Distinct modes of DNA accessibility in plant chromatin

Nature Communications

Volumn 3, Issue , 2012, Pages

  Shu, Huan ^a   Wildhaber, Thomas ^a   Siretskiy, Alexey ^b   Gruissem, Wilhelm ^a   Hennig, Lars ^a,b  

^a ETH ZURICH   (Switzerland)

^b SWEDISH UNIVERSITY OF AGRICULTURAL SCIENCES   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; HISTONE H3; PLANT DNA;

DICOTYLEDON; DNA; GENOME; METHYLATION; PROTEIN;

ARABIDOPSIS; ARTICLE; CHROMATIN; CONTROLLED STUDY; DNA EXTRACTION; GENETIC TRANSCRIPTION; HETEROCHROMATIN; NONHUMAN; NUCLEIC ACID PROBE; PLANT GENOME; PROMOTER REGION; PROTEIN METHYLATION;

ARABIDOPSIS; CENTROMERE; CHROMATIN; DNA METHYLATION; DNA, ANTISENSE; DNA, PLANT; EUCHROMATIN; GENES, PLANT; HETEROCHROMATIN; IN SITU HYBRIDIZATION, FLUORESCENCE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYCOMB-GROUP PROTEINS;

ARABIDOPSIS THALIANA;

EID: 84871796810     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms2259     Document Type: Article

References (60)

1. Li, B., Carey, M. & Workman, J. L. The role of chromatin during transcription. Cell 128, 707-719 (2007). (Pubitemid 46273570)
2. Campos, E. I. & Reinberg, D. Histones: annotating chromatin. Annu. Rev. Genet. 43, 559-599 (2009).
3. Selth, L. A., Sigurdsson, S. & Svejstrup, J. Q. Transcript elongation by RNA polymerase II. Annu. Rev. Biochem. 79, 271-293 (2010).
4. Grewal, S. I. & Jia, S. Heterochromatin revisited. Nat. Rev. Genet. 8, 35-46 (2007). (Pubitemid 46006048)
5. Hennig, L. & Derkacheva, M. Diversity of polycomb group complexes in plants: same rules, different players? Trends Genet. 25, 414-423 (2009).
6. Margueron, R. & Reinberg, D. The polycomb complex PRC2 and its mark in life. Nature 469, 343-349 (2011).
7. Zhang, X. et al. Whole-genome analysis of Histone H3 Lysine 27 trimethylation in Arabidopsis. PLoS Biol. 5, 1026-1035 (2007). (Pubitemid 46790393)
8. Oh, S., Park, S. & van Nocker, S. Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis. PLoS Genet. 4, e1000077 (2008).
9. Weinhofer, I., Hehenberger, E., Roszak, P., Hennig, L. & Köhler, C. H3K27me3 profiling of the endosperm implies exclusion of polycomb group protein targeting by DNA methylation. PLoS Genet. 6, e1001152 (2010).
10. Cheutin, T. et al. Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science 299, 721-725 (2003). (Pubitemid 36159490)
11. Cheutin, T., Gorski, S. A., May, K. M., Singh, P. B. & Misteli, T. In vivo dynamics of Swi6 in yeast: evidence for a stochastic model of heterochromatin. Mol. Cell. Biol. 24, 3157-3167 (2004). (Pubitemid 38452062)
12. Festenstein, R. et al. Modulation of heterochromatin protein 1 dynamics in primary mammalian cells. Science 299, 719-721 (2003). (Pubitemid 36159489)
13. Verschure, P. J. et al. Condensed chromatin domains in the mammalian nucleus are accessible to large macromolecules. EMBO Rep. 4, 861-866 (2003). (Pubitemid 37304402)
14. Gorisch, S. M., Lichter, P. & Rippe, K. Mobility of multi-subunit complexes in the nucleus: accessibility and dynamics of chromatin subcompartments. Histochem. Cell Biol. 123, 217-228 (2005). (Pubitemid 40674673)
15. Bell, O. et al. Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing. Nat. Struct. Mol. Biol. 17, 894-900 (2010).
16. Misteli, T. Beyond the sequence: cellular organization of genome function. Cell 128, 787-800 (2007). (Pubitemid 46273571)
17. Fransz, P. & de Jong, H. From nucleosome to chromosome: a dynamic organization of genetic information. Plant J. 66, 4-17 (2011).
18. Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815 (2000).
19. Soppe, W. J. et al. DNA methylation controls histone H3 lysine 9 methylation and heterochromatin assembly in Arabidopsis. EMBO J. 21, 6549-6559 (2002). (Pubitemid 35448432)
20. Schönrock, N., Exner, V., Probst, A., Gruissem, W. & Hennig, L. Functional genomic analysis of CAF-1 mutants in Arabidopsis thaliana. J. Biol. Chem. 281, 9560-9568 (2006). (Pubitemid 43864674)
21. Fransz, P. F. et al. Integrated cytogenetic map of chromosome arm 4s of A. thaliana: structural organization of heterochromatic knob and centromere region. Cell 100, 367-376 (2000). (Pubitemid 30353092)
22. Fransz, P., Jong, J. H. D., Lysak, M., Castiglione, M. R. & Schubert, I. Interphase chromosomes in Arabidopsis are organized as well defined chromocenters from which euchromatin loops emanate. Proc. Natl Acad. Sci. USA 99, 14584-14589 (2002). (Pubitemid 35257714)
23. Sperling, K. et al. DNase I sensitivity in facultative and constitutive heterochromatin. Chromosoma 93, 38-42 (1985). (Pubitemid 16193278)
24. Gendrel, A. V., Lippman, Z., Yordan, C., Colot, V. & Martienssen, R. A. Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene. DDM1. Science 297, 1871-1873 (2002). (Pubitemid 35024346)
25. Jackson, J. P., Lindroth, A. M., Cao, X. & Jacobsen, S. E. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416, 556-560 (2002). (Pubitemid 34288860)
26. Weil, M. R., Widlak, P., Minna, J. D. & Garner, H. R. Global survey of chromatin accessibility using DNA microarrays. Genome Res. 14, 1374-1381 (2004). (Pubitemid 39029235)
27. Eskeland, R. et al. Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination. Mol. Cell. 38, 452-464 (2010).
28. Bantignies, F. et al. Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila. Cell 144, 214-226 (2011).
29. Naughton, C., Sproul, D., Hamilton, C. & Gilbert, N. Analysis of active and inactive X chromosome architecture reveals the independent organization of 30 nm and large-scale chromatin structures. Mol. Cell. 40, 397-409 (2010).
30. Mathieu, O., Probst, A. V. & Paszkowski, J. Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J. 24, 2783-2791 (2005). (Pubitemid 41170027)
31. Tran, R. K. et al. DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes. Curr. Biol. 15, 154-159 (2005).
32. Zhang, X. et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126, 1189-1201 (2006). (Pubitemid 44380289)
33. Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T. & Henikoff, S. Genomewide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 39, 61-69 (2007). (Pubitemid 46026502)
34. Lyko, F., Ramsahoye, B. H. & Jaenisch, R. DNA methylation in Drosophila melanogaster. Nature 408, 538-540 (2000).
35. Baubec, T., Pecinka, A., Rozhon, W. & Scheid, O. M. Effective, homogeneous and transient interference with cytosine methylation in plant genomic DNA by zebularine. Plant J. 57, 542-554 (2008).
36. Mathieu, O., Reinders, J., Caikovski, M., Smathajitt, C. & Paszkowski, J. Transgenerational stability of the Arabidopsis epigenome is coordinated by CG methylation. Cell 130, 851-862 (2007). (Pubitemid 47334929)
37. Jones, P. A. & Taylor, S. M. Cellular differentiation, cytidine analogs and DNA methylation. Cell 20, 85-93 (1980). (Pubitemid 10117303)
38. Vongs, A., Kakutani, T., Martienssen, R. A. & Richards, E. J. Arabidopsis thaliana DNA methylation mutants. Science 260, 1926-1928 (1993). (Pubitemid 23258270)
39. Saze, H., Scheid, O. M. & Paszkowski, J. Maintenance of cpg methylation is essential for epigenetic inheritance during plant gametogenesis. Nat. Genet. 34, 65-69 (2003). (Pubitemid 36548792)
40. Kakutani, T., Munakata, K., Richards, E. J. & Hirochika, H. Meiotically and mitotically stable inheritance of DNA hypomethylation induced by ddm1 mutation of Arabidopsis thaliana. Genetics 151, 831-838 (1999). (Pubitemid 29082948)
41. Lister, R. et al. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133, 523-536 (2008).
42. Henikoff, S. & Shilatifard, A. Histone modification: cause or cog? Trends Genet. 27, 389-396 (2011).
43. Volpe, T. A. et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833-1837 (2002). (Pubitemid 35024336)
44. Chen, E. S. et al. Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature 451, 734-737 (2008). (Pubitemid 351220568)
45. Lu, J. & Gilbert, D. M. Proliferation-dependent and cell cycle regulated transcription of mouse pericentric heterochromatin. J. Cell. Biol. 179, 411-421 (2007). (Pubitemid 350074787)
46. Kloc, A., Zaratiegui, M., Nora, E. & Martienssen, R. RNA interference guides histone modification during the S phase of chromosomal replication. Curr. Biol. 18, 490-495 (2008).
47. Bantignies, F., Grimaud, C., Lavrov, S., Gabut, M. & Cavalli, G. Inheritance of Polycomb-dependent chromosomal interactions in Drosophila. Genes Dev. 17, 2406-2420 (2003). (Pubitemid 37214789)
48. Francis, N. J., Kingston, R. E. & Woodcock, C. L. Chromatin compaction by a Polycomb group protein complex. Science 306, 1574-1577 (2004). (Pubitemid 39564957)
49. Lorincz, M. C., Dickerson, D. R., Schmitt, M. & Groudine, M. Intragenic DNA methylation alters chromatin structure and elongation efficiency in mammalian cells. Nat. Struct. Mol. Biol. 11, 1068-1075 (2004). (Pubitemid 39453335)
50. Zilberman, D., Coleman-Derr, D., Ballinger, T. & Henikoff, S. Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks. Nature 456, 125-129 (2008).
51. Chang, S. & Pikaard, C. S. Transcript profiling in Arabidopsis reveals complex responses to global inhibition of DNA methylation and histone deacetylation. J. Biol. Chem. 280, 796-804 (2005). (Pubitemid 40165048)
52. Sabo, P. J. et al. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat. Methods 3, 511-518 (2006). (Pubitemid 43941768)
53. Rehrauer, H. et al. AGRONOMICS1: A new resource for Arabidopsis transcriptome profiling. Plant Physiol. 152, 487-499 (2010).
54. R Development Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, Austria, 2010).
55. Johnson, W. E. et al. Model-based analysis of tiling-arrays for ChIP-chip. Proc. Natl Acad. Sci. USA 103, 12457-12462 (2006).
56. Bengtsson, H., Simpson, K., Bullard, J. & Hansen, K. aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory. Tech Report No.745, Department of Statistics, University of California, Berkeley (2008).
57. Gottardo, R., Li, W., Johnson, W. E. & Liu, X. S. A flexible and powerful Bayesian hierarchical model for ChIP-Chip experiments. Biometrics 64, 468-478 (2008). (Pubitemid 351691922)
58. Nicol, J. W., Helt, G. A., Blanchard, Jr S. G., Raja, A. & Loraine, A. E. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25, 2730-2731 (2009).
59. Hsieh, T. F. et al. Genome-wide demethylation of Arabidopsis endosperm. Science 324, 1451-1454 (2009).
60. Müller, M., Patrignani, A., Rehrauer, H., Gruissem, W. & Hennig, L. Evaluation of alternative RNA labeling protocols for transcript profiling with Arabidopsis AGRONOMICS1 tiling arrays. Plant Meth. 8, 18 (2012).