Mbd4

554 amino acids

MeCP2

484 amino acids

Methyl Binding Transcriptional Domain Repression Domain

Figure 6.5 Murine methyl-CpG-binding (MBD) proteins.

In commenting on the studies of Nan et al.,57 Jones et al.,58 Bestor60 suggested that deacetylation might exert two structural effects on chromatin that favor gene silencing: First, deacetylation of lysine e-amino groups might permit greater ionic interactions between the positively charged amino-terminal histone tails and the negatively charged phosphate backbone of DNA, which would interfere with the binding of transcription factors to their specific DNA sequences. Second, deacetylation might favor interactions between adjacent nucleosomes and lead to compaction of the chromatin. The higher affinity of deacetylated histone tails for DNA favored the first explanation while the crystal structure of the nucleosome favored the second. Whether the effects of histone acetyla-tion acted at intra- or internucleosome levels was unclear.60 Nevertheless, the results of Nan et al.57 and Jones et al.58 clearly established a direct causal relationship between DNA methylation-transcriptional silencing and modification of chromatin.

The events of the 1990s can be summed up as follows. At the beginning of this decade, evidence from studies on many model systems had demonstrated that most regions of invertebrate genomes were free of methylation. In contrast, all regions of vertebrate genome were subject to methylation primarily at sites rich in CpG dinucleotides. However, the methylated sites were distributed unevenly throughout the genome in patches of low and high density. At the beginning of this period, Dnmt1 was the only mammalian DNA methyltransferase and no methyl-CpG-binding protein was known. By the close of this decade, the mechanism of the methylation reaction had been worked out; four mammalian Dmnts and five methyl-CpG-binding proteins were known61 (Figures 6.4 and 6.5).

With these new findings in hand, questions regarding the function of DNA methylation and the relation of histone acetylation and DNA methylation to chromatin remodeling and to repression of gene activity were beginning to yield to experimental scrutiny. Acetylation of conserved lysines on the amino terminals of the core histones was shown to be an important mechanism by which chromatin structure is altered. Histone acetylation was associated with an open chromatin conformation allowing for gene transcription, while histone deacety-lation maintained the chromatin in the closed, nontranscribed state. Aided by the tools of molecular biology, investigators had learned how CpG dinucleotides were targeted for methylation, and how the patterns of methylation were read, maintained, and in most cases faithfully transmitted from one generation to the next.

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