FACTOID # 11: Oklahoma has the highest rate of women in State or Federal correctional facilities.
 
 Home   Encyclopedia   Statistics   States A-Z   Flags   Maps   FAQ   About 
   
 
WHAT'S NEW
 

SEARCH ALL

FACTS & STATISTICS    Advanced view

Search encyclopedia, statistics and forums:

 

 

(* = Graphable)

 

 


Encyclopedia > Junk DNA

In molecular biology, "junk" DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified. About 80-90% of the human genome has been designated as "junk", including most sequences within introns and most intergenic DNA. 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. Moreover, the conservation of some junk DNA over many millions of years of evolution may imply an essential function. 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). 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 being expressed, which supports the view that the term "junk DNA" may be a misnomer.[1] Image File history File links Merge-arrow. ... It has been suggested that junk DNA be merged into this article or section. ... Molecular biology is the study of biology at a molecular level. ... The structure of part of a DNA double helix Deoxyribonucleic acid, or DNA, is a nucleic acid molecule that contains the genetic instructions used in the development and functioning of all known living organisms. ... Figure 1: A representation of a condensed eukaryotic chromosome, as seen during cell division. ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... A graphical representation of the normal human karyotype. ... Diagram of the location of introns and exons within a gene. ... An Intergenic region is a stretch of DNA sequences located between clusters of genes that comprise a large percentage of the human genome but contain few or no genes. ... This article is about evolution in biology. ... Conservation is a high degree of similarity in the primary or higher structure of homologous proteins amongst various phyla. ... This article is about evolution in biology. ... This article does not cite any references or sources. ... It has been suggested that junk DNA be merged into this article or section. ... Transposons are sequences of DNA that can move around to different positions within the genome of a single cell, a process called Transposition. ...


Broadly, the science of functional genomics has developed widely accepted techniques to characterize protein-coding genes, RNA genes, and regulatory regions. 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). 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). Still, a large amount of sequence in these genomes falls under no existing classification other than "junk". A DNA microarray 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) to describe gene (and protein!) functions and interactions. ... For other uses, see Gene (disambiguation). ... A non-coding RNA (ncRNA) is any RNA molecule that functions without being translated into a protein. ... In biochemistry, a regulatory region is a DNA base sequence that controls gene expression. ... For other uses, see Plant (disambiguation). ... For other uses, see Animal (disambiguation). ... In the study of DNA sequences, one can distinguish two main types of repeated sequence: Tandem repeats: Satellite DNA, Minisatellite, Microsatellite; Interspersed repeats: SINEs (Short INterspersed Elements), LINEs (Long INterspersed Elements). ... A genealogical DNA test examines the nucleotides at specific locations on a persons DNA for genetic genealogy purposes. ... In biology, phylogenetics (Greek: phylon = tribe, race and genetikos = relative to birth, from genesis = birth) is the study of evolutionary relatedness among various groups of organisms (e. ...


Overall genome size, and by extension the amount of junk DNA, appears to have little relationship to organism complexity: the genome of the unicellular Amoeba dubia has been reported to contain more than 200 times the amount of DNA in humans"[2] [3]. Genome size refers to the total amount of DNA contained within one copy of a genome. ... The Amoeba dubia is the largest species of the genus 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. 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]. Genera Amblyrhynchotes Arothron Auriglobus Canthigaster Carinotetraodon Chelonodon Colomesus Contusus Ephippion Feroxodon Fugu Gastrophysus Javichthys Lagocephalus Liosaccus Marilyna Monotretus Omegaphora Pelagocephalus Polyspina Reicheltia Sphoeroides Takifugu Tetractenos Tetraodon Torquigener Tylerius Xenopterus For species see Genera articles. ... For other uses, see Fugu (disambiguation). ... 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 species. ...

Contents

Hypotheses of origin and function

There are some hypotheses, none conclusively established, 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). 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]. 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]
  • Junk DNA may act as a protective buffer against genetic damage and harmful mutations. For example, a high proportion of nonfunctional sequence makes it unlikely that a functional element will be destroyed in a chromosomal crossover event, possibly making a species more tolerant to this important mechanism of genetic recombination.
  • 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[8].
  • New Age Speculation and some Intelligent Design advocates purport that junk DNA may represent intentionally re-ordered or "unplugged" sequences. [citation needed]
  • Similarly, proponents of extraterrestrial origin theories suggest that junk DNA may be lying dormant, waiting for a signal from the creators of the human race.
  • 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[9], and/or development of certain organs/organelles[10].
  • 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.[11] 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[12]. 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.

A pseudogene is a nucleotide sequences that is similar to a normal gene, but is not expressed as a functional protein. ... Retrotransposons are genetic elements than can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. ... Endogenous retroviruses are retroviruses thought to be derived from ancient infections of germ cells in humans, mammals and other vertebrates; as such their proviruses are passed on to the next generation and as such now remain in the genome. ... Thomas Hunt Morgans illustration of crossing over (1916) Homologous Recombination is the process by which two chromosomes, paired up during prophase I of meiosis, exchange some distal portion of their DNA. Crossover occurs when two chromosomes, normally two homologous instances of the same chromosome, break and then reconnect but... Genetic recombination is the process by which a strand of DNA is broken and then joined to the end of a different DNA molecule. ... New Age describes a broad movement characterized by alternative approaches to traditional Western culture. ... For other uses, see Intelligent design (disambiguation). ... Extraterrestrial, as an adjective, refers to something that originates, occurs, or is located outside Earth or its atmosphere. ... Ribbon diagram of the enzyme TIM, surrounded by the space-filling model of the protein. ... For other uses, see Embryo (disambiguation). ... A non-coding RNA (ncRNA) is any RNA molecule that is not translated into a protein. ... Individuals in the mollusk species Donax variabilis show diverse coloration and patterning in their phenotypes. ...

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 genomics is the study of relationships between the genomes of different species or strains. ... Darwins illustrations of beak variation in the finches of the Galápagos Islands, which hold 13 closely related species that differ most markedly in the shape of their beaks. ... Orthologs are genes in different species which evolved from a common ancestral gene. ...


Comparative studies of several mammalian genomes suggest that approximately 5% of the human genome has evolved under purifying selection[13] 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 is known functional sequence. Stabilizing selection, also known as purifying selection or negative selection, is a type of natural selection in which genetic diversity decreases as the population stabilizes on a particular trait value. ...


A surprising recent finding was the discovery of nearly 500 ultraconserved elements[14], 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[14][15][16] 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 [12].


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 (3) Retrotransposon insertions of nonfunctional sequence occurring faster than evolution can eliminate it. These are all hypotheses for which the time scales involved in evolution may make it difficult for humans to investigate rigorously. Retrotransposons are genetic elements than can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. ...


Functions for 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. [3]
  • A 2003 study from Tel Aviv University found crucial uses for "junk" sequences in human DNA. [4]
  • 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." [5]
  • An article from BioEd Online details DNA which appears crucial although no function has yet been discovered. [6]
  • A 2005 study from the National Institutes of Health found that social behavior in rodents (and, possibly humans [7]) was affected by portions of the genetic code once thought to be "junk." [8]
  • A 2005 study from University of California-San Diego suggested that junk DNA is "critically important to an organism’s evolutionary survival." [9]
  • 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." [10]
  • A 2006 study by the McKusick-Nathans Institute of Genetic Medicine (Johns Hopkins) stated that "Junk DNA may not be so junky after all." [11]
  • 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. [12]
  • A mathematical analysis of the genetic code by IBM identified patterns that suggested junk DNA had an important role after all. [13]
  • In 2006, University of Iowa researchers documented segments of RNA (previously considered "junk") that regulated protein production, and could generate microRNAs. [14]
  • 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."[15]

Ribonucleic acid or RNA is a nucleic acid polymer consisting of nucleotide monomers that plays several important roles in the processes that translate genetic information from deoxyribonucleic acid (DNA) into protein products; RNA acts as a messenger between DNA and the protein synthesis complexes known as ribosomes, forms vital portions... The stem-loop secondary structure of a pre-microRNA from Brassica oleracea. ...

See also

This page is about the biological term Atavism. ... An Alu sequence is a short stretch of DNA characterized by the action of the Alu restriction endonuclease. ... Eukaryotic chromosome fine structure refers to the structure of sequences for eukaryotic chromosomes. ... A genealogical DNA test examines the nucleotides at specific locations on a persons DNA for genetic genealogy purposes. ... Diagram of the location of introns and exons within a gene. ... In the study of DNA sequences, one can distinguish two main types of repeated sequence: Tandem repeats: Satellite DNA, Minisatellite, Microsatellite; Interspersed repeats: SINEs (Short INterspersed Elements), LINEs (Long INterspersed Elements). ... Retrotransposons are genetic elements than can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. ... Satellite DNA consists of highly repetitive DNA, and is so called because repetitions of a short DNA sequence tend to produce a different frequency of the nucleotides adenine, cytosine, guanine and thymine, and thus have a different density from bulk DNA - such that they form a second or satellite band... Selfish DNA is DNA which is prevalent in the genome, not because its phenotypic effect is beneficial, but because it has properties which cause the number of copies of it within the genome to increase with time. ...

References

  1. ^ Pennisi, Elizabeth (2007). "DNA Study Forces Rethink of What It Means to Be a Gene". Science 316 (5831): 1556-7. 
  2. ^ Gregory, T.R. and P.D.N. Hebert . (1999). "The modulation of DNA content: proximate causes and ultimate consequences". Genome Research 9: 317-324. 
  3. ^ Gregory, T.R. (2005). Animal Genome Size Database. http://www.genomesize.com.
  4. ^ Wahls, W.P., et al. (1990). "Hypervariable minisatellite DNA is a hotspot for homologous recombination in human cells". Cell 60 (1): 95-103. PMID 2295091. 
  5. ^ S. Blaise , N. de Parseval and T. Heidmann (2005). "Functional characterization of two newly identified Human Endogenous Retrovirus coding envelope genes". Retrovirology 2 (19). doi:10.1186/1742-4690-2-19. 
  6. ^ P.L. Deininger, M.A. Batzer (October 2002). "Mammalian retroelements". Genome Res. 12 (10): 1455-1465. PubMed. 
  7. ^ [1] [2]
  8. ^ "...Professor Christina Cheng's group from the University of Illinois has found the gene for the cod antifreeze protein has come from a non-coding region of their DNA sometimes referred to as 'junk DNA'." http://www.sebiology.org.uk/Publications/pageview.asp?S=7&mid=&id=554
  9. ^ Woolfe, A., et al. (2005). "Highly conserved non-coding sequences are associated with vertebrate development". PLoS Biol 3 (1): e7. PMID 15630479 doi:10.1371/journal.pbio.0030007. 
  10. ^ Simons and Pellionisz (2006). Genomics, morphogenesis and biophysics: Triangulation of Purkinje cell development.
  11. ^ http://www.imb.uq.edu.au/index.html?page=11681&pid=11669]
  12. ^ a b 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 (7011): 988-993. doi:10.1038/nature03022. 
  13. ^ Mouse Genome Sequencing Consortium (December 2002). "Initial sequencing and comparative analysis of the mouse genome". Nature 420 (6915): 520-562. doi:10.1038/nature01262. 
  14. ^ a b G. Bejerano et al. "Ultraconserved Elements in the Human Genome". Science 304:1321-1325, May 2004. Discussed in "'Junk' DNA reveals vital role", Nature (2004).
  15. ^ Woolfe, A., et al. (2005). "Highly conserved non-coding sequences are associated with vertebrate development". PLoS Biol 3 (1): e7. PMID 15630479 doi:10.1371/journal.pbio.0030007. 
  16. ^ Sandelin, A., et al. (December 2004). "Arrays of ultraconserved elements span the loci of key development genes in vertebrate genomes". BMC Genomics 5 (1): 99. 

A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ... A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ... Nature is one of the most prominent scientific journals, first published on 4 November 1869. ... A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ... Also see: 2002 (number). ... A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ... Year 2004 (MMIV) was a leap year starting on Thursday of the Gregorian calendar. ... Nature is one of the most prominent scientific journals, first published on 4 November 1869. ... A digital object identifier (or DOI) is a standard for persistently identifying a piece of intellectual property on a digital network and associating it with related data, the metadata, in a structured extensible way. ...

Further reading

  • 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.)

  Results from FactBites:
 
Junk DNA: ScienCentral Video News (719 words)
They did see the expected differences in the shared genes from the common ancestor, but they were surprised to find long stretches of shared "junk" DNA that were exactly the same in humans and rodents.
"There were about five hundred stretches of DNA in the human genome that hadn't changed at all in the millions and millions of years that separated the human from the mouse and the rat," says Haussler.
Long stretches of "junk" DNA are exactly the same in humans and rodents.
Junk DNA - EvoWiki (2053 words)
The total amount of DNA per haploid cell in an organism is referred to as the C value; the failure of C values to correspond to phylogenetic complexity is called the C-value paradox.
Regulatory elements are stretches of DNA associated with genes that assist the molecular machinery of gene expression in determining which genes, and which exons within those genes, should be expressed.
Junk DNA may therefore have a role in reducing the rate of mutation.
  More results at FactBites »

 
 

COMMENTARY     


Share your thoughts, questions and commentary here
Your name
Your comments

Want to know more?
Search encyclopedia, statistics and forums:

 


Press Releases |  Feeds | Contact
The Wikipedia article included on this page is licensed under the GFDL.
Images may be subject to relevant owners' copyright.
All other elements are (c) copyright NationMaster.com 2003-5. All Rights Reserved.
Usage implies agreement with terms, 1022, m