Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation.
BACKGROUND
The heterochromatin of many eukaryotes is marked by both DNA methylation and histone H3 lysine 9 (H3-K9) methylation, though the exact relationship between these epigenetic modifications is unknown. In Neurospora, H3-K9 methylation is required for the maintenance of all known DNA methylation. In Arabidopsis, H3-K9 methylation directs some of the CpNpG and asymmetric methylation. However, it is not known in any organism whether DNA methylation may also direct histone H3 methylation.


RESULTS
Using chromatin immunoprecipitation (ChIP) assays, we show that Arabidopsis heterochromatin is associated with H3-K9 methylation. This histone methylation is dependent on the KRYPTONITE and DDM1 genes (SU[VAR]3-9 and SWI2/SNF2 homologs, respectively). We also find that a decrease in DNA methylation does not directly cause a loss of H3-K9 methylation. Instead, a decrease in H3-K9 methylation is only seen at loci where transcription is derepressed.


CONCLUSIONS
We conclude that DNA methylation does not control the methylation of histone H3-K9. We propose that loss of H3-K9 methylation is due to transcriptional reactivation, coupled with deposition of unmethylated nucleosomes. These findings are consistent with recent observations of DNA replication-independent deposition of histone H3.3 in Drosophila. Our results also suggest that, in Arabidopsis, DNA methylation is sufficient for gene silencing, but H3-K9 methylation is not.
Johnson
Lianna
L
Life Science Core Curriculum, Los Angeles, CA 90095-1606, USA.
Cao
Xiaofeng
X
Jacobsen
Steven
S
D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics / Q000378:metabolism; D019175:DNA Methylation; D018744:DNA, Plant / Q000378:metabolism*; D015257:DNA-Cytosine Methylases / Q000235:genetics / Q000378:metabolism; D020868:Gene Silencing; D017343:Genes, Plant; D006657:Histones / Q000378:metabolism*; D008745:Methylation; D011233:Precipitin Tests; D018626:Retroelements / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics
D029681:Arabidopsis Proteins; D002843:Chromatin; D018744:DNA, Plant; D006657:Histones; D018626:Retroelements; D014157:Transcription Factors; C096661:superman protein, Arabidopsis; D015257:DNA-Cytosine Methylases; C499608:MET1 protein, Arabidopsis; C429766:CMT3 protein, Arabidopsis; D004248:DNA (Cytosine-5-)-Methyltransferases