Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis

Abstract

Transcriptional activity and structure of chromatin are correlated with patterns of covalent DNA and histone modification. Previous studies have revealed that high levels of histone H3 dimethylation at lysine 9 (H3K9me2), characteristic of transcriptionally silent heterochromatin in Arabidopsis, require hypermethylation of DNA at CpG sites. Here, we report that CpG hypermethylation characteristic of heterochromatin specifically prevented H3K27 trimethylation (H3K27me3). H3K27 mono- and dimethylation mark silent heterochromatin independently of DNA methylation. Upon loss of CpG methylation, there was target-specific enrichment of H3K27me3 in heterochromatin that correlated with transcriptional reactivation. Moreover, using the kyp mutant affected in H3K9me2, we showed that changes in H3K27me3 occurred independently of the levels of H3K9me2. Therefore, CpG methylation provides distinct and direct information for a specific subset of histone methylation marks. The observed independence of the regulation of H3K9 and H3K27 methylation by CpG methylation refines the recently proposed combinatorial histone code involving these two marks.

Figure 1

Reduction in DNA methylation affected the distribution of H3K27me3 but not of H3K27me1 and H3K27me2. Immunolocalization experiments (using parformaldehyde-fixed nuclei) showing the distribution of H3K27me1 (A) H3K27me2 (B) and H3K27me3 (C) in interphase nuclei of wild type (Columbia (Col) and Zurich (Line A)) and hypomethylated mutants met1-3 and ddm1-5. White arrows in (C) indicate the H3K27me3-enriched foci, and the percent of nuclei showing this staining pattern is indicated. At least 80 nuclei from different preparations were evaluated for each genotype.

Figure 2

Depletion of DNA methylation induced enrichment in H3K27me3 correlating with transcriptional reactivation. (A) ChIP analysis using antibodies specific for the three H3K27 methylation states (me1, me2 and me3). Representative gel pictures of three independent replicates are shown. (B) Fold enrichment of a particular sequence in the pull-down of met1-3 versus wild type, normalized by the amplification of Tubulin8 (TUB8) and Actin2/7 genes. No changes in the H3K27 methylation patterns for the euchromatic genes TUB8 and ACTIN2/7 were observed when comparing equal amounts of tissues. The results of three independent ChIP experiments are shown and the standard error of the mean is indicated on each bar. (C) RT–PCR analysis of transcripts with (+) and without (–) reverse transcriptase (RT).

Figure 3

met1-3 mutation caused drastic reduction in CpG methylation. (A) Targets were PCR amplified using primer pairs used in Figure 2, after digestion of the DNA with the restriction enzymes indicated ( × 2 indicates that two restriction sites are present). (B) Undigested DNA served as PCR control.

Figure 4

5S rDNA repeats became specifically enriched in H3K27me3 and contributed partly to the appearance of H3K27me3-enriched spots in DNA hypomethylation mutants. (A) ChIP analysis using antibodies specific for the three H3K27 methylation states (me1, me2 and me3). Representative gel pictures of three independent replicates are shown. (B) Immuno-DNA FISH results revealing the colocalization (white arrows) of a selection of 5S rDNA loci with chromatin foci enriched in H3K27me3 in met1-3 and ddm1-5 interphase nuclei.

Figure 5

Reduction of H3K9me2 methylation in the kyp mutant did not affect the distribution of H3K27 methylation states and induced an increase in H3K4me2 only in a transcription-dependent manner. (A) ChIP analysis using antibodies specific for the three H3K27 methylation states (me1, me2 and me3) in Columbia (Col) wild-type and kyp plants. Representative gel pictures of three independent replicates are shown. (B) ChIP analysis using antibodies against H3K9me2 and H3K4me2 in Col and kyp plants. (C) RT–PCR analysis of transcripts with (+) and without (−) reverse transcriptase (RT).

Figure 6

Summary of the influence of CpG methylation on distinct histone H3 modifications in Arabidopsis. CpG methylation maintained by MET1 represses H3K27me3 and H3K4me2, which mark active chromatin. Conversely, methylated CpGs stimulate H3K9me2, a hallmark of silent chromatin, which in turn can induce CpNpG methylation via the chromomethylase CMT3. At some specific target sequences, H3K9me2 may also restrain H3K4me2 in a transcription-dependent manner (dotted lines). The heterochromatin marks H3K27me1 and H3K27me2 are not influenced by DNA methylation and are modulated by as yet unknown factors.