Complete genome sequencing has allowed the different types of noncoding DNA to be specified more precisely in a variety of organisms. It came as a great surprise to learn that in the human genome only about 2.5% of the genome actually codes for proteins. The other 97.5% includes sequences we have encountered earlier, including introns, noncoding DNA, and various other types of repetitive sequences.

In Fig. 13.10, we see the composition of the human genome, including the principal types of repeated sequences. Earlier we saw how repeated sequences could be classified as dispersed or tandem according to their organization in the genome. In Fig. 13.10 the repeated sequences are classified according to their function. Among the repeated sequences is alpha (α) satellite DNA, which consists of tandem copies of a 171-bp sequence repeated near each centromere an average of 18,000 times. The α satellite DNA is essential for attachment of spindle fibers to the centromeres during cell division (Chapter 11).

Fig. 13.10 also shows the proportions of several types of repeated sequence collectively known as transposable elements (abbreviated TE; they are also called transposons), which are DNA sequences that can replicate and insert themselves into new positions in the genome. As a result, they have the potential to increase their copy number in the genome over time. Transposable elements are sometimes referred to as “selfish” DNA because it seems that their only function is to duplicate themselves and proliferate in the genome, making them the ultimate parasite.

Transposable elements make up about 45% of the DNA in the human genome. They can be grouped into two major classes based on the way they replicate. One class consists of DNA transposons, which replicate and transpose by DNA replication and repair. The other class consists of elements that transpose by means of an RNA intermediate. These are sometimes called retrotransposons because their RNA is used as a template to synthesize complementary strands of DNA, a process that reverses the usual flow of genetic information from DNA into RNA (retro- means “backward”). More than 40% of the human genome consists of various types of retrotransposons, whereas only about 3% of human DNA consists of DNA transposons.

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Over the course of evolutionary time, the amount of repetitive DNA in a genome can change drastically, in large part because of the accumulation of transposable elements (Fig. 13.10). In some genomes repetitive DNA is maintained over long periods of time even as new species evolve and diversify, whereas in other genomes the amount of repetitive DNA is held in check because of deletion and other processes. The result is that the genomes of different species can contain vastly differing amounts of repetitive DNA, and this accounts in large part for the C-value paradox.