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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, enhancers and silencers 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 Fugu rubripes 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 be the genetic basis for evolution. Over time many mutations accrue, most of which, statistically speaking, will affect the junk DNA and not the functional DNA. Furthermore these mutations may change parts of the junk DNA until they become functional, thus giving the organism a new feature or attribute.
- 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 phenotype³. 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.
By now, it is fairly certain that a combination of these are true, or partly true. A large portion of 'junk' DNA seems to have crucial functions in gene regulation; in humans, for example, only 2% of transcribed DNA gets translated into proteins. Therefore, the term 'junk DNA' should be avoided as it confers an outdated and completely misleading view of genetic functions on the genomic level. A more precise term like 'noncoding DNA' is to be preferred. True 'junk' elements in the genome can be recognized by comparisons between species, as in such DNA elements, mutations would be expected to occur randomly and in comparatively large amounts.
It should be noted that the assumption of high proportions of 'junk' DNA - like the '97%' figure in humans - can by no means be reconciled with evolutionary theory. Replication of such a large amount of useless information each time a cell divides would place a high burden on an organism; much energy would simply be wasted in creating the nucleotides for such useless stretches. Over an evolutionary time-scale, therefore, elimination of 'junk' sequences by deletion mutations would have to reduce the amount of 'junk' sequences to a level that can be maintained with the available energy and compounds without incurring a punitive loss of fitness. The fact that 'junk DNA' sequences indeed do exist (although much less common than it was assumed as late as 2002) suggests that the natural selection-driven need to conserve energy is somewhat less stringent than it is generally assumed to be in popular science.
- 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", 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.
- Mattick, John S. (2004) "The Hidden Layer of Noncoding RNA: a Digital Control System Underpinning Mammalian Development and Diversity", HGM Symposium 2004 Session 4/16.
- Alu repeat
- repetitive sequence
- satellite DNA
- molecular evolution
- selfish DNA
- ABC News: Genius of Junk (DNA)
- Focus Online - News from Harvard Schools - Junk DNA Yields New Kind of Gene
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