DNA methylation patterns and epigenetic memory Adrian Bird The identity of a cell is determined by its proteins, which result from specific gene expression patterns. Key determinants of gene expression are transcription factors that activate or repress genes by recognizing DNA sequences in promoter regions. However, the types of transcription factors present in a cell are not sufficient to define its gene activity spectrum, as gene expression can be restricted during development. This restriction likely explains the low efficiency of cloning animals from differentiated cell nuclei. A "transcription factors only" model would predict that the gene expression pattern of a differentiated nucleus would be reversible upon exposure to new factors. Although many aspects of expression can be reprogrammed, some marks of differentiation are stable and cannot be erased by an alien cytoplasm. The genomic sequence of a differentiated cell is similar to that of the zygote, suggesting that developmental history marks are not due to somatic mutation. Epigenetic mechanisms, which involve heritable changes in gene function not explained by DNA sequence changes, include DNA methylation and the Polycomb-trithorax group (Pc-G/trx) protein complexes. This review focuses on DNA methylation, discussing its generation, inheritance, and biological significance in mammalian development. Data suggest that DNA methylation may only affect genes already silenced by other mechanisms in the embryo. Embryonic transcription may exclude the DNA methylation machinery. The heritability of methylation states and the secondary nature of the decision to invite or exclude methylation support the idea that DNA methylation is adapted for a specific cellular memory function in development. DNA methylation and Pc-G/trx may represent alternative systems of epigenetic memory that have been interchanged over evolutionary time. DNA methylation patterns vary widely in animals. In C. elegans, there is no detectable 5mC, while in Drosophila, very low levels of 5mC are found. Most invertebrate genomes have moderately high levels of methyl-CpG. Vertebrate genomes have the highest levels of 5mC. Vertebrate methylation is dispersed over much of the genome, referred to as global methylation. The variety of DNA methylation patterns in animals highlights the possibility that different distributions reflect different functions for the DNA methylation system. In human somatic cells, 5mC accounts for ~1% of total DNA bases and affects 70%–80% of all CpG dinucleotides. This average pattern conceals intriguing temporal and spatial variation. During early mouse development, methylation levels decline sharply. De novo methylation restores normal levels by implantation. A much more limited drop in methylation occurs in the frog Xenopus laevis, and no drop is seen in the zebrafish. Even within vertebrates, interspecies variation is seen that could reflect differences in the precise role played by methylation in these organisms. The most striking featureDNA methylation patterns and epigenetic memory Adrian Bird The identity of a cell is determined by its proteins, which result from specific gene expression patterns. Key determinants of gene expression are transcription factors that activate or repress genes by recognizing DNA sequences in promoter regions. However, the types of transcription factors present in a cell are not sufficient to define its gene activity spectrum, as gene expression can be restricted during development. This restriction likely explains the low efficiency of cloning animals from differentiated cell nuclei. A "transcription factors only" model would predict that the gene expression pattern of a differentiated nucleus would be reversible upon exposure to new factors. Although many aspects of expression can be reprogrammed, some marks of differentiation are stable and cannot be erased by an alien cytoplasm. The genomic sequence of a differentiated cell is similar to that of the zygote, suggesting that developmental history marks are not due to somatic mutation. Epigenetic mechanisms, which involve heritable changes in gene function not explained by DNA sequence changes, include DNA methylation and the Polycomb-trithorax group (Pc-G/trx) protein complexes. This review focuses on DNA methylation, discussing its generation, inheritance, and biological significance in mammalian development. Data suggest that DNA methylation may only affect genes already silenced by other mechanisms in the embryo. Embryonic transcription may exclude the DNA methylation machinery. The heritability of methylation states and the secondary nature of the decision to invite or exclude methylation support the idea that DNA methylation is adapted for a specific cellular memory function in development. DNA methylation and Pc-G/trx may represent alternative systems of epigenetic memory that have been interchanged over evolutionary time. DNA methylation patterns vary widely in animals. In C. elegans, there is no detectable 5mC, while in Drosophila, very low levels of 5mC are found. Most invertebrate genomes have moderately high levels of methyl-CpG. Vertebrate genomes have the highest levels of 5mC. Vertebrate methylation is dispersed over much of the genome, referred to as global methylation. The variety of DNA methylation patterns in animals highlights the possibility that different distributions reflect different functions for the DNA methylation system. In human somatic cells, 5mC accounts for ~1% of total DNA bases and affects 70%–80% of all CpG dinucleotides. This average pattern conceals intriguing temporal and spatial variation. During early mouse development, methylation levels decline sharply. De novo methylation restores normal levels by implantation. A much more limited drop in methylation occurs in the frog Xenopus laevis, and no drop is seen in the zebrafish. Even within vertebrates, interspecies variation is seen that could reflect differences in the precise role played by methylation in these organisms. The most striking feature