Chromosomal Elements:- Eukaryotic Genes and Chromosomes Are Very Complex
Many bacterial species have only one chromosome per cell and, in nearly all cases, each chromosome contains only one copy of each gene. A very few genes, such as those for rRNAs, are repeated several times. Genes and regulatory sequences account for almost all the DNA in prokaryotes. Moreover, almost every gene is precisely colinear with the amino acid sequence (or RNA sequence) for which it codes (Fig. 24–2). The organization of genes in eukaryotic DNA is structurally and functionally much more complex. The study of eukaryotic chromosome structure, and more recently the sequencing of entire eukaryotic genomes, has yielded many surprises. Many, if not most, eukaryotic genes have a distinctive and puzzling structural feature: their nucleotide sequences contain one or more intervening segments of DNA that do not code for the amino acid sequence of the polypeptide product. These nontranslated inserts interrupt the otherwise colinear relationship between the nucleotide sequence of the gene and the amino acid sequence of the polypeptide it encodes. Such nontranslated DNA segments in genes are called intervening sequences or introns, and the coding segments are called exons. Few prokaryotic genes contain introns In higher eukaryotes, the typical gene has much more intron sequence than sequences devoted to exons. For example, in the gene coding for the single polypeptide chain of the avian egg protein ovalbumin (Fig. 1), the introns are much longer than the exons; altogether, seven introns make up 85% of the gene’s DNA. In the gene for the subunit of hemoglobin, a single intron contains more than half of the gene’s DNA. The gene for the muscle protein titin is the intron cham pion, with 178 introns. Genes for histones appear to have no introns. In most cases the function of introns is not clear. In total, only about 1.5% of human DNA is “coding” or exon DNA, carrying information for protein or RNA products. However, when the much larger introns are included in the count, as much as 30% of the hu man genome consists of genes. The relative paucity of genes in the human genome leaves a lot of DNA unaccounted for. Figure 2 provides a summary of sequence types. Much of the nongene DNA is in the form of repeated sequences of several kinds. Perhaps most surprising, about half the human genome is made up of moderately repeated sequences that are derived from transposable elements— segments of DNA, ranging from a few hundred to several thousand base pairs long, that can move from one location to another in the genome. Transposable elements (transposons) are a kind of molecular parasite, efficiently making a home within the host genome. Many have genes encoding proteins that catalyze the trans position process. Some transposons in the human genome are active, moving at a low frequency, but most are inactive relics, evolutionarily altered by mutations. Although these elements generally do not encode proteins or RNAs that are used in human cells, they have played a major role in human evolution: movement of transposons can lead to the redistribution of other genomic sequences.
FIGURE 1 Introns in two eukaryotic genes. The gene for ovalbumin has seven introns (A to G), splitting the coding sequences into eight exons (L, and 1 to 7). The gene for the β subunit of hemoglobin has two introns and three exons, including one intron that alone contains more than half the base pairs of the gene.
Another 3% or so of the human genome consists of highly repetitive sequences, also referred to as simple-sequence DNA or simple sequence repeats (SSR). These short sequences, generally less than 10 bp long, are sometimes repeated millions of times per cell. The simple-sequence DNA has also been called satellite DNA, so named because its unusual base composition often causes it to migrate as “satellite” bands (separated from the rest of the DNA) when fragmented cellular DNA samples are centrifuged in a cesium chloride density gradient. Studies suggest that simple sequence DNA does not encode proteins or RNAs. Un like the transposable elements, the highly repetitive DNA can have identifiable functional importance in human cellular metabolism, because much of it is associated with two defining features of eukaryotic chromosomes: centromeres and telomeres.
FIGURE 2 Types of sequences in the human genome. This pie chart divides the genome into transposons (transposable elements), genes, and miscellaneous sequences. There are four main classes of transposons. Long interspersed elements (LINEs), 6 to 8 kbp long (1 kbp=1,000 bp), typically include a few genes encoding proteins that catalyze transposition. The genome has about 850,000 LINEs. Short interspersed elements (SINEs) are about 100 to 300 bp long. Of the 1.5 million in the human genome more than 1 million are Alu elements, so called because they generally include one copy of the recognition sequence for AluI, a restriction endonuclease . The genome also contains 450,000 copies of retroviruslike transposons, 1.5 to 11 kbp long. Although these are “trapped” in the genome and cannot move from one cell to another, they are evolutionarily related to the retroviruses, which include HIV. A final class of transposons (making up <1% and not shown here) consists of a variety of transposon remnants that differ greatly in length. About 30% of the genome consists of sequences included in genes for proteins, but only a small fraction of this DNA is in exons (coding sequences). Miscellaneous sequences include simple-sequence re peats (SSR) and large segmental duplications (SD), the latter being segments that appear more than once in different locations. Among the unlisted sequence elements (denoted by a question mark) are genes encoding RNAs (which can be harder to identify than genes for proteins) and remnants of transposons that have been evolutionarily altered so that they are now hard to identify.
The centromere (Fig. 3) is a sequence of DNA that functions during cell division as an attachment point for proteins that link the chromosome to the mitotic spindle. This attachment is essential for the equal and orderly distribution of chromosome sets to daughter cells. The centromeres of Saccharomyces cerevisiae have been isolated and studied. The sequences essential to centromere function are about 130 bp long and are very rich in A=T pairs. The centromeric sequences of higher eukaryotes are much longer and, un like those of yeast, generally contain simple-sequence DNA, which consists of thousands of tandem copies of one or a few short sequences of 5 to 10 bp, in the same orientation. The precise role of simple-sequence DNA in centromere function is not yet understood. Telomeres (Greek telos, “end”) are sequences at the ends of eukaryotic chromosomes that help stabilize the chromosome. The best-characterized telomeres are those of the simpler eukaryotes. Yeast telomeres end with about 100 bp of imprecisely repeated sequences of the form
where x and y are generally between 1 and 4. The num ber of telomere repeats, n, is in the range of 20 to 100 for most single-celled eukaryotes and generally more than 1,500 in mammals. The ends of a linear DNA mol ecule cannot be routinely replicated by the cellular repli cation machinery (which may be one reason why bacterial DNA molecules are circular). Repeated telomeric sequences are added to eukaryotic chromosome ends primarily by the enzyme telomerase. Artificial chromosomes have been con structed as a means of better understanding the functional significance of many structural features of eukaryotic chromosomes. A reasonably stable artificial linear chromosome requires only three components: acentro mere, telomeres at each end, and sequences that allow the initiation of DNA replication. Yeast artificial chromo somes have been developed as a research tool in biotechnology. Similarly, human artificial chromosomes (HACs) are being developed for the treat ment of genetic diseases by somatic gene therapy.
