Structural basis of transcriptional gene silencing mediated by Arabidopsis MOM1

PLoS Genetics

Volumn 8, Issue 2, 2012, Pages

  Nishimura, Taisuke ^a,b,c   Molinard, Guillaume ^a   Petty, Tom J ^a   Broger, Larissa ^a   Gabus, Caroline ^a   Halazonetis, Thanos D ^a   Thore, Stéphane ^a   Paszkowski, Jerzy ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c NAGOYA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS PROTEIN; PROTEIN MOM1; SMALL INTERFERING RNA; UNCLASSIFIED DRUG; MOM PROTEIN, ARABIDOPSIS; NUCLEAR PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; CHROMOSOME; DIMERIZATION; EPIGENETICS; GENE LOCUS; GENE REPRESSION; GENE SILENCING; GENETIC COMPLEMENTATION; GENETIC REGULATION; GENETIC TRANSCRIPTION; MUTAGENESIS; NONHUMAN; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN STRUCTURE; TRANSCRIPTION REGULATION; TRANSGENICS; X RAY CRYSTALLOGRAPHY; AMINO ACID SEQUENCE; ARABIDOPSIS; CHEMISTRY; GENE EXPRESSION REGULATION; GENETIC EPIGENESIS; GENETICS; MOLECULAR GENETICS; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN MULTIMERIZATION; PROTEIN TERTIARY STRUCTURE; STRUCTURE ACTIVITY RELATION; TRANSGENIC PLANT;

ARABIDOPSIS;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARABIDOPSIS PROTEINS; CRYSTALLOGRAPHY, X-RAY; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, PLANT; GENE SILENCING; MOLECULAR SEQUENCE DATA; MUTAGENESIS; NUCLEAR PROTEINS; PLANTS, GENETICALLY MODIFIED; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, TERTIARY; RNA, SMALL INTERFERING; STRUCTURE-ACTIVITY RELATIONSHIP; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 84859196351     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002484     Document Type: Article

References (46)

1. Law JA, Jacobsen SE, (2010) Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11: 204-220.
2. Kankel MW, Ramsey DE, Stokes TL, Flowers SK, Haag JR, et al. (2003) Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163: 1109-1122.
3. 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.
4. Woo HR, Dittmer TA, Richards EJ, (2008) Three SRA-Domain Methylcytosine-Binding Proteins Cooperate to Maintain Global CpG Methylation and Epigenetic Silencing in Arabidopsis. PLoS Genet 4: e1000156 doi:10.1371/journal.pgen.1000156.
5. Kraft E, Bostick M, Jacobsen SE, Callis J, (2008) ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases. Plant J 56: 704-715.
6. Bartee L, Malagnac F, Bender J, (2001) Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Gene Dev 15: 1753-1758.
7. Lindroth AM, Cao XF, Jackson JP, Zilberman D, McCallum CM, et al. (2001) Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292: 2077-2080.
8. Lindroth AM, Shultis D, Jasencakova Z, Fuchs J, Johnson L, et al. (2004) Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J 23: 4146-4155.
9. Matzke M, Kanno T, Claxinger L, Huettel B, Matzke AJM, (2009) RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol 21: 367-376.
10. Bernatavichute YV, Zhang XY, Cokus S, Pellegrini M, Jacobsen SE, (2008) Genome-Wide Association of Histone H3 Lysine Nine Methylation with CHG DNA Methylation in Arabidopsis thaliana. PLoS ONE 3: e3156 doi:10.1371/journal.pone.0003156.
11. Malagnac F, Bartee L, Bender J, (2002) An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J 21: 6842-6852.
12. Jackson JP, Lindroth AM, Cao XF, Jacobsen SE, (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416: 556-560.
13. Johnson LM, Bostick M, Zhang XY, Kraft E, Henderson I, et al. (2007) The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol 17: 379-384.
14. Soppe WJJ, Jasencakova Z, Houben A, Kakutani T, Meister A, et al. (2002) DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J 21: 6549-6559.
15. Tariq M, Saze H, Probst AV, Lichota J, Habu Y, et al. (2003) Erasure of CpG methylation in Arabidopsis alters patterns of histone H3 methylation in heterochromatin. Pros Natl Acad Sci U S A 100: 8823-8827.
16. Mathieu O, Reinders J, Čaikovski M, Smathajitt C, Paszkowski J, (2007) Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130: 851-862.
17. Amedeo P, Habu Y, Afsar K, Mittelsten Scheid O, Paszkowski J, (2000) Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature 405: 203-206.
18. Steimer A, Amedeo P, Afsar K, Fransz P, Mittelsten Scheid O, et al. (2000) Endogenous targets of transcriptional gene silencing in Arabidopsis. Plant Cell 12: 1165-1178.
19. Probst AV, Fransz PF, Paszkowski J, Mittelsten Scheid O, (2003) Two means of transcriptional reactivation within heterochromatin. Plant J 33: 743-749.
20. Habu Y, Mathieu O, Tariq M, Probst AV, Smathajitt C, et al. (2006) Epigenetic regulation of transcription in intermediate heterochromatin. EMBO Rep 7: 1279-1284.
21. Vaillant I, Schubert I, Tourmente S, Mathieu O, (2006) MOM1 mediates DNA-methylation-independent silencing of repetitive sequences in Arabidopsis. EMBO Rep 7: 1273-1278.
22. Numa H, Kim JM, Matsui A, Kurihara Y, Morosawa T, et al. (2010) Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana. EMBO J 29: 352-362.
23. Yokthongwattana C, Bucher E, Caikovski M, Vaillant I, Nicolet J, et al. (2010) MOM1 and Pol-IV/V interactions regulate the intensity and specificity of transcriptional gene silencing. EMBO J 29: 340-351.
24. Čaikovski M, Yokthongwattana C, Habu Y, Nishimura T, Mathieu O, et al. (2008) Divergent evolution of CHD3 proteins resulted in MOM1 refining Epigenetic control in vascular plants. PLoS Genet 4: e1000165 doi:10.1371/journal.pgen.1000165.
25. Morel JB, Mourrain P, Beclin C, Vaucheret H, (2000) DNA methylation and chromatin structure affect transcriptional and post-transcriptional transgene silencing in Arabidopsis. Curr Biol 10: 1591-1594.
26. Petty TJ, Nishimura T, Emamzadah S, Gabus C, Paszkowski J, et al. (2010) Expression, crystallization and preliminary X-ray diffraction analysis of the CMM2 region of the Arabidopsis thaliana Morpheus' molecule 1 protein. Acta Crystallogr F 66: 916-918.
27. Crick FHC, (1953) The fourier transform of a coiled-coil. Acta Crystallogr 6: 685-689.
28. Brown JH, Cohen C, Parry DA, (1996) Heptad breaks in alpha-helical coiled coils: Stutters and stammers. Proteins 26: 134-145.
29. Hicks MR, Holberton DV, Kowalczyk C, Woolfson DN, (1997) Coiled-coil assembly by peptides with non-heptad sequence motifs. Fold Des 2: 149-158.
30. Henderson IR, Jacobsen SE, (2008) Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading. Gene Dev 22: 1597-1606.
31. Elmayen T, Proux F, Vaucheret H, (2005) Arabidopsis RPA2: a genetic link among transcriptional gene silencing, DNA repair, and DNA replication. Curr Biol 15: 1919-1925.
32. Stetefeld J, Jenny M, Schulthess T, Landwehr R, Engel J, et al. (2000) Crystal structure of a naturally occurring parallel right-handed coiled coil tetramer. Nat Struct Biol 7: 772-776.
33. Lee LK, Stewart AG, Donohoe M, Bernal RA, Stock D, (2010) The structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase. Nat Struct Mol Biol 17: 373-378.
34. Maekawa T, Cheng W, Spiridon LN, Töller A, Lukasik E, et al. (2011) Coiled-coil domain-dependent homodimerization of intracellular barley immune reseptors defines a minimal functional module for triggering cell death. Cell Host Microbe 9: 187-199.
35. Khraiwesh B, Arif MA, Seumel GI, Ossowski S, Weigel D, et al. (2010) Transcriptional control of gene expression by microRNAs. Cell 140: 111-122.
36. Zhou Y, Zhang J, Lin H, Guo G, Guo Y, (2010) MORPHEUS' MOLECULE1 is required to prevent aberrant RNA transcriptional read-through in Arabidopsis. Plant Physiol 154: 1272-1280.
37. Nakamura S, Mano S, Tanaka Y, Ohnishi M, Nakamori C, et al. (2010) Gateway binary vectors with the bialaphos resistance gene, bar, as a selection marker for plant transformation. Biosci Biotech Bioch 74: 1315-1319.
38. Clough SJ, Bent AF, (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16: 735-743.
39. Schneider TR, Sheldrick GM, (2002) Substructure solution with SHELXD. Acta Crystallogr D 58: 1772-1779.
40. Sheldrick GM, (2008) A short history of SHELX. Acta Crystallogr A 64: 112-122.
41. Sheldrick GM, (2010) Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr D 66: 479-485.
42. Bricogne G, Vonrhein C, Flensburg C, Schiltz M, Paciorek W, (2003) Generation, representation and flow of phase information in structure determination: recent developments in and around SHARP 2.0. Acta Crystallogr D 59: 2023-2030.
43. Cowtan K, (1994) 'dm': An automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31: 34.
44. Emsley P, Cowtan K, (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D 60: 2126-2132.
45. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D 66: 213-221.
46. Diederichs K, Karpus PA, (1997) Improved R-factors for diffraction data analysis in macromolecular crystallography. Nat Struct Biol 4: 269-275.