Epigenome dynamics: A quantitative genetics perspective

Nature Reviews Genetics

Volumn 9, Issue 11, 2008, Pages 883-890

  Johannes, Frank ^a   Colot, Vincent ^b   Jansen, Ritsert C ^a,c  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b ECOLE NORMALE SUPÉRIEURE   (France)

^c UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; TRANS ACTING FACTOR;

CHROMATIN; DNA METHYLATION; DNA SEQUENCE; EPIGENETICS; GENOME ANALYSIS; GENOTYPE; HIGH THROUGHPUT SCREENING; MEIOSIS; MITOSIS; NONHUMAN; PHENOTYPE; PHENOTYPIC VARIATION; PLANT GENETICS; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS MAPPING; REVIEW; SEQUENCE ANALYSIS;

BASE SEQUENCE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; EPIGENESIS, GENETIC; EVOLUTION, MOLECULAR; GENETICS, POPULATION; PHENOTYPE; QUANTITATIVE TRAIT LOCI; VARIATION (GENETICS);

EID: 54149109197     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg2467     Document Type: Review

References (50)

1. Vaughn, M. W. et al. Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol. 5, e174 (2007).
2. Zhang, X., Shiu, S., Cal, A. & Borevitz, J. O. Global analysis of genetic, epigenetic and transcriptional polymorphisms in Arabidopsis thaliana using whole genome tiling arrays. PLoS Genet. 4, e1000032 (2008).
3. Riddle, N. C. & Richards, E. J. The control of natural variation in cytosine methylation in Arabidopsis. Genetics 162, 355-363 (2002).
4. Riddle, N. C. & Richards, E. J. Genetic variation in epigenetic inheritance of ribosomal RNA gene methylation in Arabidopsis. Plant J. 41, 524-532 (2005).
5. Kakutani, T., Munakata, K., Richards, E. J. & Hirochika, H. Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana. Genetics 151, 831-838 (1999).
6. Peaston, A. E. & Whitelaw, E. Epigenetics and phenotypic variation in mammals. Mamm. Genome 17, 365-374 (2006).
7. Richards, E. J. Inherited epigenetic variation - revisiting soft inheritance. Nature Rev. Genet. 7, 395-401 (2006).
8. Henderson, I. R. & Jacobsen, S. E. Epigenetic inheritance in plants. Nature 447, 418-424 (2007).
9. Chan, S. W., Henderson, I. R. & Jacobsen, S. E. Gardening the genome: DNA methylation in Arabidopsis thaliana. Nature Rev. Genet. 6, 351-360 (2005).
10. Martienssen, R. A. & Colot, V. DNA methylation and epigenetic inheritance in plants and filamentous fungi. Science 293, 1070-1074 (2001).
11. Stam, M., Belele, C., Dorweiler, J. E. & Chandler, V. L. Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev. 16, 1906-1918 (2002).
12. Soppe, W. J. et al. The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol. Cell 6, 791-802 (2000).
13. Das, O. P. & Messing, J. Variegated phenotype and developmental methylation changes of a maize allele originating from epimutation. Genetics 136, 1121-1141 (1994).
14. Rakyan, V. K., Blewitt, M. E., Druker, R., Preis, J. I. & Whitelaw, E. Metastable epialleles in mammals. Trends Genet. 18, 348-351 (2002).
15. Penterman, J. et al. DNA demethylation in the Arabidopsis genome. Proc. Natl Acad. Sci. USA 104, 6752-6757 (2007).
16. Mathieu, O., Reinders, J., Caikovski, M., Smathajitt, C. & Paszkowski, J. Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130, 851-862 (2007).
17. Richards, E. J. Population epigenetics. Curr. Opin. Genet. Dev. 18, 221-226 (2008).
18. Zilberman, D. & Henikoff, S. Genome-wide analysis of DNA methylation patterns. Development 134, 3959-3965 (2007).
19. Schones, D. E. & Zhao, K. Genome-wide approaches to studying chromatin modifications. Nature Rev. Genet. 9, 179-191 (2008).
20. Suzuki, M. M. & Bird, A. DNA methylation landscapes: provocative insights from epigenomics. Nature Rev. Genet. 9, 465-476 (2008).
21. Cokus, S. J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215-219 (2008).
22. Weber, M. et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nature Genet. 37, 853-862 (2005).
23. Zhang, X. et al. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol. 5, e129 (2007).
24. Zhang, X. et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189-1201 (2006).
25. Zilberman, D. The human promoter methylome. Nature Genet. 39, 442-443 (2007).
26. Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T. & Henikoff, S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nature Genet. 39, 61-69 (2007).
27. Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 2, 395-397 (2008).
28. Jansen, R. C. Studying complex biological systems using multifactorial perturbation. Nature Rev. Genet. 4, 145-151 (2003).
29. Mager, J. & Bartolomei, M. S. Strategies for dissecting epigenetic mechanisms in the mouse. Nature Genet. 37, 1194-1200 (2005).
30. Petronis, A. Epigenetics and twins: three variations on the theme. Trends Genet. 22, 347-350 (2006).
31. Rockman M. V. & Kruglyak L. Genetics of global gene expression. Nature Rev. Genet. 7, 862-872 (2006).
32. Rosa G. J.M, et al. Review of microarray experimental design strategies for genetical genomics studies. Physiol. Genomics 28, 15-23 (2006).
33. Li Y. et al. Mapping determinants of gene expression plasticity by genetical genomics in C. elegans. PLoS Genet. 2, e222 (2006).
34. Li Y. et al. Generalizing genetical genomics: getting added value from environmental perturbation. Trends Genet. 24, 518-524 (2008).
35. Smith E. N. & Kruglyak L. Gene-environment interaction in yeast gene expression. PLoS Biol. 6, e83 (2008).
36. Bossdorf, O., Richards, C. L. & Pigliucci, M. Epigenetics for ecologists. Ecol. Lett. 11, 106-115 (2008).
37. Jones, P. A. & Baylin, S. B. The epigenomics of cancer. Cell 128, 683-692 (2007).
38. Meissner et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766-770 (2008).
39. Farthing et al. Global mapping of DNA methylation in mouse promoters reveals epigenetic reprogramming of pluripotency genes. PLoS Genet. 4, e1000116 (2008).
40. Mikkelsen et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553-560 (2007).
41. Bjornsson, H. T., Fallin, M. D. & Feinberg, A. P. An integrated epigenetic and genetic approach to common human disease. Trends Genet. 20, 350-358 (2004).
42. Johannes, F. Mapping temporally varying quantitative trait loci in time-to-failure experiments. Genetics 175, 855-865 (2007).
43. Wu, R. & Lin, M. Functional mapping - how to map and study the genetic architecture of dynamic complex traits. Nature Rev. Genet. 7, 229-237 (2006).
44. Henckaerts, E., et al. Genetically determined variation in the number of phenotypically defined hematopoietic progenitor and stem cells and their response to early acting cytokines. Blood 99, 3947-3954 (2002).
45. Cheverud, J. M., et al. Quantitative trait loci for murine growth. Genetics 142, 1305-1319 (1996).
46. Wolf J. B., et al. Genome-wide analysis reveals a complex pattern of genomic imprinting in mice. PLoS Genet. 4, e1000091 (2008).
47. Sollars, V. et al. Evidence for an epigenetic mechanism by which Hsp90 acts as a capacitor for morphological evolution. Nature Genet. 33, 70-74 (2003).
48. Csaba, P. Plasticity, memory and the adaptive landscape of the genotype. Proc. R. Soc. Lond. B 265, 1319-1323 (1998).
49. Pal, C. & Miklos, I. Epigenetic inheritance, genetic assimilation and speciation. J. Theor. Biol. 200, 19-37 (1999).
50. Rando, O. J. & Verstrepen, K. J. Timescales of genetic and epigenetic inheritance. Cell 128, 655-668 (2007).