Quantitative epigenetics: DNA sequence variation need not apply

Genes and Development

Volumn 23, Issue 14, 2009, Pages 1601-1605

  Richards, Eric J ^a  

^a United States Department of Agriculture Agricultural Research Service and Boyce Thompson Institute for Plant Research   (United States)

Author keywords

DNA methylation; Epigenetics; Epigenome maps; Methylation profiling

Indexed keywords

ALLELE; ARABIDOPSIS; DNA SEQUENCE; EPIGENETICS; GENE MUTATION; GENETIC STABILITY; GENETIC VARIABILITY; NONHUMAN; PHENOTYPIC VARIATION; PRIORITY JOURNAL; QUANTITATIVE GENETICS; QUANTITATIVE TRAIT; RECOMBINANT INBRED STRAIN; REVIEW; TRANSPOSON; ARTICLE; GENETIC EPIGENESIS; GENETICS; GENOMIC INSTABILITY; INBREEDING; MUTATION; PHENOTYPE;

ARABIDOPSIS;

ARABIDOPSIS; DNA TRANSPOSABLE ELEMENTS; EPIGENESIS, GENETIC; GENETIC VARIATION; GENOMIC INSTABILITY; INBREEDING; MUTATION; PHENOTYPE;

EID: 67650590646     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.1824909     Document Type: Review

References (34)

1. Bossdorf O, Richards CL, Pigliucci M. 2008. Epigenetics for ecologists. Ecol Lett 11: 106-115.
2. Brennecke J, Malone CD, Aravin AA, Sachidanandam R, Stark A, Hannon GJ. 2008. An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 322: 1387-1392.
3. Chen RZ, Pettersson U, Beard C, Jackson-Grusby L, Jaenisch R. 1998. DNA hypomethylation leads to elevated mutation rates. Nature 395: 89-93.
4. Cubas P, Vincent C, Coen E. 1999. An epigenetic mutation responsible for natural variation in floral symmetry. Nature 401: 157-161.
5. Gal-Yam EN, Saito Y, Egger G, Jones PA. 2008. Cancer epigenetics: Modifications, screening, and therapy. Annu Rev Med 59: 267-280.
6. Garfinkel MD, Sollars VE, Lu X, Ruden DM. 2004. Multigenerational selection and detection of altered histone acetylation and methylation patterns: Toward a quantitative epigenetics in Drosophila. Methods Mol Biol 287: 151-168.
7. Jablonka E, Lamb MJ. 1995. Epigenetic inheritance and evolution: The lamarckian dimension. Oxford University Press, USA.
8. Jacobsen SE, Sakai H, Finnegan EJ, Cao X, Meyerowitz EM. 2000. Ectopic hypermethylation of flower-specific genes in Arabidopsis. Curr Biol 10: 179-186.
9. Jeddeloh JA, Stokes TL, Richards EJ. 1999. Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet 22: 94-97.
10. Johannes F, Colot V, Jansen RC. 2008. Epigenome dynamics: A quantitative genetics perspective. Nat Rev Genet 9: 883-890.
11. Johannes F, Porcher E, Teixeira FK, Saliba-Colombani V, Simon M, Agier N, Bulski A, Albuisson J, Heredia F, Audigier P, et al. 2009. Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet 5: e1000530. doi: 10.1371/journal.pgen.1000530.
12. Kakutani T, Munakata K, Richards EJ, Hirochika H. 1999. Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana. Genetics 151: 831-838.
13. Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, Jeddeloh JA, Riddle NC, Verbsky ML, Richards EJ. 2003. Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163: 1109-1122.
14. Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T. 2003. Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr Biol 13: 421-426.
15. Lippman Z, Gendrel AV, Black M, Vaughn MW, Dedhia N, McCombie WR, Lavine K, Mittal V, May B, Kasschau KD, et al. 2004. Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476.
16. Mathieu O, Reinders J, Caikovski M, Smathajitt C, Paszkowski J. 2007. Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130: 851-862.
17. McClintock B. 1984. The significance of responses of the genome to challenge. Science 226: 792-801.
18. Miura A, Yonebayashi S, Watanabe K, Toyama T, Shimada H, Kakutani T. 2001. Mobilization of transposons by a mutation abolishing full DNA methylation in Arabidopsis. Nature 411: 212-214.
19. Rapp RA,Wendel JF. 2005. Epigenetics and plant evolution. New Phytol 168: 81-91.
20. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J. 2008. Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Genome Res 18: 469-476.
21. Reinders J, Wulff BB, Mirouze M, Marí-Ordóñez A, Dapp M, Rozhon W, Bucher E, Theiler G, Paszkowski J. 2009. Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Genes & Dev 23: 939-950.
22. Richards EJ. 2006. Inherited epigenetic variation - Revisiting soft inheritance. Nat Rev Genet 7: 395-401.
23. Richards EJ. 2008. Population epigenetics. Curr Opin Genet Dev 18: 221-226.
24. Riddle NC, Richards EJ. 2002. The control of natural variation in cytosine methylation in Arabidopsis. Genetics 162: 355-363.
25. Rutherford SL, Henikoff S. 2003. Quantitative epigenetics. Nat Genet 33: 6-8.
26. Saze H, Mittelsten Scheid O, Paszkowski J. 2003. Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet 34: 65-69.
27. Slotkin RK, Vaughn M, Borges F, Tanurdzić M, Becker JD, Feijó JA, Martienssen RA. 2009. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136: 461-472.
28. Sollars V, Lu X, Xiao L, Wang X, Garfinkel MD, Ruden DM. 2003. Evidence for an epigenetic mechanism by which Hsp90 acts as a capacitor for morphological evolution. Nat Genet 33: 70-74.
29. Tariq M, Saze H, Probst AV, Lichota J, Habu Y, Paszkowski J. 2003. Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Proc Natl Acad Sci 100: 8823-8827.
30. Teixeira FK, Heredia F, Sarazin A, Roudier F, Boccara M, Ciaudo C, Cruaud C, Poulain J, Berdasco M, Fraga MF, et al. 2009. A role for RNAi in the selective correction of DNA methylation defects. Science 323: 1600-1604.
31. Vaughn MW, Tanurd Ić M, Lippman Z, Jiang H, Carrasquillo R, Rabinowicz PD, Dedhia N, McCombie WR, Agier N, Bulski A, et al. 2007. Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol 5: e174. doi: 10.1371/journal.pbio. 0050174.
32. Vongs A, Kakutani T, Martienssen RA, Richards EJ. 1993. Arabidopsis thaliana DNA methylation mutants. Science 260: 1926-1928.
33. Whitelaw NC, Whitelaw E. 2008. Transgenerational epigenetic inheritance in health and disease. Curr Opin Genet Dev 18: 273-279.
34. Youngson NA, Whitelaw E. 2008. Transgenerational epigenetic effects. Annu Rev Genomics Hum Genet 9: 233-257.