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.
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.
Authors: Jennifer M Hurley; Arko Dasgupta; Jillian M Emerson; Xiaoying Zhou; Carol S Ringelberg; Nicole Knabe; Anna M Lipzen; Erika A Lindquist; Christopher G Daum; Kerrie W Barry; Igor V Grigoriev; Kristina M Smith; James E Galagan; Deborah Bell-Pedersen; Michael Freitag; Chao Cheng; Jennifer J Loros; Jay C Dunlap Journal: Proc Natl Acad Sci U S A Date: 2014-10-31 Impact factor: 11.205
Authors: Pablo D Rabinowicz; Lance E Palmer; Bruce P May; Michael T Hemann; Scott W Lowe; W Richard McCombie; Robert A Martienssen Journal: Genome Res Date: 2003-12 Impact factor: 9.043
Authors: Muhammad Tariq; Hidetoshi Saze; Aline V Probst; Jacek Lichota; Yoshiki Habu; Jerzy Paszkowski Journal: Proc Natl Acad Sci U S A Date: 2003-07-09 Impact factor: 11.205
Authors: Christopher I Cazzonelli; Abby J Cuttriss; Susan B Cossetto; William Pye; Peter Crisp; Jim Whelan; E Jean Finnegan; Colin Turnbull; Barry J Pogson Journal: Plant Cell Date: 2009-01-27 Impact factor: 11.277