos I., Huynh T., Miranda K., Tsirigos A., McHardy A., and Platt D. Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. Proc. Natl. Acad. Sci. USA 103 (2006) 6605-6610
25. Griffiths-Jones S., Saini H.K., van Dongen S., and Enright A.J. miRBase: tools for microRNA genomics. Nucleic Acids Res. 36 (2008) D154-D158
26. Krek A., Grun D., Poy M.N., Wolf R., Rosenberg L., Epstein E.J., MacMenamin P., da Piedade I., Gunsalus K.C., Stoffel M., et al. Combinatorial microRNA target predictions. Nat. Genet. 37 (2005) 495-500
27. Lewis B.P., Burge C.B., and Bartel D.P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120 (2005) 15-20
28. Jazdzewski K., Murray E.L., Franssila K., Jarzab B., Schoenberg D.R., and de la Chapelle A. Common SNP in pre-miR-146a decreases mature miR expression and predisposes to papillary thyroid carcinoma. Proc. Natl. Acad. Sci. USA 105 (2008) 7269-7274
29. Saunders M.A., Liang H., and Li W.H. Human polymorphism at microRNAs and microRNA target sites. Proc. Natl. Acad. Sci. USA 104 (2007) 3300-3305
30. Takahashi M., Matsuda F., Margetic N., and Lathrop M. Automated identification of single nucleotide polymorphisms from sequencing data. J. Bioinform. Comput. Biol. 1 (2003) 253-265
31. Stephens M., and Donnelly P. A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am. J. Hum. Genet. 73 (2003) 1162-1169
32. Rozas J., Sanchez-DelBarrio J.C., Messeguer X., and Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (2003) 2496-2497
33. Excoffier L., Laval G., and Schneider S. Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1 (2005) 47-50
34. Voight B.F., Kudaravalli S., Wen X., and Pritchard J.K. A map of recent positive selection in the human genome. PLoS Biol. 4 (2006) e72
35. Wall J.D. Recombination and the power of statistical tests of neutrality. Genet. Res. 74 (1999) 65-79
36. Laval G., and Excoffier L. SIMCOAL 2.0: A program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history. Bioinformatics 20 (2004) 2485-2487
37. Voight B.F., Adams A.M., Frisse L.A., Qian Y., Hudson R.R., and Di Rienzo A. Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc. Natl. Acad. Sci. USA 102 (2005) 18508-18513
38. Beaumont M.A., and Rannala B. The Bayesian revolution in genetics. Nat. Rev. Genet. 5 (2004) 251-261
39. Beaumont M.A., Zhang W., and Balding D.J. Approximate Bayesian computation in population genetics. Genetics 162 (2002) 2025-2035
40. Fagundes N.J., Ray N., Beaumont M., Neuenschwander S., Salzano F.M., Bonatto S.L., and Excoffier L. Statistical evaluation of alternative models of human evolution. Proc. Natl. Acad. Sci. USA 104 (2007) 17614-17619
41. Seitz H., and Zamore P.D. Rethinking the microprocessor. Cell 125 (2006) 827-829
42. Brennecke J., Stark A., Russell R.B., and Cohen S.M. Principles of microRNA-target recognition. PLoS Biol. 3 (2005) e85
43. Lai E.C. Predicting and validating microRNA targets. Genome Biol. 5 (2004) 115
44. Nielsen R. Molecular signatures of natural selection. Annu. Rev. Genet. 39 (2005) 197-218
45. Sabeti P.C., Schaffner S.F., Fry B., Lohmueller J., Varilly P., Shamovsky O., Palma A., Mikkelsen T.S., Altshuler D., and Lander E.S. Positive natural selection in the human lineage. Science 312 (2006) 1614-1620
46. Nielsen R., Hellmann I., Hubisz M., Bustamante C., and Clark A.G. Recent and ongoing selection in the human genome. Nat. Rev. Genet. 8 (2007) 857-868
47. Kreitman M. Methods to detect selection in populations with applications to the human. Annu. Rev. Genomics Hum. Genet. 1 (2000) 539-559
48. Akey J.M., Eberle M.A., Rieder M.J., Carlson C.S., Shriver M.D., Nickerson D.A., and Kruglyak L. Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol. 2 (2004) e286
49. Pluzhnikov A., Di Rienzo A., and Hudson R.R. Inferences about human demography based on multilocus analyses of noncoding sequences. Genetics 161 (2002) 1209-1218
50. Barreiro L.B., Laval G., Quach H., Patin E., and Quintana-Murci L. Natural selection has driven population differentiation in modern humans. Nat. Genet. 40 (2008) 340-345
51. Sabeti P.C., Varilly P., Fry B., Lohmueller J., Hostetter E., Cotsapas C., Xie X., Byrne E.H., McCarroll S.A., Gaudet R., et al. Genome-wide detection and characterization of positive selection in human populations. Nature 449 (2007) 913-918
52. Weir B.S., and Cockerham C.C. Estimating F-statistics for the analysis of population structure. Evolution 38 (1984) 1358-1370
53. Kiss T. Small nucleolar RNAs: An abundant group of noncoding RNAs with diverse cellular functions. Cell 109 (2002) 145-148
54. Frazer K.A., Ballinger D.G., Cox D.R., Hinds D.A., Stuve L.L., Gibbs R.A., Belmont J.W., Boudreau A., Hardenbol P., Leal S.M., et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 449 (2007) 851-861
55. Chen K., and Rajewsky N. Natural selection on human microRNA binding sites inferred from SNP data. Nat. Genet. 38 (2006) 1452-1456
56. * species has substantial influence on microRNA and 3′ UTR evolution. Nat. Struct. Mol. Biol. 15 (2008) 354-363
57. Takagi S., Nakajima M., Mohri T., and Yokoi T. Post-transcriptional regulation of human pregnane X receptor by micro-RNA affects the expression of cytochrome P450 3A4. J. Biol. Chem. 283 (2008) 9674-9680
58. Thompson E.E., Kuttab-Boulos H., Witonsky D., Yang L., Roe B.A., and Di Rienzo A. CYP3A variation and the evolution of salt-sensitivity variants. Am. J. Hum. Genet. 75 (2004) 1059-1069