Mechanisms underlying epigenetic regulation in arabidopsis thaliana

Integrative and Comparative Biology

Volumn 54, Issue 1, 2014, Pages 61-67

  Jones, Ashley L ^a   Sung, Sibum ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84903590553     PISSN: 15407063     EISSN: 15577023     Source Type: Journal    
DOI: 10.1093/icb/icu030     Document Type: Conference Paper

References (65)

1. Albani MC, Castaings L, Wötzel S, Mateos J L, Wunder J, Wang R, Coupland G. 2012. PEP1 of Arabis alpina is encoded by two overlapping genes that contribute to natural genetic variation in perennial flowering. PLoS Genet 8:1-14.
2. Allfrey G, Faulkner R, Mirsky AE. 1964. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc Natl Acad Sci 315:786-94.
3. Bartee L, Malagnac F, Bender J. 2001. Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Gen Dev 15:1753-8. (Pubitemid 32905632)
4. Bender J, Fink GR. 1995. Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of Arabidopsis. Cell 83:725-34.
5. Berger SL, Kouzarides T, Shiekhattar R, Shilatifard A. 2009. An operational definition of epigenetics. Gen Dev 23:781-3.
6. Bernatavichute Y, Zhang X, Cokus S, Pellegrini M, Ja cobsen S. 2008. Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana. PLoS One 3:1-11.
7. Cao X, Jacobsen S. 2002. Role of the arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing. Curr Biol 12:1138-44. (Pubitemid 34766938)
8. Chan S, Henderson I, Zhang X, Shah G, Chien J, Jacobsen S. 2006a . RNAi, DRD1, and histone methylation activel y target developmentally important non-CG DNA methylation in arabidopsis. PLoS Genet 2:791-7.
9. Chan S, Zhang X, Bernatavichute Y, Jacobsen S. 2006b . Twostep recruitment of RNA-directed DNA methylation to tandem repeats. PLoS Biol 4:1923-33. (Pubitemid 44760009)
10. De Lucia F, Crevillen P, Jones A, Greb T, Dean C. 2008. A PHD-polycomb repressive complex 2 triggers the epigenetic silencing of FLC during vernalization. Proc Natl Acad 105:16831-6.
11. Finnegan EJ, Kovac KA, Jaligot E, Sheldon CC, Peacock WJ, Dennis ES. 2005. The downregulation of FLOWERI NG LOCUS C (FLC) expression in plants with low levels of DNA methylation and by vernalization occurs by distinct mechanisms. Plant J 44:420-32.
12. Foerster A, Dinh H, Sedman L, Wohlrab B, Mittelsten Scheid O. 2011. Genetic rearrangements can modify chromatin features at epialleles. PLoS Genet 7:1-13.
13. Fujimoto R, Kinoshita Y, Kawabe A, Kinoshita T, Takashima K, Nordborg M, Kakutani T. 2008. Ev olution and control of imprinted FWA genes in the genus Arabidopsis. PLoS Genet 4:1-11.
14. Greenberg M, Ausin I, Chan S, Cokus S, Cuperus J, Feng S, Jacobsen S. 2011. Identification of genes r equired for de novo DNA methylation in Arabidopsis. Epigenetics 6:344-54.
15. Gruenbaum Y, Naveh-Many T, Cedar H, Razin A. 1981. Sequence specificity of methylation in higher plant DNA. Nature 292:860-2. (Pubitemid 11015506)
16. Grunstein M. 1997. Histone acetylation in chromatin structure and transcription. Nature 389:349-52. (Pubitemid 27415209)
17. Heo JB, Sung S. 2011. Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA. Science 331:76-9.
18. Hepworth S, Valverde F, Ravenscroft D, Mouradov A, Coupland G. 2002. Antagonistic regulation of floweringtime gene SOC1 by CONSTANS and FLC via separate promot er motifs. EMBO J 21:4327-37.
19. Jackson JP, Lindroth AM, Cao X, Jacobsen SE. 2002. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416:556-60. (Pubitemid 34288860)
20. Jacobsen SE, Meyerowitz EM. 1997. Hypermethylated SUPERMAN epigenetic alleles in arabidopsis. Science 277:1100-3. (Pubitemid 27371632)
21. Jenuwein T, Allis CD. 2001. Translating the histone code. Science 293:1074-80. (Pubitemid 32758077)
22. Johannes F., Porcher E.,Teixeira F.K.,Saliba-Colombani V.,Simon M.,Agier N.,Colot V. 2009. Assessing the impact of transgenerational epigenetic variation on complex traits. PLoS Genet 5 1-11.
23. Johnson LM, Bostick M, Zhang X, Kraft E, Henderson I, Callis J, Jacobsen SE. 2007. The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol 17: 379-84. (Pubitemid 46241885)
24. Johnson LM, Law J, Khattar A, Henderson IR, Jacobsen SE. 2008. SRA-domain proteins required for DRM2-mediated de novo DNA methylation. PLoS Genet 4:1-13.
25. Kakutani T, Jeddeloh J, Flowers SK, Munakata K, Richards EJ. 1996. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations. Proc Natl Acad Sci USA 93:12406-11. (Pubitemid 26367156)
26. Kinoshita T, Miura A, Choi Y, Kinoshita Y, Cao X, Jacobsen SE, Kakutani T. 2004. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303:521-3. (Pubitemid 38120849)
27. Koorn neef M, Hanhart CJ, van der Veen JH. 1991. A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana. Mol Gen Genet 229:57-66.
28. Kothapalli N, Camporeale G, Kueh A, Chew YC, Oommen AM, Griffin JB, Zempleni J. 2005. Biological functions of biotinylated histones. J Nutr Biochem 16: 446-8. (Pubitemid 40916215)
29. Law JA, Jacobsen SE. 2010. Establish patterns in plants and animals. Nat Rev Genet 11: 204-20.
30. Lindroth AM, Shultis D, Jasencakova Z, Fuchs J, Johnson L, Schubert D, Jacobsen SE. 2004. Dual histone H3 methylation marks at lysines 9 and 27 required for interactio n with CHROMOMETHYLASE3. EMBO J 23:4286-96. (Pubitemid 39546166)
31. Lippman Z, et al. 2004. Role of transposable elements in heterochromatin and epigenetic control. Nature 430:471-6. (Pubitemid 38987911)
32. Lister R, O'Ma lley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar H, Ecker JR. 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523-36.
33. Lister R, Pelizzol a M, Dowen RH, Hawkins RD, Hon G, Nery JR, Ecker JR. 2009. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315-22.
34. Liu J, He Y, Amasino R, Chen X. 2004. siRNAs targeting an intronic transposon in the regulation of natural flowering behavior in Arabidopsis. Gen Dev 18:2873-8. (Pubitemid 39602306)
35. Liu S, Yu Y, Ruan Y, Meyer D, Wolff M, Xu L, Shen WH. 2007. Plant SET-And RING-Associated domain proteins in heterochromatinization. Plant J 52:914-26. (Pubitemid 350157757)
36. Liu X, Jiang F, Kalidas S, Smith D, Liu Q. 2006. Dicer-2 and R2D2 coordinately bind siRNA to promote assembly of the siRISC complexes. RNA 12:1514-20. (Pubitemid 44141531)
37. Mathieu O, Reinders J, Caikovski M, Smathajitt C, Paszkowski J. 2007. Transgenerational stability of the Arabidopsis epigenome is coordin ated by CG methylation. Cell 130:851-62. (Pubitemid 47334929)
38. Nordborg M, Weigel D. 2008. Next-generation genetics in plants. Nature 456:720-3.
39. Pham A, Sauer F. 2000. Ubiquitin-Activating/conjugating activity of TAF250, a mediator of activation of gene expression in Drosophila. Science 289:2357-60.
40. Popova OV, Dinh HQ, Aufsatz W, Jo nak C. 2013. The RdDM pathway is required for basal heat tolerance in Arabidopsis. Mol Plant 6:396-410.
41. Rangwala SH, Elumalai R, Vanier C, Ozkan H, Galbraith DW, Richards EJ. 2006. Meiotica lly stable natural epialleles of Sadhu, a novel Arabidopsis retroposon. PLoS Genet 2:270-81.
42. Reinders J, Wulff BB, Mirouze M, Mar| A. 2009. Compromised stability of DNA methylation and transposon immobilization in mosaic Arabidopsis epigenomes. Gen Dev 23:939-50.
43. Riddle NC,Richards EJ. 2005. Genetic variation in epigenetic inheritance of ribosomal RNA gene methylation in Arabidopsis Plant J 41 524-32. (Pubitemid 40307414)
44. Saze H, Kakutani T. 2007. Heritable epigenetic mutation of a transposon-flanked Arabidopsis gene due to lack of the chromatin-remodeling factor DDM1. EMBO J 26: 3641-52. (Pubitemid 47236873)
45. Shiio Y, Eis enman RN. 2003. Histone sumoylation is associated with transcriptional repression. Proc Natl Acad Sci USA 100:13225-30. (Pubitemid 37444723)
46. Soppe WJ, Jacobsen SE, Alonso-Blanco C, Jackson JP, Kakutani T, Koornneef M, Peeters J. 2000. The late flowering phenotype of fwa mutants is caused by gain-of-function epigenetic alleles of a homeodomain gene. Mol Cell 6:791-802.
47. Strahl BD, Allis CD. 2000. The language of covalent histone modications. Nature 403:41-5.
48. Swiezewski S, Liu F, Magusin A, Dean C. 2009. Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature 462:799-802.
49. Teif VB, Rippe K. 2009. Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities. Nucleic Acids Res 37:5641-55.
50. Trevaskis B , Hemming MN, Dennis ES, Peacock WJ. 2007. The molecular basis of vernalization-induced flowering in cereals. Trends Plant Sci 12:352-7. (Pubitemid 47187749)
51. Vanyushin BF. 2006. DNA methylation and epigenetics. Russ J Genet 42:985-97. (Pubitemid 44450867)
52. Wagner D. 2003. Chromatin regulation of plant development. Curr Opin Plant Biol 6:20-8. (Pubitemid 36064211)
53. Wang R, Farrona S, Vincent C, Joecker A, Schoof H, Turck F, Albani MC. 2009. PEP1 regulates perennial flowering in Arabis alpina. Nature 459:423-7.
54. Wei Y, Yu L, Bowen J, Gorovsky MA, Allis CD. 1999. Phosphorylation of histone H3 is required for proper chromosome condensation and segregation. Cell 97:99-109. (Pubitemid 29165893)
55. Weinberg MS, Morris KV. 2013. Long non-coding RNA targeting and transcriptional de-repression. Nucleic Acid Ther 23:9-14.
56. Whitehouse I, Flaus A, Cairns BR, White MF, Workman JL, Owen-Hughes T. 1999. Nucleosome mobilization catalysed by the yeast SWI/SNF complex. Nature 400:784-7. (Pubitemid 29399542)
57. Wierzbicki A, Ream T, Jeremy H, Pikaard C. 2009. RNA Polymerase V transcription guides ARGONAUTE4 to chromatin. Nat Genet 41:630-34.
58. Woo HR, Dittmer T, Richards EJ. 2008. Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis. PLoS Genet 4:1-13.
59. Wood CC, Robertson M , Tanner G, Peacock WJ, Dennis ES, Helliwell C. 2006. The Arabidopsis thaliana vernalization response requires a polycomb-like protein complex that also includes VERNALIZATION INSENSITIVE 3. Proc Natl Acad Sci USA 103:14631-6. (Pubitemid 44484801)
60. Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, ZilbermanD,Carrington JC. 2004. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol 2:642-52.
61. Zemach A, Kim MY, Hsieh PH, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heter ochromatin. Cell 153:193-205.
62. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, Chen H, Ecker JR. 2006. Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidop sis. Cell 126:1189-201. (Pubitemid 44380289)
63. Zheng B, Wang Z, Li S, Yu B, Liu JY, Chen X. 2009. Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silen cing in Arabidopsis. Gen Dev 23:2850-60.
64. Zilberman D,Cao X,Jacobsen SE. 2003. ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation Science 299 716-9. (Pubitemid 36159488)
65. Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004. Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats. Curr Biol 14:1214-20. (Pubitemid 38893986)