Plants, pairing and phenotypes - Two's company?

Trends in Genetics

Volumn 20, Issue 4, 2004, Pages 188-195

  Grant Downton, Robert T ^a   Dickinson, Hugh G ^a  

^a Department of Plant Sciences ^*  (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

RNA; ZEIN;

ALLELE; CHROMOSOME PAIRING; ENDOSPERM; EPIGENETICS; GENE EXPRESSION REGULATION; GENE SEQUENCE; HOMOZYGOSITY; HYBRID; HYBRIDIZATION; INBREEDING DEPRESSION; NONHUMAN; PHENOTYPE; PLANT; PLANT DEVELOPMENT; PRIORITY JOURNAL; REVIEW;

EMBRYOPHYTA; TRANSPOSONS;

EID: 1642286026     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2004.02.005     Document Type: Article

References (78)

1. Hamilton A.J., Baulcombe D.C. A species of small antisense RNA in posttranscriptional gene silencing in plants. Science. 286:1999;950-952.
2. Dalmay T., et al. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell. 101:2000;543-553.
3. Fagard M., et al. AGO1, QDE2 and RDE1 are related proteins required for post-transcriptonal gene silencing in plants, quelling in fungi, and RNA interference in animals. Proc. Natl. Acad. Sci. U. S. A. 97:2000;11650-11654.
4. Schauer S.E., et al. DICER-LIKE1: blind men and elephants in Arabidopsis development. Trends Plant Sci. 7:2002;487-491.
5. Waterhouse P.M., et al. Gene silencing as an adaptive defence against viruses. Nature. 411:2001;834-841.
6. Jones L. Revealing micro-RNAs in plants. Trends Plant Sci. 7:2002;473-475.
7. Kidner C.A., Martienssen R.A. Macro effects of microRNAs in plants. Trends Genet. 19:2003;13-16.
8. Rhoades M.W., et al. Prediction of plant microRNA targets. Cell. 110:2002;513-520.
9. Tang G., et al. A biochemical framework for RNA silencing in plants. Genes Dev. 17:2003;49-63.
10. Llave C., et al. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science. 297:2002;2053-2056.
11. Reinhart B.J., Bartel D.P. Small RNAs correspond to centromere heterochromatic repeats. Science. 297:2002;1831.
12. Volpe T.A., et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science. 297:2002;1833-1837.
13. Sleutels F., et al. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature. 415:2002;810-813.
14. Franke A., Baker B.S. Dosage compensation rox! Curr. Opin. Cell Biol. 12:2000;351-354.
15. Avner P., Heard E. X chromosome inactivation: counting, choice and initiation. Nat. Rev. Genet. 2:2001;59-67.
16. Citovsky V., Zambryski P. Systemic transport of RNA in plants. Trends Plant Sci. 5:2000;52-54.
17. Klahre U., et al. High molecular weight RNAs and small interfering RNAs induce systemic post-transcriptional gene silencing in plants. Proc. Natl. Acad. Sci. U. S. A. 99:2002;11981-11986.
18. Hollick J.B., et al. Paramutation and related allelic interactions. Trends Genet. 13:1997;302-308.
19. Chandler V.L., et al. Paramutation in maize. Plant Mol. Biol. 43:2000;121-145.
20. Herman H., et al. Trans allele methylation and paramutation-like effects in mice. Nat. Genet. 34:2003;199-202.
21. Stam M., et al. Differential chromatin structure within a tandem array 100 kb upstream of the maize b1 locus is associated with paramutation. Genes Dev. 16:2002;1906-1918.
22. Sidorenko L.V., Peterson T. Transgene-induced silencing identifies sequences invoved in the establishment of paramutation of the maize p1 gene. The Plant Cell. 13:2001;319-335.
23. Qin H., et al. Epigenetic interactions between Arabidopsis transgenes: characterization in light of transgene integration sites. Plant Mol. Biol. 52:2003;217-231.
24. Mittelsten Scheid O., et al. Formation of stable epialleles and their paramutation-like interaction in tetraploid Arabidopsis thaliana. Nat. Genet. 34:2003;450-454.
25. Matzke M., et al. A test for transvection in plants: DNA pairing may lead to trans-activation or silencing of complex heteroalleles in tobacco. Genetics. 158:2001;451-461.
26. Klöti A., et al. Tissue-specific silencing of a transgene in rice. Proc. Natl. Acad. Sci. U. S. A. 99:2002;10881-10886.
27. Kusaba M., et al. Monoallelic expression and dominance interactions in anthers of self-incompatible Arabidopsis lyrata. Plant Physiol. 128:2002;17-20.
28. Hiraoka Y., et al. The onset of homologous chromosome pairing during Drosophila melanogaster embryogenesis. J. Cell Biol. 120:1993;591-600.
29. Avivi L., Feldman M. Arrangement of chromosomes in the interphase nucleus of plants. Hum. Genet. 55:1980;281-295.
30. Fransz P., et al. Interphase chromosomes in Arabidopsis are organised as well-defined chromocenters from which euchromatin loops emanate. Proc. Natl. Acad. Sci. U. S. A. 99:2002;14584-14589.
31. Dong F., Jiang J. Non-Rabl patterns of centromere and telomere distribution in the interphase nuclei of plant cells. Chromosome Res. 6:1998;551-558.
32. Aragon-Alcaide L., et al. Association of homologous chromosomes during floral development. Curr. Biol. 7:1997;905-990.
33. Martínez-Pérez E., et al. The Ph1 locus is needed to ensure specific somatic and meiotic centromere association. Nature. 411:2001;204-207.
34. Abranches R., et al. Widely separated multiple transgene integration sites in wheat chromosomes are brought together at interphase. Plant J. 24:2000;713-723.
35. Kato N., Lam E. Chromatin of endoreduplicated pavement cells has greater range of movement than that of diploid guard cells in Arabidopsis thaliana. J. Cell Sci. 116:2003;2195-2201.
36. William R.R.E. Transcription and the territory: the ins and outs of gene positioning. Trends Genet. 19:2003;298-302.
37. Cook P.R. The transcriptional basis of chromosome pairing. J. Cell Sci. 110:1997;1033-1040.
38. Renauld H., Gasser S.M. Heterochromatin: a meiotic matchmaker? Trends Cell Biol. 7:1997;201-205.
39. Allen E., et al. High concentrations of long interspersed nuclear element sequences distinguish monoallelically expressed genes. Proc. Natl. Acad. Sci. U. S. A. 100:2003;9940-9945.
40. Frank-Kamenetskii M.D., Mirkin S.M. Triplex DNA structures. Annu. Rev. Biochem. 64:1995;65-95.
41. Ohno M., et al. Triplex-forming DNAs in the human interphase nucleus visualized in situ by polypurine/polypyrimidine DNA probes and antitriplex antibodies. Chromosoma. 111:2002;201-213.
42. Sakamoto N., et al. Sticky DNA: self-association properties of long GAA.TTC repeats in R.R.Y triplex structures from Friedrich's ataxia. Mol. Cell. 3:1999;465-475.
43. Sakamoto N., et al. Sticky DNA, a self-associated complex formed at long GAA TTC Repeats in intron 1 of the Frataxin gene, inhibits transcription. J. Biol. Chem. 276:2001;27171-27177.
44. Goobes R., et al. Unique condensation patterns of triplex DNA: physical and physiological implications. Nucleic Acids Res. 30:2002;2154-2161.
45. Jacobsen S.E., et al. Ectopic hypermethylation of flower-specific genes in Arabidopsis. Curr. Biol. 10:2000;179-186.
46. LaSalle J.M., Lalande M. Homologous association of oppositely imprinted chromosomal domains. Science. 272:1996;725-728.
47. Jones R.N. B chromosomes in plants. New Phytol. 131:1995;411-434.
48. Jones R.N., Rees H. An anomalous variation due to B chromosomes in rye. Heredity. 24:1969;265-271.
49. Birchler J.A., et al. In search of the molecular basis of heterosis. The Plant Cell. 15:2003;2236-2239.
50. Tsaftaris S.A. Molecular aspects of heterosis. Physiol. Plant. 94:1995;362-370.
51. Crow J.F. Dominance and overdominance. Gowen J.W. Heterosis: A Record of Researches Directed Toward Explaining and Utilising the Vigor of Hybrids. 1964;282-297 Hafner Publishing Company.
52. Song R., Messing J. Gene expression of a gene family in maize based on noncollinear haplotypes. Proc. Natl. Acad. Sci. U. S. A. 100:2003;9055-9060.
53. 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.
54. Chaudhury A.M., et al. Control of early seed development. Annu. Rev. Cell Dev. Biol. 17:2001;677-699.
55. Spielman M., et al. The epigenetic basis of gender in flowering plants and mammals. Trends Genet. 17:2001;705-711.
56. Osborn T.C., et al. Understanding mechanisms of novel gene expression in polyploids. Trends Genet. 19:2003;141-147.
57. Stokes T.L., Richards E.J. Induced instability of two Arabidopsis constitutive pathogen-response alleles. Proc. Natl. Acad. Sci. U. S. A. 99:2002;7792-7796.
58. Comai L., et al. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. The Plant Cell. 12:2000;1551-1568.
59. Chase S.S. Monoploids and diploids of maize: a comparison of genotypic equivalents. Am. J. Bot. 51:1964;928-933.
60. Henikoff S., Comai L. Trans-sensing effects: the ups and downs of being together. Cell. 93:1998;329-332.
61. Wu C.-T., Morris J.R. Transvection and other homology effects. Curr. Opin. Genet. Dev. 9:1999;237-246.
62. Pirrotta V. Transvection and chromosomal trans-interaction effects. Biochim. Biophys. Acta. 1424:1999;M1-M8.
63. Duncan I.W. Transvection effects in Drosophila. Annu. Rev. Genet. 36:2002;521-556.
64. Lewis E.B. The theory and application of a new method of detecting chromosomal rearrangements in Drosophila melanogaster. Am. Nat. 88:1954;225-239.
65. Bantignies F., et al. Inheritance of Polycomb-dependent chromosomal interactions in Drosophila. Genes Dev. 17:2003;2406-2420.
66. Goodrich J., Tweedie S. Remembrance of things past: chromatin remodeling in plant development. Annu. Rev. Cell Dev. Biol. 18:2002;707-746.
67. Alvarez-Venegas R., et al. ATX-1, an Arabidopsis homolog of Trithorax, activates flower homeotic genes. Curr. Biol. 13:2003;627-637.
68. Dorweiler J.E., et al. mediator of paramutation1 is required for establishment and maintenance of paramutation at multiple maize loci. The Plant Cell. 12:2000;2101-2118.
69. Lisch D., et al. A mutation that prevents paramutation in maize also reverses Mutator transposon methylation and silencing. Proc. Natl. Acad. Sci. U. S. A. 99:2002;6130-6135.
70. Hollick J.B., Chandler V.L. Genetic factors required to maintain repression of paramutagenic maize pl allele. Genetics. 157:2001;369-378.
71. Reinhart B.J., Bartel D.P. Small RNAs correspond to centromere heterochromatic repeats. Science. 297:2002;1831.
72. Volpe T.A., et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science. 297:2002;1833-1837.
73. Soppe W.J.J., et al. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J. 21:2002;6549-6559.
74. Mittelsten Scheid O., et al. Two regulatory levels of transcriptional gene silencing in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 99:2002;13659-13662.
75. Shiu P.K.T., et al. Meiotic silencing of unpaired DNA. Cell. 107:2001;905-916.
76. Dalmay T., et al. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell. 101:2000;543-553.
77. Bean C.J., et al. Meiotic pairing and imprinted X chromatin assembly in Caenorhabditis elegans. Nat. Genet. 36:2003;100-105.
78. Dekker J. A closer look at long-range chromosomal interactions. Trends Biochem. Sci. 28:2003;277-280.