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PMID: 16157865 Published · epublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S.

Methylation patterns of histone H3 Lys 4, Lys 9 and Lys 27 in transcriptionally active and inactive Arabidopsis genes and in atx1 mutants.

Nucleic acids research ·Vol. 33 ·No. 16 ·2005-00-00 ·Pages 5199-207

Alvarez-Venegas R, Avramova Z

Abstract

Covalent modifications of histone-tail amino acid residues communicate information via a specific 'histone code'. Here, we report histone H3-tail lysine methylation profiles of several Arabidopsis genes in correlation with their transcriptional activity and the input of the epigenetic factor ARABIDOPSIS HOMOLOG OF TRITHORAX (ATX1) at ATX1-regulated loci. By chromatin immunoprecipitation (ChIP) assays, we compared modification patterns of a constitutively expressed housekeeping gene, of a tissue-specific gene, and among genes that differed in degrees of transcriptional activity. Our results suggest that the di-methylated isoform of histone H3-lysine4 (m2K4/H3) provide a general mark for gene-related sequences distinguishing them from non-transcribed regions. Lys-4 (K4/H3), lys-9 (K9/H3) and lys-27 (K27/H3) nucleosome methylation patterns of plant genes may be gene-, tissue- or development-regulated. Absence of nucleosomes from the LTP-promotor was not sufficient to provoke robust transcription in mutant atx1-leaf chromatin, suggesting that the mechanism repositioning nucleosomes at transition to flowering functioned independently of ATX1.

MeSH Terms
Arabidopsis/genetics,metabolism Arabidopsis Proteins/genetics,physiology Chromatin/metabolism Gene Expression Regulation, Plant Histone-Lysine N-Methyltransferase Histones/chemistry,metabolism Lysine/metabolism Methylation Mutation Nucleosomes/metabolism Plant Leaves/genetics,metabolism Promoter Regions, Genetic Transcription Factors/genetics,physiology Transcription, Genetic
Chemicals
Arabidopsis Proteins Chromatin Histones Nucleosomes Transcription Factors At2g31650 protein, Arabidopsis Histone-Lysine N-Methyltransferase Lysine
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Alvarez-Venegas Raul
School of Biological Sciences, UNL, Lincoln, NE 68588-011, USA.
Avramova Zoya
References (28)
28 references, click to expand
  1. Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity.
    Mol Cell. 2003 Mar;11(3):709-19 PMID: 12667453
  2. ATX-1, an Arabidopsis homolog of trithorax, activates flower homeotic genes.
    Curr Biol. 2003 Apr 15;13(8):627-37 PMID: 12699618
  3. Histone lysine methylation: a signature for chromatin function.
    Trends Genet. 2003 Nov;19(11):629-39 PMID: 14585615
  4. Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin.
    Mol Cell. 2003 Nov;12(5):1325-32 PMID: 14636589
  5. Histone H3 lysine 4 methylation patterns in higher eukaryotic genes.
    Nat Cell Biol. 2004 Jan;6(1):73-7 PMID: 14661024
  6. Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3.
    Nature. 2004 Jan 8;427(6970):159-64 PMID: 14712276
  7. Vernalization requires epigenetic silencing of FLC by histone methylation.
    Nature. 2004 Jan 8;427(6970):164-7 PMID: 14712277
  8. Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana.
    Chromosoma. 2004 Mar;112(6):308-15 PMID: 15014946
  9. A plant dialect of the histone language.
    Trends Plant Sci. 2004 Feb;9(2):84-90 PMID: 15102374
  10. Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome.
    Proc Natl Acad Sci U S A. 2004 May 11;101(19):7357-62 PMID: 15123803
  11. DNA and histone methylation in plants.
    Trends Genet. 2004 Jun;20(6):244-51 PMID: 15145577
  12. The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote.
    Genes Dev. 2004 Jun 1;18(11):1263-71 PMID: 15175259
  13. Role of transposable elements in heterochromatin and epigenetic control.
    Nature. 2004 Jul 22;430(6998):471-6 PMID: 15269773
  14. Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3.
    EMBO J. 2004 Oct 27;23(21):4286-96 PMID: 15457214
  15. A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis.
    Genetics. 1998 May;149(1):307-18 PMID: 9584105
  16. Plant defense peptides.
    Biopolymers. 1998;47(6):479-91 PMID: 10333739
  17. Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications.
    Nucleic Acids Res. 2004;32(22):6511-8 PMID: 15598823
  18. Histone modifications defining active genes persist after transcriptional and mitotic inactivation.
    EMBO J. 2005 Jan 26;24(2):347-57 PMID: 15616580
  19. Profiling histone modification patterns in plants using genomic tiling microarrays.
    Nat Methods. 2005 Mar;2(3):213-8 PMID: 16163802
  20. The language of covalent histone modifications.
    Nature. 2000 Jan 6;403(6765):41-5 PMID: 10638745
  21. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries.
    Science. 2001 Aug 10;293(5532):1150-5 PMID: 11498594
  22. 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. 2001 Nov 1;29(21):4319-33 PMID: 11691919
  23. Heterochromatin in animals and plants. Similarities and differences.
    Plant Physiol. 2002 May;129(1):40-9 PMID: 12011336
  24. SET-domain proteins of the Su(var)3-9, E(z) and trithorax families.
    Gene. 2002 Feb 20;285(1-2):25-37 PMID: 12039029
  25. Methylation of histone H3 Lys 4 in coding regions of active genes.
    Proc Natl Acad Sci U S A. 2002 Jun 25;99(13):8695-700 PMID: 12060701
  26. Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation.
    Curr Biol. 2002 Aug 20;12(16):1360-7 PMID: 12194816
  27. Active genes are tri-methylated at K4 of histone H3.
    Nature. 2002 Sep 26;419(6905):407-11 PMID: 12353038
  28. Histone modifications in Arabidopsis- high methylation of H3 lysine 9 is dispensable for constitutive heterochromatin.
    Plant J. 2003 Feb;33(3):471-80 PMID: 12581305
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gki830
Published
2005-00-00
Epub
2005-00-12
Pages
5199-207
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1214549
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gki830 PMC Full Text View journal details
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