Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation- dependent heterochromatin formation

Cell

Volumn 120, Issue 5, 2005, Pages 613-622

  Onodera, Yasuyuki ^a,b   Haag, Jeremy R ^a   Ream, Thomas ^a   Nunes, Pedro Costa ^c   Pontes, Olga ^a   Pikaard, Craig S ^a  

^a WASHINGTON UNIVERSITY   (United States)

^b HOKKAIDO UNIVERSITY   (Japan)

^c INSTITUTO SUPERIOR DE AGRONOMIA   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID TRANSPORTER; ARABIDOPSIS PROTEIN; CYTOSINE; DNA DIRECTED RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE III; MUTANT PROTEIN; NONRAPID PROGRESSION OF DISEASE 1 PROTEIN; NONRAPID PROGRESSION OF DISEASE 2 PROTEIN; PLANT DNA; RIBONUCLEIC ACID POLYMERASE IV; RNA 5S; RNA POLYMERASE; RNA POLYMERASE II; SMALL INTERFERING RNA; SYSTEM N AMINO ACID TRANSPORTER 1; UNCLASSIFIED DRUG;

ARTICLE; CELL VIABILITY; CONTROLLED STUDY; DNA METHYLATION; ENZYME ACTIVE SITE; EUKARYOTE; GENE CLUSTER; GENE DISRUPTION; GENE TARGETING; HETEROCHROMATIN; HYPOTHESIS; MOLECULAR GENETICS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FUNCTION;

EUKARYOTA;

EID: 14844302397     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2005.02.007     Document Type: Article

References (36)

1. Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 408 2000 796 815
2. J. Archambault, and J.D. Friesen Genetics of eukaryotic RNA polymerases I, II, and III Microbiol. Rev. 57 1993 703 724
3. W. Aufsatz, M.F. Mette, J. van der Winden, A.J. Matzke, and M. Matzke RNA-directed DNA methylation in Arabidopsis Proc. Natl. Acad. Sci. USA Suppl. 99 2002 16499 16506
4. D. Baulcombe RNA silencing in plants Nature 431 2004 356 363
5. J. Bender Chromatin-based silencing mechanisms Curr. Opin. Plant Biol. 7 2004 521 526
6. B.R. Campell, Y. Song, T.E. Posch, C.A. Cullis, and C.D. Town Sequence and organization of 5S ribosomal RNA-encoding genes of Arabidopsis thaliana Gene 112 1992 225 228
7. X. Cao, and S.E. Jacobsen Role of the Arabidopsis DRM methyltransferases in de novo DNA methylation and gene silencing Curr. Biol. 12 2002 1138 1144
8. X. Cao, W. Aufsatz, D. Zilberman, M.F. Mette, M.S. Huang, M. Matzke, and S.E. Jacobsen Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation Curr. Biol. 13 2003 2212 2217
9. S.W. Chan, D. Zilberman, Z. Xie, L.K. Johansen, J.C. Carrington, and S.E. Jacobsen RNA silencing genes control de novo DNA methylation Science 303 2004 1336
10. Z.J. Chen, L. Comai, and C.S. Pikaard Gene dosage and stochastic effects determine the severity and direction of uniparental rRNA gene silencing (nucleolar dominance) in Arabidopsis allopolyploids Proc. Natl. Acad. Sci. USA 95 1998 14891 14896
11. P. Cramer, D.A. Bushnell, J. Fu, A.L. Gnatt, B. Maier-Davis, N.E. Thompson, R.R. Burgess, A.M. Edwards, P.R. David, and R.D. Kornberg Architecture of RNA polymerase II and implications for the transcription mechanism Science 288 2000 640 649
12. P. Cramer, D.A. Bushnell, and R.D. Kornberg Structural basis of transcription: RNA polymerase II at 2.8 Å resolution Science 292 2001 1863 1876
13. P. Fransz, J.H. De Jong, M. Lysak, M.R. Castiglione, and I. Schubert Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate Proc. Natl. Acad. Sci. USA 99 2002 14584 14589
14. I. Grummt Life on a planet of its own: regulation of RNA polymerase I transcription in the nucleolus Genes Dev. 17 2003 1691 1702
15. A. Hamilton, O. Voinnet, L. Chappell, and D. Baulcombe Two classes of short interfering RNA in RNA silencing EMBO J. 21 2002 4671 4679
16. Herr, A., Jensen, M.B., Dalmay, T., and Baulcombe, D.C. (2005). RNA polymerase IV directs silencing of endogenous DNA. Science, in press. Published online February 3, 2005. 10.1126/science.1106910.
17. A. Houben, N.D. Belyaev, B.M. Turner, and I. Schubert Differential immunostaining of plant chromosomes by antibodies recognizing acetylated histone H4 variants Chromosome Res. 4 1996 191 194
18. R.M. Larkin, G. Hagen, and T.J. Guilfoyle Arabidopsis thaliana RNA polymerase II subunits related to yeast and human RPB5 Gene 231 1999 41 47
19. Lippman, Z., May, B., Yordan, C., Singer, T., and Martienssen, R. (2003). Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol. 1(3) e67 DOI: 10.1371/journal.pbio.0000067.
20. M. McClelland, M. Nelson, and E. Raschke Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases Nucleic Acids Res. 22 1994 3640 3659
21. O. Pontes, N. Neves, M. Silva, M.S. Lewis, A. Madlung, L. Comai, W. Viegas, and C.S. Pikaard Chromosomal locus rearrangements are a rapid response to formation of the allotetraploid Arabidopsis suecica genome Proc. Natl. Acad. Sci. USA 101 2004 18240 18245
22. E.J. Richards, and S.C. Elgin Epigenetic codes for heterochromatin formation and silencing: rounding up the usual suspects Cell 108 2002 489 500
23. M.R. Rountree, and E.U. Selker DNA methylation inhibits elongation but not initiation of transcription in Neurospora crassa Genes Dev. 11 1997 2383 2395
24. J. Saez-Vasquez, and C.S. Pikaard Extensive purification of a putative RNA polymerase I holoenzyme from plants that accurately initiates rRNA gene transcription in vitro Proc. Natl. Acad. Sci. USA 94 1997 11869 11874
25. J. Saez-Vasquez, and C.S. Pikaard RNA polymerase I holoenzyme-promoter interactions J. Biol. Chem. 275 2000 37173 37180
26. J. Sambrook, and D.R. Russell Molecular Cloning: A Laboratory Manual Third Edition 2001 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
27. L. Schramm, and N. Hernandez Recruitment of RNA polymerase III to its target promoters Genes Dev. 16 2002 2593 2620
28. L.B. Schwartz, and R.G. Roeder Purification and subunit structure of deoxyribonucleic acid-dependent ribonucleic acid polymerase I from mouse myeloma, MOPC 315 J. Biol. Chem. 249 1974 5898 5906
29. H.G. Schwarzacher, and W. Mosgoeller Ribosome biogenesis in man: current views on nucleolar structures and function Cytogenet. Cell Genet. 91 2000 243 252
30. W.J. Soppe, Z. Jasencakova, A. Houben, T. Kakutani, A. Meister, M.S. Huang, S.E. Jacobsen, I. Schubert, and P.F. Fransz DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis EMBO J. 21 2002 6549 6559
31. M. Wassenegger RNA-directed DNA methylation Plant Mol. Biol. 43 2000 203 220
32. N.A. Woychik, and M. Hampsey The RNA polymerase II machinery: structure illuminates function Cell 108 2002 453 463
33. Xie, Z., Johansen, L.K., Gustafson, A.M., Kassachau, K.D., Lellis, A.D., Zilberman, D., Jacobsen, S.E., and Carrington, J.C. (2004). Genetic and functional diversification of small RNA pathways in plants. PLoS Biol. 2(5):, e104 DOI: 10.1371/journal.pbio.0020104.
34. G. Zhang, E.A. Campbell, L. Minakhin, C. Richter, K. Severinov, and S.A. Darst Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution Cell 98 1999 811 824
35. D. Zilberman, X. Cao, and S.E. Jacobsen ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation Science 299 2003 716 719
36. D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, and S.E. Jacobsen Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats Curr. Biol. 14 2004 1214 1220