Genome-wide association of histone H3 lysine nine methylation with CHG DNA methylation in Arabidopsis thaliana.
Methylation of histone H3 lysine 9 (H3K9) is a hallmark of transcriptional silencing in many organisms. In Arabidopsis thaliana, dimethylation of H3K9 (H3K9m2) is important in the silencing of transposons and in the control of DNA methylation. We constructed a high-resolution genome-wide map of H3K9m2 methylation by using chromatin immunoprecipitation coupled with whole genome Roche Nimblegen microarrays (ChIP-chip). We observed a very high coincidence between H3K9m2 and CHG methylation (where H is either A,T or C) throughout the genome. The coding regions of genes that are associated exclusively with methylation in a CG context did not contain H3K9m2. In addition, we observed two distinct patterns of H3K9m2. Transposons and other repeat elements present in the euchromatic arms contained small islands of H3K9m2 present at relatively low levels. In contrast, pericentromeric/centromeric regions of Arabidopsis chromosomes contained long, rarely interrupted blocks of H3K9m2 present at much higher average levels than seen in the chromosome arms. These results suggest a complex interplay between H3K9m2 and different types of DNA methylation and suggest that distinct mechanisms control H3K9m2 in different compartments of the genome.
Bernatavichute
Yana V
YV
Molecular Biology Institute, University of California Los Angeles, Los Angeles, California, United States of America.
Zhang
Xiaoyu
X
Cokus
Shawn
S
Pellegrini
Matteo
M
Jacobsen
Steven E
SE
D017360:Arabidopsis / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000378:metabolism; D002843:Chromatin / Q000737:chemistry; D047369:Chromatin Immunoprecipitation; D019175:DNA Methylation; D004251:DNA Transposable Elements; D044127:Epigenesis, Genetic; D017343:Genes, Plant; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D006570:Heterochromatin / Q000378:metabolism; D006657:Histones / Q000737:chemistry*; D008239:Lysine / Q000737:chemistry*; D008745:Methylation; D034741:RNA, Small Interfering / Q000378:metabolism; D014158:Transcription, Genetic
D029681:Arabidopsis Proteins; D002843:Chromatin; D004251:DNA Transposable Elements; D006570:Heterochromatin; D006657:Histones; D034741:RNA, Small Interfering; D008239:Lysine
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