Plant epigenetics: From genomes to epigenomes

Notulae Botanicae Horti Agrobotanici Cluj-Napoca

Volumn 38, Issue 2, 2010, Pages 9-15

  Rival, Alain ^a   Beulé, Thierry ^a   Aberlenc Abertossi, Frédérique ^a   Tregear, James ^a   Jaligot, Estelle ^a  

^a INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

Author keywords

Chromatin; DNA methylation; Epigenetics; Gene expression; Silencing

Indexed keywords

EID: 78049320344     PISSN: 0255965X     EISSN: 18424309     Source Type: Journal    
DOI: None     Document Type: Article

References (23)

1. Barski, A., S. Cuddapah, K. Cui, T. Y. Roh, D. E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao (2007). High-Resolution Profiling of Histone Methylations in the Human Genome. Cell 129 (4):823-837.
2. Beck, S. and V. K. Rakyan (2008). The methylome: approaches for global DNA methylation profiling. Trends in Genetics 24(5):231-237.
3. Bird, A. (2001). Molecular biology. Methylation talk between histones and DNA. Science 294(5549):2113-2115.
4. Callinan, P. A. and A. P. Feinberg (2006). The emerging science of epigenomics, Hum. Mol. Genet. 15 Spec. 1:R95-R101.
5. Chan, S. W. L., I. R. Henderson and S. E. Jacobsen (2005). Gardening the genome: DNA methylation in Arabidopsis thaliana. Nature Reviews Genetics 6:351-360.
6. Cokus, S. J., S. Feng, X. Zhang, Z. Chen, B. Merriman, C. D. Haudenschild, S. Pradhan, S. F. Nelson, M. Pellegrini and S. E. Jacobsen (2008). Shotgun bisulfite sequencing of the Arabidopsis genome reveals DNA methylation patterning, Nature 452:215-219.
7. Esteller, M. (2006). The necessity of a human epigenome project, Carcinogenesis 27:1121-1125.
8. Fields, S. (2007). Molecular biology: site-seeing by sequencing, Science 316:1441-1442.
9. Henderson, I. R. and S. E. Jacobsen. Epigenetic inheritance in plants. Nature 447:418-424. doi:10.1038/nature05917.
10. Johnson, L. M., X. F. Cao and S. E. Jacobsen (2002). Interplay between two epigenetic marks: DNA methylation and histone H3 lysine methylation. Current Biology 12:1360-1367.
11. Kuo, M. H. and C. D. Allis (1999). In vivo cross-linking and immunoprecipitation for studying dynamic protein:DNA associations in a chromatin environment. Methods 19:425-433.
12. Mathieu, O. and J. Bender (2004). RNA-directed DNA methylation. Journal of Cell Science 117:4881-4888.
13. Metzker, M. L. (2010). Sequencing technologies-the next generation. Nature Reviews Genetics 11:31-46.
14. Morozova, O., M. A. Marra (2008). Applications of next-generation sequencing technologies in functional genomics. Genomics 92(5), 255-264
15. Ren, B., F. Robert, J. J. Wyrick, O. Aparicio, E. G. Jennings, I. Simon, J. Zeitlinger, J. Schreiber, N. Hannett, E. Kanin, T. L. Volkert, C. J. Wilson, S. P. Bell and R. A. Young (2000). Genome-wide location and function of DNA binding proteins. Science 290:2306-2309.
16. Roh, T. Y., W. C. Ngau, K. Cui, D. Landsman and K. Zhao (2004). High-resolution genome-wide mapping of histone modifications, Nat. Biotechnol. 22:1013-1016.
17. Schones, D. E. and K. Zhao (2008). Genome-wide approaches to studying chromatin modifications. Nat. Rev. Genet. 9:179-191.
18. Shendure, J. and H. Ji (2008). Next-generation DNA sequencing. Nature Biotechnology 26:1135-1145.
19. Suzuki, M. M., A. Bird (2008). DNA methylation landscapes: provocative insights from epigenomics. Nature Reviews Genetics 9:465-476
20. Taylor, K. H., R. S. Kramer, J. W. Davis, J. Guo, D. J. Duff, D. Xu, C. W. Caldwell and H. Shi (2007). Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing, Cancer Res. 67: 8511-8518.
21. Vaucheret, H. (2006). Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev. 2006 20: 759-771.
22. Xueyong, Li, X. Wang, K. He, Y. Ma, N. Su, H. He, V. Stolc, W. Tongprasit, W. Jin, J. Jiang, W. Terzaghi, S. Li and X. W. Deng (2008). High-Resolution Mapping of Epigenetic Modifications of the Rice Genome Uncovers Interplay between DNA Methylation, Histone Methylation, and Gene Expression. The Plant Cell 20:259-276.
23. Zhang, X., J. Yazaki, A. Sundaresan, S. Cokus, S. W. Chan, H. Chen, I. R. Henderson, P. Shinn, M. Pellegrini, S. E. Jacobsen and J. R. Ecker (2006). Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126(6):1189-1201.