O O

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methylation

.XWTtTTTTTTTTTTTTT,

proteins that bind methylated dma

histone deacetylase chromatin remodeling complex gene completely OFF

gene completely OFF

FIGURE 17-24 Switching a gene off through DNA methylation and histone modification.

In its unmodified state, the mammalian gene shown can readily switch between being expressed or not expressed in tf>e presence of activators and Ihe transcription machinery, as shown in the top line. In this situation. expression is never fimily shut off - it is leaky. Often that is not good enough-sometimes a gene must be completely shut off, on occasion permanently This is achieved through methylation of the DNA and modification of the local nudeosomes fhus, when the gene is not being expressed, a DNA methyftransferase (a methylase) can gain access and methylate cytosines within the promoter sequence, the gene itself, and the upsteam activator binding sites. The methyl group is added to the 5' position in the cytosine nr,g, generating 5-methylcytosine (see Chapter 6) Thts modification alone can disrupt binding of the transcription machinery and activators in some cases. But it also binds other proteins (for example, MeCP2) that recognise DNA sequences containing rnethylc/tosine. These proteins, in turn, recruit complexes that remodel and modify local nucleo-scmes, switching off expression of the gene completely.

one copy on a chromosome inherited from the father, the other on the equivalent chromosome from the mother. In most cases, the two alleles are expressed at comparable levels. This is hardly surprising: they carry the same regulatory sequences and are in the presence of the same regulators; they are also located in an equivalent region of two very similar chromosomes. But there are a few cases where one copy of a gene is expressed while the other is silent.

Two well-studied examples are Ihe human H19 and ]gf2 genes (Figure 17-25). These are locateri close to each other on human chromosome 11. In a given cell, one copy of 1119 (that on the maternal chromosome) is expressed, while the other copy (on the paternal chromosome) is switched off; for ig/2 the reverse is true—the paternal copy is on and the maternal copy off.

Two regulatory sequences are critical for the differential expression of these genes: an enhancer (downstream of the Ifl9 gene) and an insulator (located between the 1119 and ]gf2 genes). The enhancer

FIGURE 17-25 Imprinting. Shown are two examples of genes controlled by imprinting—Ihe mammalian Igf2 and HI9 genes. As described in the text, in a given cell, the H)9 gene ts expressed from only the maternal chromosome, Igt? from the paternal chromosome. Tbe metbylabon state of the insulator element determines whether or not the insulator binding protein (CfCr) can bind and block activation of the HIS gene from the downstream enhancer.

b paternal chrosome insulator

a insulator enhancnr

(.when bound by activators) can, in principle, activate either of the two genes. So why does it activate only H19 on the maternal chromosome and Igf2 on the paternal chromosome? The answer lies in the role of (he insulator and its rnethylation state, Thus, the enhancer cannol activate the Jgf2 gene on the maternal chromosome because on that chromosome, the insulator binds a protein, CTCF, that blocks activators at the enhancer from activating the Ig/2 gene. On the paternal chromosome, in contrast, the insulator element and the H19 promoter are methylated. In that state, the transcription machinery cannot hind the Hi 9 promoter, and CTCF cannot bind the insulator. As a result, the enhancer now activates the ig/2 gene. The Hi9 gene is further repressed on the paternal chromosome by the binding of MeCP2 to the methylated insulator. This, as we have seen, recruits deacetylases, and these repress the H19 promoter.

Some States of Gene Expression Are Inherited through Cell Division even when the Initiating Signal Is No Longer Present

Patterns of gene expression must sometimes be inherited. A signal released by one cell during development causes neighboring cells to switch on specific genes. Those genes may have to remain switched on in those cells for many cell generations, even if the signal that induced them is present only fLeetingly. The inheritance of gene expression pot-terns, in the absence of either mutation or the initiating signal, is called epigenetic regulation. The imprinting example we discussed above reveals one way the expression of a gene can be regulated epigenetically.

Contrast this with some of the examples of gene regulation we have discussed. If a gene is controlled by an activator, and that activator is only active in the presence of a given signal, then the gene will remain on only as long as the signal is present. Indeed, under normal conditions, the lac genes of E. coli will only be expressed while lactose is present and glucose absent. Likewise the GAL genes of yeast ;ue expressed only as long as glucose is absent and galactose present, and human ^-interferon is made only while cells are stimulated by viral infection. But we have also already encountered an example of gene regulation which can be inherited epigenetically. The reason that case, maintenance of a phage X. lysogen (Chapter 16), can be described as epigenetic is discussed in Box 17-3, X Lysogens and the Epigenetic K witch.

CTCF^

FIGURE 17-25 Imprinting. Shown are two examples of genes controlled by imprinting—Ihe mammalian Igf2 and HI9 genes. As described in the text, in a given cell, the H)9 gene ts expressed from only the maternal chromosome, Igt? from the paternal chromosome. Tbe metbylabon state of the insulator element determines whether or not the insulator binding protein (CfCr) can bind and block activation of the HIS gene from the downstream enhancer.

insulator enhancer a maternal chromosome

CTCF^

b paternal chrosome insulator enhancer

Nucleosome and DNA modifications nan provide thfi basis for epigenetic inheritance, Consider a gene switched off by methylation of locat histones. When that region of the chromosome is replicated during cell division, the methylated histones from the parental DNA molecule end up distributed equally between die two daughter duplexes (see Figure 7-42). Thus, each of the daughter molecules carries some methylated and some tinmethylated nucleosides. The methylated nucleosomes recruit proteins hearing ehromodoraains, including the histone methylase itself which then methylates the adjacent unmodified nucleosomes. A daughter strand that lacked methylated histones altogether (that is, one from an unmethylated parent) would not recruit the methylase. In this way, the state of chromatin modification can be maintained through generations.

DNA methylation is even mom reliably inherited, as shown in Figure 17-26. Thus, certain DNA methylases can methylate, at low frequency, previously unmodified DNA; but far more efficiently, so-called maintenance methylases modify hemimethylated DNA—the very substrate provided by replication of fully methylated DNA. In mammalian cells, DNA methylation may be the primary marker of regions of the genome that are silenced. After DNA replication.

FIGURE 17-26 Patterns of ONA methylation can be maintained through cell division.

As we saw in Figure 17-24, DMA invoked in expression of a vertebrate gene can get methylated, and expression of that gene switched oft. This initial methylation is performed by a de novo methylase. For the shutdown state to keep a gene off permanently, the methylation state must be inherited through cell division this figure shows how that is achieved A DNA sequence is shown in which two cytokines arc present on each strand, one methylated, the other not This pattern is maintained through cell division, because, upon DMA replication, a maintenance methylase recognizes the hemimethylated DMA, and adds a methyl group to the unmethylated cytosme within it. The completely unmethylated sequence is not recognized by this enzyme, and so remains unmethylated. Thus, both daughter DMA duplexes end up with the same pattern of methylation as the parent (Source: Adapted from Alberts B et ai. 20D2 Molecular biology of the cell, 4th edition, p. 48 T, fig 7 8?. Copyright © 2002. Reproduced by perm is sion of Routledge/Taylor & Francis Books, Inc.)

FIGURE 17-26 Patterns of ONA methylation can be maintained through cell division.

As we saw in Figure 17-24, DMA invoked in expression of a vertebrate gene can get methylated, and expression of that gene switched oft. This initial methylation is performed by a de novo methylase. For the shutdown state to keep a gene off permanently, the methylation state must be inherited through cell division this figure shows how that is achieved A DNA sequence is shown in which two cytokines arc present on each strand, one methylated, the other not This pattern is maintained through cell division, because, upon DMA replication, a maintenance methylase recognizes the hemimethylated DMA, and adds a methyl group to the unmethylated cytosme within it. The completely unmethylated sequence is not recognized by this enzyme, and so remains unmethylated. Thus, both daughter DMA duplexes end up with the same pattern of methylation as the parent (Source: Adapted from Alberts B et ai. 20D2 Molecular biology of the cell, 4th edition, p. 48 T, fig 7 8?. Copyright © 2002. Reproduced by perm is sion of Routledge/Taylor & Francis Books, Inc.)

Box 17-3 X Lysogens and the Epigenetic Switch

Heritable patterns of gene expression can be established without the use of nudeosome, or DNA, modification. Consider a bacterial example we discussed trt Chapter 16, a k lysogen. in a lysogen, the phage is in a dormant state within the bacterial host cell. This state is associated with a specific pattern of gene expression, and in particular with sustained expression of the k repressor protein (see Figure 16 27)

Lysogemc gene expression is established tn an infected cell in response to poor growth conditions. Once established, however, the lysogen ic state is maintained stably despite improvements in growth conditions: moving a Jysogen into rich giowth medium does not lead to induction And indeed, induction essentially never occurs until a suitable indudng signal (such as UV light) is received.

Maintenance of the lysogcnic state through cell division is thus an example of epigenetic regulation Instead of any form of modification, this epigenetic control results from a two-step strategy for repressor synthesis. In the first, systhesis is initially established through activation of the repressor (cl) gene by the activator CI1 (which is sensitive to growth conditions). In the second step, re pressor synthesis is maintained by autoregulation: repressor acti vates expression of its own gene (see Chapter 16, Figure 16-35). In this way, when the lysogenic cell divides, each daughter cell tn-hents a copy of the dormant phage genome and some repressor protein. That repressor is sufficient to stimulate further repressor synthesis from the phage genome in both cells. Much of gene regulation during the development of muticellutar organisms works in just this way. W/e will see examples in the next chapter.

hemirnethylated sites are re methylated. These can then be recognized by the repressor MeCP2, which in turn recruits histone deacetylases and rnethylases, reestablishing silencing (Figure 17-24).

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  • THOMAS SCHWAB
    When two genes are situated very close to each other in a chrosome ,then?
    4 years ago

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