siRNAs and DNA methylation: seedy epigenetics

Trends in Plant Science

Volumn 15, Issue 4, 2010, Pages 204-210

  Mosher, Rebecca A ^a   Melnyk, Charles W ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

SMALL INTERFERING RNA;

ARABIDOPSIS; DNA METHYLATION; ENDOSPERM; GENE EXPRESSION REGULATION; GENETICS; GENOME IMPRINTING; METABOLISM; PLANT SEED; REVIEW; TRANSPOSON;

ARABIDOPSIS; DNA METHYLATION; DNA TRANSPOSABLE ELEMENTS; ENDOSPERM; GENE EXPRESSION REGULATION, PLANT; GENOMIC IMPRINTING; RNA, SMALL INTERFERING; SEEDS;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

EID: 77950518292     PISSN: 13601385     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tplants.2010.01.002     Document Type: Review

References (77)

1. Gehring M., et al. Extensive demethylation of repetitive elements during seed development underlies gene imprinting. Science 324 (2009) 1447-1451
2. Hsieh T.F., et al. Genome-wide demethylation of Arabidopsis endosperm. Science 324 (2009) 1451-1454
3. Mosher R.A., et al. Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature 460 (2009) 283-286
4. Slotkin R.K., et al. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell 136 (2009) 461-472
5. Sun G., et al. Archaefructaceae, a new basal angiosperm family. Science 296 (2002) 899-904
6. Berger F., et al. Double fertilization - caught in the act. Trends Plant Sci. 13 (2008) 437-443
7. Xie Z., et al. Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2 (2004) e104
8. Herr A.J., et al. RNA polymerase IV directs silencing of endogenous DNA. Science 308 (2005) 118-120
9. Kanno T., et al. Atypical RNA polymerase subunits required for RNA-directed DNA methylation. Nat. Genet. 37 (2005) 761-765
10. Onodera Y., et al. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell 120 (2005) 613-622
11. Pontier D., et al. Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Gene. Dev. 19 (2005) 2030-2040
12. Luo J., and Hall B.D. A multistep process gave rise to RNA polymerase IV of land plants. J. Mol. Evol. 64 (2007) 101-112
13. He X.J., et al. An effector of RNA-directed DNA methylation in Arabidopsis is an ARGONAUTE 4-and RNA-binding protein. Cell 137 (2009) 498-508
14. Huang L.F., et al. An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II. Nat. Struct. Mol. Biol. 16 (2009) 91-93
15. Lahmy S., et al. PolV(PolIVb) function in RNA-directed DNA methylation requires the conserved active site and an additional plant-specific subunit. Proc. Natl. Acad. Sci. U. S. A. 106 (2009) 941-946
16. Ream T.S., et al. Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II. Mol. Cell 33 (2009) 192-203
17. Mosher R.A., et al. PolIVb influences RNA-directed DNA-methylation independently of its role in siRNA biogenesis. Proc. Natl. Acad. Sci. U. S. A. 105 (2008) 3145-3150
18. Zhang X., et al. Role of RNA polymerase IV in plant small RNA metabolism. Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 4536-4541
19. Wierzbicki A.T., et al. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135 (2008) 635-648
20. Wierzbicki A.T., et al. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat. Genet. 41 (2009) 630-634
21. Zheng X., et al. ROS3 is an RNA-binding protein required for DNA demethylation in Arabidopsis. Nature 455 (2008) 1259-1262
22. Kinoshita T., et al. Imprinting of the MEDEA polycomb gene in the Arabidopsis endosperm. Plant Cell 11 (1999) 1945-1952
23. Kinoshita T., et al. One-way control of FWA imprinting in Arabidopsis endosperm by DNA methylation. Science 303 (2004) 521-523
24. Kohler C., et al. The Arabidopsis thaliana MEDEA Polycomb group protein controls expression of PHERES1 by parental imprinting. Nat. Genet. 37 (2005) 28-30
25. Jullien P.E., et al. Maintenance of DNA methylation during the Arabidopsis life cycle is essential for parental imprinting. Plant Cell 18 (2006) 1360-1372
26. Tiwari S., et al. MATERNALLY EXPRESSED PAB C-TERMINAL, a novel imprinted gene in Arabidopsis, encodes the conserved C-terminal domain of polyadenylate binding proteins. Plant Cell 20 (2008) 2387-2398
27. Fitz Gerald J.N., et al. Polycomb group-dependent imprinting of the actin regulator AtFH5 regulates morphogenesis in Arabidopsis thaliana. Development 136 (2009) 3399-3404
28. Garnier O., et al. Genomic imprinting in plants. Epigenetics 3 (2008) 14-20
29. Wilkinson L.S., et al. Genomic imprinting effects on brain development and function. Nat. Rev. Neurosci. 8 (2007) 832-843
30. Haig D., and Westoby M. Parent-specific gene expression and the triploid endosperm. Am. Nat. 134 (1989) 147-155
31. Renfree M.B., et al. Evolution of genomic imprinting: insights from marsupials and monotremes. Annu. Rev. Genomics Hum. Genet. 10 (2009) 241-262
32. Adams S., et al. Parent-of-origin effects on seed development in Arabidopsis thaliana require DNA methylation. Development 127 (2000) 2493-2502
33. Xiao W., et al. Regulation of seed size by hypomethylation of maternal and paternal genomes. Plant Physiol. 142 (2006) 1160-1168
34. Choi Y., et al. DEMETER, a DNA glycosylase domain protein, is required for endosperm gene imprinting and seed viability in Arabidopsis. Cell 110 (2002) 33-42
35. Xiao W., et al. Imprinting of the MEA Polycomb gene is controlled by antagonism between MET1 methyltransferase and DME glycosylase. Dev. Cell 5 (2003) 891-901
36. Jullien P.E., et al. Retinoblastoma and its binding partner MSI1 control imprinting in Arabidopsis. PLoS Biol. 6 (2008) e194
37. Chan S.W.-L., et al. Two-step recruitment of RNA-directed DNA methylation to tandem repeats. PLoS Biol. 4 (2006) e363
38. Vielle-Calzada J.P., et al. Delayed activation of the paternal genome during seed development. Nature 404 (2000) 91-94
39. Pan Y.B., and Peterson P.A. Spontaneous activation of quiescent uq transposable elements during endosperm development in Zea mays. Genetics 119 (1988) 457-464
40. Schoft V.K., et al. Induction of RNA-directed DNA methylation upon decondensation of constitutive heterochromatin. EMBO Rep. 10 (2009) 1015-1021
41. Arazi T., et al. Cloning and characterization of micro-RNAs from moss. Plant J. 43 (2005) 837-848
42. Axtell M.J., and Bartel D.P. Antiquity of microRNAs and their targets in land plants. Plant Cell 17 (2005) 1658-1673
43. Axtell M.J., et al. Common functions for diverse small RNAs of land plants. Plant Cell 19 (2007) 1750-1769
44. Fattash I., et al. Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution. BMC Plant Biol. 7 (2007) 1-19
45. Dolgosheina E.V., et al. Conifers have a unique small RNA silencing signature. RNA 14 (2008) 1508-1515
46. Morin R.D., et al. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa. Genome Res. 18 (2008) 571-584
47. Cho S.H., et al. Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development. PLoS Genet. 4 (2008) e1000314
48. Osborn T.C., et al. Understanding mechanisms of novel gene expression in polyploids. Trends Genet. 19 (2003) 141-147
49. McClintock B. The significance of responses of the genome to challenge. Science 226 (1984) 792-801
50. Blumenstiel J.P., and Hartl D.L. Evidence for maternally transmitted small interfering RNA in the repression of transposition in Drosophila virilis. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 15965-15970
51. Kalmykova A.I., et al. Argonaute protein PIWI controls mobilization of retrotransposons in the Drosophila male germline. Nucleic Acids Res. 33 (2005) 2052-2059
52. Brennecke J., et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128 (2007) 1089-1103
53. Chambeyron S., et al. piRNA-mediated nuclear accumulation of retrotransposon transcripts in the Drosophila female germline. Proc. Natl. Acad. Sci. U. S. A. 105 (2008) 14964-14969
54. Josefsson C., et al. Parent-dependent loss of gene silencing during interspecies hybridization. Curr. Biol. 16 (2006) 1322-1328
55. Selinger D.A., and Chandler V.L. B-Bolivia, an allele of the maize b1 gene with variable expression, contains a high copy retrotransposon-related sequence immediately upstream. Plant Physiol. 125 (2001) 1363-1379
56. Kermicle J.L. Dependence of the R-mottled aleurone phenotype in maize on mode of sexual transmission. Genetics 66 (1970) 69-85
57. Chaudhuri S., and Messing J. Allele-specific parental imprinting of dzr1, a posttranscriptional regulator of zein accumulation. Proc. Natl. Acad. Sci. U. S. A. 91 (1994) 4867-4871
58. Lund G., et al. Maternal-specific demethylation and expression of specific alleles of zein genes in the endosperm of Zea mays L. Plant J. 8 (1995) 571-581
59. Lund G., et al. Endosperm-specific demethylation and activation of specific alleles of alpha-tubulin genes of Zea mays L. Mol. Gen. Genet. 246 (1995) 716-722
60. Suzuki S., et al. Genomic imprinting of IGF2, p57(KIP2) and PEG1/MEST in a marsupial, the tammar wallaby. Mech. Dev. 122 (2005) 213-222
61. Warren W.C., et al. Genome analysis of the platypus reveals unique signatures of evolution. Nature 453 (2008) 175-183
62. Pask A.J., et al. Analysis of the platypus genome suggests a transposon origin for mammalian imprinting. Genome Biol. 10 (2009) R1
63. Jahnke S., and Scholten S. Epigenetic resetting of a gene imprinted in plant embryos. Curr. Biol. 19 (2009) 1677-1681
64. Molinier J., et al. Transgeneration memory of stress in plants. Nature 442 (2006) 1046-1049
65. Chinnusamy V., and Zhu J.K. RNA-directed DNA methylation and demethylation in plants. Sci. China C Life Sci. 52 (2009) 331-343
66. Teixeira F.K., et al. A role for RNAi in the selective correction of DNA methylation defects. Science 323 (2009) 1600-1604
67. Palauqui J.C., et al. Systemic acquired silencing: transgene-specific post-transcriptional silencing is transmitted by grafting from silenced stocks to non-silenced scions. EMBO J. 16 (1997) 4738-4745
68. Voinnet O., and Baulcombe D.C. Systemic signalling in gene silencing. Nature 389 (1997) 553
69. Fire A., et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391 (1998) 806-811
70. Vielle-Calzada J.P., et al. Maintenance of genomic imprinting at the Arabidopsis medea locus requires zygotic DDM1 activity. Genes Dev. 13 (1999) 2971-2982
71. Luo M., et al. Expression and parent-of-origin effects for FIS2, MEA, and FIE in the endosperm and embryo of developing Arabidopsis seeds. Proc. Natl. Acad. Sci. U. S. A 97 (2000) 10637-10642
72. Baroux C., et al. Dynamic regulatory interactions of Polycomb group genes: MEDEA autoregulation is required for imprinted gene expression in Arabidopsis. Genes Dev. 20 (2006) 1081-1086
73. Jullien P.E., et al. Polycomb group complexes self-regulate imprinting of the Polycomb group gene MEDEA in Arabidopsis. Curr. Biol. 16 (2006) 486-492
74. Kinoshita Y., et al. Control of FWA gene silencing in Arabidopsis thaliana by SINE-related direct repeats. Plant J. 49 (2007) 38-45
75. Kohler C., et al. The Polycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1. Genes Dev. 17 (2003) 1540-1553
76. Makarevich G., et al. Mechanism of PHERES1 imprinting in Arabidopsis. J. Cell Sci. 121 (2008) 906-912
77. Villar, C.B. et al. (2009) Control of PHERES1 imprinting in Arabidopsis by direct tandem repeats. Molecular Plant 2, 654-660