Os03g0226800 - Revision history

Rice2012: /* Structured Information */

2015-06-12T05:36:10Z

‎Structured Information

Jin Xiaoyang at 04:09, 8 June 2014

2014-06-08T04:09:01Z

Show changes

Buddyma: CMT3 is a key determinant for non-CG methylation.

2014-06-08T02:29:38Z

CMT3 is a key determinant for non-CG methylation.

Buddyma: /* References */

2014-06-08T02:27:30Z

‎References

Buddyma: /* Expression */

2014-06-08T02:21:32Z

‎Expression

Buddyma: /* Labs working on this gene */

2014-06-08T02:19:58Z

‎Labs working on this gene

Buddyma: /* Evolution */

2014-06-08T02:18:38Z

‎Evolution

Buddyma: /* Evolution */

2014-06-08T02:18:04Z

‎Evolution

Buddyma: /* References */

2014-06-08T02:16:52Z

‎References

Buddyma: /* Expression */

2014-06-08T01:48:26Z

‎Expression

@@ Line 112: / Line 112: @@
 </ref>
 </references>
 ==Structured Information==
 [[Category:Genes]]
 [[Category:Japonica mRNA]]

@@ Line 47: / Line 47: @@
 ===Expression===
-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.
+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.
 ===Evolution===
-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.[10]
+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.[10]
+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]
 [[File:Os03g0226800 1.jpg]]

@@ Line 95: / Line 95: @@
 [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] A. Zemach, D. Zilberman. (2010) "Evolution of eukaryotic DNA methylation and the pursuit of safer sex" ''Curr. Biol''., 20 (2010), pp. R780–R785.
+[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.
 ==Structured Information==

@@ Line 47: / Line 47: @@
 ===Expression===
-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]
+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.
 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.

@@ Line 61: / Line 61: @@
 ==Labs working on this gene==
-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 90095, USA.
-Robert Fischer Lab，University of California, Berkeley
+▪ Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.
-Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
+▪ Robert Fischer Lab，University of California, Berkeley
-Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.
+▪ Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
-Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, USA.
+▪ Department of Biochemistry and Molecular Biology, Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland 21205, USA.
-Department of Agronomy, University of Wisconsin-Madison, 1575 Linden Drive, Madison, Wisconsin 53706, USA.
+▪ Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, California, USA.
 ==References==

@@ Line 76: / Line 76: @@
 ==References==
-[1] Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Jackson, J.P., Lindroth, A.M., Cao, X., Jacobsen, S.E. Nature (2002)
+[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] Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation. Lindroth, A.M., Cao, X., Jackson, J.P., Zilberman, D., McCallum, C.M., Henikoff, S., Jacobsen, S.E. Science (2001)
+[2] 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] Arabidopsis cmt3 chromomethylase mutations block non-CG methylation and silencing of an endogenous gene. Bartee, L., Malagnac, F., Bender, J. Genes Dev. (2001)
+[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] DNA methylation is critical for Arabidopsis embryogenesis and seed viability. Xiao, W., Custard, K.D., Brown, R.C., Lemmon, B.E., Harada, J.J., Goldberg, R.B., Fischer, R.L. Plant Cell (2006)
+[4] 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] Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. 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. EMBO J. (2004)
+[5] 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] Chromatin and siRNA pathways cooperate to maintain DNA methylation of small transposable elements in Arabidopsis. 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. Genome Biol. (2005)
+[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] A histone methylation-dependent DNA methylation pathway is uniquely impaired by deficiency in Arabidopsis s-adenosylhomocysteine hydrolase. Mull, L., Ebbs, M.L., Bender, J. Genetics (2006)
+[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] RNAi, DRD1, and Histone Methylation Actively Target Developmentally Important Non-CG DNA Methylation in Arabidopsis. Chan, S.W., Henderson, I.R., Zhang, X., Shah, G., Chien, J.S., Jacobsen, S.E. PLoS Genet. (2006)
+[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] Maize chromomethylase Zea methyltransferase2 is required for CpNpG methylation. Papa, C.M., Springer, N.M., Muszynski, M.G., Meeley, R., Kaeppler, S.M. Plant Cell (2001)
+[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''.
 ==Structured Information==