From RiceWiki
Jump to: navigation, search

Annotated Information


High impact information on CMT3

▪ 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 ofendogenous retrotransposon sequences.[1]

▪CpNpG DNA methylation is controlled by histone H3 Lys 9 methylation, through interaction ofCMT3 with methylated chromatin.[1]

▪ A genetic screen for suppressors of a hypermethylated clark kent mutant identified nine loss-of-function alleles of CHROMOMETHYLASE3 (CMT3), a novel cytosine methyltransferase homolog.[2]

▪These cmt3 mutants display a wild-type morphology but exhibit decreased CpXpG methylation of the SUP gene and of other sequences throughout the genome.[2]

▪ Thus, CMT3 is a key determinant for non-CG methylation.[3]

Biological context of CMT3

▪ Plants have DNA methylation at CpNpG and CpNpN sites, maintained, in part, by the CHROMOMETHYLASE3 (CMT3) DNA methyltransferase.[4]

▪ Arabidopsis thaliana embryos with loss-of-function mutations in MET1 and CMT3 develop improperly, display altered planes and numbers of cell division, and have reduced viability.[4]

▪ A model in which H3K9 methylation by KYP, and H3K27 methylation by an unknown enzyme provide a combinatorial histone code for the recruitment of CMT3 to silent loci.[5]

▪ CMT3 and KYP targets show similar proximal distributions that correspond to the overall distribution of transposable elements of all types, whereas DRM targets are distributed more distally along the chromosome.[6]

Associations of CMT3 with chemical compounds.

▪ The CMT3 pathway depends on histone H3 lysine 9 methylation (H3 mK9) to guide DNA methylation. Other interactions of CMT3.[7]

Other interactions of CMT3

▪ These signals act in at least three partially intersecting pathways that control the locus-specific patterning of non-CGmethylation by the DRM2 and CMT3 methyltransferases.[8]

▪ The sequence of ZMET2 is similar to that of the Arabidopsis chromomethylases CMT1 and CMT3, with C-terminal motifs characteristic of eukaryotic and prokaryotic DNA methyltransferases.[9]

Analytical, diagnostic and therapeutic context of CMT3

▪ Using chromatin immunoprecipitation analysis and immunohistolocalization experiments, researchers found that H3K27 methylation colocalizes with H3K9 methylation at CMT3-controlled loci.[5]


In many eukaryotes, including mammals, higher plants, and some species of fungi, cytosine methylation plays an important role in genome stability and development by altering chromatin structure and patterns of gene expression. In mammalian genomes, methylation is found primarily at cytosines in the symmetric context 5′-CG-3′ (CG), whereas in plant and fungal genomes methylation is found on both CG and non-CG residues (Yoder et al. 1997; Colot and Rossignol 1999; Finnegan and Kovac 2000). Mammals and higher plants carry related cytosine methyltransferases of the Dnmt1/MET1 class that have been implicated by mutational analysis as enzymes that maintain the bulk of genomic methylation (Li et al. 1992; Finnegan et al. 1996;Ronemus et al. 1996). Another class of chromomethylases (CMTs) has been identified by analysis of Arabidopsis thaliana genomic sequences (Henikoff and Comai 1998; McCallum et al. 2000). The CMT class is characterized by the presence of a chromodomain amino acid motif between the cytosine methyltransferase catalytic motifs I and IV. There are three CMT genes encoded in Arabidopsis: CMT1, CMT2, and CMT3 (Henikoff and Comai 1998; Finnegan and Kovac 2000; McCallum et al. 2000). In the Wassilewskija (WS) strain background used for this study, CMT2and CMT3 are predicted to encode functional proteins, whereas the CMT1 coding sequence is disrupted by an Eve1(Henikoff and Comai 1998) retroelement insertion (J. Bender, unpubl.).CMT genes have also been identified in several other plant species including Brassica and maize, but not in fungal or animal systems (Rose et al. 1998; Finnegan and Kovac 2000). Recently,Arabidopsis CMT3 (Lindroth et al. 2001) and the maize CMT homolog ZMET2 (Papa et al. 2001) have been implicated in the maintenance of CNG methylation.[10]

CMT3 encodes a chromomethylase involved in methylating cytosine residues at non-CG sites. Involved in preferentially methylating transposon-related sequences, reducing their mobility. CMT3 interacts with an Arabidopsis homologue of HP1 (heterochromatin protein 1), which in turn interacts with methylated histones.CMT3 involved in gene silencing.


The genetic code underpins all of life with almost invariant consistency, but imagine, for a moment, if this were not so. After all, a given codon is not intrinsically better suited to represent leucine than phenylalanine or aspartic acid. What if evolution could break the informational straightjacket, allowing species to tweak the code to their needs? It would be, to say the least, extremely inconvenient. To interpret each genome, the code would have to be cracked anew. We would need to understand how the code has evolved, which features are ancient, which are specific to major lineages, and which commonly fluctuate between species. DNA methylation may not be as old as the genetic code but is nonetheless exceedingly ancient. Methylation of the fifth carbon of cytosine, is mediated by the same enzymatic superfamily in bacteria, archaea, and eukaryotes. Like the genetic code, semiconservative inheritance of methylation states of palindromic sites can propagate information through cellular generations. However, the biological meaning of methylated bases is flexible. Considering that mechanistic studies of DNA methylation are confined to a small number of model organisms, uncovering the evolutionary history of this process is required to know which lessons from, for example, the mustard weed Arabidopsis thaliana are directly applicable to mammals, which will be useful for distantly related crop plants, and which are esoteric to the genus. Recent advances in sequencing technology have allowed us to read the methylation patterns of entire genomes. The quest to decipher the meaning of these patterns is just beginning.[11]

Eukaryotic Methyltransferase Families Dnmt1 and Dnmt3 are two generally accepted families of functional eukaryotic DNA methyltransferases that predate the divergence of plants and animals. Dnmt1 and the accessory protein UHRF1 mediate methylation of hemimethylated CG dinucleotides following DNA replication, allowing faithful propagation of methylation patterns. Because of this functionality, Dnmt1 is generally considered a maintenance methyltransferase. Dnmt1 is the lynchpin of eukaryotic methylation: with the exception of a lineage of ascomycete fungi, all plants, animals and fungi that methylate DNA possess Dnmt1 (Figures 1 and 2). Dnmt3 enzymes establish methylation of previously unmethylated sequences in plants and animals. Animal Dnmt3s methylate CG sites, while land plant Dnmt3s (called DRMs for Domains Rearranged Methyltransferases because of a rearrangement of the catalytic domain) can methylate cytosine in any context. DRMs are recruited to their sites of action by the RNA interference pathway. Dnmt3 enzymes appear to be more dispensable than Dnmt1. Dnmt3 homologs have not been found in any fungal genome, and Dnmt3 has been lost in some green algae and animal lineages (Figure 2). The green alga Chlorella sp. NC64A, the silk moth Bombyx mori and zygomycete and basidiomycete fungi have robust Dnmt1-mediated CG methylation without Dnmt3. In B. mori and basidiomycetes, Dnmt1 is the only methyltransferase family, indicating that Dnmt1 can establish as well as maintain DNA methylation, at least in some species. CMT and Dim-2 are Dnmt1-related methyltransferases found in plants and fungi, respectively. Both enzymes methylate transposable elements and other repeats, are dependent on methylation of lysine 9 of histone H3, and have acidic carboxy-terminal tails. Consistent with the structural and functional similarities, CMT and Dim-2 form a monophyletic group distinct from the Dnmt1 proteins of plants, animals, and fungi (Figure 1), leading us to propose the CMT/Dim-2 enzyme family. Neither CMT-like nor Dim-2-like proteins are present in animals, indicating that this family has been lost early in animal evolution (Figure 2). Finally, plants, animals and fungi share the highly conserved Dnmt2 proteins. Dnmt2 contains all catalytic motifs expected of a DNA methyltransferase, but shows no such activity in vitro. Instead, Dnmt2 specifically and efficiently methylates cytosine 38 of tRNAAsp in vitro, and can reestablish this methylation in A. thaliana, mouse and fruit fly Dnmt2-deficient cells. The sequence around cytosine 38 is conserved among organisms that have Dnmt2, but is diverged in species lacking Dnmt2. Several studies have put forth evidence for in vivo DNA methylation by Dnmt2, most recently in early Drosophila embryos. However, whole-genome analysis of fruit fly embryos at the same stage did not reveal significant methylation. While the possibility that Dnmt2 can function as a DNA methyltransferase remains, the preponderance of evidence so far suggests that Dnmt2 is a very specific RNA methyltransferase with no activity on DNA.[11]

Os03g0226800 1.jpg

Os03g0226800 2.JPG

Labs working on this gene

▪ Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles 90095, USA.

▪ Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.

▪ Robert Fischer Lab,University of California, Berkeley

▪ Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.

▪ Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.

▪ Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, USA.

▪ Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, Wisconsin 53706, USA.


  1. 1.0 1.1 Jackson, J.P., Lindroth, A.M., Cao, X., Jacobsen, S.E. (2002) "Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase." Nature.
  2. 2.0 2.1 Lindroth, A.M., Cao, X., Jackson, J.P., Zilberman, D., McCallum, C.M., Henikoff, S., Jacobsen, S.E. (2001) "Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation." Science.
  3. Bartee, L., Malagnac, F., Bender, J. (2001) "Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene." Genes Dev.
  4. 4.0 4.1 Xiao, W., Custard, K.D., Brown, R.C., Lemmon, B.E., Harada, J.J., Goldberg, R.B., Fischer, R.L. (2006) "DNA methylation is critical for Arabidopsis embryogenesis and seed viability." Plant Cell.
  5. 5.0 5.1 Lindroth, A.M., Shultis, D., Jasencakova, Z., Fuchs, J., Johnson, L., Schubert, D., Patnaik, D., Pradhan, S., Goodrich, J., Schubert, I., Jenuwein, T., Khorasanizadeh, S., Jacobsen, S.E. (2004) "Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3." EMBO J.
  6. Tran, R.K., Zilberman, D., de Bustos, C., Ditt, R.F., Henikoff, J.G., Lindroth, A.M., Delrow, J., Boyle, T., Kwong, S., Bryson, T.D., Jacobsen, S.E., Henikoff, S. (2005) "Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis." Genome Biol.
  7. Mull, L., Ebbs, M.L., Bender, J. (2006) "A histone methylation-dependent DNA methylation pathway is uniquely impaired by deficiency in Arabidopsis s-adenosylhomocysteine hydrolase." Genetics.
  8. Chan, S.W., Henderson, I.R., Zhang, X., Shah, G., Chien, J.S., Jacobsen, S.E. (2006) "RNAi, DRD1, and Histone Methylation Actively Target Developmentally Important Non-CG DNA Methylation in Arabidopsis." PLoS Genet.
  9. Papa, C.M., Springer, N.M., Muszynski, M.G., Meeley, R., Kaeppler, S.M. (2001) "Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation." Plant Cell.
  10. Bartee L, Malagnac F, Bender J. (2001) "Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene." Gen Dev., 15 (2001), pp. 1753-8.
  11. 11.0 11.1 A. Zemach, D. Zilberman. (2010) "Evolution of eukaryotic DNA methylation and the pursuit of safer sex" Curr. Biol., 20 (2010), pp. R780–R785.

Os03g0226800 3.JPG

Structured Information