Genomic and Gene-Level Distribution of Histone H3 Dimethyl Lysine-27 (H3K27me2) in Arabidopsis

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Park, Sunchung ^a   Oh, Sookyung ^a   van Nocker, Steve ^a  

^a MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; HISTONE H3 DIMETHYL LYSINE 27; UNCLASSIFIED DRUG;

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; DNA METHYLATION; DNA MODIFICATION; GENE ACTIVITY; GENE CLUSTER; GENE EXPRESSION; GENE FUNCTION; GENE LOCATION; GENE MAPPING; GENETIC TRANSCRIPTION; H3K27 GENE; NONHUMAN; NUCLEOSOME; PLANT GENE; PLANT GENOME; PROMOTER REGION; PSEUDOGENE; TRANSPOSON;

3' FLANKING REGION; 5' FLANKING REGION; ARABIDOPSIS; CHROMOSOME MAPPING; CLUSTER ANALYSIS; DNA TRANSPOSABLE ELEMENTS; EUCHROMATIN; GENES, PLANT; GENOMICS; HISTONES; LYSINE; OPEN READING FRAMES;

ARABIDOPSIS; ARABIDOPSIS THALIANA; EUKARYOTA;

EID: 84871677774     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0052855     Document Type: Article

References (48)

1. Yanowitz J, (2010) Meiosis: making a break for it. Curr Opin Cell Biol 22: 744-751.
2. Schatz DG, Ji Y, (2011) Recombination centres and the orchestration of V(D)J recombination. Nat Rev Immunol 11: 251-263.
3. Cedar H, Bergman Y, (2009) Linking DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 10: 295-304.
4. van Attikum H, Gasser SM, (2009) Crosstalk between histone modifications during the DNA damage response. Trends Cell Biol 19: 207-217.
5. Li G, Reinberg D, (2011) Chromatin higher-order structures and gene regulation. Curr Opin Genet Dev 21: 175-186.
6. Talbert PB, Henikoff S, (2010) Histone variants-ancient wrap artists of the epigenome. Nat Rev Mol Cell Biol 11: 264-275.
7. Strahl BD, Allis CD, (2000) The language of covalent histone modifications. Nature 403: 41-45.
8. Kouzarides T, (2007) Chromatin modifications and their function. Cell 128: 693-705.
9. Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, et al. (2002) Active genes are tri-methylated at K4 of histone H3. Nature 419: 407-411.
10. Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, et al. (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120: 169-181.
11. Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, et al. (2005) Genome wide map of nucleosome acetylation and methylation in yeast. Cell 122: 517-527.
12. Vakoc CR, Sachdeva MM, Wang H, Blobel GA, (2006) Profile of histone lysine methylation across transcribed mammalian chromatin. Mol Cell Biol 26: 9185-9195.
13. Oh S, Park S, van Nocker S, (2008) Genic and global functions for Paf1C in chromatin modification and gene expression in Arabidopsis. PLoS Genet 4: e1000077.
14. Li X, Wang X, He K, Ma Y, Su N, et al. (2008) High-resolution mapping of epigenetic modifications of the rice genome uncovers interplay between DNA methylation, histone methylation, and gene expression. Plant Cell 20: 259-276.
15. Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, et al. (2003) Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol 23: 4207-4218.
16. Bannister AJ, Schneider R, Myers FA, Thorne AW, Crane-Robinson C, et al. (2005) Spatial distribution of di- and tri-methyl lysine 36 of histone H3 at active genes. J Biol Chem 280: 17732-17736.
17. Nakayama J, Rice JC, Strahl BD, Allis CD, Grewal SI, (2001) Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292: 110-113.
18. Snowden AW, Gregory PD, Case CC, Pabo CO, (2002) Gene-specific targeting of H3K9 methylation is sufficient for initiating repression in vivo. Curr Biol 12: 2159-2166.
19. Fischer A, Hofmann I, Maumann K, Reuter G, (2006) Heterochromatin proteins and the control of heterochromatic gene silencing in Arabidopsis. J Plant Physiol 163: 358-368.
20. 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: 4286-4296.
21. Mathieu O, Probst AV, Paszkowski J, (2005) Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis. EMBO J 24: 2783-2791.
22. Maluszynska J, Heslop-Harrison JS, (1991) Localization of tandemly repeated DNA sequences in Arabidopsis thaliana. Plant J 1: 159-166.
23. Jacob Y, Feng S, LeBlanc CA, Bernatavichute YV, Stroud H, et al. (2009) ATXR5 and ATXR6 are novel H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol 16: 763-8.
24. Baumbusch LO, Thorstensen T, Krauss V, Fischer A, Naumann K, et al. (2001) The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes. Nucleic Acids Res 29: 4319-4333.
25. Jacob Y, Stroud H, Leblanc C, Feng S, Zhuo L, et al. (2010) Regulation of heterochromatic DNsA replication by histone H3 lysine 27 methyltransferases. Nature 466: 987-991.
26. Naumann K, Fischer A, Hofmann I, Krauss V, Phalke S, et al. (2005) Pivotal role of AtSUVH2 in heterochromatic histone methylation and gene silencing in Arabidopsis. EMBO J 24: 1418-1429.
27. Shi J, Dawe RK, (2006) Partitioning of the maize epigenome by the number of methyl groups on histone H3 lysines 9 and 27. Genetics 173: 1571-1583.
28. Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini,M, et al, (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5: e129.
29. Schwartz YB, Pirrotta B, (2007) Polycomb silencing mechanisms and the management of genomic programmes. Nat Rev Genet 8: 9-22.
30. Turck F, Roudier F, Farrona S, Martin-Magniette M-L, Guillaume E, et al. (2007) Arabidopsis TFL2/LHP1 specifically associates with genes marked by trimethylation of histone H3 lysine 27. PLoS Genet 3: e86.
31. Schubert D, Primavesi L, Bishopp A, Roberts G, Doonan J, et al. (2006) Silencing by plant Polycomb-group genes requires dispersed trimethylation of histone H3 at lysine 27. EMBO J 25: 4638-4649.
32. Roudier F, Ahmed I, Bérard C, Sarazin A, Mary-Huard T, et al. (2011) Integrative epigenomic mapping defines four main chromatin states in Arabidopsis. EMBO J 30: 1928-1938.
33. Nekrasov M, Klymenko T, Fraterman S, Papp B, Oktaba K, et al. (2007) Pcl-PRC2 is needed to generate high levels of H3-K27 trimethylation at Polycomb target genes. EMBO J 26: 4078-4088.
34. Sarma K, Margueron R, Ivanov A, Pirrotta V, Reinberg D, (2008) Ezh2 requires PHF1 to efficiently catalyze H3 lysine 27 trimethylation in vivo. Mol Cell Biol 28: 2718-2731.
35. Ji H, Wong WH, (2005) TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics 21: 3629-3636.
36. Bernatavichute YV, Zhang X, 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.
37. Bastow R, Mylne JS, Lister C, Lippman Z, Martienssen R, et al. (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427: 164-167.
38. Krichevsky A, Gutgarts H, Kozlovsky SV, Tzfira T, Sutton A, et al. (2006) C2H2 zinc finger-SET histone methyltransferase is a plant-specific chromatin modifier. Dev Biol 303: 259-269.
39. Li H, He Z, Lu G, Lee SC, Alonso J, et al. (2007) A WD40 domain cyclophilin interacts with histone H3 and functions in gene repression and organogenesis in Arabidopsis. Plant Cell 19: 2403-2416.
40. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan SW, et al. (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126: 1189-1201.
41. Johnson L, Mollah S, Garcia BA, Muratore TL, Shabanowitz J, et al. (2004) Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications. Nucleic Acids Res 32: 6511-6518.
42. Tie F, Banerjee R, Stratton CA, Prasad-Sinha J, Stepanik V, et al. (2009) CBP-mediated acetylation of histone H3 lysine 27 antagonizes Drosophila Polycomb silencing. Development 136: 3131-3141.
43. Reynolds N, Salmon-Divon M, Dvinge H, Hynes-Allen A, Balasooriya G, et al. (2011) NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression. EMBO J 31: 593-605.
44. Zhang K, Sridhar VV, Zhu J, Kapoor A, Xhu JK, (2007) Distinctive core histone post-translational modification patterns in Arabidopsis thaliana. PLoS One 2: e1210.
45. Ahmad K, Henikoff S, (2002) The histone variant H3.3 marks active chromatin by replication-independent nucleosome assembly. Mol Cell 9: 1191-1200.
46. Lu F, Cui X, Zhang S, Jenuwein T, Cao X, (2011) Arabidopsis REF6 is a histone H3 lysine 27 demethylase. Nat Genet 43: 715-719.
47. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, et al. (2005) A gene expression map of Arabidopsis thaliana development. Nat Genet 37: 501-506.
48. Schug J, Schuller WP, Kappen C, Salbaum JM, Bucan M, et al. (2005) Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol 6: R33.