Unexpected consequences of a sudden and massive transposon amplification on rice gene expression

Feschotte, C. Transposable elements and the evolution of regulatory networks. Nature Rev. Genet. 9, 397–405 (2008)

Feschotte, C., Jiang, N. & Wessler, S. R. Plant transposable elements: where genetics meet genomics. Nature Rev. Genet. 3, 329–341 (2002)

Naito, K. et al. Dramatic amplification of a rice transposable element during recent domestication. Proc. Natl Acad. Sci. USA 103, 17620–17625 (2006)

McClintock, B. The significance of responses of the genome to challenge. Science 226, 792–801 (1984)

Britten, R. J. & Davidson, E. H. Gene regulation for higher cells: a theory. Science 165, 349–357 (1969)

Britten, R. J. & Davidson, E. H. Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Q. Rev. Biol. 46, 111–138 (1971)

Jiang, N. et al. Active DNA transposon family in rice. Nature 421, 163–167 (2003)

Kikuchi, K., Terauchi, K., Wada, M. & Hirano, H. Y. The plant MITE mPing is mobilized in anther culture. Nature 421, 167–170 (2003)

Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005)

Arnold, C. & Hodgson, I. J. Vectorette PCR: a novel approach to genomic walking. PCR Methods Appl. 1, 39–42 (1991)

Itoh, T. et al. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana . Genome Res. 17, 175–183 (2007)

Cresse, A. D., Hulbert, S. H., Brown, W. E., Lucas, J. R. & Bennetzen, J. L. Mu1-related transposable elements of maize preferentially insert into low copy number DNA. Genetics 140, 315–324 (1995)

Liao, G. C., Rehm, E. J. & Rubin, G. M. Insertion site preferences of the P transposable element in Drosophila melanogaster . Proc. Natl Acad. Sci. USA 97, 3347–3351 (2000)

Miyao, A. et al. Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell 15, 1771–1780 (2003)

Piffanelli, P. et al. Large-scale characterization of Tos17 insertion sites in a rice T-DNA mutant library. Plant Mol. Biol. 65, 587–601 (2007)

Kolesnik, T. et al. Establishing an efficient Ac/Ds tagging system in rice: Large-scale analysis of Ds flanking sequences. Plant J. 37, 301–314 (2004)

Yu, J. et al. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296, 79–92 (2002)

Mavrich, T. N. et al. Nucleosome organization in the Drosophila genome. Nature 453, 358–362 (2008)

Kaplan, N. et al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458, 362–366 (2009)

Shimono, M. et al. WRKY45 plays a crucial role in benzothiadiazole-inducible blast resistance. Plant Cell 19, 2064–2076 (2007)

Jiang, N. et al. Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics 161, 1293–1305 (2002)

Monden, Y. et al. High potential of a transposon mPing as a marker system in japonica × japonica cross in rice. DNA Res. 16, 131–140 (2009)

Higo, K., Ugawa, Y., Iwamoto, M. & Korenaga, T. Plant cis-acting regulatory DNA elements (PLACE) database. Nucleic Acids Res. 27, 297–300 (1999)

McClintock, B. The relation of homozygous deficiencies to mutations and allelic series in maize. Genetics 29, 478–502 (1944)

Yang, G., Zhang, F., Hancock, C. N. & Wessler, S. R. Transposition of a rice miniature inverted-repeat transposable element mPing in Arabidopsis thaliana . Proc. Natl Acad. Sci. USA 104, 10962–10967 (2007)

Capy, P., Gasperi, G., Biemont, C. & Bazin, C. Stress and transposable elements: co-evolution or useful parasites? Heredity 85, 101–106 (2000)

Feschotte, C., Zhang, X. & Wessler, S. R. in Mobile DNA II Ch. 50 (eds Craig, N. L., Craigie, R., Gellert, M. & Lambowitz, A. M.) 1147–1158 (ASM Press, 2002)

Delihas, N. Small mobile sequences in bacteria display diverse structure/function motifs. Mol. Microbiol. 67, 475–481 (2007)

Curtis, M. D. & Grossniklaus, U. A gateway cloning vector set for high-throughput functional analysis of genes in planta . Plant Physiol. 133, 462–469 (2003)

Clough, S. J. & Bent, A. F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana . Plant J. 16, 735–743 (1998)