▲ FIGURE 10-3 Comparative density of genes in «80-kb regions of genomic DNA from humans and the yeast S. cerevisiae. (a) In the diagram of the p-globin gene cluster on human chromosome 11, the green boxes represent exons of p-globin-related genes. Exons spliced together to form one mRNA are connected by caret-like spikes. The human p-globin gene cluster contains two pseudogenes (white); these regions are related to the functional globin-type genes but are not transcribed. Each red arrow indicates the location of an Alu sequence, an «300-bp noncoding repeated sequence that is abundant in the human genome. (b) In the diagram of yeast DNA from chromosome III, the green boxes indicate open reading frames. Most of these potential protein-coding sequences probably are functional genes without introns. Note the much higher proportion of noncoding-to-coding sequences in the human DNA than in the yeast DNA. [Part (a), see F S. Collins and S. M. Weissman, 1984, Prog. Nucl. Acid Res. Mol. Biol. 31:315; part (b), see S. G. Oliver et al., 1992, Nature 357:28.]
species within each of these phylogenetic classes varies by a factor of 100.
Detailed sequencing and identification of exons in chromosomal DNA have provided direct evidence that the genomes of higher eukaryotes contain large amounts of noncoding DNA. For instance, only a small portion of the P-globin gene cluster of humans, about 80 kb long, encodes protein (Figure 10-3a). Moreover, compared with other regions of vertebrate DNA, the p-globin gene cluster is unusually rich in protein-coding sequences, and the introns in globin genes are considerably shorter than those in many human genes. In contrast, a typical 80-kb stretch of DNA from the yeast cerevisiae, a single-celled eukaryote (Figure 10-3b) contains many closely spaced protein-coding sequences without introns and relatively much less noncoding DNA.
The density of genes varies greatly in different regions of human chromosomal DNA, from "gene-rich" regions, such as the p-globin cluster, to large gene-poor "deserts." Of the 94 percent of human genomic DNA that has been sequenced, only «1.5 percent corresponds to protein-coding sequences (exons). Most human exons contain 50-200 base pairs, although the 3' exon in many transcription units is much longer. Human introns vary in length considerably. Although many are «90 bp long, some are much longer; their median length is 3.3 kb. Approximately one-third of human genomic DNA is thought to be transcribed into pre-mRNA precursors, but some 95 percent of these sequences are in introns, which are removed by RNA splicing.
Different selective pressures during evolution may account, at least in part, for the remarkable difference in the amount of nonfunctional DNA in unicellular and multicellu-
lar organisms. For example, microorganisms must compete for limited amounts of nutrients in their environment, and metabolic economy thus is a critical characteristic. Since synthesis of nonfunctional (i.e., noncoding) DNA requires time and energy, presumably there was selective pressure to lose nonfunctional DNA during the evolution of microorganisms. On the other hand, natural selection in vertebrates depends largely on their behavior. The energy invested in DNA synthesis is trivial compared with the metabolic energy required for the movement of muscles; thus there was little selective pressure to eliminate nonfunctional DNA in vertebrates.
Protein-Coding Genes May Be Solitary or Belong to a Gene Family
The nucleotide sequences within chromosomal DNA can be classified on the basis of structure and function, as shown in Table 10-1. We will examine the properties of each class, beginning with protein-coding genes, which comprise two groups.
In multicellular organisms, roughly 25-50 percent of the protein-coding genes are represented only once in the haploid genome and thus are termed solitary genes. A well-studied example of a solitary protein-coding gene is the chicken lysozyme gene. The 15-kb DNA sequence encoding chicken lysozyme constitutes a simple transcription unit containing four exons and three introns. The flanking regions, extending for about 20 kb upstream and downstream from the transcription unit, do not encode any detectable mRNAs. Lysozyme, an enzyme that cleaves the polysaccharides in bacterial cell walls, is an abundant
TABLE 10-1 Major Classes of Eukaryotic DNA and Their Representation in the Human Genome
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