Essential Cell Biology 5th edition

350 CHAPTER 10 Analyzing the Structure and Function of Genes
polymerase has added the labeled, chain-terminating nucleotide, a photo
of the slide is taken and the identity of the nucleotide added at each cluster
is recorded; the label and the chain-terminator are then stripped away,
allowing DNA polymerase to add the next nucleotide (Figure 10–21).
More recent technological advances have led to the development of thirdgeneration
sequencing methods that permit the sequencing of just a single
molecule of DNA. One of these techniques, called Single Molecule Real
Time sequencing, employs a special apparatus in which a single DNA
polymerase and a DNA template with an attached primer are anchored
together in a tiny compartment with differently colored fluorescent
dNTPs. As DNA synthesis proceeds, the attachment of each nucleotide
to the growing DNA strand is determined one base at a time, revealing
the sequence of the template; as in other sequencing methods, large
numbers of reactions are measured in parallel in separate compartments.
In another method, still under development, a single DNA molecule is
pulled slowly through a tiny channel, like thread through the eye of a
needle. Because each of the four nucleotides has different, characteristic
chemical properties, the way a nucleotide obstructs the pore as it passes
through reveals its identity—information that is then used to compile the
sequence of the DNA molecule. Further refinement of these and other
technologies will continue to drive down the amount of time and money
required to sequence a human genome.
Comparative Genome Analyses Can Identify Genes and
Predict Their Function
Strings of nucleotides, at first glance, reveal nothing about how that
genetic information directs the development of a living organism—or
even what type of organism it might encode. One way to learn something
about the function of a particular nucleotide sequence is to compare it
with the multitude of sequences available in public databases. Using a
computer program to search for sequence similarity, one can determine
whether a nucleotide sequence contains a gene and what that gene is
likely to do—based on the gene’s known activity in other organisms.
Comparative analyses have revealed that the coding regions of genes
from a wide variety of organisms show a large degree of sequence conservation
(see Figure 9−20). The sequences of noncoding regions, however,
tend to diverge rapidly over evolutionary time (see Figure 9−19). Thus, a
search for sequence similarity can often indicate from which organism a
particular piece of DNA was derived, and which species are most closely
related. Such information is particularly useful when the origin of a DNA
sample is unknown—because it was extracted, for example, from a sample
of soil or seawater or the blood of a patient with an undiagnosed
infection.
EXPLORING GENE FUNCTION
Knowing where a nucleotide sequence comes from—or even what activity
it might have—is only the first step toward determining what role it has
in the development or physiology of an organism. The knowledge that a
particular DNA sequence encodes a transcription regulator, for example,
does not reveal when and where that protein is produced, or which
genes it might regulate. To learn that, investigators must head back to
the laboratory.
This is where creativity comes in. There are as many ways to study how
genes function as there are scientists with an interest in studying the
question. The techniques an investigator chooses often depend on his or