Structural Basis of Transcriptional Gene Silencing Mediated by MOM1
Shifts between epigenetic states of transcriptional activity are typically correlated with changes in epigenetic marks. However, exceptions to this rule suggest the existence of additional, as yet uncharacterized, layers of epigenetic regulation. MOM1, a protein of 2,001 amino acids that acts as a transcriptional silencer, represents such an exception. Here we define the 82 amino acid domain called CMM2 (Conserved MOM1 Motif 2) as a minimal MOM1 fragment capable of transcriptional regulation. As determined by X-ray crystallography, this motif folds into an unusual hendecad-based coiled-coil. Structure-based mutagenesis followed by transgenic complementation tests in plants demonstrate that CMM2 and its dimerization are effective for transcriptional suppression at chromosomal loci co-regulated by MOM1 and the siRNA pathway but not at loci controlled by MOM1 in an siRNA–independent fashion. These results reveal a surprising separation of epigenetic activities that enable the single, large MOM1 protein to coordinate cooperating mechanisms of epigenetic regulation.
Vyšlo v časopise:
Structural Basis of Transcriptional Gene Silencing Mediated by MOM1. PLoS Genet 8(2): e32767. doi:10.1371/journal.pgen.1002484
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1002484
Souhrn
Shifts between epigenetic states of transcriptional activity are typically correlated with changes in epigenetic marks. However, exceptions to this rule suggest the existence of additional, as yet uncharacterized, layers of epigenetic regulation. MOM1, a protein of 2,001 amino acids that acts as a transcriptional silencer, represents such an exception. Here we define the 82 amino acid domain called CMM2 (Conserved MOM1 Motif 2) as a minimal MOM1 fragment capable of transcriptional regulation. As determined by X-ray crystallography, this motif folds into an unusual hendecad-based coiled-coil. Structure-based mutagenesis followed by transgenic complementation tests in plants demonstrate that CMM2 and its dimerization are effective for transcriptional suppression at chromosomal loci co-regulated by MOM1 and the siRNA pathway but not at loci controlled by MOM1 in an siRNA–independent fashion. These results reveal a surprising separation of epigenetic activities that enable the single, large MOM1 protein to coordinate cooperating mechanisms of epigenetic regulation.
Zdroje
1. LawJAJacobsenSE 2010 Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet 11 204 220
2. KankelMWRamseyDEStokesTLFlowersSKHaagJR 2003 Arabidopsis MET1 cytosine methyltransferase mutants. Genetics 163 1109 1122
3. SazeHMittelsten ScheidOPaszkowskiJ 2003 Maintenance of CpG methylation is essential for epigenetic inheritance during plant gametogenesis. Nat Genet 34 65 69
4. WooHRDittmerTARichardsEJ 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. KraftEBostickMJacobsenSECallisJ 2008 ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases. Plant J 56 704 715
6. BarteeLMalagnacFBenderJ 2001 Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Gene Dev 15 1753 1758
7. LindrothAMCaoXFJacksonJPZilbermanDMcCallumCM 2001 Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Science 292 2077 2080
8. LindrothAMShultisDJasencakovaZFuchsJJohnsonL 2004 Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J 23 4146 4155
9. MatzkeMKannoTClaxingerLHuettelBMatzkeAJM 2009 RNA-mediated chromatin-based silencing in plants. Curr Opin Cell Biol 21 367 376
10. BernatavichuteYVZhangXYCokusSPellegriniMJacobsenSE 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. MalagnacFBarteeLBenderJ 2002 An Arabidopsis SET domain protein required for maintenance but not establishment of DNA methylation. EMBO J 21 6842 6852
12. JacksonJPLindrothAMCaoXFJacobsenSE 2002 Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416 556 560
13. JohnsonLMBostickMZhangXYKraftEHendersonI 2007 The SRA methyl-cytosine-binding domain links DNA and histone methylation. Curr Biol 17 379 384
14. SoppeWJJJasencakovaZHoubenAKakutaniTMeisterA 2002 DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J 21 6549 6559
15. TariqMSazeHProbstAVLichotaJHabuY 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. MathieuOReindersJČaikovskiMSmathajittCPaszkowskiJ 2007 Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130 851 862
17. AmedeoPHabuYAfsarKMittelsten ScheidOPaszkowskiJ 2000 Disruption of the plant gene MOM releases transcriptional silencing of methylated genes. Nature 405 203 206
18. SteimerAAmedeoPAfsarKFranszPMittelsten ScheidO 2000 Endogenous targets of transcriptional gene silencing in Arabidopsis. Plant Cell 12 1165 1178
19. ProbstAVFranszPFPaszkowskiJMittelsten ScheidO 2003 Two means of transcriptional reactivation within heterochromatin. Plant J 33 743 749
20. HabuYMathieuOTariqMProbstAVSmathajittC 2006 Epigenetic regulation of transcription in intermediate heterochromatin. EMBO Rep 7 1279 1284
21. VaillantISchubertITourmenteSMathieuO 2006 MOM1 mediates DNA-methylation-independent silencing of repetitive sequences in Arabidopsis. EMBO Rep 7 1273 1278
22. NumaHKimJMMatsuiAKuriharaYMorosawaT 2010 Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana. EMBO J 29 352 362
23. YokthongwattanaCBucherECaikovskiMVaillantINicoletJ 2010 MOM1 and Pol-IV/V interactions regulate the intensity and specificity of transcriptional gene silencing. EMBO J 29 340 351
24. ČaikovskiMYokthongwattanaCHabuYNishimuraTMathieuO 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. MorelJBMourrainPBeclinCVaucheretH 2000 DNA methylation and chromatin structure affect transcriptional and post-transcriptional transgene silencing in Arabidopsis. Curr Biol 10 1591 1594
26. PettyTJNishimuraTEmamzadahSGabusCPaszkowskiJ 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. CrickFHC 1953 The fourier transform of a coiled-coil. Acta Crystallogr 6 685 689
28. BrownJHCohenCParryDA 1996 Heptad breaks in alpha-helical coiled coils: Stutters and stammers. Proteins 26 134 145
29. HicksMRHolbertonDVKowalczykCWoolfsonDN 1997 Coiled-coil assembly by peptides with non-heptad sequence motifs. Fold Des 2 149 158
30. HendersonIRJacobsenSE 2008 Tandem repeats upstream of the Arabidopsis endogene SDC recruit non-CG DNA methylation and initiate siRNA spreading. Gene Dev 22 1597 1606
31. ElmayenTProuxFVaucheretH 2005 Arabidopsis RPA2: a genetic link among transcriptional gene silencing, DNA repair, and DNA replication. Curr Biol 15 1919 1925
32. StetefeldJJennyMSchulthessTLandwehrREngelJ 2000 Crystal structure of a naturally occurring parallel right-handed coiled coil tetramer. Nat Struct Biol 7 772 776
33. LeeLKStewartAGDonohoeMBernalRAStockD 2010 The structure of the peripheral stalk of Thermus thermophilus H+-ATPase/synthase. Nat Struct Mol Biol 17 373 378
34. MaekawaTChengWSpiridonLNTöllerALukasikE 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. KhraiweshBArifMASeumelGIOssowskiSWeigelD 2010 Transcriptional control of gene expression by microRNAs. Cell 140 111 122
36. ZhouYZhangJLinHGuoGGuoY 2010 MORPHEUS' MOLECULE1 is required to prevent aberrant RNA transcriptional read-through in Arabidopsis. Plant Physiol 154 1272 1280
37. NakamuraSManoSTanakaYOhnishiMNakamoriC 2010 Gateway binary vectors with the bialaphos resistance gene, bar, as a selection marker for plant transformation. Biosci Biotech Bioch 74 1315 1319
38. CloughSJBentAF 1998 Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16 735 743
39. SchneiderTRSheldrickGM 2002 Substructure solution with SHELXD. Acta Crystallogr D 58 1772 1779
40. SheldrickGM 2008 A short history of SHELX. Acta Crystallogr A 64 112 122
41. SheldrickGM 2010 Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr D 66 479 485
42. BricogneGVonrheinCFlensburgCSchiltzMPaciorekW 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. CowtanK 1994 ‘dm’: An automated procedure for phase improvement by density modification. Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography 31 34
44. EmsleyPCowtanK 2004 Coot: model-building tools for molecular graphics. Acta Crystallogr D 60 2126 2132
45. AdamsPDAfoninePVBunkocziGChenVBDavisIW 2010 PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D 66 213 221
46. DiederichsKKarpusPA 1997 Improved R-factors for diffraction data analysis in macromolecular crystallography. Nat Struct Biol 4 269 275
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
2012 Číslo 2
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
Najčítanejšie v tomto čísle
- Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA
- Contrasting Properties of Gene-Specific Regulatory, Coding, and Copy Number Mutations in : Frequency, Effects, and Dominance
- Homeobox Genes Critically Regulate Embryo Implantation by Controlling Paracrine Signaling between Uterine Stroma and Epithelium
- Nondisjunction of a Single Chromosome Leads to Breakage and Activation of DNA Damage Checkpoint in G2