REFERENCES
- Aasland, R., T. J. Gibson, and A. F. Stewart. 1995. The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem. Sci. 20:56–59.
- Bennetzen, J. L. 2000. Transposable element contributions to plant gene and genome evolution. Plant Mol. Biol. 42:251–269.
- Boeke, J. D., and V. G. Corces. 1989. Transcription and Reverse Transcription of Retrotransposons. Annu. Rev. Microbiol. 43:403–433.
- Bowen, N. J., and I. K. Jordan. 2002. Transposable elements and the evolution of eukaryotic complexity. Curr. Issues Mol. Biol. 4:65–76.
- Britten, R. J. 1995. Active gypsy/Ty3 retrotransposons or retroviruses in Caenorhabditis elegans.. Proc. Natl. Acad. Sci. USA 92:599–601.
- Capilli, A. D., D. C. Schultz, F. J. Rauscher, and K. L. B. Borden. 2001. Solution structure of the PHD domain from KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains. EMBO J. 20:165–177.
- Day, A., M. Schimer-Rahire, M. R. Kuchka, S. P. Mayfield, and J. D. Rochaix. 1988. A transposon with an unusual arrangement of long terminal repeats in the green alga Chlamydomonas reinhardtii.. EMBO J. 7:1917–1927.
- Day, A., and J. D. Rochaix. 1991. Structure and inheritance of sense and anti-sense transcripts from a transposon in the green alga Chlamydomonas reinhardtii.. J. Mol. Biol. 218:273–291.
- Eissenberg, J. C. 2001. Molecular biology of the chromo domain: an ancient chromatin module comes of age. Gene 275:19–29.
- Grandbastein, M. A. 1998. Activation of plant retrotransposons under stress conditions. Trends Plant Sci. 3:181–187.
- Harris, E. H. 1989. The Chlamydomonas sourcebook: a comprehensive guide to biology and laboratory use. Academic Press, New York, N.Y.
- Hirochika, H. 1997. Retrotransposons of rice: their regulation and use for genome analysis. Plant Mol. Biol. 35:231–240.
- Hirochika, H., H. Okamoto, and T. Kakutani. 2000. Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation. Plant Cell 12:357–368.
- James, T. C., and S. C. Elgin. 1986. Identification of a nonhistone chromosomal protein associated with heterochromatin in Drosophila melanogaster and its gene. Mol. Cell. Biol. 6:3862–3872.
- Kapitonov, V. V., and J. Jurka. 2003. The Esterase and PHD Domains in CR1-Like Non-LTR Retrotransposons. Mol. Biol. Evol. 20:38–46.
- Kidwell, M. G., and D. R. Lisch. 2001. Perspective: transposable elements, parasitic DNA, and genome evolution. Evolution 55:1–24.
- Kim, A. I., C. Terzian, P. Santamaria, A. Pélisson,. N. Prud'homme, and A. Bucheton. 1994. Retroviruses in invertebrates: the gypsy retrotransposon is apparently an infectious retrovirus of Drosophila melanogaster.. Proc. Natl. Acad. Sci. USA 91:1285–1289.
- Kindle, K. L., R. A. Schnell, E. Fernández, and P. A. Lefebvre. 1989. Stable nuclear transformation of Chlamydomonas using the Chlamydomonas gene for nitrate reductase. J. Cell Biol. 109:2589–2601.
- Koonin, E. V., S. Zhou, and J. C. Lucchesi. 1995. The chromo superfamily: new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin. Nucleic Acids Res. 23:4229–4233.
- Kumar, A., and J. L. Bennetzen. 1999. Plant retrotransposons. Annu. Rev. Genet. 33:479–532.
- Kumekawa, N., H. Ohtsubo, T. Horiuchi, and E. Ohtsubo. 1999. Identification and characterization of novel retrotransposons of the gypsy type in rice. Mol. Gen. Genet. 260:593–602.
- Leeton, P. R., and D. R. Smyth. 1993. An abundant LINE-like element amplifies in the genome of Lilium speciosum.. Mol. Gen. Genet. 237:97–104.
- Li, Y., D. A. Kirschmann, and L. L. Wallrath. 2002. Does heterochromatin protein 1 always follow code. Proc. Natl. Acad. Sci. USA 99:16462–16469.
- Liu, B., and J. F. Wendel. 2000. Retrotransposon activation followed by rapid repression in introgressed rice plants. Genome 43:874–880.
- Malik, H. S., and T. H. Eickbush. 1999. Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR retrotransposons. J. Virol. 73:5186–5190.
- Manninen, I., and A. H. Schulman. 1993. BARE-1, a copia-like retroelement in barley (Hordeum vulgare L.). Plant Mol. Biol. 22:829–846.
- Marsano, R. M., R. Moschetti, C. Caggese, C. Lanave, P. Barsanti, and R. Caizzi. 2000. The complete Tirant transposable element in Drosophila melanogaster shows a structural relationship with retrovirus-like retrotransposons. Gene 247:87–95.
- Mount, S. M., and G. M. Rubin. 1995. Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins. Mol. Cell. Biol. 5:1630–1638.
- Nakayashiki, H., H. Matsuo, I. Chuma, K. Ikeda, S. Betsuyaku, M. Kusaba, Y. Tosa, and S. Mayama. 2001. Pyret, a Ty3/Gypsy retrotransposon in Magnaporthe grisea contains an extra domain between the nucleocapsid and protease domains. Nucleic Acids Res. 29:4106–4113.
- Navarro, M. T., E. Guerra, E. Fernández, and A. Galván. 2000. Nitrite reductase mutants as an approach to understanding nitrite assimilation in Chlamydomonas reinhardtii.. Plant Physiol. 122:1–7.
- Ogas, J., S. Kaufmann, J. Henderson, and C. Somerville. 1999. PICKLE is a CHD3 chromatin-remodeling factor that regulates the transition from embryonic to vegetative development in Arabidopsis.. Proc. Natl. Acad. Sci. USA 96:13839–13844.
- O′Neill, R. J. M., M. J. O′Neill, and J. A. M. Graves. 1998. Under-methylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid. Nature. 393:68–72.
- Paro, R., and D. S. Hogness. 1991. The Polycomb protein shares a homologous domain with a heterochromatin-associated protein of Drosophila.. Proc. Natl. Acad. Sci. USA 88:263–267.
- Parraga, G., S. J. Horvath, A. Eisen, W. E. Taylor, L. Hood, E. T. Young, and R. E. Klevit. 1988. Zinc-dependent structure of a single-finger domain of yeast ADR1. Science 241:1489–1492.
- Pearce, S. R., G. Harrison, J. S. Heslop-Harrison, A. J. Flavell, and A. Kumar. 1997. Characterization and genomic organization of the Ty1-copia group retrotransposons in rye (Secale cereale). Genome 40:617–625.
- Pimpinelli, S., M. Berloco, L. Fanti, P. Dimitri, S. Bonaccorsi, E. Marchetti, R. Caizzi, C. Caggese, and M. Gatti. 1995. Transposable elements are stable structural components of the Drosophila melanogaster heterochromatin. Proc. Natl. Acad. Sci. USA 92:3804–3808.
- Prieto, R., A. Dubus, A. Galván, and E. Fernández. 1996. Isolation and characterization of two regulatory mutants for nitrate assimilation in Chlamydomonas reinhardtii.. Mol. Gen. Genet. 251:461–471.
- Quesada, A., A. Galván, R. Schnell, P. A. Lefebvre, and E. Fernández. 1993. Five nitrate assimilation related loci are clustered in Chlamydomonas reinhardtii.. Mol. Gen. Genet. 240:387–394.
- Quesada, A., I. Gomez, and E. Fernández. 1998. Clustering of the nitrite reductase gene and a light-regulated gene with nitrate assimilation loci in Chlamydomonas reinhardtii.. Planta 206:259–265.
- Rexach, J., E. Fernández, and A. Galván. 2000. The Chlamydomonas reinhardtii Nar1 gene encodes a cloroplast membrane protein involved in nitrite transport. Plant Cell 12:1441–1453.
- Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
- Sanmiguel, P., and J. L. Bennetzen. 1998. Evidence that a recent increase maize genome size was caused by the massive amplification of integrase retrotransposons. Ann. Bot. 81:37–44.
- Schloss, J. A., C. D. Silflow, and J. L. Rosenbaum. 1984. mRNA abundance changes during flagellar regeneration in Chlamydomonas reinhardtii.. Mol. Cell. Biol. 4:424–434.
- Varmus, H., and P. Brown. 1989. Mobile DNA, p. 53–108. In D. E. Berg and M. M. Howe (ed.), Retroviruses. American Society for Microbiology, Washington, D.C.
- Wolffe, A. P., and M. A. Matzke. 1999. Epigenetics: Regulation through repression. Science. 286:481–486.
- Xiong, Y., and T. H. Eickbush. 1990. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 9:3353–3362.
- Yochum, G. S., and D. E. Ayer. 2001. Pf1, a novel PHD zinc finger protein that links the TLE corepressor to the mSin3A-histone deacetylase complex. Mol. Cell. Biol. 21:4110–4118.
- Zhou, Y., E. B. Cambareri, and J. A. Kinsey. 2001. DNA methylation inhibits expression and transposition of the Neurospora Tad retrotransposon. Mol. Genet. Genomics 265:748–754.