Paramutation: The chromatin connection

Plant Cell

Volumn 16, Issue 6, 2004, Pages 1358-1364

  Della Vedova, Chris B ^a   Cone, Karen C ^a  

^a UNIVERSITY OF MISSOURI   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA; MAMMALIA; ZEA MAYS;

EID: 2942694469     PISSN: 10404651     EISSN: None     Source Type: Journal    
DOI: 10.1105/tpc.160630     Document Type: Review

References (42)

1. Alleman, M., and Doctor, J. (2000). Genomic imprinting in plants: Observations and evolutionary implications. Plant Mol. Biol. 43, 147-161.
2. Andersen, A.A., and Panning, B. (2003). Epigenetic gene regulation by noncoding RNAs. Curr. Opin. Cell Biol. 15, 281-289.
3. Brink, R.A. (1956). A genetic change associated with the R locus in maize which is directed and potentially reversible. Genetics 41, 872-889.
4. Brzeski, J., and Jerzmanowski, A. (2003). Deficient in DNA Methylation 1 (DDM1) defines a novel family of chromatin-remodeling factors. J. Biol. Chem. 278, 823-828.
5. Chan, S.W.-L., Zilberman, D., Xie, Z., Johansen, L.K., Carrington, J.C., and Jacobsen, S.E. (2004). RNA silencing genes control de novo DNA methylation. Science 303, 1336.
6. Colot, V., Maloisel, L., and Rossignol, J.-L. (1996). Interchromosomal transfer of epigenetic states in Ascobolus: Transfer of DNA methylation is mechanistically related to homologous recombination. Cell 86, 855-864.
7. Comai, L., Tyagi, A.P., Winter, K., Holmes-Davis, R., Reynolds, S.H., Stevens, Y., and Byers, B. (2000). Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12, 1551-1567.
8. Dorweiler, J.E., Carey, C.C., Kubo, K.M., Hollick, J.B., Kermicle, J., and Chandler, V.L. (2000). mediator of paramutation1 is required for establishment and maintenance of paramutation at multiple maize loci. Plant Cell 12, 2101-2118.
9. Emmert-Buck, M.R., Bonner, R.F., Smith, P.D., Chuaqui, R.F., Zhuang, Z., Goldstein, S.R., Weiss, R.A., and Liotta, L.A. (1996). Laser capture microdissection. Science 274, 998-1001.
10. Geiman, T.M., and Robertson, K.D. (2002). Chromatin remodeling, histone modifications, and DNA methylation-how does it all fit together? J. Cell. Biochem. 87, 117-125.
11. Guo, M., and Birchler, J.A. (1994). Trans-acting dosage effects on the expression of model gene systems in maize aneuploids. Science 266, 1999-2002.
12. He, P., Friebe, B.R., Gill, B.S., and Zhou, J.M. (2003). Allopolyploidy alters gene expression in the highly stable hexaploid wheat. Plant Mol. Biol. 52, 401-414.
13. Henikoff, S., and Comai, L. (1998). Trans-sensing effects: The ups and downs of being together. Cell 93, 329-332.
14. Herman, H., Lu, M., Anggraini, M., Sikora, A., Chang, Y., Yoon, B.J., and Soloway, P.D. (2003). Trans allele methylation and paramutation-like effects in mice. Nat. Genet. 34, 199-202.
15. Higashiyama, T., Yabe, S., Sasaki, N., Nishimura, Y., Miyagishima, S.-y., Kuroiwa, H., and Kuroiwa, T. (2001). Pollen tube attraction by the synergid cell. Science 293, 1480-1483.
16. Jeddeloh, J.A., Bender, J., and Richards, E.J. (1998). The DNA methylation locus DDM1 is required for maintenance of gene silencing in Arabidopsis. Genes Dev. 12, 1714-1725.
17. Kermicle, J., Eggleston, W.B., and Alleman, M. (1995). Organization of paramutagenicity in R-stippled maize. Genetics 141, 361-372.
18. Lyle, R., Watanabe, D., te Vruchte, D., Wutz, A., Schageman, J., Hahner, L., Davies, C., and Barlow, D.P. (2000). The imprinted antisense RNA at the Igf2r locus overlaps but does not imprint Mas1. Nat. Genet. 25, 19-21.
19. Madlung, A., Masuelli, R.W., Watson, B., Reynolds, S.H., Davison, J., and Comai, L. (2002). Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol. 129, 733-746.
20. Martienssen, R. (2003). Maintenance of heterochromatin by RNA interference of tandem repeats. Nat. Genet. 35, 213-214.
21. Mette, M.F., Aufsatz, W., van der Winden, J., Matzke, M.A., and Matzke, A.J.M. (2000). Transcriptional silencing and promoter methylation triggered by double-stranded RNA. EMBO J. 19, 5194-5201.
22. Meyer, P., and Saedler, H. (1996). Homology-dependent gene silencing in plants. Annu. Rev. Plant Physiol. Plant Mol. Biol. 47, 23-48.
23. Mittelsten Scheid, O., Afsar, K., and Paszkowski, J. (2003). Formation of stable epialleles and their paramutation-like interaction in tetraploid Arabidopsis thaliana. Nat. Genet. 34, 450-454.
24. Mittelsten Scheid, O., Jakovleva, L., Afsar, K., Maluszynska, J., and Paszkowski, J. (1996). A change of ploidy can modify epigenetic silencing. Proc. Natl. Acad. Sci. USA 93, 7114-7119.
25. Murphy, S.K., and Jirtle, R.L. (2003). Imprinting evolution and the price of silence. Bioessays 25, 577-588.
26. Osborn, T.C., Pires, J.C., Birchler, J.A., Auger, D.L., Chen, Z.J., Lee, H.S., Comai, L., Madlung, A., Doerge, R.W., Colot, V., and Martienssen, R. (2003). Understanding mechanisms of novel gene expression in polyploids. Trends Genet. 19, 141-147.
27. Panavas, T., Weir, J., and Walker, E.L. (1999). The structure and paramutagenicity of the R-marbled haplotype of Zea mays. Genetics 153, 979-991.
28. Patterson, G.I., Thorpe, C.J., and Chandler, V.L. (1993). Paramutation, an allelic interaction, is associated with a stable and heritable reduction of transcription of the maize b regulatory gene. Genetics 135, 881-894.
29. Riddle, N.C., and Birchler, J.A. (2003). Effects of reunited diverged regulatory hierarchies in allopolyploids and species hybrids. Trends Genet. 19, 597-600.
30. Shaked, H., Kashkush, K., Ozkan, H., Feldman, M., and Levy, A.A. (2001). Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13, 1749-1759.
31. Sleutels, F., Tjon, G., Ludwig, T., and Barlow, D.P. (2002). Imprinted silencing of Slc22a2 and Slc22a3 does not need transcriptional overlap between Igf2r and Air. EMBO J. 15, 3696-3704.
32. Stam, M., Belele, C., Dorweiler, J.E., and Chandler, V.L. (2002a). Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev. 16, 1906-1918.
33. Stam, M., Belele, C., Ramakrishna, W., Dorweiler, J.E., Bennetzen, J.L., and Chandler, V.L. (2002b). The regulatory regions required for B' paramutation and expression are located far upstream of the maize b1 transcribed sequences. Genetics 162, 917-930.
34. Styles, E.D. (1970). Paramutation of the R locus in maize trisomics and comparison of paramutation systems in maize and tomato. Can. J. Genet. Cytol. 12, 941-946.
35. Vance, V.B., and Vaucheret, H. (2001). RNA silencing in plants: Defense and counterdefense. Science 292, 2277-2280.
36. Verdel, A., Jia, S., Gerber, S., Sugiyama, T., Gygi, S., Grewal, S.I.S., and Moazed, D. (2004). RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303, 672-676.
37. Verona, R.I., Mann, M.R.W., and Bartolomei, M.S. (2003). Genomic imprinting: Intricacies of epigenetic regulation in clusters. Annu. Rev. Cell Dev. Biol. 19, 237-259.
38. Walker, E.L., and Panavas, T. (2001). Structural features and methylation patterns associated with paramutation at the r1 Locus of Zea mays. Genetics 159, 1201-1215.
39. Wendel, J.F. (2000). Genome evolution in polyploids. Plant Mol. Biol. 42, 225-249.
40. Wendel, J.F., Cronn, R.C., Johnston, J.S., and Price, H.J. (2002). Feast and famine in plant genomes. Genetica 115, 37-47.
41. Wutz, A., Smrzka, O.W., Schweifer, N., Schellanders, K., Wagner, E.F., and Barlow, D.P. (1997). Imprinted expression of the Igf2r gene depends on an intronic CpG island. Nature 389, 745-749.
42. Yoon, B.J., Herman, H., Sikora, A., Smith, L.T., Plass, C., and Soloway, P.D. (2002). Regulation of DNA methylation of Rasgrf1. Nat. Genet. 30, 92-96.