Dependence of Heterochromatic Histone H3 Methylation Patterns on the Arabidopsis Gene DDM1

Abstract

The Arabidopsis gene DDM1 is required to maintain DNA methylation levels and is responsible for transposon and transgene silencing. However, rather than encoding a DNA methyltransferase, DDM1 has similarity to the SWI/SNF family of adenosine triphosphate-dependent chromatin remodeling genes, suggesting an indirect role in DNA methylation. Here we show that DDM1 is also required to maintain histone H3 methylation patterns. In wild-type heterochromatin, transposons and silent genes are associated with histone H3 methylated at lysine 9, whereas known genes are preferentially associated with methylated lysine 4. In ddm1 heterochromatin, DNA methylation is lost, and methylation of lysine 9 is largely replaced by methylation of lysine 4. Because DNA methylation has recently been shown to depend on histone H3 lysine 9 methylation, our results suggest that transposon methylation may be guided by histone H3 methylation in plant genomes. This would account for the epigenetic inheritance of hypomethylated DNA once histone H3 methylation patterns are altered.

ThePolycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box genePHERES1

“…The DDM1 protein has homology to the SWI/SNF family of chromatin-remodeling factors, and may have an indirect role in modulating DNA methylation patterns (Jeddeloh et al 1999). DDM1 appears to be required for the maintenance of histone H3 methylation patterns at heterochromatic sites, suggesting that in ddm1 mutants, H3K9 methylated histones are redistributed from heterochromatic to euchromatic regions, giving rise to an activation of transcriptionally silenced loci (Gendrel et al 2002). In contrast to DDM1, the SWI/SNF-like protein MOM is required for the maintenance of transcriptional gene silencing independent of changes in methylation across the silenced locus.…”

Chromatin assembly factor 1 ensures the stable maintenance of silent chromatin states in Arabidopsis

“…A MULE DNA transposon, AtMu1, on chromosome 4 and a hypothetical gene, T5L23.26, at a heterochromatin knob of chromosome 4 are methylated at cytosine residues and transcriptionally silenced in a wild-type background (Gendrel et al 2002;Lippman et al 2003). We investigated whether these silent genes at different chromosomal locations (Fig.…”

“…Aliquots of total RNA treated with DNase I were reverse transcribed with oligo (dT) primer and Superscript II reverse transcriptase (Invitrogen), and the cDNA was amplified using Takara EX taq DNA polymerase (Takara). PCR conditions were as follows: for CACTA, 40 cycles (96 °C, 30 s; 55 °C, 30 s; 72 °C, 100 s) with primers SP15 and SP40 (Kato et al 2003); for AtMu1, 35 cycles (94 °C, 30 s; 60 °C, 30 s; 72 °C, 2 min) with primers AtMu1F and AtMu1R (Lippman et al 2003); for T5L23.26, 35 cycles (94 °C, 30 s; 58 °C, 30 s; 72 °C, 2 min) with primers T5L23.26F and T5L23.26R (Gendrel et al 2002); for AP2 as a control, 32 cycles (96 °C, 30 s; 55 °C, 30 s; 72 °C, 1 min) with primers AP2A and AP2R.…”

Mobile small RNAs and their role in regulating cytosine methylation of DNA

“…The association between the total cellular population of sRNAs and H3K9me2 has been established clearly, 27,61,62 whereas the associations observed here between mobile methylation loci and H3K27me3, H3K36me2 and H3K36me3 histone Figure 3. Number of overlaps per kilobase (KB) per KB between locus class types and histone peaks.…”