Victoria H. Clark

Methylation of genomes and genes at the invertebrate-vertebrate boundary.

Patterns of DNA methylation in animal genomes are known to vary from an apparent absence of modified bases, via methylation of a minor fraction of the genome, to genome-wide methylation. Representative genomes from 10 invertebrate phyla comprise predominantly nonmethylated DNA and (usually but not always) a minor fraction of methylated DNA. In contrast, all 27 vertebrate genomes that have been examined display genome-wide methylation. Our studies of chordate genomes suggest that the transition from fractional to global methylation occurred close to the origin of vertebrates, as amphioxus has a typically invertebrate methylation pattern whereas primitive vertebrates (hagfish and lamprey) have patterns that are typical of vertebrates. Surprisingly, methylation of genes preceded this transition, as many invertebrate genes have turned out to be heavily methylated. Methylation does not preferentially affect genes whose expression is highly regulated, as several housekeeping genes are found in the heavily methylated fraction whereas several genes expressed in a tissue-specific manner are in the nonmethylated fraction.

Absence of genome-wide changes in DNA methylation during development of the zebrafish.

nature genetics • volume 23 • october 1999 139 CpGs in the vertebrate genome are targets for DNA cytosine methyltransferases. Methylation leads to local transcriptional repression and is essential for normal development in the mouse1. Both gametogenesis and early embryogenesis of mouse are accompanied by changes in global levels of DNA methylation2,3. Methylation levels are lowest in blastocyst DNA, but are restored to normal by the time of implantation. Several single-copy genes, repetitive sequences and transgenes have been shown to lose methylation in the early embryonic stages4. Notably, some imprinted regions have been shown to remain highly methylated through the blastocyst stage despite global hypomethylation4,5. The functional significance of reduced methylation is not known, but it has been suggested that gametic methylation patterns must be reset in the early embryo to re-programme the genome for the next round of somatic development2,4. If so, it might be expected that global loss of Absence of genome-wide changes in DNA methylation during development of the zebrafish

CpG island libraries from human chromosomes 18 and 22: landmarks for novel genes.

Abstract. CpG islands are found at the 5′ end of approximately 60% of human genes and so are important genomic landmarks. They are concentrated in early-replicating, highly acetylated gene-rich regions. With respect to CpG island content, human Chrs 18 and 22 are very different from each other: Chr 18 appears to be CpG island poor, whereas Chr 22 appears to be CpG island rich. We have constructed and validated CpG island libraries from flow-sorted Chrs 18 and 22 and used these to estimate the difference in number of CpG islands found on these two chromosomes. These libraries contain normalized collections of sequences from the 5′ end of genes. Clones from the libraries were sequenced and compared with the sequence databases; one third matched ESTs, thus anchoring these ESTs at the 5′ end of their gene. However, it was striking that many clones either had no match or matched only existing CpG island clones. This suggests that a significant proportion of 5′ gene sequences are absent from databases, presumably either because they are difficult to clone or the gene is poorly expressed and/or has a restricted expression pattern. This point should be taken into consideration if the currently available libraries are those used for the elucidation of complete, as opposed to partial, gene sequences. The Chr 18 and 22 CpG island libraries are a sequence resource for the isolation of such 5′ gene sequences from specific human chromosomes.