Junk DNA

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 genetic code. 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" DNA sequences that are known to be important. These include origin of replication, which define the starting points of DNA replication, and regulatory sequences such as promoters, enhancers and silencer (DNA)s 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. In this way, it 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 serves the role as "meta-DNA", being involved in the development of an organism from embryo to adult. as of 2004 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 had 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. 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. ==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) "[http://www.nature.com/nsu/040503/040503-9.html 'Junk' DNA reveals vital role]", ''Nature (journal)''. # 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 (journal)'', 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. == See also == * intron * centromere * telomere * Alu repeat * repetitive sequence * satellite DNA * molecular evolution * selfish DNA ==External links== *[http://www.abc.net.au/catalyst/stories/s898887.htm ABC News: Genius of Junk (DNA)] *[http://focus.hms.harvard.edu/2004/June4_2004/genetics.html Focus Online - News from Harvard Schools - Junk DNA Yields New Kind of Gene] *[http://www.noncodingdna.com noncodingDNA.com] DNA

Junk DNA

Since these days Science, Nature, Scientific American (and many hundreds of present-day links) deal with this subject, the reader may benefit from visiting www.fractogene.com , and www.junkdna.com "the portal to junk DNA". The portal contains links to Malcolm Simons US "junk DNA" patents, Andras Pellionisz' US "FractoGene" Patent Pending, venture opportunities and a wide range of references. --- Is this an official term? "Official" in what sense? It is the term most often used by modern geneticists. --LDC -- And what about post-modern geneticists? ;-) - shouldn't it be called "noncoding DNA" ? --- Any distinction from intron? sodium Introns occur inside active genes; most junk DNA is in the bulk of the chromosome between active genes. :I think an intron is DNA that made sense at some time and is slowly degrading (or changing - it might become activated again when the exon-intron-"border" gets mutated), whereas "junk DNA" aims more at highly repetitive sequences and the like if it doesn't serve any "structural" purpose. --user:Magnus Manske WHat is being talked about in these sentences: " In some cases, the positioning, rather than precise sequence, may be important. There are known examples in the yeast Saccharomyces. " I find them mysterious. User:168... 21:41 5 Jun 2003 (UTC) *My POVmeter pings at the last two paragraphs. Could use some rephrasing. -- User:Jakenelson 06:50, 2003 Aug 21 (UTC) Really? Seems O.K. to me. What exactly is your concern?User:168... 17:16, 21 Aug 2003 (UTC) : I think he took exception to the phrase "''the term "junk" is somewhat a misnomer''" which to my mind does express an opinion. I changed it to "''The term "junk" is recognized as something of a misnomer''" where we can assume the implied object of "recognized" is the scientific community. : Also, the clause "''which might suggest uses for much or all of the junk''" in the second sentence was speculative, and contained no information. So I chopped it. -- User:Clarknova 03:36, 23 Jun 2004 (UTC) ---- Removed this sentence (mentioned above) : In some cases, the positioning, rather than precise sequence, may be important. There are known examples in the yeast ''Saccharomyces''. because it's vague, and therefore somewhat dubious. It should give some indication of what these non-junk sequences actually do. Anyway, the fact that the nucleotide sequence is only loosely important to the function of the sequence is not the point; the question is whether the sequence has a known function or not. --------- Deleted: :The 2003 November issue of Scientific American published an article "Gems in the Junk", in which it stated that "The failure to recognize the importance of introns 'may well go down as one of the biggest mistakes in the history of molecular biology'". [and] "What was damned as junk because if was not understood may, in fact, turn out to be the very basis of human complexity" I don't like the SciAm reference. First of all, scholars reference authors, not publications. Second of all the author of that piece is a journalist, not a scientist, so I don't think it deserves quoting unless it is a truly fascinating and original opinion, and if so then it should be represented as such and not as the conservative view of a world authority. Second of all, many of the articles in SciAm are what would be considered secondary source material. Some of them are stories by journalists who are offering their interpretation or sketch of what researchers reported in an academic journal article. In that case, the journal article is the primary source. There also an inbetween category of popular articles written by scientists in collaboration with journalists, in which they rehash what the scientists themselves reported in a journal in a way ordinary readers can understand. But the scientists know that the SciAm will not be taken very seriously by their peers and won't be peer reviewed, so many of them are bolder in the claims they make in these articles. If the SciAm is an ''essay'' or other sort of opinion piece by a scientist, then it might be appropriate to reference some opinion from it and attribute it to the scientist. The magazine and issue number shouldn't appear except as a footnote. If the opinion is a journalist's, I don't think it deserves quoting unless it is a truly fascinating and original opinion, but then it should be represented as such and not as the conservative view of a world authority.User:168... 06:12, 22 Jan 2004 (UTC)User:168... 06:20, 22 Jan 2004 (UTC) : I think you raise some good points against the Sci-Am reference. I agree that the author seems to be a science writer, and not a scientist, and it's clear (e.g. from the quotes from the article I deleted) that some of the scientists have used the opportunity for PR for their particular research agenda, although the same kind of thing happens in more serious scientific journals as well. : I'm not sure what is meant by "scholars reference authors, not publications". Does that concern refer to the deleted text, or to the Wikipedia article as it stands? : I'm inclined to disagree with your standard for deciding when a science writer can be cited. Although the Sci-Am article has its flaws, I found it a reasonable review of some recent developments in the field, admittedly for a more popular audience. I think that overview is valuable, and for a general encyclopedia, may be more relevant to a greater portion of the readership. It would be nice to have a more serious reference in addition, but I'm not aware of a serious reference with the same scope. (I think there have probably been some perspective articles in Science/Nature in the last year, since there have been a number of papers on finding functional things other than protein-coding genes recently). : Anyway, if you were to remove the reference, I wouldn't get into an edit war, but I think it has some merit for this Wikipedia article. : User:Zashaw 00:06, 23 Jan 2004 (UTC) By "scholars reference authors, not publications" I meant that the attribution should be to a person and not a magazine. I imagine you're right about the article being reasonable (because I respect the SciAm journalists), and seeing that you claim to be a grad student, I'm inclined to trust your opinion that it ''is'' reasonable. Thing is, that doesn't mean that others should be obliged to trust you, you who are not referenced or listed as this article's author. If it's going to be on your authority that we take this journalist as fairly representing scientific opinion, then I suggest you just state the opinion as fact rather than implying either that journalists are scientific authorities or that the referenced source is a scientist and not a journalist. That said, if it didn't strike me as clearly improper, I'd recommend we reference the journalist over a random academic review paper, since those papers tend to be shameless propaganda pieces (they're a little like journalism, since generally they're unrefereed). User:168... 00:29, 23 Jan 2004 (UTC) ---- == Repetitive or random sequence? == What does the "junk" look like? Is it sometimes random or always highly repetitive like "CACACACACACACA" for hundreds of thousands of bases? Thanks ---- I deleted this paragraph on SNPs: * There are about three million SNPs or 'snips', i.e. differences in the genomes of any two unrelated people, but of these only about 10,000 or so are likely to have any effect on the organism � i.e. 0.3%. Extrapolating to the human genome, which has about 800 MBytes of information, 0.3% of this is 2.6 MB of really functional DNA, which is roughly the amount of information in the approximately 20,000 genes. This implies that the junk DNA may truly be junk. I don't get the logic here, and it seems like it's not a very strong case, and not necessarily a widely considered hypothesis. On the other hand, it's apparent that some thought went into it. Please respond if you have evidence that it's widely held (like refs in decent journals), or could explain it a bit better. At any rate, whatever the logic, it's certainly conceivable that much of what we currently consider junk is really junk, although I think most people would be skeptical of this hypothesis, because it seems burdensome for organisms to have so much useless DNA. User:Zashaw 00:38, 9 Dec 2004 (UTC) The logic is quite simple and does not depend on any POV. The reference on the SNPs is e.g. from http://www.pbs.org/wgbh/nova/genome/debate.html - " 'snips' -- genespeak for the sites littered throughout our DNA that frequently vary between unrelated people. About three million differences exist in the genomes of any two unrelated people, but of these only about 10,000 or so are likely to have any functional consequences. " All I did on top of that was to estrapolate from SNPs to the Genome - a reasonable assumption, as there is no reason why SNPs should be exceptional locations in the genome. : I'm still dubious, since (1) there are a lot of assumptions, (2) I still don't see a reference on this work using SNPs to estimate the likelihood of function in "junk" DNA. It seems like your work, and Wikipedia doesn't publish original research. As for the assumptions, first, the quote says "are _likely_ to", which makes it sound like they have very little idea. SNPs and researching diseases using them is still an open field, so I doubt they know exactly how many are functional. Okay, if the 10000/3000000 number is right, I don't see why you can multiply that by 3 billion nucleotides. 3 million is, I assume, the number of SNPs that have been discovered anywhere in the human genome. If so, our best current estimate is that there are 3 million SNPs in the human genome (we might estimate more, if we think we've missed some). Even if we accept this, the argument that the predicted number of SNP nucleotides equals the amount of coding DNA seems pretty specious: (a) detection of how many SNPs are functional is biased to coding DNA (which we're relatively good at understanding), so this number may ignore functional SNPs in functional, but non-coding DNA -- a circular argument, (b) I'm pretty sure most coding DNA is not SNPs (i.e. it's conserved in all tested humans), (c) at best it's a back-of-the-envelope estimate, so if any of our biological knowledge, or the simple assumptions made are wrong, the estimate may be way off -- so, it doesn't tell us much about the likelihood of function in junk DNA, IMHO. User:Zashaw 22:59, 9 Dec 2004 (UTC) :: The reference is good - Kevin Davies is a respected researcher (founder of NATURE Genetics !! ) talking here on PBS. He gives 3 references, but admittedly it is not clear if they apply to SNPs or if he is talking from his extensive experience in the field. It might be best to query him directly for clarification. Then your counter-argument is somewhat confused. The facts are simple - 3 million SNPS have been identified, though there may be more. Of these it has been shown that only 0.3% are effective. As far as I understand it the SNPs are quite evenly distributed in the genome - with a mean spacing of about 1000 base pairs. Thus some fall in coding regions and some in junk. Sounds like a sort of Mont Carlo sampling of the 3,000,000,000 base pairs. I.e. the 3 million SNPs are fairly representative of all base pairs. Let's test this: in http://snp.cshl.org/naturepaper.shtml it says that 60000 SNPs of a 1.42 million sample fall in Exons - that's 4%, where 1.5% would be expected for a uniform distribution, i.e. a potential bias of 3:1, due either to sampling bias or to an actual preponderance of SNPs in exons. Not serious though, as if only 10,000 are effective anyway, it shows that at most 1/6 of EXON SNPs are effective - otherwise a much smaller fraction of junk SNPs is effective. So my argument of scaling up this result to the genome as a whole is not so outlandish. --User:Hdeasy 13:18, 10 Dec 2004 (UTC) :I'm not sure if we're talking about the same thing in terms of references. What I would like to see is an article in a peer-reviewed journal that states that junk DNA is probably not functional specifically because the estimated number of SNPs is equal to the amount of "information" in coding genes in the human genome. It's not enough to have references that support the 10000 functional SNPs out of 3 million (because that isn't about the analysis per se, it just supports an assumption underlying the analysis) and it's not enough to have references that suggest that junk DNA may indeed be junk based on other reasons (because that's clearly a possibility anyway; and BTW, the Nature/mouse reference is great). I'd consider a quote from an authority on this analysis. (I'll accept Kevin Davies as an authority, but he doesn't seem to say anything about your analysis; from what I can see, he just gives the 10000 functional SNPs number.) :In the interests of expediency, let me restate that you seem to imply that the analysis you present is your work, and not, for example, the work of Kevin Davies. So, unless you can offer references of this analysis in a refereed journal, I would refer you to Wikipedia's policy on no original research. BTW, I'm not saying that your theory is necessarily wacky, just that it doesn't belong in Wikipedia. (As for the analysis, I now understand your logic in multiplying 10000/3million by 3billion bases, which is not outlandish, although I still think the analysis overall is problematic. Write on my talk page if you're interested in discussing further, assuming there are no references.) :User:Zashaw 06:57, 11 Dec 2004 (UTC) Additional evidence that large stretches of the DNA are non-functional, even the ulta-conserved sections, is given in http://www.i-sis.org.uk/AUEI.php - "There are 481 segments in the human genome longer than 200 bp that are 100% identical with rat and mouse genomes. Nearly all are also conserved in the chicken (467/481) and dog (477/481) genomes ... 481x200 = 96200 bp ... actually 106 767 bp or 26692 Bytes ultraconserved... But researchers revealed that mice with big chunks for such ultraconserved sequences deleted get on very well without them. Edward Rubin's team at the Lawrence Berkeley National Laboratory in California deleted two huge regions of DNA from mice containing nearly 1 000 highly conserved sequences shared between human and mice. One region was 1.6 million DNA bases long, the other over 800,000 bases long. The researchers expected the mice to show big problems as the result of the deletions. But the mutant mice were no different from normal mice in every respect: growth, metabolic functions, lifespan and overall development. "We were quite amazed," said Rubin, who presented the findings at a meeting of the Cold Spring Harbor Laboratory in New York earlier this year. "It may say as much about our inability to detect any phenotypes as it says about the function of this region, " said David Haussler of the University of California, Santa Cruz, whose team described the "ultra-conserved regions" in mammals, "What's most mysterious is that we don',t know any molecular mechanism that would demand conservation like this." " Or better still - http://www.nature.com/news/2004/041018/pf/041018-7_pf.html - " Published online: 20 October 2004; Mice do fine without 'junk DNA' Roxanne Khamsi - Mice born without large portions of their 'junk DNA' seem to survive normally. The result contradicts the beliefs of many scientists who have sought to uncover the function of these parts of the genome. More than 90% the genome of organisms such as mice and humans does not appear to code for any proteins. And yet this DNA shows striking similarities between species. If they had no function, over time mutations would scramble the sequences. Why have these bits of the genome remained so highly conserved? " Thus several independent sources confirm the conclusion in the excised paragraph. May I therefore restore it with references? --User:Hdeasy 11:47, 9 Dec 2004 (UTC) : I think the Nature paper is a great experiment, and I agree. I've taken the liberty of boldly adding that to the article (along with the point that junk DNA may have functions). See what you think. User:Zashaw 22:59, 9 Dec 2004 (UTC) Not too bad, I suppose - although even there the later 3% removal might be mentioned, though it is not as well tested experimentally as the 1% level in the mouse genome.--User:Hdeasy 08:26, 10 Dec 2004 (UTC) : A-ha, I was confused about the 1% vs 3% inconsistency. I don't feel strongly about which number to use. User:Zashaw 06:57, 11 Dec 2004 (UTC) == Repressor -> Silencer == I changed the (red) link to repressor to a (red) link to silencer (DNA) even though I know nothing about genetics, based on the following e-mail: :In the main text about "Junk DNA' "repressor" is quoted as a kind of junk DNA. Repressors are proteins coded by DNA. The position of the word, just after "enhancer", suggests that may be the author thought about "silencer", the sequence of DNA silencing expression of a given gene. :Magdalena Fikus :Institute of Biochemistry and Biophysics Polish Academy of Sciences. User:The Epopt 23:08, 6 Mar 2005 (UTC) *yes, I wrote that and what I really meant was silencer (DNA), not repressors. Thanks for fixing the mistake. --User:Tycho 01:39, 7 Mar 2005 (UTC) == I feel so proud! == I just joined the Wiki comunity and already are my comments being saved! I wrote the theory of the conection between junk DNA and evolution myself and already its taking off! (I'm also soooooo wierd, arn't I?) ----- Moved this link from article to talk page: : For a non-silly discussion of junk DNA, see the EvoWiki [http://www.evowiki.org/index.php/Junk_DNA Junk DNA page] Basically, I think there's some interesting info at that article, but IMHO I really don't think it's a serious discussion about Junk DNA. It seems to be a polemical anti-creationism site (trying to score points at all times) and presents a fairly narrow view of the science. If someone thinks I'm being unfair, please say so & I'll say more. (Otherwise I'll feel I'm rambling.) Something interesting in that article: "one species of deer has ~20% more DNA than another very similar species of deer in the same genus... [ One species either lost or gained a lot of DNA with only trivial resulting change ]. ... this implies that this DNA is not very important." I couldn't find the claimed citation for this, and Google didn't help. But if true, this seems interesting (though about as significant as the 3%-genome-deleted mouse). User:Zashaw 03:54, 16 Jun 2005 (UTC)

Junk dna

#redirect junk DNA

See other meanings of words starting from letter:

J

JA | JB | JC | JD | JE | JF | JG | JH | JI | JK | JL | JM | JN | JO | JP | JR | JS | JT | JU | JW | JX | JY | JZ |

Words begining with Junk_DNA:

Junk_DNA
Junk_DNA
Junk_dna