Contribution of the epigenetic mark H3K27me3 to functional divergence after whole genome duplication in Arabidopsis

Genome Biology

Volumn 13, Issue 10, 2012, Pages

  Berke, Lidija ^a   Sanchez Perez, Gabino F ^a,b,c,d   Snel, Berend ^a  

^a UTRECHT UNIVERSITY   (Netherlands)

^b Netherlands Consortium for Systems Biology   (Netherlands)

^c Applied Bioinformatics ^*  (Puerto Rico)

^d WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; HISTONE H3K27ME3; UNCLASSIFIED DRUG; HISTONE; VEGETABLE PROTEIN;

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; EPIGENETICS; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENE FATE; GENE FUNCTION; GENE LOCATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC PARAMETERS; GENETIC VARIABILITY; HISTONE METHYLATION; MOLECULAR EVOLUTION; NONHUMAN; PARALOGY; DNA METHYLATION; GENETIC EPIGENESIS; GENETICS; METABOLISM; PLANT GENOME; PROCEDURES;

ANIMALIA; ARABIDOPSIS; ARABIDOPSIS THALIANA;

ARABIDOPSIS; DNA METHYLATION; EPIGENESIS, GENETIC; EPIGENOMICS; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; HISTONES; PLANT PROTEINS;

EID: 84866879241     PISSN: None     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2012-13-10-R94     Document Type: Article

References (39)

1. Margueron R, Reinberg D. The Polycomb complex PRC2 and its mark in life. Nature 2011, 469:343-349.
2. Köhler C, Villar CBR. Programming of gene expression by Polycomb group proteins. Trends Cell Biol 2008, 18:236-243.
3. Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J, Jacobsen SE. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 2007, 5:e129.
4. Hennig L, Derkacheva M. Diversity of Polycomb group complexes in plants: same rules, different players?. Trends Genet 2009, 25:414-423.
5. Holec S, Berger F. Polycomb group complexes mediate developmental transitions in plants. Plant Physiol 2012, 158:35-43.
6. Makarevich G, Leroy O, Akinci U, Schubert D, Clarenz O, Goodrich J, Grossniklaus U, Köhler C. Different Polycomb group complexes regulate common target genes in Arabidopsis. EMBO Rep 2006, 7:947-952.
7. Zheng B, Chen X. Dynamics of histone H3 lysine 27 trimethylation in plant development. Curr Opin Plant Biol 2011, 14:112-129.
8. Adrian J, Torti S, Turck F. From decision to commitment: the molecular memory of flowering. Mol Plant 2009, 2:628-642.
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 2010, 6:e1001152.
10. Lee TI, Jenner RG, Boyer L A, Guenther MG, Levine SS, Kumar RM, Chevalier B, Johnstone SE, Cole MF, Isono K, Koseki H, Fuchikami T, Abe K, Murray HL, Zucker JP, Yuan B, Bell GW, Herbolsheimer E, Hannett NM, Sun K, Odom DT, Otte AP, Volkert TL, Bartel DP, Melton D A, Gifford DK, Jaenisch R, Young R. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 2006, 125:301-313.
11. Boyer L A, Plath K, Zeitlinger J, Brambrink T, Medeiros L A, Lee TI, Levine SS, Wernig M, Tajonar A, Ray MK, Bell GW, Otte AP, Vidal M, Gifford DK, Young R A, Jaenisch R. Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 2006, 441:349-353.
12. Schwartz YB, Kahn TG, Nix D A, Li X-Y, Bourgon R, Biggin M, Pirrotta V. Genome-wide analysis of Polycomb targets in Drosophila melanogaster. Nat Genet 2006, 38:700-705.
13. Gu Z, Nicolae D, Lu HH-S, Li WH. Rapid divergence in expression between duplicate genes inferred from microarray data. Trends Genet 2002, 18:609-613.
14. Makova KD, Li W-H. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res 2003, 13:1638-1645.
15. Blanc G, Wolfe KH. Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 2004, 16:1679-1691.
16. Haberer G, Hindemitt T, Meyers BC, Mayer KFX. Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis. Plant Physiol 2004, 136:3009-3022.
17. Casneuf T, De Bodt S, Raes J, Maere S, Van de Peer Y. Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol 2006, 7:R13.
18. Ganko EW, Meyers BC, Vision TJ. Divergence in expression between duplicated genes in Arabidopsis. Mol Biol Evol 2007, 24:2298-2309.
19. Bowers JE, Chapman BA, Rong J, Paterson AH. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 2003, 422:433-438.
20. Drummond DA, Wilke CO. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 2008, 134:341-352.
21. Drummond DA, Bloom JD, Adami C, Wilke CO, Arnold FH. Why highly expressed proteins evolve slowly. Proc Natl Acad Sci USA 2005, 102:14338-14343.
22. Lu F, Cui X, Zhang S, Jenuwein T, Cao X. Arabidopsis REF6 is a histone H3 lysine 27 demethylase. Nat Genet 2011, 43:715-719.
23. Farrona S, Thorpe FL, Engelhorn J, Adrian J, Dong X, Sarid-Krebs L, Goodrich J, Turck F. Tissue-specific expression of FLOWERING LOCUS T in Arabidopsis is maintained independently of polycomb group protein repression. Plant Cell 2011, 23:3204-3214.
24. De Bodt S, Carvajal D, Hollunder J, Van den Cruyce J, Movahedi S, Inzé D. CORNET: a user-friendly tool for data mining and integration. Plant Physiol 2010, 152:1167-1179.
25. Geiler-Samerotte KA, Dion MF, Budnik BA, Wang SM, Hartl DL, Drummond DA. Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast. Proc Natl Acad Sci USA 2011, 108:680-685.
26. Yang L, Gaut BS. Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Mol Biol Evol 2011, 28:2359-2369.
27. Wright SI, Yau CBK, Looseley M, Meyers BC. Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol Biol Evol 2004, 21:1719-1726.
28. Schmid M, Davison TS, Henz SR, Pape UJ, Demar M, Vingron M, Schölkopf B, Weigel D, Lohmann JU. A gene expression map of Arabidopsis thaliana development. Nat Genet 2005, 37:501-506.
29. Castillo-Davis CI, Hartl DL, Achaz G. cis-Regulatory and protein evolution in orthologous and duplicate genes. Genome Res 2004, 14:1530-1536.
30. Freeling M, Rapaka L, Lyons E, Pedersen B, Thomas BC. G-boxes, bigfoot genes, and environmental response: characterization of intragenomic conserved noncoding sequences in Arabidopsis. Plant Cell 2007, 19:1441-1457.
31. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002, 417:399-403.
32. Lee I, Date SV, Adai AT, Marcotte EM. A probabilistic functional network of yeast genes. Science 2004, 306:1555-1558.
33. Takuno S, Gaut BS. Body-methylated genes in Arabidopsis thaliana are functionally important and evolve slowly. Mol Biol Evol 2012, 29:219-227.
34. Thomas BC, Pedersen B, Freeling M. Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res 2006, 16:934-946.
35. Berger N, Dubreucq B, Roudier F, Dubos C, Lepiniec L. Transcriptional regulation of Arabidopsis LEAFY COTYLEDON2 involves RLE, a cis-element that regulates trimethylation of histone H3 at lysine-27. Plant Cell Online 2011, 23:4065-4078.
36. TAIR. , http://www.arabidopsis.org
37. Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 2000, 16:276-277.
38. TreeSoft:TreeBeST. , http://treesoft.sourceforge.net/treebest.shtml
39. Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 2007, 24:1586-1591.