Creation of genomic methylation patterns

There are two biological properties of genomic methylation patterns that can be regarded as established. First, methylation of 5′-CpG-3′ dinucleotides within promoters represses transcription, often to undetectable levels. Second, in most cases methylation patterns are subject to clonal inheritance. These properties suit methylation patterns for a number of biological roles, although none of the current hypotheses can be regarded as proved or disproved. One hypothesis suggests that the activity of parasitic sequence elements is repressed by selective methylation. Features of invasive sequences that might allow their identification and inactivation are discussed in terms of the genome defense hypothesis. Identification of the cues that direct de novo methylation may reveal the biological role (or roles) of genomic methylation patterns.

[1]  W. Engels,et al.  Long-range cis preference in DNA homology search over the length of a Drosophila chromosome. , 1994, Science.

[2]  E. Selker Premeiotic instability of repeated sequences in Neurospora crassa. , 1990, Annual review of genetics.

[3]  G. Fink,et al.  Epigenetic control of an endogenous gene family is revealed by a novel blue fluorescent mutant of arabidopsis , 1995, Cell.

[4]  R. Jaenisch,et al.  DNA methylation, genomic imprinting, and mammalian development. , 1993, Cold Spring Harbor symposia on quantitative biology.

[5]  R. Jaenisch,et al.  Treatment of mice with 5-azacytidine efficiently activates silent retroviral genomes in different tissues. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[6]  R. Cawthon,et al.  Somatic mutations in the neurofibromatosis 1 gene in human tumors , 1992, Cell.

[7]  B. Kemper,et al.  Endonuclease VII resolves Y‐junctions in branched DNA in vitro. , 1986, The EMBO journal.

[8]  W. Gerald,et al.  Epigenetic lesions at the H19 locus in Wilms' tumour patients , 1994, Nature Genetics.

[9]  C. Schmid,et al.  Specific Alu Binding Protein from Human Sperm Chromatin Prevents DNA Methylation (*) , 1995, The Journal of Biological Chemistry.

[10]  D. Barlow,et al.  Characteristics of imprinted genes , 1995, Nature Genetics.

[11]  Z. Siegfried,et al.  Spl elements protect a CpG island from de novo methylation , 1994, Nature.

[12]  N. Craig Unity in Transposition Reactions , 1995, Science.

[13]  G. Barsh,et al.  Neomorphic agouti mutations in obese yellow mice , 1994, Nature Genetics.

[14]  W. Lipscomb,et al.  The crystal structure of Haelll methyltransferase covalently complexed to DNA: An extrahelical cytosine and rearranged base pairing , 1995, Cell.

[15]  M. Davisson,et al.  Differential expression of a new dominant agouti allele (Aiapy) is correlated with methylation state and is influenced by parental lineage. , 1994, Genes & development.

[16]  A. Bird,et al.  Gene number, noise reduction and biological complexity. , 1995, Trends in genetics : TIG.

[17]  D. Kohn,et al.  Lack of expression from a retroviral vector after transduction of murine hematopoietic stem cells is associated with methylation in vivo. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[18]  R. Roberts,et al.  M.HhaI binds tightly to substrates containing mismatches at the target base. , 1995, Nucleic acids research.

[19]  J. Herman,et al.  Silencing of the VHL tumor-suppressor gene by DNA methylation in renal carcinoma. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[20]  A. Coxon,et al.  Cytosine methylation The pros and cons of DNA methylation , 1993, Current Biology.

[21]  T. Mukai,et al.  Genomic imprinting of p57KIP2, a cyclin–dependent kinase inhibitor, in mouse , 1995, Nature Genetics.

[22]  Arthur D. Riggs,et al.  X inactivation, differentiation, and DNA methylation. , 1975, Cytogenetics and cell genetics.

[23]  A. Yang,et al.  HhaI and HpaII DNA methyltransferases bind DNA mismatches, methylate uracil and block DNA repair. , 1995, Nucleic acids research.

[24]  DP Barlow Methylation and imprinting: from host defense to gene regulation? , 1993, Science.

[25]  R Holliday,et al.  DNA modification mechanisms and gene activity during development , 1975, Science.

[26]  C. Schmid,et al.  Alu repeated DNAs are differentially methylated in primate germ cells. , 1994, Nucleic acids research.

[27]  Bernhard Horsthemke,et al.  Inherited microdeletions in the Angelman and Prader–Willi syndromes define an imprinting centre on human chromosome 15 , 1995, Nature Genetics.

[28]  T. Bestor,et al.  DNA methylation: evolution of a bacterial immune function into a regulator of gene expression and genome structure in higher eukaryotes. , 1990, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[29]  Wolfgang Stephan,et al.  The evolutionary dynamics of repetitive DNA in eukaryotes , 1994, Nature.

[30]  M. Matzke,et al.  Homology-dependent gene silencing in transgenic plants: what does it really tell us? , 1995, Trends in genetics : TIG.

[31]  J. Drake,et al.  Duplication-targeted DNA methylation and mutagenesis in the evolution of eukaryotic chromosomes. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[32]  R. Flavell Inactivation of gene expression in plants as a consequence of specific sequence duplication. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Rudolf Jaenisch,et al.  Targeted mutation of the DNA methyltransferase gene results in embryonic lethality , 1992, Cell.

[34]  T. Bestor,et al.  Regulated synthesis and localization of DNA methyltransferase during spermatogenesis. , 1995, Biology of reproduction.

[35]  S. Iguchi-Ariga,et al.  CpG methylation of the cAMP-responsive enhancer/promoter sequence TGACGTCA abolishes specific factor binding as well as transcriptional activation. , 1989, Genes & development.

[36]  T. Bestor Supercoiling-dependent sequence specificity of mammalian DNA methyltransferase. , 1987, Nucleic acids research.

[37]  K. Woodford,et al.  CGG repeats associated with DNA instability and chromosome fragility form structures that block DNA synthesis in vitro. , 1995, Nucleic acids research.

[38]  Eric S. Lander,et al.  A genetic map of the mouse with 4,006 simple sequence length polymorphisms , 1994, Nature Genetics.

[39]  M. Turker,et al.  A cis-acting element accounts for a conserved methylation pattern upstream of the mouse adenine phosphoribosyltransferase gene. , 1993, The Journal of biological chemistry.

[40]  J. Cleaver It was a very good year for DNA repair , 1994, Cell.

[41]  A. Bird,et al.  Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. , 1994, Genes & development.

[42]  A. Riggs,et al.  Polymerase chain reaction-aided genomic sequencing of an X chromosome-linked CpG island: methylation patterns suggest clonal inheritance, CpG site autonomy, and an explanation of activity state stability. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[43]  J. Finnegan,et al.  Transgene Inactivation: Plants Fight Back! , 1994, Bio/Technology.

[44]  S. S. Smith,et al.  Hairpins are formed by the single DNA strands of the fragile X triplet repeats: structure and biological implications. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[45]  C. Goyon,et al.  Perpetuation of cytosine methylation in Ascobolus immersus implies a novel type of maintenance methylase. , 1994, Journal of molecular biology.

[46]  S. Hirohashi,et al.  Silencing of the E-cadherin invasion-suppressor gene by CpG methylation in human carcinomas. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[47]  Michael Ashburner,et al.  Drosophila: A laboratory handbook , 1990 .