How can cell biologists tackle the mystery of noncoding conserved DNA? Traditionally, attempts to determine the function of a puzzling DNA sequence begin by looking at the consequences of its experimental disruption. But many DNA sequences that are crucial for an organism in the wild can be expected to have no noticeable effect on its phenotype under laboratory conditions: what is required for a mouse to survive in a laboratory cage is very much less than what is required 190,000 nucleotide pairs 100 nucleotide pairs 10,000 nucleotide pairs
Figure 4–73 The detection of multispecies conserved sequences.
In this example, genome sequences for each of the organisms shown have been compared with the indicated region of the human CFTR (cystic fibrosis transmembrane conductance regulator) gene; this region contains one exon plus a large amount of intronic DNA. For each organism, the percent identity with human for each 25-nucleotide block is plotted in green. In addition, a computational algorithm has been used to detect the sequences within this region that are most highly conserved when the sequences from all of the organisms are taken into account. besides the exon (dark blue on the line at the top of the figure), the positions of three other blocks of multispecies conserved sequences are indicated (pale blue). The function of most such sequences in the human genome is not known. (Courtesy of Eric D. green.) for it to succeed in nature. Moreover, calculations based on population genetics reveal that just a tiny selective advantage—less than a 0.1% difference in survival—can be enough to strongly favor retaining a particular DNA sequence over evolutionary time spans. One should therefore not be surprised to find that many DNA sequences that are ultraconserved can be deleted from the mouse genome without any noticeable effect on that mouse in a laboratory.
A second important approach for discovering the function of a mysterious noncoding DNA sequence uses biochemical techniques to identify proteins or RNA molecules that bind to it—and/or to any RNA molecules that it produces. Most of this task still lies before us, but a start has been made (see p. 435).
Given genome sequence information, we can tackle another intriguing question: What alterations in our DNA have made humans so different from other animals—or for that matter, what makes any individual species so different from its relatives? For example, as soon as both the human and the chimpanzee genome sequences became available, scientists began searching for DNA sequence changes that might account for the striking differences between us and chimpanzees. With 3.2 billion nucleotide pairs to compare in the two species, this might seem an impossible task. But the job was made much easier by confining the search to 35,000 clearly defined multispecies conserved sequences (a total of about 5 million nucleotide pairs), representing parts of the genome that are most likely to be functionally important. Though these sequences are conserved strongly, they are not conserved perfectly, and when the version in one species is compared with that in another they are generally found to have drifted apart by a small amount corresponding simply to the time elapsed since the last common ancestor. In a small proportion of cases, however, one sees signs of a sudden evolutionary spurt. For example, some DNA sequences that have been highly conserved in other mammalian species are found to have accumulated nucleotide changes exceptionally rapidly during the 6 million years of human evolution since we diverged from the chimpanzees. These human accelerated regions (HARs) are thought to reflect functions that have been especially important in making us different in some useful way.
About 50 such sites were identified in one study, one-fourth of which were located near genes associated with neural development. The sequence exhibiting the most rapid change (18 changes between human and chimpanzee, compared to only two changes between chimpanzee and chicken) was examined further and found to encode a 118-nucleotide noncoding RNA molecule, HAR1F (human accelerated region 1F), that is produced in the human cerebral cortex at a critical time during brain development. The function of this HAR1F RNA is not yet known, but findings of this type are stimulating research studies that may shed light on crucial features of the human brain.