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

Volumn 33, Issue 16, 2005, Pages 5199-5207

  Alvarez Venegas, Raul ^a   Avramova, Zoya ^a  

^a UNIVERSITY OF NEBRASKA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; ISOPROTEIN; LYSINE; ARABIDOPSIS PROTEIN; ATX1 PROTEIN, ARABIDOPSIS; HISTONE; TRANSCRIPTION FACTOR;

ARABIDOPSIS; ARTICLE; CHROMATIN; CORRELATION ANALYSIS; EPIGENETICS; GENE ACTIVITY; GENE CONTROL; GENE EXPRESSION PROFILING; GENE LOCATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; HOUSEKEEPING GENE; IMMUNOPRECIPITATION; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN METHYLATION; CHEMISTRY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHYLATION; MUTATION; PHYSIOLOGY; PLANT LEAF; PROMOTER REGION;

ARABIDOPSIS;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CHROMATIN; GENE EXPRESSION REGULATION, PLANT; HISTONES; LYSINE; METHYLATION; MUTATION; NUCLEOSOMES; PLANT LEAVES; PROMOTER REGIONS (GENETICS); TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 25144436494     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki830     Document Type: Article

References (29)

1. Strahl,B.D. and Allis,C.D. (2000) The language of covalent histone modifications. Nature, 403, 41-45.
2. Noma,K., Allis,C.D. and Grewal,S.I. (2001) Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science, 293, 1150-1155.
3. Sims,R.J.,3rd, Nishioka,K. and Reinberg,D. (2003) Histone lysine methylation: A signature for chromatin function. Trends Genet., 19, 629-639.
4. Loidl,P. (2004) A plant dialect of the histone language. Trends Plant Sci., 9, 84-90.
5. Ng,H.H., Robert,F., Young,R.A. and Struhl,K. (2003) Targeted recruitment of Set1 histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity. Mol. Cell, 11, 709-719.
6. Schneider,R., Bannister,A.J., Myers,F.A., Thorne,A.W., Crane-Robinson,C. and Kouzarides,T. (2004) Histone H3 lysine 4 methylation patterns in higher eukaryotic genes. Nature Cell Biol., 6, 73-77.
7. Liang,G., Lin,J.C., Wei,V., Yoo,C., Cheng,J.C., Nguyen,C.T., Weisenberger,D.J., Egger,G., Takai,D., Gonzales,F.A. et al. (2004) Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome. Proc. Natl Acad. Sci. USA, 101, 7357-7362.
8. Kouskouti,A. and Talianidis,J. (2004) Histone modifications defining active genes persist after transcriptional and mitotic inactivation. EMBO J., 24, 347-57.
9. Schubeler,D., MacAlpine,D.M., Scalzo,D., Wirbelauer,C., Kooperberg,C., van Leeuwen,F., Gottschling,D.E., O'Neill,L.P., Turner,B.M., Delrow,J. et al. (2004) The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev., 18, 1263-1271.
10. Bernstein,B.E., Humphrey,E.L., Erlich,R.L., Schneider,R., Bouman,P., Liu,J.S., Kouzarides,T. and Schreiber,S.L. (2002) Methylation of histone H3 Lys 4 in coding regions of active genes. Proc. Natl Acad. Sci. USA, 99, 8695-8700.
11. Santos-Rosa,H., Schneider,R., Bannister,A.J., Sherriff,J., Bernstein,B.E., Emre,N.C., Schreiber,S.L., Mellor,j. and Kouzarides,T. (2002) Active genes are tri-methylated at K4 of histone H3. Nature, 419, 407-411.
12. Tariq,M. and Paszkowski,J. (2004) DNA and histone methylation in plants. Trends Genet., 20, 245-251.
13. Avramova,Z.V. (2002) Heterochromatin in animals and plants. Similarities and differences. Plant Physiol., 129, 40-49.
14. Henikoff,S. and Comai,L. (1998) A DNA metyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis. Genetics, 149, 307-318.
15. Lindroth,A.M., Shultis,D., Jasencakova,Z., Fuchs,J., Johnson,L., Schubert,D., Patnaik,D., Pradhan,S., Goodrich,J., Schubert,I. et al. (2004) Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J., 23, 4286-4296.
16. Sung,S. and Amasino,R.M. (2004) Vernalization in Arabidopsis thaliana is mediated by the PHD finger protein VIN3. Nature, 427, 159-164.
17. Bastow,R., Mylne,J.S., Lister,C., Lippman,Z., Martienssen,R.A. and Dean,C. (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature, 427, 164-167.
18. Jasencakova,Z., Soppe,W.J., Meister,A., Gernand,D., Turner,B.M. and Schubert,I. (2003) Histone modifications in Arabidopsis-high methylation of H3 lysine9 is dispensable for constitutive heterochromatin. Plant J., 33, 471-480.
19. Lipman,Z., Gendrel,A.V., Black,M., Vaughn,M.W., Dedhia,N., McCombie,W.R., Lavine,K., Mittal,V., May,B., Kasschau,K.D. et al. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature, 430, 471-476.
20. Johnson,L., Mollah,S., Garcia,B.A., Muratore,T.L., Shabanowitz,J., Hunt,D.F. and Jacobsen,S.E. (2004) Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-transcriptional modifications. Nucleic Acids Res., 32, 6511-6518.
21. Alvarez-Venegas,R., Pien,S., Sadder,M., Witmer,X., Grossniklaus,U. and Avramova,Z. (2003) ATX-1, An Arabidopsis homolog of Trithorax has histone methylase activity and activates flower homeotic genes. Curr. Biol., 13, 627-637.
22. Gendrel,A.-V., Lippman,Z., Martienssen,R. and Colot,V. (2005) Profiling histone modification patterns in plants using genomic tiling microarrays. Nature Methods, 2, 213-218.
23. Johnson,L., Cao,X. and Jacobsen,S. (2002) Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr. Biol., 12, 1360-1367.
24. Jackson,J.P., Johnson,L., Jasencakova,Z., Zhang,X., Perez-Burgos,L., Singh,P.B., Cheng,X., Schubert,I., Jenuwein,T. and Jacobsen,S.E. (2004) Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana. Chromosoma, 112, 308-315.
25. Weigel,D. and Glazebrook,J. (2002) Chapter 7: How to study gene expression. In Arabidopsis: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp. 222-223.
26. Garcia-Olmedo,F., Molina,A., Alamillo,J.M. and Rodriguez-Palenzu,P. (1998) Plant defense peptides. Biopolymers, 47, 479-491.
27. Baumbusch,L.O., Thorstensen,T., Krauss,V., Fischer,A., Naumann,K., Assalkhou,R., Schulz,I., Reuter,G. and Aalen,R.B. (2001) The Arabidopsis thaliana genome contains at least 29 active genes encoding SET-domain proteins that can be assigned to four evolutionary conserved classes. Nucleic Acids Res., 29, 4319-4333.
28. Alvarez-Venegas,R. and Avramova,Z. (2002) SET-domain proteins of the Su(var)3-9, E(z) and trithorax families. Gene, 285, 25-37.
29. Santos-Rosa,H., Schneider,R., Bernstein,B.E., Karabetsou,N., Morillon,A., Weise,C., Schreiber,S.L., Mellor,J. and Kouzarides,T. (2003) Methylation of histone H3 K4 mediates association of Isw1p ATPase with chromatin. Mol. Cell, 12, 1325-1332.