>| (2) On a mechanistic level, there is a huge deal of genetic code that
>| is not used by organisms but is nonethless in their DNA. It is called
>| Junk DNA (I'm not sure if this is the official scientific term but it
>| was called this in one scientific documentary I saw).
>
>I asked a similar question the other day, but no answers yet so I'll
>repeat it here: How can it be known that this DNA "is not used by
>organisms"? Is current understanding of genetics really that good?
>
>Stein
Short of the obvious fact that scientific knowledge is never absolute, the
genetics (and just as importantly, the comparative evolutionary biology) is
really that good. Obviously "Junk DNA" is a loose term that glosses over a
lot of details. See further description below.
The fact is, the genomes contain segments of DNA having a variety of
functional relevance to the organisms bearing them. The concept of the
gene has been modified over the years. It used to mean a segment of DNA
that codes for a polypeptide chain or specifies a functional RNA
molecule. Now a more accurate definition is a DNA segment that performs a
specific function, whether as a protein-coding (transcribed and
translated), RNA-specifying (only transcribed), or regulatory (many not
even transcribed) gene. There are also DNA regions, such as those that cap
the tips of chromosomes (telomeres) or at the middle (centromeres) that
have function only in a gross structural sense. Within protein-coding
genes, there are portions that actually specify the amino-acids of the
protein (exons) and those that do not (introns). There are also segments
of DNA (often as large or larger that the genes themselves) between genes
(intergenic spacers).
Each of these types of regions with their associated functions comprise
different constraints on the mutations which can occur without there being
any effect on function/fitness of the organism. Within exons, variation in
the third position of each codon has less affect than second or third
position. Within introns, most nucleotide substitutions have no
effect. And in intergenic spacers, large deletions or insertions of DNA
have little or no effect.
There are also many examples of duplications, and at a variety of
levels. Duplicates of parts of genes often occur next to the complete
gene. These can be shown to be functionless relative to the complete
gene. They are called pseudogenes; as they are released from selection
(since they do notfunction), they accumulate mutations more rapidly than
the neighboring complete gene. Likewise, complete genes or stretches of
multiple genes and intergenic spacers, are observed as duplicates in
genomes. They can be shown to be of redundant function by experiments that
remove them from an organism (variation in their presence is also seen in
nature among different populations, etc.). Finally, many organisms
represent complete duplications of the genome, being called polyploids.
Finally, within nongenic regions of the genome (and occassionally within
genes, where they often have deleterious effects) there are also repetitive
DNA elements of little functional relevance. The smallest of these are
called microsatellites, and are comprised of hundreds-thousands of short
nucleotide repeats (e.g., CACACACACACACACACA). The length of these
stretches is variable within species, and are known to occur by common
slippage mechanisms in DNA replication. And there are also rogue DNA
segments of viral origin that have become inserted into host genomes. Some
of these can snip themselves out and relocate or duplicate themselves
within the host genome according to their own propensities, etc. Thus,
except when they interrupt genes in the organisms, they expand and mutate
but are undetected by natural selection at the organismal/population
level. Hence, they are called "selfish DNA".
Finally, fairly closely related organisms are known to differ substantially
in overall genome size, due almost entirely to differences in nongenic
DNA. This is called the C-value paradox. Here is a relevant summary of
the issues surrounding this phenomenon from _Molecular evolution_ by W-H Li
(Sinauer Press, 1997):
# begin quote #
Solving the C-value paradox and accounting for the structure of the
eukaryotic genome require finding evolutionary mechanisms for the long-term
maintenance of vast quantities of nongenic, seemingly superfluous
DNA. This, in turn, is intimately linked with the question of what
function this DNA might have, if any. Numerous attempts have been made to
provide evolutionary explanations for this phenomenon. The following are
four such hypotheses:
1. The nongenic DNA performs essential function, such as global regulation
of gene expression (Zuckerkandl 1976). According to this hypothesis, the
ecess of DNA is only apparent, and the DNA is wholly
functional. Consequently, deletions or removal of such DNA will have
deleterious effects on fitness.
2. The nongenic DNA is useless "junk" (Ohno 1972), carried passively by
the chromosome merely because of its physical linkage to functional
genes. According to this view, the excess DNA does not affect the fitness
of the organisms and thus will be carried indefinitely from generation to
generation.
3. The nongenic DNA is a functionless "parasite" (Ostergren 1945) or
"selfish DNA" (Orgel and Crick 1980; Doolittle and Sapienza 1980) that
accumulates and is actively maintained by intragenomic selection.
4. The DNA has a structural or nucleoskeletal function, i.e., function
related to the determination of nuclear volume but unrelated to the task of
carrying genetic information (Cavalier-Smith 1978).
There is very little evidence for the first hypothesis. In fact, most
indications are that most nongenic DNA is indeed devoid of function and can
be deleted without discernable phenotypic effects (see the review by John
and Miklos 1988). It also seems that excess DNA is eukaryotes does not
greatly tax the metabolic system and that the cost in energy and nutrients
of maintaining and replicating large amounts of nongenic DNA is not
excessive. It is thus possible that most nongenic DNA is indeed junk or
selfish DNA.
# end quote #
Thus, "junk DNA" is a term used to describe the general consensus about
nongenic DNA. It does not form a hard fast declaration about specific DNA
regions. The functional constraints on each DNA region are evaluated
individually. Now, if I might get my two cents in here, comparative
analysis (i.e., using expressly evolutionary models) have been instrumental
in acquiring this knowledge; evolutionary biology is a very useful and
fruitful science.
Doug
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