Evolution of Arabidopsis thaliana microRNAs from random sequences

RNA

Volumn 14, Issue 12, 2008, Pages 2455-2459

  De Felippes, Felipe Fenselau ^a   Schneeberger, Korbinian ^a   Dezulian, Tobias ^b   Huson, Daniel H ^b   Weigel, Detlef ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

^b UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

Arabidopsis thaliana; Evolution; MicroRNAs

Indexed keywords

DNA; MICRORNA;

ARABIDOPSIS; GENE SEQUENCE; GENETIC ANALYSIS; GENOME; INVERTED REPEAT; NONHUMAN; PRIORITY JOURNAL; REVIEW; RNA GENE;

ARABIDOPSIS; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENE DUPLICATION; MICRORNAS; MOLECULAR SEQUENCE DATA; RNA, PLANT; SEQUENCE ALIGNMENT;

ARABIDOPSIS THALIANA;

EID: 57049169777     PISSN: 13558382     EISSN: 14699001     Source Type: Journal    
DOI: 10.1261/rna.1149408     Document Type: Review

References (17)

1. Allen, E., Xie, Z., Gustafson, A.M., Sung, G.H., Spatafora, J.W., and Carrington, J.C. 2004. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat. Genet. 36: 1282-1290.
2. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
3. Axtell, M.J. 2008. Evolution of microRNAs and their targets: Are all microRNAs biologically relevant? Biochim. Biophys. Acta. doi: 10.1016/j.bbagrm.2008.02.007.
4. Chapman, E.J. and Carrington, J.C. 2007. Specialization and evolution of endogenous small RNA pathways. Nat. Rev. Genet. 8: 884-896.
5. Dermitzakis, E.T. and Clark, A.G. 2002. Evolution of transcription factor binding sites in mammalian gene regulatory regions: Conservation and turnover. Mol. Biol. Evol. 19: 1114-1121.
6. Dezulian, T., Remmert, M., Palatnik, J.F., Weigel, D., and Huson, D.H. 2006. Identification of plant microRNA homologs. Bioinformatics 22: 359-360.
7. Fahlgren, N., Howell, M.D., Kasschau, K.D., Chapman, E.J., Sullivan, C.M., Cumbie, J.S., Givan, S.A., Law, T.F., Grant, S.R., Dangl, J.L., et al. 2007. High-throughput sequencing of Arabidopsis microRNAs: Evidence for frequent birth and death of MIRNA genes. PLoS One 2: e219. doi: 10.1371/journal.pone.0000219.
8. Jones-Rhoades, M.W. and Bartel, D.P. 2004. Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol. Cell 14: 787-799.
9. Jones-Rhoades, M.W., Bartel, D.P., and Bartel, B. 2006. MicroRNAs and their regulatory roles in plants. Annu. Rev. Plant Biol. 57: 19-53.
10. Kent, W.J. 2002. BLAT: The BLAST-like alignment tool. Genome Res. 12: 656-664.
11. Koch, M.A., Haubold, B., and Mitchell-Olds, T. 2000. Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol. Biol. Evol. 17: 1483-1498.
12. Lu, C., Kulkarni, K., Souret, F.F., MuthuValliappan, R., Tej, S.S., Poethig, R.S., Henderson, I.R., Jacobsen, S.E., Wang, W., Green, P.J., et al. 2006. MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res. 16: 1276-1288.
13. Lu, J., Shen, Y., Wu, Q., Kumar, S., He, B., Shi, S., Carthew, R.W., Wang, S.M., and Wu, C.I. 2008. The birth and death of microRNA genes in Drosophila. Nat. Genet. 40: 351-355.
14. Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J.H., Senin, P., Wang, W., Ly, B.V., Lewis, K.L., et al. 2008. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452: 991-996.
15. Rajagopalan, R., Vaucheret, H., Trejo, J., and Bartel, D.P. 2006. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes & Dev. 20: 3407-3425.
16. Svoboda, P. and Di Cara, A. 2006. Hairpin RNA: A secondary structure of primary importance. Cell. Mol. Life Sci. 63: 901-908.
17. Tuskan, G.A., Difazio, S., Jansson, S., Bohlmann, J., Grigoriev, I., Hellsten, U., Putnam, N., Ralph, S., Rombauts, S., Salamov, A., et al. 2006. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.