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Within a chromosome or a genome, the "junk" DNA are those portions of the DNA for which no function has been identified.
The term "junk" is recognized as something of a misnomer, especially in light of the fact that molecular biology is a young science and segments of DNA may function in additional ways that have not yet been discovered. Recent work, as of 2004, suggests that junk DNA may indeed perform unrecognized functions.
In the genomes of most plants and animals, the biological role of an overwhelming percentage of the DNA is not known. The portions of a chromosome which are genes are often identifiable as open reading frames even when biologists lack full information about the proteins these genes presumably encode. Genome scientists find it reasonable to assume that these regions are important, even if they do not yet know exactly how. There are also "noncoding" DNA sequences that are known to be important. These include origins of replication, which define the starting points of DNA replication, and regulatory sequences such as promoters, which are involved in turning genes on and off.
About 97% of the human genome has been designated as "junk". The onion genome is 12 times the size of the human one, presumably because it contains even more junk. In contrast, the pufferfish genome is only about one tenth the size of the human, yet seems to have about the same number of genes. Therefore it seems that the ratio of functional to junk DNA differs widely between species.
Hypotheses of origin and function
There are many theories about the factors that shaped junk DNA and why it persists in the genome: -
- These chromosomal regions are trash heaps of defunct genes, sometimes known as pseudogenes, which have been cast aside and fragmented during evolution. Evidence for a related hypothesis suggests that the junk represents the accumulated DNA of failed viruses.
- Junk DNA acts as a protective buffer against genetic damage and harmful mutations. An overwhelming percentage of DNA is irrelevant to the metabolic and developmental processes, so it is unlikely any single, random insult to the nucleotide sequence will affect the organism.
- Junk DNA provides a reservoir of sequences from which potentially advantageous new genes can emerge.
- Junk DNA serves the role as "meta-DNA", being involved in the development of an organism from embryo to adult. Recent results² indicate that so-called ultraconserved elements of junk DNA are common to all vertebrates, and this could mean that this part of the genome is essential to our survival.
- Junk DNA may contain some functions that are as-yet unrecognized. For example, some non-coding RNAs have been discovered in what would have been considered junk.
- Junk DNA may contain no function. For example, recent experiments removed 1% of the mouse genome and were unable to detect any effect on the phenotype. This result suggests that the DNA is, in fact, non-functional. However, it remains a possibility that there is some function that the experiments performed on the mice were merely insufficient to detect.
It may be that a combination of these are true, or partly true.
References
- Gibbs W.W. (2003) "The unseen genome: gems among the junk", Scientific American, 289(5): 46-53. (A review, written for non-specialists, of recent discoveries of function within junk DNA.)
- Pearson, Helen (2004) "'Junk' DNA reveals vital role (http://www.nature.com/nsu/040503/040503-9.html)", Nature.
- M.A. Nobrega, Y. Zhu, I. Plajzer-Frick, V. Afzal and E.M. Rubin (2004) "Megabase deletions of gene deserts result in viable mice", Nature, 431: 988-993.
See also
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