10. Quesneville,H., Nouaud,D. and Anxolabehere,D. (2003) Detection of new transposable element families in Drosophila melanogaster and Anopheles gambiae genomes. J. Mol. Evol., 57(Suppl. 1), S50–S59. 11. Smit,A.F.A., Hubley,R. and Green,P. (1996–2004) Institute for Systems Biology. 12. Jurka,J., Klonowski,P., Dagman,V. and Pelton,P. (1996) CENSOR–a program for identiﬁcation and elimination of repetitive elements from DNA sequences. Comput. Chem., 20, 119–121. 13. Kohany,O., Gentles,A.J., Hankus,L. and Jurka,J. (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics, 7, 474. 14. Benson,G. (1999) Tandem repeats ﬁnder: a program to analyze DNA sequences. Nucleic Acids Res., 27, 573–580. 15. Kolpakov,R., Bana,G. and Kucherov,G. (2003) mreps: Efﬁcient and ﬂexible detection of tandem repeats in DNA. Nucleic Acids Res., 31, 3672–3678. 16. Eddy,S.R. (1998) Proﬁle hidden Markov models. Bioinformatics, 14, 755–763. 17. Bedell,J.A., Korf,I. and Gish,W. (2000) MaskerAid: a performance enhancement to RepeatMasker. Bioinformatics, 16, 1040–1041. 18. Chao,K.M., Zhang,J., Ostell,J. and Miller,W. (1995) A local alignment tool for very long DNA sequences. Comput. Appl. Biosci., 11, 147–153. 19. Gusﬁeld,D. (1997) Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, New York, NY. 20. Kapitonov,V. and Jurka,J. (1996) The age of Alu subfamilies. J. Mol. Evol., 42, 59–65. 21. Lippman,Z., Gendrel,A.V., Black,M., Vaughn,M.W., Dedhia,N., McCombie,W.R., Lavine,K., Mittal,V., May,B., Kasschau,K.D. et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature, 430, 471–476. 22. Zilberman,D., Gehring,M., Tran,R.K., Ballinger,T. and Henikoff,S. (2007) Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet., 39, 61–69. 23. Kurtz,S., Phillippy,A., Delcher,A.L., Smoot,M., Shumway,M., Antonescu,C. and Salzberg,S.L. (2004) Versatile and open software for comparing large genomes. Genome Biol., 5, R12. 24. Fahlgren,N., Sullivan,C.M., Kasschau,K.D., Chapman,E.J., Cumbie,J.S., Montgomery,T.A., Gilbert,S.D., Dasenko,M., Nucleic Acids Research, 2011, Vol. 39, No. 16 6931 Backman,T.W., Givan,S.A. et al. (2009) Computational and analytical framework for small RNA proﬁling by high-throughput sequencing. RNA, 15, 992–1002. 25. Miura,A., Nakamura,M., Inagaki,S., Kobayashi,A., Saze,H. and Kakutani,T. (2009) An Arabidopsis jmjC domain protein protects transcribed genes from DNA methylation at CHG sites. EMBO J., 28, 1078–1086. 26. Lister,R. and Ecker,J.R. (2009) Finding the ﬁfth base: genome-wide sequencing of cytosine methylation. Genome Res., 19, 959–966. 27. Bernatavichute,Y.V., Zhang,X., Cokus,S., Pellegrini,M. and Jacobsen,S.E. (2008) Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One, 3, e3156. 28. Hollister,J.D. and Gaut,B.S. (2009) Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res., 19, 1419–1428. 29. Pelizzola,M. and Ecker,J.R. (2010) The DNA methylome. FEBS Lett. 30. Penterman,J., Zilberman,D., Huh,J.H., Ballinger,T., Henikoff,S. and Fischer,R.L. (2007) DNA demethylation in the Arabidopsis genome. Proc. Natl Acad. Sci. USA, 104, 6752–6757. 31. Kanno,T., Bucher,E., Daxinger,L., Huettel,B., Bohmdorfer,G., Gregor,W., Kreil,D.P., Matzke,M. and Matzke,A.J. (2008) A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat. Genet., 40, 670–675. 32. Henderson,I.R. and Jacobsen,S.E. (2008) Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading. Genes Dev., 22, 1597–1606. 33. Daxinger,L., Kanno,T., Bucher,E., van der Winden,J., Naumann,U., Matzke,A.J. and Matzke,M. (2009) A stepwise pathway for biogenesis of 24-nt secondary siRNAs and spreading of DNA methylation. EMBO J., 28, 48–57. 34. Saze,H. and Kakutani,T. (2007) Heritable epigenetic mutation of a transposon-ﬂanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J., 26, 3641–3652. 35. Dooner,H.K. and Weil,C.F. (2007) Give-and-take: interactions between DNA transposons and their host plant genomes. Curr. Opin. Genet. Dev., 17, 486–492.