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The importance of methylation in DNA-protein interactions is well known. In chapter 13, we showed that a particular DNA sequence could be protected from restriction endonucleases if it were methylated. A small percentage of cytosine residues are methylated in many eukaryotic organisms, mainly in CpG sequences (see g. 13.3); 80% of the cytosines in CpG sequences in human DNA are methylated. (Often, when we refer to a sequence of two bases on the same strand of DNA, we put a p between them CpG to indicate that they are on the same strand connected by a phosphodiester bond and not on two different strands as a hydrogen-bonded base pair.) The degree of methylation of DNA is related to the silencing of a gene. Genes that are dormant in one cell type but active in another, or genes that are dormant at one stage of development but active in another, are usually less methylated when active and more fully methylated when inactive. For example, adenovirus, a cancer-causing virus, has been observed in many eukaryotic cell lines. In most lines in which the adenovirus DNA has integrated into the host chromosome, late viral genes are turned off. These genes are highly methylated at their CCGG or GCGC sites. In addition, chemicals that prevent methylation frequently activate previously dormant genes. For example, 5-azacytidine inhibits methylation; X chromosomal genes, which are normally deactivated, can be reactivated by treatment with 5-azacytidine. There are numerous other examples of the activation of genes after treatment with this chemical. The activated genes lack methylated cytosines that were previously methylated. Finally, the possibility exists that DNA methylation can affect the pattern of chromatin structure. Recent work has also indicated that the methylation itself may not prevent transcription, but rather may be a signal for transcriptional inactivity. In the thale cress plant, Arabidopsis thaliana, a protein named Mom (for Morpheus
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Figure 16.2 The rhomboid and twist genes each have three enhancer sequences that are recognized by the Dorsal transcription factor. However, the recognition sequences of the rhomboid gene are more ef cient at binding Dorsal than the recognition sequences of the twist gene. Thus, rhomboid is induced at both low and high concentrations of Dorsal, whereas twist is induced only at high concentrations.
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III. Molecular Genetics
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16. Gene Expression: Control in Eukaryotes
The McGraw Hill Companies, 2001
Control of Transcription in Eukaryotes
molecule), has been discovered that, when mutated, results in genes that have heavy methylation levels but are actively transcribed. Thus, the methylation level can be separated from the transcriptional activity of genes, although the two usually occur together. Arabidopsis is proving to be a good model in the study of the role of methylation in transcriptional activation because other common model organisms, namely fruit ies, yeast, and the nematode, Caenorhabditis elegans, do not have methylation of their DNA. Further interest has been generated in the role of methylation in controlling gene expression by the discovery of Z DNA, and the fact that Z DNA can be stabilized by methylation (see chapter 9). This observation has led to a model of transcriptional regulation based on alternative DNA structures. Sequences (such as CpG repetitions) that could exist as Z DNA exist as B DNA when being transcribed. If the gene is to be silenced (turned off), the CpG sequences are converted to stable Z DNA by methylation, which then blocks transcription.This possibility has gained some interest because of the recent discovery of an enzyme, double-stranded RNA adenosine deaminase (ADAR1), that binds to Z DNA sequences.
Signal Transduction
We return to the question of how speci c transcription activation factors appear at speci c times. As we will describe in the section on development, control of gene
expression requires that genes be expressed at speci c times and under speci c circumstances. If transcription is usually controlled by speci c transcription factors, what determines the appearance of these factors at the appropriate times and places One common mechanism is a signal transduction pathway, in which signals pass from the external environment through the cytoplasm, into the nucleus. For example, in a signal transduction pathway involved in development of the fruit y, the Toll protein spans the cell membrane ( g. 16.3). It acts as a receptor for the Sp tzle protein, which, when detected, causes a change in the cytoplasmic end of Toll, activating it. Activated Toll activates Pelle, a protein kinase that phosphorylates the Cactus protein, causing it to dissociate from Dorsal. Once Dorsal dissociates from Cactus, which acts to repress Dorsal, Dorsal becomes an active speci c transcription factor that can cross the nuclear membrane and activate its target gene ( g. 16.3). We thus see that Sp tzle attaching to its receptor protein (Toll) on the cell surface results in the activation of the target gene of the Dorsal protein in the nucleus. These pathways can become very complex, with many protein elements. More elements mean more sensitive control of various processes, often requiring that several conditions be met before a gene is activated. In addition, these pathways are usually conserved in evolution. A similar pathway, though more complex, occurs in mammals in which the
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