Modeling evolutionary growth of a microRNA-mediated regulation system

Journal of Theoretical Biology

Volumn 311, Issue , 2012, Pages 54-65

  Akita, Tetsuya ^a   Takuno, Shohei ^b   Innan, Hideki ^a,c  

^a GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Complexity; Gene duplication; Post transcriptional regulation

Indexed keywords

MICRORNA; SMALL UNTRANSLATED RNA;

ANGIOSPERM; EVOLUTIONARY BIOLOGY; GENE; GENOME; GENOMICS; GROWTH MODELING; RNA;

ARABIDOPSIS; ARTICLE; CONCEPTUAL FRAMEWORK; GENE CONTROL; GENE DUPLICATION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE INTERACTION; GENOMICS; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; MOLECULAR MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENOME; PRIORITY JOURNAL; PROCESS OPTIMIZATION; THEORETICAL STUDY; TRANSCRIPTION REGULATION;

ARABIDOPSIS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENES, PLANT; MICRORNAS; MODELS, GENETIC; RNA, PLANT;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 84864459223     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2012.07.011     Document Type: Article

References (34)

1. Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. Molecular Biology of the Cell 2008, Garland Science, New York, pp. 493-494. 5th ed.
2. Axtell M.J., Bartel D.P. Antiquity of microRNAs and their targets in land plants. Plant Cell 2005, 17:1658-1673.
3. Axtell M.J., Bowman J.L. Evolution of plant microRNAs and their targets. Trends Plant Sci. 2008, 13:343-349.
4. Backman T.W., Sullivan C.M., Cumbie J.S., Miller Z.A., Chapman E.J., Fahlgren N., Givan S.A., Carrington J.C., Kasschau K.D. Update of ASRP: the Arabidopsis Small RNA Project database. Nucl. Acids Res. 2008, 36:982-985.
5. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004, 116:281-297.
6. Bonnet, E., Wuyts, J., Rouzé, P., Van de Peer, Y., 2004. Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc. Natl. Acad. Sci. USA 101, 11511-11516.
7. Borneman A.R., Gianoulis T.A., Zhang Z.D., Yu H., Rozowsky J., Seringhaus M.R., Wang L.Y., Gerstein M., Snyder M. Divergence of transcription factor binding sites across related yeast species. Science 2007, 317:815-819.
8. Carrington J.C., Ambros V. Role of microRNAs in plant and animal development. Science 2003, 301:336-338.
9. Chen K., Rajewsky N. The evolution of gene regulation by transcription factors and microRNAs. Nat. Rev. Genet. 2007, 8:93-103.
10. Crow J.F., Kimura M. An Introduction to Population Genetics Theory 1970, Harper and Row, New York.
11. Des Marais D.L., Rausher M.D. Escape from adaptive conflict after duplication in an anthocyanin pathway gene. Nature 2008, 454:762-765.
12. Fahlgren N., Jogdeo S., Kasschau K.D., Sullivan C.M., Chapman E.J., Laubinger S., Smith L.M., Dasenko M., Givan S.A., Weigel D., Carrington J.C. MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell 2010, 22:1074-1089.
13. Floyd S.K., Bowman J.L. Gene regulation: ancient microRNA target sequences in plants. Nature 2004, 428:485-486.
14. He L., Hannon G.J. MicroRNAs: small RNAs with a big role in gene regulation. Nat. Rev. Genet. 2004, 5:522-531.
15. Hughes A.L. The evolution of functionally novel proteins after gene duplication. Proc. Biol. Sci. 1994, 256:119-124.
16. Innan H., Kondrashov F. The evolution of gene duplications: classifying and distinguishing between models. Nat. Rev. Genet. 2010, 11:97-108.
17. Jiang D., Yin C., Yu A., Zhou X., Liang W., Yuan Z., Xu Y., Yu Q., Wen T., Zhang D. Duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice. Cell Res. 2006, 16:507-518.
18. Jones-Rhoades M.W., Bartel D.P. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 2004, 14:787-799.
19. Kozomara A., Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucl. Acids Res. 2011, 39:D152-D157.
20. Llave C., Xie Z., Kasschau K.D., Carrington J.C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 2002, 297:2053-2056.
21. Lynch M. The Origins of Genome Architecture 2007, Sinauer Associates, Sunderland.
22. Ma Z., Coruh C., Axtell M.J. Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. Plant Cell 2010, 22:1090-1103.
23. Maher C., Stein L., Ware D. Evolution of Arabidopsis microRNA families through duplication events. Genome Res. 2006, 16:510-519.
24. Odom D.T., Dowell R.D., Jacobsen E.S., Gordon W., Danford T.W., MacIsaac K.D., Rolfe P.A., Conboy C.M., Gifford D.K., Fraenkel E. Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat. Genet. 2007, 39:730-732.
25. Reinhart B.J., Weinstein E.G., Rhoades M.W., Bartel B., Bartel D.P. MicroRNAs in plants. Genes Dev. 2002, 16:1616-1626.
26. Rhoades M.W., Reinhart B.J., Lim L.P., Burge C.B., Bartel B., Bartel D.P. Prediction of plant microRNA targets. Cell 2002, 110:513-520.
27. Rueffler C., Hermisson J., Wagner G.P. Evolution of functional specialization and division of labor. Proc. Natl. Acad. Sci. USA 2012, 109:326-335.
28. Schwab R., Palatnik J.F., Riester M., Schommer C., Schmid M., Weigel D. Specific effects of microRNAs on the plant transcriptome. Dev. Cell 2005, 8:517-527.
29. Takuno S., Innan H. Evolution of complexity in miRNA-mediated gene regulation systems. Trends Genet. 2008, 24:56-59.
30. Takuno S., Innan H. Selection fine-tunes the expression of microRNA target genes in Arabidopsis thaliana. Mol. Biol. Evol. 2011, 28:2429-2434.
31. Tanzer A., Reister M., Hertel J., Bermudez-Santana C.I., Gorodkin J., Hofacker I.L., Stadler P.F. Evolutionary genomics of microRNAs and their relatives. Evolutionary Genomics and Systems Biology 2010, 295-327. Wiley-Blackwell. G. Caetano-Anollés (Ed.).
32. Tanzer A., Stadler P.F. Molecular evolution of a microRNA cluster. J. Mol. Biol. 2004, 339:327-335.
33. Tischler J., Lehner B., Fraser A.G. Evolutionary plasticity of genetic interaction networks. Nat. Genet. 2008, 40:390-391.
34. Xie Z., Kasschau K.D., Carrington J.C. Negative feedback regulation of Dicer-Like1 in Arabidopsis by microRNA-guided mRNA degradation. Curr. Biol. 2003, 13:784-789.