Generating Specialized Cell Types PDF

GENERATING SPECIALIZED CELL TYPES All cells must be able to turn genes on and off in response to signals in their environment. But the cells of multicellular organisms have taken this type of transcriptional control to an extreme, using it in highly specialized ways to form organized arrays of diffe...

GENERATING SPECIALIZED CELL TYPES All cells must be able to turn genes on and off in response to signals in their environment. But the cells of multicellular organisms have taken this type of transcriptional control to an extreme, using it in highly specialized ways to form organized arrays of differentiated cell types. Such decisions present a special challenge: once a cell in a multicellular organism becomes committed to differentiate into a specific cell type, the choice of fate is generally maintained through subsequent cell divisions. This means that the changes in gene expression, which are often triggered by a transient signal, must be remembered by the cell. Such cell memory is a prerequisite for the creation of organized tissues and for the maintenance of stably differentiated cell types. In contrast, the simplest changes in gene expression in both eukaryotes and bacteria are typically only transient; the tryptophan repressor, for example, switches off the tryptophan operon in bacteria only in the presence of tryptophan; as soon as the amino acid is removed from the medium, the genes switch back on, and the descendants of the cell will have no memory that their ancestors had been exposed to tryptophan. In this section, we discuss some of the special features of transcriptional regulation that allow multicellular organisms to create and maintain specialized cell types. These cell types ultimately produce the tissues and organs that give worms, flies, and even humans their distinctive characteristics. https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 1 of 33 Eukaryotic Genes Are Controlled by Combinations of Transcription Regulators The genes we have examined thus far have all been controlled by a small number of transcription regulators. While this is true for many simple bacterial systems, most eukaryotic transcription regulators work as part of a large “committee” of regulatory proteins, all of which cooperate to express the gene in the right cell type, in response to the right conditions, at the right time, and in the required amount. The term combinatorial control refers to the process by which groups of transcription regulators work together to determine the expression of a single gene. The bacterial Lac operon we discussed earlier provides a simple example of the use of multiple regulators to control transcription (see Figure 8–9). In eukaryotes, such regulatory inputs have been amplified, so that a typical gene is controlled by dozens of transcription regulators that bind to regulatory sequences that may be spread over tens of thousands of nucleotide pairs. Together, these regulators direct the assembly of Mediator, ATP-dependent chromatin-remodeling complexes, histone-modifying enzymes, general transcription factors, and, ultimately, RNA polymerase (Figure 8–13). https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 2 of 33 Figure 8–13 Transcription regulators work together as a “committee” to control the expression of a eukaryotic gene. Whereas the general transcription factors that assemble at the promoter are the same for all genes transcribed by RNA polymerase (see Figures 8–10 and 7–12), the transcription regulators and the locations of their DNA-binding sites relative to the promoters are different for each gene. The effects of multiple transcription regulators combine to determine the final rate of transcription initiation. “Spacer” DNA sequences may play a structural role in allowing the regulatory DNA sequences to find their proper positions, but they are not recognized by any transcription regulators. At particularly complex enhancers—those that include multiple repressors and activators bound to the DNA—it has been proposed that the transcription regulators form biomolecular condensates, which help them assemble into fully functional “committees.” How the cell ultimately integrates the effects of all of these proteins to determine the final level of gene expression is only now beginning to be understood. An example of such a complex regulatory system https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 3 of 33 —one that participates in the development of a fruit fly from a fertilized egg—is described in How We Know (pp. 290–291). HOW WE KNOW GENE REGULATION—THE STORY OF EVE The ability to regulate gene expression is crucial to the proper development of a multicellular organism from a fertilized egg to an adult. Beginning at the earliest moments in development, a succession of transcriptional programs guides the differential expression of genes that allows an animal to form a proper body plan—helping to distinguish its back from its belly, and its head from its tail. These programs ultimately direct the correct placement of a wing or a leg, a mouth or an anus, a neuron or a liver cell. A central challenge in developmental biology, then, is to understand how an organism generates these patterns of gene expression, which are laid down within hours of fertilization. Among the most important genes involved in these early stages of development are those that encode transcription regulators. By interacting with different regulatory DNA sequences, these proteins instruct every cell in the embryo to switch on the genes that are appropriate for that cell at each time point during development. How can a protein binding to a piece of DNA help direct the development of a complex multicellular organism? To see how we can begin to address that broad question, we review the story of Eve. https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 4 of 33 Seeing Eve Even-skipped—Eve, for short—is a gene whose expression plays an important part in the development of the Drosophila embryo. If this gene is inactivated by mutation, many parts of the embryo fail to form and the fly larva dies early in development. But Eve is not expressed uniformly. Instead, the Eve protein is produced in a striking series of seven neat stripes, each occupying a very precise position along the length of the embryo—which, at this stage in development, is actually one giant cell containing thousands of nuclei afloat in a common cytosol. The seven stripes, each about five or six nuclei wide, correspond to seven of the 14 segments that define the body plan of the fly: three for the head, three for the thorax, and eight for the abdomen. This pattern of expression never varies: the Eve protein can be found in the very same places in every Drosophila embryo. How can the expression of a gene be regulated with such spatial precision—such that one cell will produce a protein while a neighboring nucleus does not? To find out, researchers took a trip upstream. Dissecting the DNA As we have seen in this chapter, regulatory DNA sequences control which cells in an organism will express a particular gene, and at what point during development that gene will be turned on. In eukaryotes, these regulatory sequences are frequently located upstream of the gene itself. One way to locate a regulatory DNA sequence—and study how it operates—is to remove a piece of DNA https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 5 of 33 from the region upstream of a gene of interest and insert that DNA upstream of a reporter gene—one that encodes a protein with an activity that is easy to monitor experimentally. If the piece of DNA contains a regulatory sequence, it will drive the expression of the reporter gene. When this patchwork piece of DNA is subsequently introduced into a cell or organism, the reporter gene will be expressed in the same cells and tissues that normally express the gene from which the regulatory sequence was derived (see Figure 10–26). By excising various segments of the DNA sequences upstream of Eve, and coupling them to a reporter gene, researchers found that the expression of the gene is controlled by a series of seven regulatory modules—each of which specifies a single stripe of Eve expression. In this way, researchers identified, for example, a single segment of regulatory DNA that specifies stripe 2. They could excise this regulatory segment, link it to a reporter gene, and introduce the resulting DNA segment into the fly. When they examined embryos that carried this engineered DNA, they found that the reporter gene is expressed in the precise position of stripe 2—but not at any other location (Figure 8–14). Similar experiments revealed the existence of six other regulatory modules, one for each of the other Eve stripes. https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 6 of 33 Figure 8–14 An experimental approach using a reporter gene reveals the modular construction of theEve gene regulatory region. (A) Expression of the Eve gene is controlled by a series of regulatory segments (orange) that direct the production of Eve protein in stripes along the embryo. (B) Embryos stained with antibodies to the Eve protein show the seven characteristic stripes of Eve expression. (C) In the laboratory, the regulatory segment that directs the formation of stripe 2 can be excised from the DNA shown in part (A) and inserted upstream of the E. coli LacZ gene, which encodes the enzyme β-galactosidase (see Figure 8–9). (D) When the engineered DNA containing the stripe 2 regulatory segment is introduced into the genome of a fly, the resulting embryo expresses βgalactosidase precisely in the position of the second Eve stripe. Enzyme activity is assayed by the addition of X-gal, a modified sugar that when cleaved by β-galactosidase generates an insoluble blue product. (B and D, courtesy of Stephen Small and Michael Levine.) The next question was: How does each of these seven regulatory segments direct the formation of a single stripe in a specific position? The answer, researchers found, is that each DNA segment contains a unique combination of regulatory sequences that bind different combinations of transcription regulators. These regulators, like the Eve protein itself, are distributed in unique patterns within the embryo—some toward the head, some toward the rear, and some in the middle. The regulatory segment that defines stripe 2, for example, contains regulatory DNA sequences for four transcription regulators: two that activate Eve transcription and two that repress it (Figure 8– 15). In the narrow band of tissue that constitutes stripe 2, it just so https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 7 of 33 happens that the repressor proteins are not present—but the two activator proteins are; therefore, the Eve gene is expressed. In the bands of tissue on either side of the stripe, where the repressors are present, Eve is kept quiet. And so a stripe is formed. Figure 8–15 The regulatory segment that specifies Eve stripe 2 contains binding sites for four different transcription regulators. All four regulators are responsible for the proper expression of Eve in stripe 2. Flies that are deficient in the two activators, called Bicoid and Hunchback, fail to form stripe 2 efficiently; in flies deficient in either of the two repressors, called Giant and Krüppel, stripe 2 expands and covers an abnormally broad region of the embryo. As indicated in the diagram, in some cases the binding sites for the transcription regulators overlap, and the proteins compete for binding to the DNA. For example, the binding of Bicoid and Krüppel to the site at the far right is thought to be mutually exclusive. The regulatory segment is 480 base pairs in length. The regulatory segments controlling the other stripes are thought to function along similar lines; each regulatory segment reads “positional information” provided by some unique combination of transcription regulators and expresses Eve on the basis of this information. The entire regulatory region is strung out over 20,000 nucleotide pairs of DNA and, altogether, binds more than 20 different transcription regulators. This large regulatory region is built from a series of smaller regulatory segments, each of which consists of a unique arrangement of regulatory DNA sequences recognized by specific transcription regulators. In this way, the Eve https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 8 of 33 gene can respond to an enormous combination of inputs and produce a unique, tightly controlled pattern of expression. The Eve protein is itself a transcription regulator, and it—in combination with many other regulatory proteins—controls the next series of events in the development of the fly. This complex organization of a discrete number of regulatory elements begins to explain how the development of an entire organism can be orchestrated by repeated applications of a few basic principles. The Expression of Different Genes Can Be Coordinated by a Single Protein In addition to being able to switch individual genes on and off, all cells—whether bacterial or eukaryotic—need to coordinate the expression of different genes. When a eukaryotic cell receives a signal to proliferate, for example, a number of hitherto unexpressed genes are turned on together to set in motion the events that lead eventually to cell division (discussed in Chapter 18). As discussed earlier, bacteria often coordinate the expression of a set of genes by having them clustered together in an operon under the control of a single promoter (see Figure 8–6). Such clustering is rare in eukaryotic cells, where each gene is typically transcribed and regulated individually. So how do eukaryotic cells coordinate the expression of multiple genes? In particular, given that a eukaryotic cell uses a committee of transcription regulators to control each of its genes, how can it rapidly and decisively switch whole groups of genes on or off? The answer is that even though control of gene expression is https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 9 of 33 combinatorial, the effect of a single transcription regulator can still be decisive in switching any particular gene on or off, simply by completing the combination needed to activate or repress that gene. This is like dialing in the final number of a combination lock: the lock will spring open if the other numbers have been previously entered. And just as the same number can complete the combination for different locks, the same protein can complete the combination for several different genes. As long as different genes contain regulatory DNA sequences that are recognized by the same transcription regulator, they can be switched on or off together as a coordinated unit. An example of such coordinated regulation in humans is seen in response to cortisol (see Table 16–1, p. 556). As discussed earlier in this chapter, when this hormone is present, liver cells increase the expression of many genes, including those that allow the liver to produce glucose in response to starvation or prolonged stress. To switch on such cortisol-responsive genes, the cortisol receptor —a transcription regulator—first forms a complex with a molecule of cortisol. This cortisol–receptor complex then binds to a regulatory sequence in the DNA of each cortisol-responsive gene. When the cortisol concentration decreases again, the expression of all of these genes drops to normal levels. In this way, a single transcription regulator can coordinate the expression of many different genes (Figure 8–16). https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 10 of 33 Figure 8–16 A single transcription regulator can coordinate the expression of many different genes. The action of the cortisol receptor is illustrated. On the left is a series of genes, each of which has a different activator protein bound to its respective regulatory DNA sequences. However, these bound proteins are not sufficient on their own to activate transcription efficiently. On the right is shown the effect of adding an additional transcription regulator—the cortisol–receptor complex— that binds to the same regulatory DNA sequence in each gene. The activated cortisol receptor completes the combination of transcription regulators required for efficient initiation of transcription, and all three genes are now switched on as a set. Combinatorial Control Is Used to Generate Different Cell Types The ability to switch many different genes on or off using a limited number of transcription regulators is not only useful in the day-to- https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 11 of 33 day regulation of cell function. It is also one of the means by which eukaryotic cells diversify into particular types of cells during embryonic development. A striking example occurs in the development of muscle cells. A mammalian skeletal muscle cell is distinguished from other cells by the production of a large number of characteristic proteins, such as the muscle-specific forms of actin and myosin that make up the contractile apparatus, as well as the receptor proteins and ion channel proteins in the plasma membrane that allow the muscle cell to contract in response to stimulation by nerves (discussed in Chapter 17). The genes encoding this unique array of muscle-specific proteins are all switched on coordinately as the muscle cell differentiates. Studies of developing muscle cells in culture have identified a small number of key transcription regulators, expressed only in potential muscle cells, that coordinate muscle-specific gene expression and are thus crucial for muscle-cell differentiation. This set of regulators activates transcription of the genes that code for muscle-specific proteins by binding to specific DNA sequences present in their regulatory regions. In the same way, other sets of transcription regulators can activate the expression of genes that are specific for other cell types. How different combinations of transcription regulators can tailor the development of different cell types is illustrated schematically in Figure 8–17. https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 12 of 33 Figure 8–17 Combinations of a few transcription regulators can generate many cell types during development. In this simple scheme, a “decision” to make a new transcription regulator (shown as a numbered circle) is made after each cell division; each of these regulators continues to be made in subsequent cell divisions. Repetition of this simple rule can generate eight cell types (A through H) using only three transcription regulators. Each of these hypothetical cell types would then express different sets of genes, as dictated by the combination of transcription regulators that each cell type produces. Still other transcription regulators can maintain cells in an https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 13 of 33 undifferentiated state, like the precursor cell shown in Figure 8–17. Some undifferentiated cells are so developmentally flexible they are capable of giving rise to all the specialized cell types in the body. The embryonic stem (ES) cells we discuss in Chapter 20 retain this remarkable quality, a property called pluripotency. The differentiation of a particular cell type involves changes in the expression of thousands of genes: genes that encode products needed by the cell are expressed at high levels, while those that are not needed are expressed at low levels or shut down completely. A given transcription regulator, therefore, often controls the expression of hundreds or even thousands of genes (Figure 8–18). Because each gene, in turn, is typically controlled by many different transcription regulators, a relatively small number of regulators acting in different combinations can form the enormously complex regulatory networks that generate specialized cell types. It is estimated that approximately 1000 transcription regulators are sufficient to control the 25,000 genes that give rise to an individual human. https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 14 of 33 (A) https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 15 of 33 (B) Figure 8–18 A set of three transcription regulators forms the regulatory network that specifies an embryonic stem cell. (A) These three transcription regulators—Klf4 (yellow), Oct4 (blue), and Sox2 (orange)—bind to regulatory sequences in thousands of individual genes (small green dots). These direct binding interactions are indicated by the arrays of lines that link each regulator to each of its many target genes. Although each regulator controls the expression of a unique set of genes, many of these genes are bound by more than one transcription regulator—and a substantial set (located in the center of the diagram) interacts with all three. (B) The regulators also bind to each other’s genes (blue lines) and to regulatory sequences within their own genes (red loops). These interactions generate positive feedback loops, a common form of transcriptional regulation, as we discuss later in the chapter. (A, based on data from J. Kim et al., Cell 132:1049– 1061, 2008.) The Formation of an Entire Organ Can Be Triggered by a Single Transcription Regulator We have seen that transcription regulators, working in combination, can control the expression of whole sets of genes and https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 16 of 33 can produce a variety of cell types. But in some cases a single transcription regulator can initiate the formation of not just one cell type but a whole organ. A stunning example of such transcriptional control comes from studies of eye development in the fruit fly Drosophila. Here, a single transcription regulator called Ey triggers the differentiation of all of the specialized cell types that come together to form the eye. Flies with a mutation in the Ey gene have no eyes at all, which is how the regulator was discovered. How the Ey protein coordinates the specification of each type of cell found in the eye—and directs their proper organization in three-dimensional space—is an actively studied topic in developmental biology. In essence, however, Ey functions like the transcription regulators we have already discussed, controlling the expression of multiple genes by binding to DNA sequences in their regulatory regions. Some of the genes controlled by Ey encode additional transcription regulators that, in turn, control the expression of other genes. In this way, the action of this master transcription regulator produces a cascade of regulators that, working in combination, lead to the formation of an organized group of many different types of cells. One can begin to imagine how, by repeated applications of this principle, an organism as complex as a fly—or a human—progressively self-assembles, cell by cell, tissue by tissue, and organ by organ. Master regulators such as Ey are so powerful that they can even activate their regulatory networks outside the normal location. In the laboratory, the Ey gene has been artificially expressed in fruit fly embryos in cells that would normally give rise to a leg. When https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 17 of 33 these modified embryos develop into adult flies, some have an eye in the middle of a leg (Figure 8–19). Transcription Regulators Can Be Used to Experimentally Direct the Formation of Specific Cell Types in Culture We have seen that the Ey gene, when artificially expressed in a fly embryo, can produce an eye in an unnatural location by triggering a complete developmental program in the “wrong” precursor cell. Perhaps even more Figure 8–19 A master transcription surprising is that some transcription regulator can direct the formation of regulators can be used to an entire organ. Artificially induced experimentally convert a stable, expression of the Drosophila Ey gene in differentiated cell type into an entirely the precursor cells of the leg triggers the misplaced development of an eye on different cell type. For example, when a fly’s leg. The experimentally induced organ appears to be structurally normal, the gene encoding the transcription regulator MyoD is artificially introduced containing the various types of cells found in a typical fly eye. It does not, into fibroblasts cultured from skin, the however, communicate with the fly’s brain. (Walter Gehring, courtesy of fibroblasts form musclelike cells. It Biozentrum, University of Basel.) appears that the fibroblasts, which are derived from the same broad class of embryonic cells as muscle cells, have already accumulated many of the other necessary transcription regulators required for the combinatorial control of the muscle-specific genes, and that addition of MyoD completes https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 18 of 33 the unique combination required to direct the cells to become muscle. This same type of reprogramming can produce even more impressive transformations. For example, a set of nerve-specific transcription regulators, when artificially expressed in cultured liver cells, can convert them into functional neurons (Figure 8– 20). And the combination of transcription regulators shown in Figure 8–18 can be used in the laboratory to coax differentiated cells to de-differentiate into induced pluripotent stem (iPS) cells; these reprogrammed cells behave much like naturally occurring ES cells, and they can be directed to generate a variety of specialized differentiated cells (Figure 8–21). Differentiated cells produced from human iPS cells are currently being used in the study and treatment of disease, as we discuss in Chapter 20. Taken together, these dramatic demonstrations suggest that it may someday be possible to produce in the laboratory any cell type for which the correct combination of key transcription regulators is known. Figure 8–20 A small number of transcription regulators can convert one differentiated cell https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 19 of 33 type directly into another. In this experiment, liver cells grown in culture (A) were converted into neuronal cells (B) via the artificial expression of three nerve-specific transcription regulators. The cells are labeled with a fluorescent dye. Such interconversion would never take place during normal development. The result shown here depends on an experimenter expressing the three nervespecific regulators in liver cells, where these regulators would normally be tightly shut off. (From S. Marro et al., Cell Stem Cell 9:374–382, 2011. With permission from Elsevier.) Figure 8–21 A combination of transcription regulators can induce a differentiated cell to dedifferentiate into an iPS cell. The artificial expression of a set of three genes, each of which encodes a transcription regulator, can reprogram a fibroblast into a pluripotent cell with ES cell–like properties. Each transcriptional regulator controls the expression of many genes (see Figure 8–18). Like ES cells, such iPS cells can proliferate indefinitely in culture and can be stimulated by appropriate extracellular signal molecules to differentiate into almost any cell type in the body. Differentiated Cells Maintain Their Identity Once a cell has become differentiated into a particular cell type in the body, it will generally remain differentiated, and all its progeny cells will remain that same cell type. Some highly specialized cells, including skeletal muscle cells and neurons, never divide again once they have differentiated—that is, they are terminally differentiated (as discussed in Chapter 18). But many other differentiated cells—such as fibroblasts, smooth muscle cells, and liver cells—will divide many times in the life of an individual. When https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 20 of 33 they do, these specialized cell types give rise only to cells like themselves: unless an experimenter intervenes, smooth muscle cells do not give rise to liver cells, nor liver cells to fibroblasts. For a proliferating cell to maintain its identity—a property called cell memory—the patterns of gene expression responsible for that identity must be “remembered” and passed on to its daughter cells through all subsequent cell divisions. Thus, in the model illustrated in Figure 8–17, the production of each transcription regulator, once begun, has to be continued in the daughter cells of each cell division. How is such perpetuation accomplished? Cells have several ways of ensuring that their daughters remember what kind of cells they should be. One of the simplest and most important is through a positive feedback loop, where a master transcription regulator activates transcription of its own gene, in addition to that of other cell-type-specific genes. Each time a cell divides, the regulator is distributed to both daughter cells, where it continues to stimulate the positive feedback loop (Figure 8–22). The continued stimulation ensures that the regulator will continue to be produced in subsequent cell generations. The Ey protein and the transcription regulators involved in the generation of ES cells and iPS cells take part in such positive feedback loops (see Figure 8–18B). Positive feedback is crucial for establishing the “selfsustaining” circuits of gene expression that allow a cell to commit to a particular fate—and then to transmit that decision to its progeny. https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 21 of 33 Figure 8–22 A positive feedback loop can generate cell memory. Protein A is a master transcription regulator that activates the transcription of its own gene—as well as other cell-typespecific genes (not shown). All of the descendants of the original cell will therefore “remember” that the progenitor cell had experienced a transient signal that initiated the production of protein A. As shown in Figure 8–18, each of the regulators needed to form iPS cells influences its own expression using this type of positive feedback loop. Although positive feedback loops are probably the most prevalent way of ensuring that daughter cells remember what kind of cells they are meant to be, there are other ways of reinforcing cell identity. One involves the methylation of DNA. In vertebrate cells, DNA methylation occurs on certain cytosine bases (Figure 8–23). This covalent modification generally turns off the affected genes by attracting proteins that bind to methylated cytosines and block gene transcription. DNA methylation patterns are passed on to progeny cells by the action of an enzyme that copies the https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 22 of 33 methylation pattern on the parent DNA strand to the daughter DNA strand as it is synthesized (Figure 8–24). Figure 8–23 Formation of 5-methylcytosine occurs by methylation of a cytosine base in the DNA double helix. In vertebrates, this modification is confined to selected cytosine (C) nucleotides that fall next to a guanine (G) in the sequence 5’-CG-3’. However, methylation patterns change during development, and only a subset of 5’-CG-3’ sequences in a genome are methylated at any given time. Figure 8–24 DNA methylation patterns can be faithfully inherited when a cell divides. An enzyme called a maintenance methyltransferase guarantees that once a pattern of DNA methylation has been established, it is inherited by newly synthesized DNA. Immediately after DNA replication, https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 23 of 33 each daughter double helix will contain one methylated DNA strand—inherited from the parent double helix—and one unmethylated, newly synthesized strand. The maintenance methyltransferase interacts with these hybrid double helices and methylates only those CG sequences that are basepaired with a CG sequence that is already methylated. In this way, a particular methylation pattern present in a parent cell can be transmitted to progeny cells. Another mechanism for inheriting gene expression patterns involves the covalent modification of histones. These modifications regulate gene activity by influencing the packaging of DNA. When a cell replicates its DNA, each daughter double helix receives half of its parent’s histone proteins, which contain the covalent modifications that were present on the parent chromosome. Enzymes responsible for these modifications may bind to the parental histones and confer the same modifications to the new histones nearby (see Figure 5–33). This mechanism contributes to the maintenance of heterochromatin—the condensed form of chromatin structure that silences resident genes. Because all of these cell-memory mechanisms transmit patterns of gene expression from parent to daughter cell without altering the actual nucleotide sequence of the DNA, they are considered to be forms of epigenetic inheritance. These mechanisms, which work together, play an important part in maintaining patterns of gene expression, allowing transient signals from the environment to be remembered by our cells—a fact that has important implications for understanding how cells operate and how they malfunction in disease. CHAPTER EIGHTEEN 18 “Where a cell arises, there must be a previous cell, just as animals https://nerd.wwnorton.com/nerd/231302/r/goto/cfi/130!/4?control=control-toc&lti=true 10/12/23, 8:47 PM Page 24 of 33