Periodic DNA Methylation in Maize Nucleosomes and Demethylation by Environmental Stress

Abstract

When maize seedlings were exposed to cold stress, a genome-wide demethylation occurred in root tissues. Screening of genomic DNA identified one particular fragment that was demethylated during chilling. This 1.8-kb fragment, designated ZmMI1, contained part of the coding region of a putative protein and part of a retrotransposon-like sequence. ZmMI1 was transcribed only under cold stress. Direct methylation mapping revealed that hypomethylated regions spanning 150 bases alternated with hypermethylated regions spanning 50 bases. Analysis of nuclear DNA digested with micrococcal nuclease indicated that these regions corresponded to nucleosome cores and linkers, respectively. Cold stress induced severe demethylation in core regions but left linker regions relatively intact. Thus, methylation and demethylation were periodic in nucleosomes. The following biological significance is conceivable. First, because DNA methylation in nucleosomes induces alteration of gene expression by changing chromatin structures, vast demethylation may serve as a common switch for many genes that are simultaneously controlled upon environmental cues. Second, because artificial demethylation induces heritable changes in plant phenotype (Sano, H., Kamada, I., Youssefian, S., Katsumi, M., and Wabilko, H. (1990)Mol. Gen. Genet. 220, 441–447), altered DNA methylation may result in epigenetic inheritance, in which gene expression is modified without changing the nucleotide sequence. When maize seedlings were exposed to cold stress, a genome-wide demethylation occurred in root tissues. Screening of genomic DNA identified one particular fragment that was demethylated during chilling. This 1.8-kb fragment, designated ZmMI1, contained part of the coding region of a putative protein and part of a retrotransposon-like sequence. ZmMI1 was transcribed only under cold stress. Direct methylation mapping revealed that hypomethylated regions spanning 150 bases alternated with hypermethylated regions spanning 50 bases. Analysis of nuclear DNA digested with micrococcal nuclease indicated that these regions corresponded to nucleosome cores and linkers, respectively. Cold stress induced severe demethylation in core regions but left linker regions relatively intact. Thus, methylation and demethylation were periodic in nucleosomes. The following biological significance is conceivable. First, because DNA methylation in nucleosomes induces alteration of gene expression by changing chromatin structures, vast demethylation may serve as a common switch for many genes that are simultaneously controlled upon environmental cues. Second, because artificial demethylation induces heritable changes in plant phenotype (Sano, H., Kamada, I., Youssefian, S., Katsumi, M., and Wabilko, H. (1990)Mol. Gen. Genet. 220, 441–447), altered DNA methylation may result in epigenetic inheritance, in which gene expression is modified without changing the nucleotide sequence. 5-methylcytosine 4′,6-diamidino-2-phenylindoleDAPI DNA of higher eukaryotes is characterized by the presence of 5-methylcytosine (m5C)1 nucleotides, comprising up to 30% of the total cytosines. In vertebrates, m5C is located almost exclusively in CpG, whereas in plants it occurs in both CpG and CpNpG (1Gruenbaum Y. Naveh-Many T. Cedar H. Razin A. Nature. 1981; 292: 860-862Crossref PubMed Scopus (593) Google Scholar). The distribution within the genome is non-random and varies depending on the tissue and the developmental stages. The physiological function of m5C is essentially to silence gene expression, which is important for host DNA defenses against incorporation of “parasitic” DNA (2Yoder J.A. Walsh C.P. Bestor T.H. Trends Genet. 1997; 13: 335-340Abstract Full Text PDF PubMed Scopus (1501) Google Scholar, 3Colot V. Rossignol J.L. Bioessays. 1999; 21: 402-411Crossref PubMed Scopus (271) Google Scholar). Two systems are involved: one directly blocks transcriptional machinery attached to promoter regions of genes by altering DNA structure and the other indirectly interferes with transcription by influencing nucleosome conformation and stability (4Bird A.P. Wolffe A.P. Cell. 1999; 99: 451-454Abstract Full Text Full Text PDF PubMed Scopus (1541) Google Scholar). Recent studies indicated the latter to occur frequently, as shown by various disorders due to abnormal chromosome structures that are caused by defective DNA methylation (5Robertson K.D. Wolffe A.P. Nat. Rev. Genet. 2000; 1: 11-19Crossref PubMed Scopus (869) Google Scholar). One hallmark of cancer cells is local hypermethylation and global hypomethylation of chromosomal DNA (6Smith S.S. J. Mol. Biol. 2000; 302: 1-7Crossref PubMed Scopus (42) Google Scholar). Abnormal methylation in the promoter regions of regulatory genes may indeed result in cancer development (7Jones P.A. Takai D. Science. 2001; 293: 1068-1070Crossref PubMed Scopus (1513) Google Scholar). Using antisense inhibition of DNMT1, a maintenance type DNA methyltransferase, about 10% of all genes in cultured mouse cells were found to be activated (8Jackson-Grusby L. Beard C. Possemat R. Tudoe M. Fambrough D. Csankovszki G. Dausman J. Lee P. Wilson C. Lander E. Nat. Genet. 2001; 27: 31-39Crossref PubMed Scopus (562) Google Scholar). These observations confirmed that DNA methylation functions as a global repressor of gene expression (9Bird A. Genes Dev. 2002; 16: 6-21Crossref PubMed Scopus (5330) Google Scholar). The reverse case, i.e. global demethylation has also been inferred to be critical during embryogenesis in mammals (9Bird A. Genes Dev. 2002; 16: 6-21Crossref PubMed Scopus (5330) Google Scholar, 10Reik W. Dean W. Walter J. Science. 2001; 293: 1089-1093Crossref PubMed Scopus (2395) Google Scholar). What controls the on-off switch for DNA methylation, however, is still largely unclear. While a set of DNA methyltransferases has been identified in various organisms, including plants, the presence of DNA demethylases is controversial (7Jones P.A. Takai D. Science. 2001; 293: 1068-1070Crossref PubMed Scopus (1513) Google Scholar). Among several candidate proteins, 5-methylcytosine DNA glycosylase was shown to induce genome-wide demethylation upon transfection into mouse myoblasts (11Jost J.P. Oakeley E.J. Zhu B. Benjamin D. Thiry S. Siegmann M. Jost Y.-C. Nucleic Acids Res. 2001; 29: 4452-4461Crossref PubMed Scopus (88) Google Scholar). Whatever the mechanism may be, reprogramming of DNA methylation appears to be fundamental in normal development (10Reik W. Dean W. Walter J. Science. 2001; 293: 1089-1093Crossref PubMed Scopus (2395) Google Scholar).Epigenetic inheritance is defined as change in gene expression without base sequence alteration (12Riggs A.D. Porter T.N. Russo V.E.A. Martienssen R.A. Riggs A.D. Epigenetic Mechanisms of Gene Regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY1996: 29-45Google Scholar). This typically occurs during somatic cell differentiation, in which the clonal expansion of a single cell leads to a diversity of cell types (13Holliday R. Jost J.P. Saluz H.P. DNA Methylation: Molecular Biology and Biological Significance. Birkhauser Verlag, Basel, Switzerland1993: 452-468Crossref Scopus (30) Google Scholar). Such a cellular inheritance is common during ontogeny but is usually erased before gametes are produced (14Reik W. Walter J. Nat. Rev. Genet. 2001; 2: PubMed Scopus Google Scholar). In plants, however, it has been that be as by J. Biol. PubMed Scopus Google Scholar). In case, epigenetic changes were induced by as and A. Scopus Google Scholar, Rev. 1: Scopus (42) Google Scholar). the has been that environmental induce heritable chromatin as E. J. Biol. PubMed Scopus Google Scholar). is that clonal epigenetic changes are DNA methylation (6Smith S.S. J. Mol. Biol. 2000; 302: 1-7Crossref PubMed Scopus (42) Google R. Jost J.P. Saluz H.P. DNA Methylation: Molecular Biology and Biological Significance. Birkhauser Verlag, Basel, Switzerland1993: 452-468Crossref Scopus (30) Google but is for of the latter in inheritance of R.A. V. Science. 2001; 293: PubMed Scopus Google Scholar). shown that a single of to the DNA induced H. S. M. H. Mol. Gen. Genet. Scopus Google Scholar). DNA plants a in the m5C in with DNA hypomethylation and were to for H. S. M. H. Mol. Gen. Genet. Scopus Google Scholar). Thus, the phenotype due to changes in DNA methylation was epigenetic inheritance occurs under to be for the that of DNA methylation change in the cores of nucleosomes in maize root in to cold stress environmental cues. This to that DNA methylation may function as a common switch of gene expression and that induced changes in DNA methylation may result in heritable epigenetic of gene are into on DNA by in the sequence C. S. J. J. Mol. Biol. 1997; PubMed Scopus Google Scholar). One has been to be but the is as to of to DNA been M. J. PubMed Scopus Google Scholar, S. J. A. J. Biol. Full Text Full Text PDF PubMed Scopus Google and the and DNA is in to be under nucleosome appears to on CpG methylation C. S. J. J. Mol. Biol. 1997; PubMed Scopus Google Scholar, Wolffe A.P. J. Biol. Full Text Full Text PDF PubMed Scopus Google Scholar). This a DNA and that of was shown to be for DNA methylation in and it was that of DNA methylation is on of chromatin and DNA H. Nature. 2001; PubMed Scopus Google Scholar). result periodic of DNA methylation within the structure is with and a for methylation in the chromatin also of demethylation upon environmental of genome-wide of DNA methylation for which been (11Jost J.P. Oakeley E.J. Zhu B. Benjamin D. Thiry S. Siegmann M. Jost Y.-C. Nucleic Acids Res. 2001; 29: 4452-4461Crossref PubMed Scopus (88) Google Scholar, B. Benjamin D. Y. H. Thiry S. Siegmann M. Jost J.P. S. A. 2001; PubMed Scopus Google Scholar). In m5C is and in DNA is (11Jost J.P. Oakeley E.J. Zhu B. Benjamin D. Thiry S. Siegmann M. Jost Y.-C. Nucleic Acids Res. 2001; 29: 4452-4461Crossref PubMed Scopus (88) Google Scholar). with maize that genome-wide demethylation because DNA T. H. Nucleic Acids Res. 2000; PubMed Scopus Google Scholar). and in global DNA methylation was also during of J. B. B. J. 2001; PubMed Scopus Google Scholar). demethylation is by 5-methylcytosine DNA (11Jost J.P. Oakeley E.J. Zhu B. Benjamin D. Thiry S. Siegmann M. Jost Y.-C. Nucleic Acids Res. 2001; 29: 4452-4461Crossref PubMed Scopus (88) Google Scholar, B. Benjamin D. Y. H. Thiry S. Siegmann M. Jost J.P. S. A. 2001; PubMed Scopus Google has been found in of was that demethylation occurred the nucleosome core regions as revealed by methylation as to a demethylation is for but for are nucleosome cores are to be located the which is of a of nucleosomes. regions are by the This structure 5-methylcytosine DNA glycosylase to the core to the 5-methylcytosine DNA glycosylase may be to the core by for 5-methylcytosine of the methylation mapping is demethylation CpG, CpNpG and other to only one of This for is is in for in root the be This for the demethylation in the methylation of total genomic DNA in root was that of ZmMI1 was This a distribution of m5C in the with the and ZmMI1 to be located in because demethylation occurred the including the periodic methylation found in the latter may be common to other of the of demethylation in the core regions of nucleosomes induce alteration of chromatin structure and gene in ZmMI1 The of is that expression of many genes be simultaneously it was that plants may as many as several genes upon cold stress Cold Spring Harbor Laboratory Press, Cold Spring Harbor, Scholar). is to that plants the to simultaneously a vast of genes to because of the maize genome is of J.L. Mol. Biol. 2000; PubMed Scopus Google and because demethylation has been shown to R. the global demethylation to in of other genes A. S. T. H. T. Nature. 2001; PubMed Scopus Google Scholar). the demethylation occurs only in root is One be that are with a as by the presence and of DNA in the T. H. Nucleic Acids Res. 2000; PubMed Scopus Google of epigenetic in to environmental has been and DNA methylation has been as one of (13Holliday R. Jost J.P. Saluz H.P. DNA Methylation: Molecular Biology and Biological Significance. Birkhauser Verlag, Basel, Switzerland1993: 452-468Crossref Scopus (30) Google Scholar). In however, DNA methylation are in somatic cells that upon that are are usually erased and to the (14Reik W. Walter J. Nat. Rev. Genet. 2001; 2: PubMed Scopus Google Scholar). In plants, the somatic and cells is in with of DNA methylation shown by of with a that induces demethylation of DNA in H. S. M. H. Mol. Gen. Genet. Scopus Google Scholar). plants a global demethylation and altered including The and demethylation were for up to M. Y. and H. alteration of DNA methylation induce expression of in a both of which are heritable H. S. M. H. Mol. Gen. Genet. Scopus Google that the due to methylation is but of methylation changing depending on the was The that indeed maize are of somatic cells and In the demethylation be to The that demethylation was in which cells with the to into that these latter are against environmental in of DNA a DNA methylation it result in heritable were for for is the change to be the result of hypermethylation of the gene which occurred P. C. E. Nature. 1999; PubMed Scopus Google Scholar). in plants, is as with it to directly altered methylation to the that inheritance DNA DNA of higher eukaryotes is characterized by the presence of 5-methylcytosine (m5C)1 nucleotides, comprising up to 30% of the total cytosines. In vertebrates, m5C is located almost exclusively in CpG, whereas in plants it occurs in both CpG and CpNpG (1Gruenbaum Y. Naveh-Many T. Cedar H. Razin A. Nature. 1981; 292: 860-862Crossref PubMed Scopus (593) Google Scholar). The distribution within the genome is non-random and varies depending on the tissue and the developmental stages. The physiological function of m5C is essentially to silence gene expression, which is important for host DNA defenses against incorporation of “parasitic” DNA (2Yoder J.A. Walsh C.P. Bestor T.H. Trends Genet. 1997; 13: 335-340Abstract Full Text PDF PubMed Scopus (1501) Google Scholar, 3Colot V. Rossignol J.L. Bioessays. 1999; 21: 402-411Crossref PubMed Scopus (271) Google Scholar). Two systems are involved: one directly blocks transcriptional machinery attached to promoter regions of genes by altering DNA structure and the other indirectly interferes with transcription by influencing nucleosome conformation and stability (4Bird A.P. Wolffe A.P. Cell. 1999; 99: 451-454Abstract Full Text Full Text PDF PubMed Scopus (1541) Google Scholar). Recent studies indicated the latter to occur frequently, as shown by various disorders due to abnormal chromosome structures that are caused by defective DNA methylation (5Robertson K.D. Wolffe A.P. Nat. Rev. Genet. 2000; 1: 11-19Crossref PubMed Scopus (869) Google Scholar). One hallmark of cancer cells is local hypermethylation and global hypomethylation of chromosomal DNA (6Smith S.S. J. Mol. Biol. 2000; 302: 1-7Crossref PubMed Scopus (42) Google Scholar). Abnormal methylation in the promoter regions of regulatory genes may indeed result in cancer development (7Jones P.A. Takai D. Science. 2001; 293: 1068-1070Crossref PubMed Scopus (1513) Google Scholar). Using antisense inhibition of DNMT1, a maintenance type DNA methyltransferase, about 10% of all genes in cultured mouse cells were found to be activated (8Jackson-Grusby L. Beard C. Possemat R. Tudoe M. Fambrough D. Csankovszki G. Dausman J. Lee P. Wilson C. Lander E. Nat. Genet. 2001; 27: 31-39Crossref PubMed Scopus (562) Google Scholar). These observations confirmed that DNA methylation functions as a global repressor of gene expression (9Bird A. Genes Dev. 2002; 16: 6-21Crossref PubMed Scopus (5330) Google Scholar). The reverse case, i.e. global demethylation has also been inferred to be critical during embryogenesis in mammals (9Bird A. Genes Dev. 2002; 16: 6-21Crossref PubMed Scopus (5330) Google Scholar, 10Reik W. Dean W. Walter J. Science. 2001; 293: 1089-1093Crossref PubMed Scopus (2395) Google Scholar). What controls the on-off switch for DNA methylation, however, is still largely unclear. While a set of DNA methyltransferases has been identified in various organisms, including plants, the presence of DNA demethylases is controversial (7Jones P.A. Takai D. Science. 2001; 293: 1068-1070Crossref PubMed Scopus (1513) Google Scholar). Among several candidate proteins, 5-methylcytosine DNA glycosylase was shown to induce genome-wide demethylation upon transfection into mouse myoblasts (11Jost J.P. Oakeley E.J. Zhu B. Benjamin D. Thiry S. Siegmann M. Jost Y.-C. Nucleic Acids Res. 2001; 29: 4452-4461Crossref PubMed Scopus (88) Google Scholar). Whatever the mechanism may be, reprogramming of DNA methylation appears to be fundamental in normal development (10Reik W. Dean W. Walter J. Science. 2001; 293: 1089-1093Crossref PubMed Scopus (2395) Google Scholar). Epigenetic inheritance is defined as change in gene expression without base sequence alteration (12Riggs A.D. Porter T.N. Russo V.E.A. Martienssen R.A. Riggs A.D. Epigenetic Mechanisms of Gene Regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY1996: 29-45Google Scholar). This typically occurs during somatic cell differentiation, in which the clonal expansion of a single cell leads to a diversity of cell types (13Holliday R. Jost J.P. Saluz H.P. DNA Methylation: Molecular Biology and Biological Significance. Birkhauser Verlag, Basel, Switzerland1993: 452-468Crossref Scopus (30) Google Scholar). Such a cellular inheritance is common during ontogeny but is usually erased before gametes are produced (14Reik W. Walter J. Nat. Rev. Genet. 2001; 2: PubMed Scopus Google Scholar). In plants, however, it has been that be as by J. Biol. PubMed Scopus Google Scholar). In case, epigenetic changes were induced by as and A. Scopus Google Scholar, Rev. 1: Scopus (42) Google Scholar). the has been that environmental induce heritable chromatin as E. J. Biol. PubMed Scopus Google Scholar). is that clonal epigenetic changes are DNA methylation (6Smith S.S. J. Mol. Biol. 2000; 302: 1-7Crossref PubMed Scopus (42) Google R. Jost J.P. Saluz H.P. DNA Methylation: Molecular Biology and Biological Significance. Birkhauser Verlag, Basel, Switzerland1993: 452-468Crossref Scopus (30) Google but is for of the latter in inheritance of R.A. V. Science. 2001; 293: PubMed Scopus Google Scholar). shown that a single of to the DNA induced H. S. M. H. Mol. Gen. Genet. Scopus Google Scholar). DNA plants a in the m5C in with DNA hypomethylation and were to for H. S. M. H. Mol. Gen. Genet. Scopus Google Scholar). Thus, the phenotype due to changes in DNA methylation was epigenetic inheritance occurs under to be In for the that of DNA methylation change in the cores of nucleosomes in maize root in to cold stress environmental cues. This to that DNA methylation may function as a common switch of gene expression and that induced changes in DNA methylation may result in heritable epigenetic of gene are into on DNA by in the sequence C. S. J. J. Mol. Biol. 1997; PubMed Scopus Google Scholar). One has been to be but the is as to of to DNA been M. J. PubMed Scopus Google Scholar, S. J. A. J. Biol. Full Text Full Text PDF PubMed Scopus Google and the and DNA is in to be under nucleosome appears to on CpG methylation C. S. J. J. Mol. Biol. 1997; PubMed Scopus Google Scholar, Wolffe A.P. J. Biol. Full Text Full Text PDF PubMed Scopus Google Scholar). This a DNA and that of was shown to be for DNA methylation in and it was that of DNA methylation is on of chromatin and DNA H. Nature. 2001; PubMed Scopus Google Scholar). result periodic of DNA methylation within the structure is with and a for methylation in the chromatin also of demethylation upon environmental of genome-wide of DNA methylation for which been (11Jost J.P. Oakeley E.J. Zhu B. Benjamin D. Thiry S. Siegmann M. Jost Y.-C. Nucleic Acids Res. 2001; 29: 4452-4461Crossref PubMed Scopus (88) Google Scholar, B. Benjamin D. Y. H. Thiry S. Siegmann M. Jost J.P. S. A. 2001; PubMed Scopus Google Scholar). In m5C is and in DNA is (11Jost J.P. Oakeley E.J. Zhu B. Benjamin D. Thiry S. Siegmann M. Jost Y.-C. Nucleic Acids Res. 2001; 29: 4452-4461Crossref PubMed Scopus (88) Google Scholar). with maize that genome-wide demethylation because DNA T. H. Nucleic Acids Res. 2000; PubMed Scopus Google Scholar). and in global DNA methylation was also during of J. B. B. J. 2001; PubMed Scopus Google Scholar). demethylation is by 5-methylcytosine DNA (11Jost J.P. Oakeley E.J. Zhu B. Benjamin D. Thiry S. Siegmann M. Jost Y.-C. Nucleic Acids Res. 2001; 29: 4452-4461Crossref PubMed Scopus (88) Google Scholar, B. Benjamin D. Y. H. Thiry S. Siegmann M. Jost J.P. S. A. 2001; PubMed Scopus Google has been found in of was that demethylation occurred the nucleosome core regions as revealed by methylation as to a demethylation is for but for are nucleosome cores are to be located the which is of a of nucleosomes. regions are by the This structure 5-methylcytosine DNA glycosylase to the core to the 5-methylcytosine DNA glycosylase may be to the core by for 5-methylcytosine of the methylation mapping is demethylation CpG, CpNpG and other to only one of This for is is in for in root the be This for the demethylation in the methylation of total genomic DNA in root was that of ZmMI1 was This a distribution of m5C in the with the and ZmMI1 to be located in because demethylation occurred the including the periodic methylation found in the latter may be common to other of the of demethylation in the core regions of nucleosomes induce alteration of chromatin structure and gene in ZmMI1 The of is that expression of many genes be simultaneously it was that plants may as many as several genes upon cold stress Cold Spring Harbor Laboratory Press, Cold Spring Harbor, Scholar). is to that plants the to simultaneously a vast of genes to because of the maize genome is of J.L. Mol. Biol. 2000; PubMed Scopus Google and because demethylation has been shown to R. the global demethylation to in of other genes A. S. T. H. T. Nature. 2001; PubMed Scopus Google Scholar). the demethylation occurs only in root is One be that are with a as by the presence and of DNA in the T. H. Nucleic Acids Res. 2000; PubMed Scopus Google of epigenetic in to environmental has been and DNA methylation has been as one of (13Holliday R. Jost J.P. Saluz H.P. DNA Methylation: Molecular Biology and Biological Significance. Birkhauser Verlag, Basel, Switzerland1993: 452-468Crossref Scopus (30) Google Scholar). In however, DNA methylation are in somatic cells that upon that are are usually erased and to the (14Reik W. Walter J. Nat. Rev. Genet. 2001; 2: PubMed Scopus Google Scholar). In plants, the somatic and cells is in with of DNA methylation shown by of with a that induces demethylation of DNA in H. S. M. H. Mol. Gen. Genet. Scopus Google Scholar). plants a global demethylation and altered including The and demethylation were for up to M. Y. and H. alteration of DNA methylation induce expression of in a both of which are heritable H. S. M. H. Mol. Gen. Genet. Scopus Google that the due to methylation is but of methylation changing depending on the was The that indeed maize are of somatic cells and In the demethylation be to The that demethylation was in which cells with the to into that these latter are against environmental in of DNA a DNA methylation it result in heritable were for for is the change to be the result of hypermethylation of the gene which occurred P. C. E. Nature. 1999; PubMed Scopus Google Scholar). in plants, is as with it to directly altered methylation to the that inheritance DNA are into on DNA by in the sequence C. S. J. J. Mol. Biol. 1997; PubMed Scopus Google Scholar). One has been to be but the is as to of to DNA been M. J. PubMed Scopus Google Scholar, S. J. A. J. Biol. Full Text Full Text PDF PubMed Scopus Google and the and DNA is in to be under nucleosome appears to on CpG methylation C. S. J. J. Mol. Biol. 1997; PubMed Scopus Google Scholar, Wolffe A.P. J. Biol. Full Text Full Text PDF PubMed Scopus Google Scholar). This a DNA and that of was shown to be for DNA methylation in and it was that of DNA methylation is on of chromatin and DNA H. Nature. 2001; PubMed Scopus Google Scholar). result periodic of DNA methylation within the structure is with and a for methylation in the chromatin also of demethylation upon environmental stress. of genome-wide of DNA methylation for which been (11Jost J.P. Oakeley E.J. Zhu B. Benjamin D. Thiry S. Siegmann M. Jost Y.-C. Nucleic Acids Res. 2001; 29: 4452-4461Crossref PubMed Scopus (88) Google Scholar, B. Benjamin D. Y. H. Thiry S. Siegmann M. Jost J.P. S. A. 2001; PubMed Scopus Google Scholar). In m5C is and in DNA is (11Jost J.P. Oakeley E.J. Zhu B. Benjamin D. Thiry S. Siegmann M. Jost Y.-C. Nucleic Acids Res. 2001; 29: 4452-4461Crossref PubMed Scopus (88) Google Scholar). with maize that genome-wide demethylation because DNA T. H. Nucleic Acids Res. 2000; PubMed Scopus Google Scholar). and in global DNA methylation was also during of J. B. B. J. 2001; PubMed Scopus Google Scholar). demethylation is by 5-methylcytosine DNA (11Jost J.P. Oakeley E.J. Zhu B. Benjamin D. Thiry S. Siegmann M. Jost Y.-C. Nucleic Acids Res. 2001; 29: 4452-4461Crossref PubMed Scopus (88) Google Scholar, B. Benjamin D. Y. H. Thiry S. Siegmann M. Jost J.P. S. A. 2001; PubMed Scopus Google has been found in of was that demethylation occurred the nucleosome core regions as revealed by methylation as to a demethylation is for but for are nucleosome cores are to be located the which is of a of nucleosomes. regions are by the This structure 5-methylcytosine DNA glycosylase to the core to the 5-methylcytosine DNA glycosylase may be to the core by for 5-methylcytosine of the methylation mapping is demethylation CpG, CpNpG and other to only one of This for is is in for in root the be This for the demethylation in While the methylation of total genomic DNA in root was that of ZmMI1 was This a distribution of m5C in the with the and ZmMI1 to be located in because demethylation occurred the including the periodic methylation found in the latter may be common to other of the of demethylation in the core regions of nucleosomes induce alteration of chromatin structure and gene in ZmMI1 The of is that expression of many genes be simultaneously it was that plants may as many as several genes upon cold stress Cold Spring Harbor Laboratory Press, Cold Spring Harbor, Scholar). is to that plants the to simultaneously a vast of genes to because of the maize genome is of J.L. Mol. Biol. 2000; PubMed Scopus Google and because demethylation has been shown to R. the global demethylation to in of other genes A. S. T. H. T. Nature. 2001; PubMed Scopus Google Scholar). the demethylation occurs only in root is One be that are with a as by the presence and of DNA in the T. H. Nucleic Acids Res. 2000; PubMed Scopus Google Scholar). of epigenetic in to environmental has been and DNA methylation has been as one of (13Holliday R. Jost J.P. Saluz H.P. DNA Methylation: Molecular Biology and Biological Significance. Birkhauser Verlag, Basel, Switzerland1993: 452-468Crossref Scopus (30) Google Scholar). In however, DNA methylation are in somatic cells that upon that are are usually erased and to the (14Reik W. Walter J. Nat. Rev. Genet. 2001; 2: PubMed Scopus Google Scholar). In plants, the somatic and cells is in with of DNA methylation shown by of with a that induces demethylation of DNA in H. S. M. H. Mol. Gen. Genet. Scopus Google Scholar). plants a global demethylation and altered including The and demethylation were for up to M. Y. and H. alteration of DNA methylation induce expression of in a both of which are heritable H. S. M. H. Mol. Gen. Genet. Scopus Google Scholar). that the due to methylation is but of methylation changing depending on the was The that indeed maize are of somatic cells and In the demethylation be to The that demethylation was in which cells with the to into that these latter are against environmental in of DNA a DNA methylation it result in heritable were for for is the change to be the result of hypermethylation of the gene which occurred P. C. E. Nature. 1999; PubMed Scopus Google Scholar). in plants, is as with it to directly altered methylation to the that inheritance DNA A. B. and A. for and on the