Hypotheses of origin and function

• These chromosomal regions could be composed of the now-defunct remains of ancient genes, known as pseudogenes, which were once functional copies of genes but have since lost their protein-coding ability (and, presumably, their biological function). After non-functionalization, pseudogenes are free to acquire genetic noise in the form of random mutations.
• 8% of human junk DNA has been shown to be formed by retrotransposons of Human Endogenous Retroviruses (HERVs), although as much as 25% is recognisably formed of retrotransposons. This is a lower limit on how much of the genome is retrotransposons because older remains might not be recognizable having accumulated too much mutation. New research suggests that genome size variation in at least two kinds of plants is mostly because of retrotransposons.
• In 1997, Steven Sparks proposed that "The end purpose of this "excess DNA" must be to reduce the probability of transcribable genes being cut by chromosomal crossover. Gametes can survive only when their important, transcribed genes are saved from meiotic cutting by being surrounded with "buffer DNA"."
• Junk DNA might provide a reservoir of sequences from which potentially advantageous new genes can emerge. In this way, it may be an important genetic basis for evolution.
• Some junk DNA could simply be spacer material that allows enzyme complexes to form around functional elements more easily. In this way, the junk DNA could serve an important function even though the actual sequence information it contains is irrelevant.
• Some portions of junk DNA could serve presently unknown regulatory functions, controlling the expression of certain genes, the development of an organism from embryo to adult, and/or development of certain organs/organelles.
• More and more scientists believe that in fact regulatory layer(s) in the "junk DNA", such as through non-coding RNAs, altogether contain genetic programming at least on par with, and possibly much more important than protein coding genes. But still how much of the 98% would be involved in such activity is unknown.
• Junk DNA may have 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's some function that the experiments performed on the mice were merely insufficient to detect.

  Evolutionary conservation of "junk" DNA

  Comparative genomics is a promising direction in studying the function of junk DNA. Biologically functional sequences, as the theory goes, tend to undergo mutation at a slower rate than nonfunctional sequence, since mutations in these sequences are likely to be selected against. For example, the coding sequence of a human protein-coding gene is typically about 80% identical to its mouse ortholog, while their genomes as a whole are much more widely diverged. Analyzing the patterns of conservation between the genomes of different species can suggest which sequences are functional, or at least which functional sequences are shared by those species. Functional elements stand out in such analyses as having diverged less than the surrounding sequence.
     Comparative studies of several mammalian genomes suggest that approximately 5% of the human genome has evolved under purifying selection since the divergence of the mammals. Since known functional sequence comprises less than 2% of the human genome, it appears that there may be more functional "junk" DNA in the human genome than there's known functional sequence.
     A surprising recent finding was the discovery of nearly 500 ultraconserved elements, which are shared at extraordinarily high fidelity among the available vertebrate genomes, in what had previously been designated as junk DNA. The function of these sequences is currently under intense scrutiny, and there are preliminary indications that some may play a regulatory role in vertebrate development from embryo to adult.
     It must be noted that all present results concerning evolutionarily conserved human "junk" DNA are expressed in highly preliminary, probabilistic terms, since only a handful of related genomes are available. As more vertebrate, and especially mammalian, genomes are sequenced, scientists will develop a clearer picture of this important class of sequence. However, it's always possible, though highly unlikely, that there are significant quantities of functional human DNA that are not shared among these species, and which would thus not be revealed by these studies. Conversely there are even some questions about basic hypothesis that conserved sequences all must function

A 2003 study from Tel Aviv University found crucial uses for "junk" sequences in human DNA. (External Link)

A 2004 study from the Cell Press suggests that "more than one third of the mouse and human genomes, previously thought to be non-functional, may play some role in the regulation of gene expression and promotion of genetic diversity." (External Link)

An article from BioEd Online details DNA which appears crucial although no function has yet been discovered. (External Link)

A 2005 study from the National Institutes of Health found that social behavior in rodents (and, possibly humans (External Link)) was affected by portions of the genetic code once thought to be "junk." (External Link)

A 2005 study from University of California-San Diego suggested that junk DNA is "critically important to an organism’s evolutionary survival." (External Link)

Findings from Purdue University in 2005 stated that "many DNA sequences previously believed to have no function actually may play specialized roles in cell behavior." (External Link)

A 2006 study by the McKusick-Nathans Institute of Genetic Medicine (Johns Hopkins) stated that "Junk DNA may not be so junky after all." (External Link)

Researchers at the University of Illinois Society for Experimental Biology found an antifreeze-protein gene in a species of fish which "evolved" from junk DNA. (External Link)

A mathematical analysis of the genetic code by IBM identified patterns that suggested junk DNA had an important role after all. (External Link)

In 2006, University of Iowa researchers documented segments of RNA (previously considered "junk") that regulated protein production, and could generate microRNAs. (External Link)

A 2007 study from Stanford University School of Medicine found that "Large swaths of garbled human DNA once dismissed as junk appear to contain some valuable sections."^{(External Link)}Further Information

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