Encyclopedia of Evolution.pdf - Online Reading Center

noncoding DNA. Noncoding DNA is popularly called “junk
DNA,” but geneticists have found that some of the noncoding
DNA performs important functions in cells. Unlike genes, the
useful portion of the noncoding DNA has functions that are
not as dependent upon the precise nucleotide sequence. Over
time, mutations accumulate in the noncoding DNA much
more than in the genetic DNA. natural selection does not
usually eliminate mutations from the noncoding DNA. This
is why the noncoding DNA is important in reconstructing
the evolutionary relationships among species (see DNA [evidence
for evolution]).
Noncoding DNA can occur between genes or within
genes. Within genes, the noncoding stretches of DNA are
called introns and the stretches of DNA that specify the
sequence of amino acids are called exons. During gene expression,
the intron RNA is removed. Introns take up a great deal
of room inside of some genes. For example, the section of
DNA that contains the gene for the human protein dystrophin
(a protein that is an essential component in muscle cells)
has more than two million nucleotides. Within this gene are
more than 50 introns. When the introns are removed, only
about 11,000 of the original two million nucleotides remain.
There are three broad categories of noncoding DNA:
Pseudogenes. An old gene or copy of a gene that has lost its
promoter is no longer expressed but is still present in
the DNA. These leftovers from the past are copied and
recopied but not used. They are like computer files that
have been deleted but are still present on the computer
disc. Occasionally, these old genes can be reactivated. It
is estimated that humans have 6,000 pseudogenes. For
example, humans have three hemoglobin pseudogenes.
Some pseudogenes are processed pseudogenes that have
been reverse-transcribed from RNA and inserted back into
the chromosome. Geneticists draw this conclusion because
processed pseudogenes have no introns.
Repeated segments. If, during normal DNA replication, two
strands do not line up properly, short segments of one of the
strands may get copied over and over, resulting in repeated
segments. Some of these repeated segments are next to each
other on a chromosome (tandem repeats), while others may
be scattered among several chromosomes. Variable number
tandem repeats (or minisatellites) and short segment repeats
(or microsatellites) generally contain no useful information.
They are like a page filled with one word, repeated over
and over. Each individual within a population may have a
unique number of these repeats.
Transposable elements. Some segments of DNA encode
or used to encode proteins that allow these segments to
move around within and among the chromosomes. These
transposable elements (also called transposons or jumping
genes) can insert into new locations, where they may disrupt
the expression of essential genes. About one in 700
human mutations is caused by a transposon inserting in a
location where it interferes with gene function.
noncoding DNA
Transposable elements are placed in two classes. Class I
transposable elements move around via RNA intermediates.
To accomplish this, they require reverse transcription (the
information in RNA must be transcribed back into DNA),
which requires the reverse transcriptase enzyme. Reverse
transcriptase is the hallmark of retroviruses such as HIV
(see AIDS, evolution of). These transposons are called retrotransposons.
When retrotransposons move around, they
leave a copy of themselves behind in the original location.
Most retrotransposons have lost their ability to transpose and
just remain in place, generation after generation. Almost 15
percent of human DNA consists of (mostly inactivated) retrotransposons.
They include the following:
• Long interspersed nuclear elements (LINEs) may contain
the gene for reverse transcriptase and may be able to replicate
themselves. Often called HERVs (human endogenous
retroviruses), they may be remnants of retroviruses that
infected eukaryotic cells long ago. Human DNA contains
about a hundred copies of the gene for making the enzyme
reverse transcriptase. Human chromosome 22, even though
it is one of the smallest human chromosomes, has more
than 14,000 LINEs.
• Long terminal repeats (LTRs) are also left over from retroviruses
and are found on some retrotransposons. Sometimes
an LTR is accompanied by the entire genome of a
retrovirus that lost the ability to make capsules, and sometimes
it is just the terminal repeat sequences that remain
after the virus itself has departed. When the entire genome
of the yeast was sequenced, it was discovered to have 52
complete virus genomes and 264 LTRs that viruses left
behind. Maize has 10 families of LTRs, each in 10,000 to
30,000 copies in the genome.
• Retrosequences do not encode their own reverse transcriptase.
They include short interspersed nuclear elements
(SINEs) of mammals, which were produced by reverse transcription
but do not include a copy of the reverse transcriptase
gene. Alu, a human SINE sequence, closely resembles
certain genes involved in protein transport across membranes.
A haploid complement of human DNA contains
about 1,090,000 Alu sequences. Alu sequences make up
about 10 percent of human DNA.
Class II transposable elements have a DNA intermediate.
This type of transposon is more commonly found in bacteria,
but there are some in eukaryotic cells as well.
How can a eukaryotic cell limit the potentially explosive
spread of transposable elements? First, the fact that they are
so common indicates that cells have not been entirely successful
at containing their spread. Second, crossing over (see
meiosis) breaks up transposable elements, which then stop
transposing. Third, cells can inactivate transposons (for
example through methylation) just as they inactivate genes.
Noncoding DNA, even if much of it originated from
nucleic acids that went out of control, has some important
functions in the cell. The first is alternative splicing. As the
gene is expressed, different numbers of introns may be
removed. This results in more than one kind of protein being
produced from a single gene. The second is gene regulation.