In molecular biology, "junk" DNA is a provisional label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified. Molecular biology is the study of Biology at a molecular level Deoxyribonucleic acid ( DNA) is a Nucleic acid that contains the genetic instructions used in the development and functioning of all known A chromosome is an organized structure of DNA and Protein that is found in cells. In classical genetics the genome of a Diploid Organism including Eukarya refers to a full set of chromosomes or genes in a Gamete, thereby Scientists fully expect to find functions for some, but definitely not all, of this provisionally classified collection. About 80-90% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA. The human genome is the Genome of Homo sapiens, which is stored on 23 chromosome pairs Introns, derived from the term "intragenic regions" and also called intervening sequence (IVS are DNA regions in a Gene that are not translated into An Intergenic region is a stretch of DNA sequences located between clusters of Genes that contain few or no genes While much of this sequence may be an evolutionary artifact that serves no present-day purpose, some is believed to function in ways that are not currently understood. eVolution is the third Album by eLDee, it was due to be released in 2008 Moreover, the conservation of some junk DNA over many millions of years of evolution may imply an essential function. Conservation refers to a high degree of similarity in orthologous DNA sequences protein sequences, or Protein structures amongst various eVolution is the third Album by eLDee, it was due to be released in 2008 Some consider the "junk" label as something of a misnomer, but others consider it apposite as junk is stored away for possible new uses, rather than thrown out; others prefer the term "noncoding DNA" (although junk DNA often includes transposons that encode proteins with no clear value to their host genome). A misnomer is a term which suggests an interpretation that is known to be untrue In Genetics, non-coding DNA describes DNA which does not contain instructions for making Proteins (or other cell products such as Noncoding Transposons are sequences of DNA that can move around to different positions within the Genome of a single cell, a process called transposition However it now appears that, although protein-coding DNA makes up barely 2% of the human genome, about 80% of the bases in the genome may be transcribed,^[1] but transcription by itself does not necessarily imply function.

Broadly, the science of functional genomics has developed widely accepted techniques to characterize protein-coding genes, RNA genes, and regulatory regions. Functional genomics is a field of Molecular biology that attempts to make use of the vast wealth of data produced by genomic projects (such as genome sequencing projects History See also History of genetics The existence of genes was first suggested by Gregor Mendel (1822-1884 who in the 1860s studied inheritance A non-coding RNA ( ncRNA) is any RNA molecule that is not translated into a Protein. A regulatory sequence (also called a regulatory region or a regulatory area) is a segment of DNA where regulatory proteins such as Transcription In the genomes of most plants and animals, however, these together constitute only a small percentage of genomic DNA (less than 2% in the case of humans). Plants are living Organisms belonging to the kingdom Plantae. The function, if any, of the remainder remains under investigation. Most of it can be identified as repetitive elements that have no known biological function for their host (although they are useful to geneticists for analyzing lineage and phylogeny). In the study of DNA sequences one can distinguish two main types of repeated sequence: Tandem repeats Satellite DNA, A genealogical DNA test examines the Nucleotides at specific locations on a person's DNA for Genetic genealogy purposes Still, a large amount of sequence in these genomes falls under no existing classification other than "junk".

While overall genome size, and by extension the amount of junk DNA, are correlated to organism complexity, it is not a solid rule of thumb. Genome size refers to the total amount of DNA contained within one copy of a Genome. For example, the genome of the unicellular Amoeba dubia has been reported to contain more than 200 times the amount of DNA in humans"^{[2] [3]}. The Amoeba dubia is the largest species of the kingdom Amoebozoa, more commonly referred to as Amoeba.

The pufferfish Takifugu rubripes genome is only about one tenth the size of the human genome, yet seems to have a comparable number of genes. Tetraodontidae is a family of primarily marine and estuarine fish is the Japanese word for Pufferfish and is also a Japanese dish prepared from the meat of Pufferfish (normally species of Takifugu, Lagocephalus Most of the difference appears to lie in what is now known only as junk DNA. This puzzle is known as the C-value enigma or, more conventionally, the C-value paradox^[4]. The C-value enigma or C-value paradox is a term used to describe the complex puzzle surrounding the extensive variation in nuclear Genome size among Eukaryotic

Contents 1 Hypotheses of origin and function 2 Evolutionary conservation of "junk" DNA 3 Functions for Some Subsets of Junk DNA 4 See also 5 References 5.1 Further reading

Hypotheses of origin and function

There are some hypotheses, none conclusively established, from the most academic to the less expected, for how junk DNA arose and why it persists in the genome:

• 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). Pseudogenes are defunct relatives of known Genes that have lost their Protein -coding ability or are otherwise no longer expressed 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)^[5], although as much as 25% is recognisably formed of retrotransposons^[6]. Retrotransposons (also called transposons via RNA intermediates are genetic elements that can amplify themselves in a Genome and are ubiquitous components of the Endogenous retroviruses are Retroviruses derived from ancient infections of Germ cells in Humans Mammals and other vertebrates as such their 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. ^[7]
• 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". "^[8]
• 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^[9].
• Some junk DNA could simply be spacer material that allows enzyme complexes to form around functional elements more easily. Enzymes are Biomolecules that catalyze ( ie increase the rates of Chemical reactions Almost all enzymes are Proteins 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^[10], and/or development of certain organs/organelles^[11]. An embryo (from Greek:, plural, lit "that which grows" from en- "in" + bryein "to swell be full" is a multicellular
• 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. A non-coding RNA ( ncRNA) is any RNA molecule that is not translated into a Protein. ^[12] 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^[13]. A phenotype is any observable characteristic of an Organism, such as its morphology, Development, biochemical or physiological properties 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.

Evolutionary conservation of "junk" DNA

Comparative genomics is a promising direction in studying the function of junk DNA. Comparative genomics is the study of the relationship of Genome structure and function across different biological Species or strains. 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. Natural selection is the process by which favorable Heritable traits become more common in successive Generations of a Population of 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. In Evolutionary biology, homology has come to mean any similarity between characters that is due to their shared ancestry. 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^[14] since the divergence of the mammals. Stabilizing selection, also referred to as purifying selection or ambidirectional selection, is a type of Natural selection in which Genetic diversity 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 is known functional sequence.

A surprising recent finding was the discovery of nearly 500 ultraconserved elements^[15], 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^[15][16][17] 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 is 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 ^[13].

On a theoretical note, it is often observed that the presence of high proportions of truly nonfunctional "junk" DNA would seem to defy evolutionary logic. Replication of such a large amount of useless information each time a cell divides would waste energy. Organisms with less nonfunctional DNA would thus enjoy a selective advantage, and over an evolutionary time scale, nonfunctional DNA would tend to be eliminated. If one assumes that most junk DNA is indeed nonfunctional, then there are several hypotheses for why it has not been eliminated by evolution: (1) The energy required to replicate even large amounts of nonfunctional DNA is in fact relatively insignificant on the cellular or organismal scale, so no selective pressure results (selection coefficients less than one over the population size are effectively neutral); (2) The aforementioned possible advantage of having extra DNA as a reservoir of potentially useful sequences and similarly as a protective buffer against harmful genetic damage or mutations; and (3) Retrotransposon insertions of nonfunctional sequence occurring faster than evolution can eliminate it. Retrotransposons (also called transposons via RNA intermediates are genetic elements that can amplify themselves in a Genome and are ubiquitous components of the These are all hypotheses for which the time scales involved in evolution may make it difficult for humans to investigate rigorously.

Functions for Some Subsets of Junk DNA

• A 2002 study from the University of Michigan showed that segments of junk DNA called LINE-1 elements, once thought to be "leftovers from the distant evolutionary past" now "deserve more respect" because they are capable of repairing broken strands of DNA. ^[18]

• A 2003 study from Tel Aviv University found crucial uses for "junk" sequences in human DNA. [3]

• 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. " [4]

• An article from BioEd Online details DNA which appears crucial although no function has yet been discovered. [5]

• A 2005 study from the National Institutes of Health found that social behavior in rodents (and, possibly humans [6]) was affected by portions of the genetic code once thought to be "junk. " [7]

• A 2005 study from University of California-San Diego suggested that junk DNA is "critically important to an organism’s evolutionary survival. " [8]

• 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. " [9]

• A 2006 study by the McKusick-Nathans Institute of Genetic Medicine (Johns Hopkins) stated that "Junk DNA may not be so junky after all. " [10]

• Researchers at the University of Illinois Society for Experimental Biology found an antifreeze-protein gene in a species of fish which appears to have evolved from junk DNA. [11]

• A mathematical analysis of the genetic code by IBM identified patterns that suggested junk DNA had an important role after all. [12]

• In 2006, University of Iowa researchers documented segments of RNA (previously considered "junk") that regulated protein production, and could generate microRNAs. Ribonucleic acid ( RNA) is a Nucleic acid that consists of a long chain of Nucleotide units In Genetics, microRNAs ( miRNA) are single-stranded RNA molecules of about 21–23 Nucleotides in length which regulate Gene expression [13]

• 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. "^[14]

See also

• Atavism
• Alu repeat
• Eukaryotic chromosome fine structure
• Genealogical DNA test
• Intron
• Repeated sequence (DNA)
• Retrotransposon
• Satellite DNA
• Selfish DNA

References

Further reading

• Gibbs W. W. (2003) "The unseen genome: gems among the junk", Scientific American, 289(5): 46-53. Year 2003 ( MMIII) was a Common year starting on Wednesday of the Gregorian calendar. Scientific American is a Popular science magazine, published (first weekly and later monthly since August 28, 1845, making it (A review, written for non-specialists, of recent discoveries of function within junk DNA. )

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