Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase

Abstract

Gene silencing in eukaryotes is associated with the formation of heterochromatin, a complex of proteins and DNA that block transcription. Heterochromatin is characterized by the methylation of cytosine nucleotides of the DNA, the methylation of histone H3 at lysine 9 (H3 Lys 9), and the specific binding of heterochromatin protein 1 (HP1) to methylated H3 Lys 9 (refs 1-7). Although the relationship between these chromatin modifications is generally unknown, in the fungus Neurospora crassa, DNA methylation acts genetically downstream of H3 Lys 9 methylation. Here we report the isolation of KRYPTONITE, a methyltransferase gene specific to H3 Lys 9, identified in a mutant screen for suppressors of gene silencing at the Arabidopsis thaliana SUPERMAN (SUP) locus. Loss-of-function kryptonite alleles resemble mutants in the DNA methyltransferase gene CHROMOMETHYLASE3 (CMT3), showing loss of cytosine methylation at sites of CpNpG trinucleotides (where N is A, C, G or T) and reactivation of endogenous retrotransposon sequences. We show that CMT3 interacts with an Arabidopsis homologue of HP1, which in turn interacts with methylated histones. These data suggest that CpNpG DNA methylation is controlled by histone H3 Lys 9 methylation, through interaction of CMT3 with methylated chromatin.

Dynamic and reversibility of heterochromatic gene silencing in human disease

“…In Neurospora crassa, mutations in Su(var)3-9 H3K9 methyltransferases (dim-5) gene are responsible for a genome wide demethylation of methylated CpGs [72]. The same result was obtained in A. thaliana by mutations of Kryptonite gene, a relative of Su(var)H3-K9 methyltransferase, in this case the CpNpG methylated sequences were largely demethylated while methylation status of CpGs remained unchanged [73]. In mice, mutation of the two Su(var)3-9 homologs has a relatively minor effect on cytosine methylation and causes partial demethylation of major satellite regions of pericentromeric heterochromatin [74].…”

Gradual development of a genome‐wide H3‐K9 trimethylation pattern in paternally derived pig pronucleus

“…has been observed in diverse biological systems (Tamaru and Selker, 2001;Fahrner et al, 2002;Jackson et al, 2002;Fuks et al, 2003;Lehnertz et al, 2003;Tariq et al, 2003;Freitag et al, 2004). Therefore, the different H3-m 3 K9 states in the two species prompted us to investigate DNA methylation states in sperm-derived chromatins.…”

Imprinting centers, chromatin structure, and disease

“…Tamaru and Selker [2001] showed that CpG methylation in Neurospora is dependent on the function of the H3 Lys9 methyltransferase encoded by dim-5. Subsequently, Jackson et al [2002] showed that CpNpG methylation in Arabidopsis thaliana requires function of the Kryptonite (Kyp) H3 Lys9 methyltransferase. Lehnertz et al [2003] showed that mouse ES cells homozygously mutated for Suv39h1 and Suv39h2 (which encode closely-related histone H3 Lys9 methyltransferases specific for centromeric heterochromatin) have reduced DNA methylation of pericentric satellite repeats, but not of other repeat sequences.…”