What is junk DNA, and what is it

worth?
Feb 12, 2007

Wojciech Makalowski, a Pennsylvania State University biology professor and researcher

in computational evolutionary genomics, answers this query.

Our genetic blueprint consists of 3.42 billion nucleotides packaged in 23 pairs of linear
chromosomes. Most mammalian genomes are of comparable sizethe mouse script is
3.45 billion nucleotides, the rat's is 2.90 billion, the cow's is 3.65 billionand code for a
similar number of genes: about 35,000. Of course, extremes exist: the bent-winged bat
(Miniopterus schreibersi) has a relatively small 1.69-billion-nucleotide genome; the red
viscacha rat (Tympanoctomys barrerae) has a genome that is 8.21 billion nucleotides
long. Among vertebrates, the highest variability in genome size exists in fish: the green
puffer fish (Chelonodon fluviatilis) genome contains only 0.34 billion nucleotides, while
the marbled lungfish (Protopterus aethiopicus) genome is gigantic, with almost 130
billion. Interestingly, all animals have a large excess of DNA that does not code for the
proteins used to build bodies and catalyze chemical reactions within cells. In humans,
for example, only about 2 percent of DNA actually codes for proteins.

For decades, scientists were puzzled by this phenomenon. With no obvious function,
the noncoding portion of a genome was declared useless or sometimes called "selfish
DNA," existing only for itself without contributing to an organism's fitness. In 1972 the
late geneticist Susumu Ohno coined the term "junk DNA" to describe all noncoding
sections of a genome, most of which consist of repeated segments scattered randomly
throughout the genome.

Typically these sections of junk DNA come about through transposition, or movement
of sections of DNA to different positions in the genome. As a result, most of these
regions contain multiple copies of transposons, which are sequences that literally copy
or cut themselves out of one part of the genome and reinsert themselves somewhere
else.

Elements that use copying mechanisms to move around the genome increase the
amount of genetic material. In the case of "cut and paste" elements, the process is
slower and more complicated, and involves DNA repair machinery. Nevertheless, if
1

transposon activity happens in cells that give rise to either eggs or sperm, these genes
have a good chance of integrating into a population and increasing the size of the host
genome.

Although very catchy, the term "junk DNA" repelled mainstream researchers from
studying noncoding genetic material for many years. After all, who would like to dig
through genomic garbage? Thankfully, though, there are some clochards who, at the
risk of being ridiculed, explore unpopular territories. And it is because of them that in
the early 1990s, the view of junk DNA, especially repetitive elements, began to change.
In fact, more and more biologists now regard repetitive elements as genomic treasures.
It appears that these transposable elements are not useless DNA. Instead, they
interact with the surrounding genomic environment and increase the ability of the
organism to evolve by serving as hot spots for genetic recombination and by providing
new and important signals for regulating gene expression.

Genomes are dynamic entities: new functional elements appear and old ones become
extinct. And so, junk DNA can evolve into functional DNA. The late evolutionary
biologist Stephen Jay Gould and paleontologist Elisabeth Vrba, now at Yale University,
employed the term "exaptation" to explain how different genomic entities may take on
new roles regardless of their original functioneven if they originally served no
purpose at all. With the wealth of genomic sequence information at our disposal, we
are slowly uncovering the importance of non-protein-coding DNA.

In fact, new genomic elements are being discovered even in the human genome, five
years after the deciphering of the full sequence. Last summer developmental biologist
Gill Bejerano, then a postdoctoral fellow at the University of California, Santa Cruz, and
now a professor at Stanford University, and his colleagues discovered that during
vertebrate evolution, a novel retroposona DNA fragment, reverse-transcribed from
RNA, that can insert itself anywhere in the genomewas exapted as an enhancer, a
signal that increases a gene's transcription. On the other hand, anonymous sequences
that are nonfunctional in one species may, in another organism, become an exona
section of DNA that is eventually transcribed to messenger RNA. Izabela Makalowska
of Pennsylvania State University recently showed that this mechanism quite often leads

to another interesting feature in the vertebrate genomes, namely overlapping genes

that is, genes that share some of their nucleotides.

These and countless other examples demonstrate that repetitive elements are hardly
"junk" but rather are important, integral components of eukaryotic genomes. Risking
the personification of biological processes, we can say that evolution is too wise to
waste this valuable information.