Molecular Biology of the Cell - Volume 2 - Alberts B., Bray D., Lewis J., Raff M., Roberts K., Watson J. 1993

Control of gene expression
Organization and evolution of the nuclear genome

A significant portion of the evolutionary history of living organisms is recorded in their genomes. Some of these pages can be deciphered by studying the DNA sequences of these organisms. Widely used DNA Sequencing Methods make it possible to analyze large numbers of DNA molecules and shed light on how genes encoding specific Proteins emerged over tens of millions of years. Studying random chromosomal changes happening today sheds additional light on the mechanisms responsible for evolutionary shifts in the past. This section introduces several molecular-genetic approaches aimed at studying the Organization and Evolution of the nuclear genome in higher eukaryotes.

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10.5.1. Point Mutations drive minor genome alterations, whereas genome reorganization or expansion occurs through genetic recombination [54]

The nucleotide sequence in DNA must be precisely replicated and conserved. Chapter 5 discussed the complex mechanisms that allow DNA to be inherited with extraordinary fidelity: roughly only one nucleotide pair out of every thousand changes randomly every 200,000 years (see Section 5.2). Even at this mutation rate in a population of 10,000 individuals, every possible nucleotide substitution will be "tested" about fifty times over a million years. If a particular sequence variant confers an advantage, it will rapidly spread through natural Selection. Consequently, one would expect the function of most genes in any species to be optimized against variations arising from point mutations.

While point mutations serve to finely "tune" The Genome, long-term Evolutionary Processes must rely on more radical genetic changes. Genetic recombination performs this function; through it, genomes can expand or contract (via duplication or deletion), and segments can relocate from one region to another to form novel combinations. The constituent parts of genes (their exons and regulatory elements) can shuffle, giving rise to new proteins with entirely novel Functions. Furthermore, if a Gene is represented by two copies in the genome, one of them may undergo mutation, leading to copy divergence and specialization for subtly different roles. In this way, the genome as a whole gradually grows more complex and refined. For example, in mammals almost every gene exists in multiple variants: different Actin genes for various types of contractile Cells, different rhodopsin genes for perceiving different colors, different Collagen genes for various types of Connective Tissues, and so on. The expression of each gene is tightly and specifically regulated. DNA sequencing reveals that many genes, even those differing significantly from one another, may share related modular regions. For instance, a specific segment of rhodopsin genes shares a common ancestor with a set of genes encoding certain Hormones and receptors (see Section 12.3.13); this shared sequence is likely also present in other proteins (see Section 3.3.8).

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Figure 10-63. A family of tandemly repeated genes loses and regains its copies As a result of Crossing over between sister chromatids carrying these genes. This occurs quite frequently because long stretches of homologous DNA sequences serve as an excellent substrate for general genetic recombination.

Genetic recombination serves as the foundation for The Emergence of such gene families and gene segments. The MOLECULAR MECHANISMS OF general and Site-Specific Recombination were discussed earlier. This section explores several outcomes of recombination's impact on the genome.

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10.5.2. Tandemly repeated DNA sequences tend to remain unchanged [55]

Gene duplications are typically attributed to rare events catalyzed by specific recombination Enzymes. However, higher eukaryotes possess an efficient enzymatic system that joins the ends of a broken DNA molecule. Thus, duplications (as well as inversions, deletions, and translocations of DNA segments) can arise in these organisms due to the erroneous rejoining of chromosome fragments that were broken for various reasons. When duplicated sequences join HEAD-to-tail, they are referred to as tandem repeats. The appearance of a single tandem repeat can easily lead to The formation of a long series of repeats via Unequal Crossing Over between two sister chromatids, since long stretches of pairing sequences represent an ideal substrate for standard recombination (Figure 10-63). DNA duplication followed by unequal crossing over underlies DNA Amplification, a process shown to contribute to the genesis of cancer cells (see Figure 21-26). During unequal crossing over, the number of tandemly repeated genes can either increase or decrease (see Figure 10-63). A high copy number of repeated genes will be maintained by natural selection only if the presence of extra copies proves beneficial to the Organism. As noted above, in vertebrates a tandem repeat encodes a large ribosomal RNA precursor, which is required to meet the high demand of growing cells for new Ribosomes (see Section 9.4.16). Clusters of tandemly repeated genes also encode other structural RNAs in vertebrates, including 5S rRNA, U1, and U2 snRNAs. Tandem repeats are likewise characteristic of histone genes, which synthesize the large amounts of protein required during every S phase.

Figure 10-64. Two Types of events that preserve DNA sequences in a tandem arrangement and keep them highly similar to one another. A. Continuous expansion and contraction of gene copy number within a tandem array via unequal crossing over (see Figure 10-63) homogenizes all gene sequences within the cluster. B. During Gene Conversion, one copy acts as a template that transfers all or part of its DNA sequence to another gene copy. In higher eukaryotes, these processes appear characteristic of genes located adjacent to one another on a chromosome. In lower eukaryotes, such as Fungi, where gene conversion has been studied in much greater detail, the process is not limited solely to neighboring genes.

One might expect that during evolution, the sequences of tandemly arranged genes—as well as the non-transcribed spacer DNA between them—would diverge due to random mutations altering one or more gene copies. In reality, however, the sequences of tandemly repeated genes and their spacer DNA are usually nearly identical. Two mechanisms are believed to be responsible for this: first, unequal crossing over, which leads to the successive expansion and contraction of regions containing tandemly repeated sequences (computer modeling of such crossing over shows that sequences tend to remain conserved in the process, Figure 10-64A); and second, gene conversion (which has been shown to drive the homogenization of related DNA sequences, Figure 10-64B).

10.5.3. The globin gene family illustrates how random DNA duplications drive organismal evolution [56]

DNA duplications are of paramount importance for the evolution of new proteins. To see this, we can examine the globin gene family, as its evolutionary history is understood in exceptional detail. Clear homologies in the Amino acid sequences and structures of modern globin genes point to their descent from a common ancestor, even though some members of this family now reside in completely different chromosomal locations in mammalian genomes.

By analyzing Hemoglobin forms across organisms at various rungs of the phylogenetic ladder, we can reconstruct several events that led to the emergence of diverse types of this protein. The appearance of hemoglobin-like molecules during evolution evidently facilitated the growth in size of Multicellular animals. For large animals, simple diffusion is no longer sufficient to maintain an adequate oxygen supply in tissues. Consequently, hemoglobin molecules are found in all vertebrates and many invertebrates. The most primitive oxygen-carrying molecule is a single globin polypeptide chain about 150 Amino Acids long, found in many marine worms, insects, and primitive fish. The hemoglobin molecule in higher vertebrates has a more complex Structure, consisting of two types of globin chains. Apparently, about 500 million years ago during the evolution of higher fish, a series of mutations and a duplication of the corresponding gene occurred. As a result of these events, two slightly different genes initially formed, encoding the a- and ß-globin chains in the genome of each individual. In modern higher vertebrates, each hemoglobin molecule is a complex composed of two a- and two ß-chains (Figure 10-65). Such a structure functions far more efficiently than a single-chain hemoglobin molecule. The four oxygen-binding sites within the a₂ß₂ molecule interact with one another. This interaction results in cooperative allosteric Changes in the molecule upon oxygen binding and release, allowing much larger amounts of oxygen to be delivered to tissues.

During the subsequent evolution of mammals, the gene for the ß-chain apparently underwent mutations and duplications, giving rise to a second type of hemoglobin synthesized exclusively in the embryo. The resulting hemoglobin molecule exhibits a higher oxygen affinity compared to adult hemoglobin, thereby facilitating oxygen transfer from mother to fetus. The gene encoding this novel, ß-chain-like hemoglobin molecule once again underwent successive mutations and duplications, yielding two new genes, ε and γ. The ε-chain is synthesized at earlier developmental stages (forming a₂ε₂) than the embryonic γ-chain, which forms the a₂γ₂ variant (see Figure 10-39B). A later duplication of the adult ß-chain gene during primate evolution led to the Generation of the δ-globin gene and, correspondingly, a minor adult globin form (a₂δ₂) found exclusively in adult primates (Figure 10-66). Each of these duplicated genes was subsequently modified by point mutations affecting The properties of the final hemoglobin molecule, as well as by changes in regulatory regions that dictate the timing and level of Gene Expression (see Figure 10-73).

Figure 10-65. Three-dimensional structure of single-chain and four-chain globins. The four-chain hemoglobin shown here is a complex composed of two a- and two ß-globin chains. In some primitive vertebrates, the single-chain globin forms a dimer that dissociates upon oxygen binding, representing an intermediate stage in the evolution of the four-chain globin.

Figure 10-66. Evolutionary pathway of globin chains using the ß-like globin gene family as an example (see Figure 10-39). Relatively recent duplications of the γ-chain gene gave rise to the γ^G- and γ^A-chains, which are ß-like and possess identical functions.

Fig. 10-67. Structure of an antibody (immunoglobulin) molecule. This molecule consists of two identical heavy chains and two identical light chains (highlighted in color). Each heavy chain contains four similar covalently linked domains. Each light chain contains two such domains. Each domain is encoded by a separate exon; presumably, all exons arose from the duplication of a single ancestral exon.

The end result of the Gene Duplication process that led to the divergence of globin chains is clearly visible when examining genes derived from the ancestral ß-gene and arranged as a series of homologous DNA sequences within a 50,000-nucleotide-pair DNA segment (see Fig. 10-39, A). In humans, the a-globin gene cluster is located on a different chromosome. Based on the fact that in birds and mammals the a- and ß-globin gene clusters are found on different Chromosomes, whereas in the frog Xenopus they lie adjacent to each other, it is believed that the two genes separated as a result of a translocation approximately 300 million years ago (Fig. 10-66). Such translocations likely help stabilize duplicated genes with distinct functions by preventing them from undergoing the homogenization that frequently affects nearby sequences with similar compositions (see Fig. 10-64).

There are several duplicated globin DNA sequences within the a- and ß-globin gene clusters that are inactive. These are Examples of pseudogenes, which exhibit a high degree of Homology with active genes but are nonfunctional due to mutations that prevent their expression. The existence of such pseudogenes is hardly surprising, since not all DNA duplications lead to the emergence of new active genes, while inactive sequences are not immediately eliminated from the genome.

By comparing the DNA sequences of many gene families across animals at different stages of phylogeny, a significant portion of our evolutionary history can be traced (see Fig. 4-62).

10.5.4. Genes Encoding Novel Proteins Can Arise via Exon Shuffling [54]

The Role of DNA duplication in evolution is not limited to its contribution to large gene families. Duplications can also play a crucial role in THE ORIGIN OF new single genes. Proteins encoded by such genes can be recognized by the presence of repeating, similar Protein domains that are sequentially linked to one another by covalent bonds. For example, IMMUNOGLOBULINS (Fig. 10-67), albumins, and most Fibrous proteins (such as spectrins and collagens) are encoded by genes that arose through multiple duplications of an initial DNA sequence.

In genes that evolved in this manner, each exon often encodes a distinct subunit or domain within the protein (see Section 3.3.4). The organization of DNA coding sequences as a series of such exons separated by long introns greatly facilitated the evolution of new proteins. For instance, the duplications required to form a single gene encoding a protein with repeating domains can occur through DNA breakage and rejoining anywhere within the long introns flanking the exon. Without introns, an ancestral gene would have had very few recombination sites capable of producing a domain duplication. By increasing the number of potential sites for duplication, introns significantly raise the likelihood that a duplication will prove advantageous.

The presence of introns greatly increases the probability that random recombination will join two initially separate DNA sequences encoding different protein domains (see Fig. 10-71). The outcomes of such events can be observed in many modern proteins (see Fig. 3-38). Thus, the vast distances between exons encoding individual domains in higher eukaryotes accelerate the emergence of novel proteins and, consequently, enhance the evolutionary efficiency of highly complex organisms.

10.5.5. Most Proteins Are Likely Encoded by Genes Composed of Many Small Exons [57]

The discovery in 1977 that eukaryotic genes are interrupted came as a complete surprise. All genes studied prior to that time were of bacterial origin and contained no introns. Bacteria, as is well known, lack a nucleus and internal membranes, and their genome is smaller than that of eukaryotes; it was traditionally assumed that bacteria resembled the ancient, simple Cell from which The Introduction/5.html">Eukaryotic Cell evolved. It is hardly surprising, therefore, that many biologists initially viewed introns as a quirky, late evolutionary addition. Today, however, the prevailing view is that interrupted genes are extremely ancient, and that bacteria lost their introns only after the majority of their proteins had already evolved.

The idea that introns appeared very early in evolution aligns with the modern view of Protein Evolution through trial and error via the recombination of individual exons encoding distinct protein domains. Furthermore, Evidence for the ancient origin of introns has come from studies of genes encoding the ubiquitous enzyme Triosephosphate isomerase. Triosephosphate isomerase plays a vital role in the METABOLISM of all cells, catalyzing a central step in Glycolysis and Gluconeogenesis—the interconversion of glyceraldehyde-3-phosphate and dihydroxyacetone phosphate (see Fig. 2-38). By comparing the Amino Acid Sequence of this enzyme across various organisms, it can be concluded that the enzyme arose before the divergence of PROKARYOTES AND EUKARYOTES from a common ancestor, since 46% of The amino acid sequence is identical between humans and bacteria. In vertebrates (chicken and human), the gene encoding this enzyme contains six introns, five of which are located in the exact same positions in maize. This implies that these five introns already existed in the gene before plants and animals diverged during eukaryotic evolution, an event estimated to have occurred 10⁹ years ago (Fig. 10-68).

Small unicellular organisms are subject to strong selection pressure, which has driven them to reproduce via Cell Division at the maximum rate permitted by the nutrient availability in their environment. Consequently, they are forced to minimize The amount of unnecessary DNA that must be synthesized during each cell division cycle. For larger predatory organisms and Multicellular Organisms in general—whose cell division rates are governed by other factors—such intense selection pressure to purge excess DNA from the genome is absent. This circumstance most likely explains why bacteria have lost their introns, whereas eukaryotes have retained them. This explanation is further supported by data from studies on triosephosphate isomerase: while the multicellular fungus Aspergillus contains five introns in the gene encoding this enzyme, its unicellular relative, the Yeast Saccharomyces, contains none at all.

Fig. 10-68. Evolution of interrupted genes since ancient times. A. STRUCTURE OF THE triosephosphate isomerase gene in plants and vertebrates. Identical intron positions in maize (kernel) and vertebrates are indicated by black arrows, whereas differing positions are highlighted with red arrows. Given that plants and vertebrates are estimated to have diverged from a common ancestor about a billion years ago, the shared Introns must be of very ancient origin. B. Hypothetical pathway for the emergence of a specific gene. Exon sequences are colored, and intron sequences are shown in black. The gene shown here encodes a protein essential for all cells. Much like triosephosphate isomerase, this protein apparently acquired its definitive three-dimensional structure before bacteria, archaebacteria, and eukaryotes split from their common ancestor. This common ancestor is designated in the figure as the "ancestral gene." The dashed line indicates the approximate timing of the endosymbiotic events that led to the origin of Mitochondria and Chloroplasts. (A—after W. Gilbert, M. Marchionni, and G. Mc. Knight, Cell 46: 151-154, 1987.)

What is The Mechanism of intron loss? It is possible that introns were lost through gradual random deletions of short DNA segments, but it is more likely that Eukaryotic cells (and perhaps also bacterial ancestors) possess a mechanism for the precise and selective deletion of an entire intron from their genomes. For example, the cells of most vertebrates contain only a single Insulin gene with two introns, yet rats have an additional insulin gene nearby that contains only one intron. Apparently, this second gene arose relatively recently through duplication and subsequently lost one of its introns. Because intron loss requires the precise rejoining of coding DNA sequences, it is believed that the second gene originated from a rare event: the incorporation into the genome of a cDNA copy of the corresponding mRNA from which the introns had been precisely spliced out. Such intron-free copies can be generated via The activity of reverse transcriptases. Recombination enzymes are thought to enable these copies to pair with the original sequence, which is then "corrected" using the intron-less template in a process resembling gene conversion.

Reverse transcriptases are synthesized in cells by transposable elements (see Table 10-3) and all Retroviruses. The generation of DNA copies from genomic regions via reverse Transcription has evidently also contributed to the evolution of higher organism genomes.

10.5.6. The major fraction of DNA in higher eukaryotes consists of repetitive, noncoding nucleotide sequences [58]

Eukaryotic Genomes contain not only introns but also A large number of copies of noncoding, apparently superfluous DNA. The presence of such repetitive DNA sequences in higher eukaryotes was first discovered using Hybridization methods that estimate gene copy number (see Section 4.6.7). In this Procedure, the genome is mechanically sheared into short double-stranded fragments about 1,000 nucleotide pairs in length; these fragments are then denatured to yield single-stranded DNA. The rate at which single-stranded DNAs hybridize in a mixture depends on the complementarity of the fragments. For the majority of fragments, this reaction proceeds very slowly. For example, the haploid genome of a mammalian cell is represented by approximately 6 million different DNA fragments of 1,000 NUCLEOTIDES, and any single-copy sequence must randomly collide with 6 million noncomplementary strands before encountering its homolog.

DNA hybridization analysis of human cells has shown that approximately 70% of single-stranded fragments hybridize very slowly—that is, precisely as one would expect for a large collection of unique (nonrepetitive) sequences (complete hybridization takes several days). However, the remaining 30% of DNA strands hybridize much more rapidly. These strands contain sequences that are repeated many times in the genome and can therefore find their partners relatively quickly. Most of this DNA does not encode proteins; roughly one-third consists of tandemly repeated satellite sequences, while the remaining two-thirds comprise interspersed repetitive DNA. These dispersed repeats apparently originated from transposable elements that proliferated within our genome and reached exceptionally high copy numbers.

10.5.7. The function of satellite DNA remains unknown [59]

The bulk of rapidly hybridizing DNA strands typically consists of very long tandem repeats of a single short nucleotide sequence (Fig. 10-69). The repeating unit in such a sequence may be as short as one or two nucleotides, though most repeats are longer; in mammals, they are typically composed of variants of a short sequence organized into repeats several hundred nucleotides long. These simple-sequence tandem repeats are called satellite DNA because the first such DNA discovered had an unusual nucleotide composition, allowing it to be separated from total cellular DNA AS A minor component (or "satellite"). Satellite DNA sequences are generally not transcribed and are most frequently localized in the heterochromatin of centromeric chromosomal regions (see Section 10.3.8). In some mammals, satellite DNA accounts for 10% or more of the total DNA (satellite sequences may even occupy an entire chromosome arm).

Fig. 10-69. A satellite DNA sequence formed by a series of repeating blocks of seven nucleotides. This sequence was found in the Drosophila genome.

Satellite DNA sequences are capable of rapid change; moreover, they have shifted their chromosomal positions over the course of evolution. For instance, when comparing two homologous chromosomes in any given individual, certain satellite DNA sequences are found at different locations. Similarly, closely related species often have significantly divergent satellite DNA sequences, whereas DNA sequences in other genomic regions remain highly conserved. The functional role of satellite DNA sequences remains unknown to this day: all attempts to demonstrate its involvement in chromosome pairing or nuclear organization have failed. It has been suggested that this is "selfish DNA," which merely "ensures" the preservation of its own sequences within the genome without contributing to the survival of the cells that harbor it. Other sequences generally regarded as selfish DNA include transposable elements or Transposons.

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10.5.8. Genome Evolution Is Accelerated by Transposable Elements of at Least Three Types [60]

Genomes typically contain A wide variety of transposable elements, or transposons. These elements were first discovered in the maize genome; some of them have been characterized and even had their Primary Structure determined. Transposons are best understood in Drosophila, where more than 30 types are known. The length of these transposons ranges from 2,000 to 10,000 nucleotide pairs; the majority of them are present in the genome at 5 to 10 copies per diploid cell. Currently, three Major Classes of transposons are distinguished based on the Structural Features of their sequences (Table 10-3). Some elements move through the genome as DNA, whereas in others the process involves the formation of an intermediate product (which serves as RNA). In either case, transposons are capable of replicating, excising from some sites, and inserting into others; their behavior can be described as parasitic.

Table 10-3. Three major families of transposons

The length of these elements varies from 2,000 to 12,000 nucleotide pairs. Each family contains many different elements, and only a few of them are listed in the table.

Figure 10-70. Several changes in chromosomal DNA sequences resulting from transposon mobility. The insertion of a transposon invariably creates a short duplication of the chromosomal sequence, 3–12 nucleotide pairs in length. Site-specific recombination enzymes encoded by the element also participate in the subsequent excision of the transposon. Such excision frequently fails to restore the original chromosomal DNA sequence, as shown in the four examples.

Transposons account for at least 10% of the genomic DNA in higher eukaryotes. Most of these elements move only infrequently, but because their cellular copy number is high, transposition exerts a significant impact on species diversity. For example, more than half of the spontaneous mutations studied in Drosophila are caused by transposon insertion within or near the mutated gene.

Mutations can arise either when an element inserts into a gene or when it mobilizes to a new Location. All known transposons give rise to short target-site duplications as a consequence of their insertion mechanism (see Fig. 5-67, B). When a transposon is excised from a chromosome, it typically leaves behind one of the duplication-constituting copies (Figure 10-70). Thus, transposon mobility is accompanied by insertions and deletions in the nucleotide sequence.

Transposons also contribute to genome Variability by other means. If two transposons recognized by the same site-specific recombination enzyme (transposase) integrate into neighboring chromosomal sites, the DNA segment between them can become a substrate for transposase-mediated transposition. Because this is a highly efficient pathway for exon shuffling, it is valid to state that transposons can facilitate the formation of new genes (Figure 10-71).

Figure 10-71. Exon shuffling that can occur as a result of transposon insertion. When two transposons of the same type (highlighted in color) lie close to one another on a chromosome, transposition may involve the ends of two different elements (instead of the two ends of a single element); as a result, the chromosomal DNA enclosed between them is relocated to a new chromosomal region. Because introns are very large compared to exons (see Figure 9-7), the insertion of a new exon into a pre-existing intron, as depicted here, is by no means an improbable event.

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10.5.9. Transposons Can Influence Gene Regulation [61]

DNA sequence rearrangements driven by transposons frequently alter the expression of neighboring genes, which can lead to various developmental abnormalities in animals or plants, such as pigmentation defects (Figure 10-72). The majority of such gene-regulation changes tend to be detrimental to the organism, but some may prove advantageous.

The properties of transposon-induced mutations are unusual and distinguish them from mutations arising from errors in DNA Replication or repair. One important difference is that when a transposon moves, new sequences often end up in the vicinity of a gene, acting as recognition sites for site-specific DNA-binding proteins, including transposase and transcription-regulating proteins carried within the transposon. Thus, these sequences can act as enhancers and stimulate the transcription of genes located thousands of nucleotide pairs away. An example of this type of effect on pigment GENE EXPRESSION IN maize is shown in Figure 10-72. A similar effect may contribute to the genesis of cancer cells: the relocation of regulatory sequences to regions adjacent to a proto-oncogene can convert it into an oncogene.

Figure 10-72. Transposons can cause profound changes in gene regulation. For each of the three organisms, an example is shown of inherited alterations in pigment distribution caused by the insertion of transposable elements (TEs) into the regulatory regions of genes. Similar processes can drive morphological changes in an organism by affecting cell growth and differentiation. A. Insertion into regulatory elements located upstream of the white gene promoter in Drosophila results in red pigment expression restricted to the dorsal and ventral Regions of the eye. B. Insertion upstream of the promoter of a pigment-determining gene in snapdragons results in flowers that lack pigment everywhere except in groups of cells where the element was excised via transposition. Subsequent excision of the transposon throughout the plant gives rise to pale patches on a limited area of the flower. C. An example of regulated kernel color variation in maize caused by a transposon. In this case, the transposon acts as a regulatory protein that partially restores pigmentation in all cells of a kernel that would otherwise remain uncolored. Furthermore, the transposase catalyzes the random excision of the element, producing distinct intensely colored spots. (A, after G.M. Rubin et al., Cold Spring Harbor Symp. Quant. Biol. 50: 329–335, 1985; B, after E.S. Coen, R. Carpenter, and C. Martin, Cell 47: 285–296, 1986; C, after Zs. Schwarz-Sommer et al., EMBO J. 6: 287–294, 1987.)

Figure 10-73. The combined action of individual enhancer modules determines The Cell-specific pattern of gene expression. Because the mix of regulatory proteins binding to each enhancer varies from Cell to Cell, the function of an enhancer differs in different cell types. This diagram is based on results obtained in Drosophila, where numerous enhancers can be analyzed by independently evaluating their activity in transgenic flies. For simplicity, the stimulating (+) and inhibiting (—) effects of each enhancer (a, β, γ, δ, or ε) are scored with numbers from +3 to -3, assuming that these values are additive in calculating the net enhancer activity that dictates the level of gene expression.

The genomes of higher eukaryotes, in which long stretches of noncoding DNA are interspersed with relatively short coding regions, represent fertile ground for the integration and excision of mobile elements. Because gene transcription is influenced by sequences located tens of thousands of nucleotide pairs away, one would expect many transposition-induced genomic changes to affect gene expression as well. Conversely, very few rearrangements are likely to disrupt the short exons containing coding sequences.

Could the vast excess of noncoding DNA in higher eukaryotes be evolutionarily maintained thanks to the regulatory plasticity it confers upon an organism harbouring numerous diverse transposons? Current knowledge of the regulatory systems controlling genes in higher eukaryotes is consistent with this possibility. Enhancers, much like exons, appear to function as discrete modules, and gene activity depends on the cumulative influence of a set of enhancers on the promoter (Figure 10-73). By shuttling enhancers around the genome, transposons may help optimize gene regulation to ensure organismal survival across generations.

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10.5.10. Transposition Bursts Drive Substantial Genomic Changes and Enhance Biological Diversity [62]

Another unique feature distinguishing transposons from conventional mutagens is their ability to remain dormant within the chromosome for extended periods. From time to time, transposon mobility undergoes a surge of rapid activation in a portion of the population, accompanied by a corresponding spike in mutagenic activity. These drastic genomic alterations, known as transposition bursts, involve the almost simultaneous mobilization of multiple types of transposons. Transposition bursts were first discovered in developing corn plants. A similar phenomenon occurs during the interbreeding of certain fly strains—a well-documented occurrence known as "hybrid dysgenesis." When such bursts take place in germline cells, they induce widespread genomic modifications in the offspring of an individual fly or plant.

By altering an organism's traits, transposition bursts increase the likelihood that two novel characteristics—neither of which confers a selective advantage on its own—will prove beneficial when expressed together in a single individual within a population. Evidence suggests that in certain plants, transposition bursts can be triggered by severe environmental stress. This results in a diverse array of randomly modified descendants, some of which may be better adapted for survival under novel conditions. It is plausible that, at least in these species, a mechanism exists to activate transposons, operating as mutagens that generate a large pool of variant organisms precisely when such diversity is most urgently needed. Consequently, transposons should not be viewed merely as genetic parasites; in some instances, they act as beneficial symbionts, enhancing the survival of the host species that harbor them.

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10.5.11. Approximately 10% of The Human Genome is occupied by two families of transposons that appear to have proliferated only recently [63]

Primate DNA is unusual in at least one respect: it contains a massive number of copies of two sequences that literally "infest" our chromosomes. Both types of these sequences move through the genome via an RNA-mediated process requiring Reverse Transcriptase. One of these sequences—L1—resembles the F element in Drosophila and the Cin4 element in maize. It is believed to encode a reverse transcriptase (see Table 10-3). Transposons typically operate under the control of feedback regulatory systems that tightly restrict their copy number within each cell (thereby sparing the cell from potential catastrophe); nevertheless, in humans, L1 elements account for approximately 4% of the total genome mass.

An even more unusual sequence, the Alu sequence, is quite short (about 350 nucleotide pairs) and moves by inserting a copy directly into a target site. It originated from a deletion within the host cell's 7SL RNA gene. This gene encodes the RNA component of the signal-recognition particle (SRP), which plays a key role in Protein Synthesis. Consequently, it remains debatable whether the Alu sequence should be classified as a transposon or more accurately regarded as a processed pseudogene. The copy number of the Alu sequence in the haploid human genome is roughly 500,000 (accounting for about 5% of the DNA), meaning this sequence appears on average once every 5,000 nucleotide pairs of DNA. Alu DNA is transcribed from the 7SL RNA promoter, which is recognized by RNA polymerase III and is located internally within the transcript. Thus, this sequence carries all the information required for its own transcription.

Fig. 10-74. Schematic model of the putative evolution of repetitive Alu-like sequences found in mouse and human genomes. Both of these transposable DNA elements are thought to have originated from the vital 7SL RNA gene. However, considering the specific chromosomal distribution and Sequence homology of these highly repetitive elements, it is evident that their amplification occurred independently of one another.

A comparison of the sequence and chromosomal distribution of L1 and Alu-like elements across various mammals leads to the Conclusion that these elements have proliferated and reached high copy numbers relatively recently (Fig. 10-74). It is difficult to imagine that these sequences, dispersed throughout the entire genome, exert no noticeable effect on neighboring genes.

Summary

Functional DNA sequences in the genomes of higher eukaryotes appear to be assembled from small genetic modules of at least two types. Blocks of coding sequences combine in numerous ways to synthesize proteins, while regulatory sequences are scattered among lengthy non-coding regions to control gene expression. Both coding sequences (exons) and regulatory sequences (enhancers) typically span no more than a few hundred nucleotide pairs in length. Genomes undergo diverse genetic recombination events that drive gene duplication and the relocation of DNA segments. In some cases, entire genes are duplicated and subsequently acquire novel functions. Recombination can also generate new proteins through exon shuffling or alter gene expression via the recombination of enhancers. Sequence rearrangement is of paramount importance for organismal evolution, and in eukaryotes, this process is greatly facilitated by their interrupted gene structure. Crucially, eukaryotic genes are subject to a multitude of activating and repressing influences exerted by various combinations of distant enhancers.

Genomes contain various types of transposons, which collectively account for more than 10% of the genomic DNA in both Drosophila and vertebrates. Periodically, germline cells undergo "transposition bursts," leading to numerous heritable changes in gene expression within a single individual. Transposons are believed to play a specialized evolutionary role by driving organismal diversity.

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