Talk:Noncoding DNA

From Wikipedia, the free encyclopedia
Jump to: navigation, search
WikiProject Genetics (Rated C-class, Mid-importance)
WikiProject icon This article is within the scope of WikiProject Genetics, a collaborative effort to improve the coverage of Genetics on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.
C-Class article C  This article has been rated as C-Class on the project's quality scale.
 Mid  This article has been rated as Mid-importance on the project's importance scale.
 
WikiProject Molecular and Cellular Biology (Rated C-class, Mid-importance)
WikiProject icon This article is within the scope of the WikiProject Molecular and Cellular Biology. To participate, visit the WikiProject for more information.
C-Class article C  This article has been rated as C-Class on the project's quality scale.
 Mid  This article has been rated as Mid-importance on the project's importance scale.
 

Merge request[edit]

Set up merge request. "Junk DNA" is a non-scientific throwaway term that should be avoided. All that can be said is that this stuff does not get translated into proteins and in many - though quite likely not even "most" - cases, apparently also not transcribed into RNA, hence, it is non-coding. Anything beyond that is not based on evidence (though lack of a function is hard to prove in the current state of knowledge and research technology), and while some apparently randomly-evolving sequences indeed do not seem to have any function at all, the question of whether this stuff might have some function is only seriously being researched since maybe 2000; essentially it were Gregory's C-value enigma papers that kicked it off - and in astoundingly many cases where research is being conducted, non-coding DNA does appear to have some sort of function, namely in gene regulation (it appears that the largest part of the "regulatory" code of the genome is contained in some way or another in noncoding sequences). See also Non-coding RNA, Science: 632-635, and the recent reviews by Biemont/Vieira (PMID 17024082) and Willingham/Gingeras (PMID 16814704), and recent Takifugu and gulper eel publications.
A possible way to merge would be to copy/paste, rm "junk" with "noncoding" as appropriate and add an intro statement like:

Noncoding DNA, colloquially also referred to as "junk DNA" (but see below), ...

Dysmorodrepanis 12:15, 4 December 2006 (UTC)

It was discussed before,, on Talk:Junk DNA and most people disagreed. You should reply to arguments there if you have new idea. --Baldzac 15:14, 4 December 2006 (UTC)

The regions of the code we're talking about are so vast, that some will always be described as "junk". This term was coined by the leading researchers, and is just as "scientific" as any other term. Do not merge. —Preceding unsigned comment added by 205.118.81.24 (talk) 21:56, 23 October 2007 (UTC)

"Coined" yes, "used today" no. Do a PubMed search and

Dysmorodrepanis (talk) 10:29, 12 December 2007 (UTC) -> see Talk:Junk DNA


Junk DNA refers to the 98% of DNA of unknown function, non-coding DNA is a subset of junk DNA.

Speh 12:29, 16 January 2008 (UTC)

Simply because a portion of DNA does not code for anything (non-coding) does not mean that it has no known function (junk DNA). enhancers, promoters, operators, and many other sequences that code for nothing (produce no RNA) have functions. Increasing or decreasing the rate at which genes are depending on what proteins are binding, but these sequences themselves do not code for anything. On the other hand, junk DNA could code for something, it could code for an RNA that hasn't yet been discovered or a protein that similarly hasn't been discovered. Junk DNA simply indicates that the DNA's purpose has no known function, non-coding is a statement that the DNA has some function that doesn't produce RNA or protein. The line, I would have to admit is hazy, but I think that there's enough of a line that I would recommend not merging. —Preceding unsigned comment added by 12.216.237.235 (talk) 05:06, 25 February 2008 (UTC)

Wow. How can Wikipedia get something so wrong for such a long time? Wiki politics will ensure that it'll never be corrected either. Non-coding DNA is entirely different from junk DNA. Merging these articles is simply wrong and misleading. Get it fixed. —Preceding unsigned comment added by 88.104.237.107 (talk) 10:57, 17 June 2010 (UTC)

New Scientist article[edit]

There's an article in this week's New Scientist 'Junk' DNA gets credit for making us who we are which should be useful for references. Richerman (talk) 02:11, 21 March 2010 (UTC)

Junk DNA[edit]

Regarding this paragraph: "A large amount of sequence in these genomes falls under no existing classification other than "junk". For example, one experiment removed 0.1% of the mouse genome with no detectable effect on the phenotype. This result suggests that the removed DNA was largely nonfunctional."

I object to the suggested conclusion that the removed DNA was largely nonfunctional. Although I would not go the the opposite extreme and declare that all junk DNA is functional unless proven otherwise, it is very difficult to exclude all potential functions experimentally.

Even if the 0.1% removed DNA is not normally functional, it may still provide survival value in unusual situations and natural environments. For example:

1. Part of the removed noncoding DNA may cause increased production of an enzyme that detoxifies a protein in some food the mature female mouse can tolerate but is lethal to a fetus. Since this toxic protein was not in the labchow, this possibility was not excluded by the experiment.

2. Perhaps the removed noncoding DNA may cause altered behavior during exposure to environmental stresses that would cause infertility in mice that fail to alter their behavior. This would not be detected by protocols that do not include such stresses, or prevent such altered behavior, or do not test for effects on fertility.

3. Perhaps some of the noncoding DNA may provide antigen-like templates that enhance antibody immunity to pathogens that mice frequently encounter in a garbage pit, but not in a clean lab.

4. Similarly, perhaps some of the noncoding DNA provided antigen-like templates that cause colon cells to recognize normal flora as friendly and exempts them from immune attack.

I'm sure you can think of dozens of possibilities that were not excluded experimentally. Greensburger (talk) 05:30, 25 April 2010 (UTC)

For example, one experiment removed 0.1% of the mouse genome...[edit]

1% changed to 0.1% Paper abstract says "We deleted two large non-coding intervals, 1,511 kilobases and 845 kilobases in length, from the mouse genome". It's 2.3Mbp in total. Mouse genome length is ca. 2.5-2.7Gbp ( http://www.informatics.jax.org/mgihome/other/mouse_facts1.shtml ), thus only 0.1% was deleted. 89.251.107.8 (talk) 16:18, 29 August 2010 (UTC)

non-coding RNA[edit]

The article defines non-coding DNA as DNA which does not code for protein. If you are following this definition, then you have made some rather significant omissions (e.g. tRNA, snRNA, rRNA, telomerase RNA, etc). —Preceding unsigned comment added by 24.65.85.66 (talk) 02:53, 16 October 2010 (UTC)

Non-coding RNA has its own article...Not all non-coding DNA produces RNA (or non-coding RNA), so they're separate topics. Then again, most of the topics you list are discussed here, with links to individual articles. Did you bother reading the page? — Scientizzle 03:55, 16 October 2010 (UTC)

Junk Dna reins exposed:[edit]

The nice thing about scanning articles is that sometimes something really sticks. Ergo:

In a revealing experiment, a mouse was bioengineered to be deficient in one essential growth factor. It was kept alive by the inclusion of the missing 'element' in it's diet. After three generations an offspring produced AN ANCIENT FORM of this 'missing' enzyme that had and has THE ABILITY TO PRODUCE THE MISSING COFACTOR {Q. and this came from where? A. Junk Dna}.

When this can happen for this 'one [isolated] example', the same applies to all of the other 50,000 enzyme systems; meaning that the purpose of the content of Junk Dna is now clear, and that the phrase non-coding is at best erroneous, and at worst misleading. ~ Best Regards Betaclamp (talk) 06:38, 16 January 2011 (UTC)

Your conclusion is erroneous on a few levels. First, it is a hasty generalization to extrapolate the results of one study on one enzyme to the genetics of every enzyme. [Also, I couldn't find a citation for this study...care to share?] Secondly, while much of what is often called "junk DNA" (erroneously, and most commonly by the lay press who won't let the term die) is actually genetic information of as-yet-undetermined function, some of it does likely meet any reasonable definition of "junk". There are sequences (e.g., pseudogenes) that are without present function but can serve as the raw materials for future evolution--they might be imagined as the junk that was just thrown into the recycle bin and may serve future use! A huge portion of the genome, however, is made up of viral and mobile elements that, for the organism harboring said genome, very often do fit within the definition of DNA that provides "little specificity and conveys little or no selective advantage to the organism", as stated in the article.
In reply to "the phrase non-coding is at best erroneous, and at worst misleading", I have to object strongly. There's a rather simple delineation between a coding sequence and a non-coding sequence: the former produces a protein product, the latter does not. Many examples exist of important gene products that lack a protein endpoint (see noncoding RNA). Through mutation, a non-coding sequence can become a coding sequence (particularly those psuedogenes that have had an inactivating mutation reversed). "Non-coding" should not be inferred to mean "never capable of resulting in a coding sequence following selective pressure" and I don't think such an interpretation actually flows from the material on this page...if so, please point out the offending passages. — Scientizzle 16:27, 17 January 2011 (UTC)

20% verses 80%[edit]

"About 80 percent of the nucleotide bases in the human genome may be transcribed" but the reference article claims that about 90% of the transcribed yeast genome is non-coding, which translates to (100%-98%)/(100%-90%) = 20% of the human genome may be transcribed, not 80%. Mollwollfumble (talk) 16:37, 5 April 2011 (UTC)

ENCODE project[edit]

This page is probably 'junk' now lol needs some serious revision re ENCODE project....

Jinx69 (talk) 03:28, 7 September 2012 (UTC)

Roger that. Quoting from ENCODE Project Writes Eulogy for Junk DNA; Elizabeth Pennisi; Science 7 September 2012: Vol. 337 no. 6099 pp. 1159-1161 DOI: 10.1126/science.337.6099.1159:

"This week, 30 research papers, including six in Nature and additional papers published by Science, sound the death knell for the idea that our DNA is mostly littered with useless bases. A decadelong project, the Encyclopedia of DNA Elements (ENCODE), has found that 80% of the human genome serves some purpose, biochemically speaking. “I don't think anyone would have anticipated even close to the amount of sequence that ENCODE has uncovered that looks like it has functional importance,” says John A. Stamatoyannopoulos, an ENCODE researcher at the University of Washington, Seattle." and

"ENCODE drives home, however, that there are many “genes” out there in which DNA codes for RNA, not a protein, as the end product. The big surprise of the pilot project was that 93% of the bases studied were transcribed into RNA; in the full genome, 76% is transcribed. ENCODE defined 8800 small RNA molecules and 9600 long noncoding RNA molecules, each of which is at least 200 bases long. Thomas Gingeras of Cold Spring Harbor Laboratory in New York has found that various ones home in on different cell compartments, as if they have fixed addresses where they operate. Some go to the nucleus, some to the nucleolus, and some to the cytoplasm, for example. “So there's quite a lot of sophistication in how RNA works,” says Ewan Birney of the European Bioinformatics Institute in Hinxton, U.K., one of the key leaders of ENCODE"

Someone who understands the topic well enough to accurately preserve the historical sense of Junk DNA while correcting this article needs to have a go... Cheers - Williamborg (Bill) 17:50, 10 September 2012 (UTC)
I removed a good portion of this because its presentation mistakenly conflates "junk DNA" with noncoding DNA. I will continue to work in relevant pieces of the ENCODE findings. — Scientizzle 20:44, 10 September 2012 (UTC)
Appears to walk the middle while resolving some of the misimpressions this article created.

Keep up the good work - Williamborg (Bill) 04:22, 12 September 2012 (UTC)

Misinterpretation of ENCODE?[edit]

I know nothing about the subject, but reading online I see many claims that the popular media's representation of ENCODE's discoveries is skewed. The article's current version seems to mirror the media's. Can someone knowledgeable in this subject review this? Ratzd'mishukribo (talk) 20:12, 10 September 2012 (UTC)

Working on it. Many editors have conflated noncoding DNA with "Junk DNA". The former describes all DNA sequences that do not encode for a protein product, whether the sequences have a known function or not. The latter is largely a media-driven term that refers to the ever-decreasing proportion of the genome with no known--and no likely--function in the genetic regulation of an organism. There still is "junk DNA" to be sure: endogenous retroviruses, for example, are "junk" by any reasonable interpretation of the word. That the vast majority of noncoding DNA has known or likely regulatory functions, though, isn't really a surprise to modern geneticists. — Scientizzle 20:43, 10 September 2012 (UTC)
  • From Talk:ENCODE, a good link discussing this problem: Most of what you read was wrong: how press releases rewrote scientific history. Repeating myths may make good stories, but it breeds confusion. See the ENCODE news, John Timmer, Ars Technica, September 10 2012 — Scientizzle 21:27, 10 September 2012 (UTC)
  • Another similar link: Special AMA: The Encyclopedia of DNA Elements (ENCODE) Consortium on reddit. I like this quote from one of the ENCODE researchers, Michael Hoffman, task group chair (large-scale behavior) and a lead analyst (genomic segmentation):

    Part of the problem is that there are multiple definitions of "biological function" and "junk DNA." Things that are "functional" under some definitions are "junk" under others. It's especially worth noting that the definition of "junk DNA" used most often by the public and even by most scientists is different from the original definition used by evolutionary biologists.

    Under one definition ("reproducible biochemical activity"), the ENCODE Project Consortium found that 80% of the genome had function. If you use a definition based on looking only at regions of the genome under purifying selection, you might get as little as 5%. I feel like these are upper and lower bounds and that any other definition will be somewhere in the middle depending on what their threshold for "function" is.

    TL;DR: Between 5% and 80%, depending on how you define function.

    This was in response to a question from Larry Moran, who has been very critical of some of the ENCODE reporting.[1]Scientizzle 21:38, 10 September 2012 (UTC)

There are two sections at Talk:ENCODE rather relevant to this discussion. — Scientizzle 14:07, 11 September 2012 (UTC)

Thanks! Ratzd'mishukribo (talk) 17:56, 11 September 2012 (UTC)
ENCODE's theories have been debunked. They made the error of y failing to appreciate the crucial difference between "junk DNA" and "garbage DNA".

http://gbe.oxfordjournals.org/content/early/2013/02/20/gbe.evt028.short?rss=1 QuentinUK (talk) 12:24, 24 February 2013 (UTC)

Transcribing DNA to RNA consumes energy. Moving the transcriber proteins along the chromosomes consumes energy. Opening and closing the DNA double (or sometimes triple) helix consumes energy. Large amounts of "noise" activity is energetically absurd. And what about the missing inheritance? The argument used against ENCODE, that there would be too many fatal mutations if most DNA was not unnecessary, thus only shows that there must be function-sensitive genetic correction mechanisms multiple times more efficient than natural selection (genetic diseases cured by the organisms themselves by natural self-splicing outnumbering those eliminated by natural selection several to one).

95.209.69.116 (talk) 16:27, 6 May 2013 (UTC)

Unsourced statement in introduction[edit]

The Encyclopedia of DNA Elements (ENCODE) project[1] reported in September 2012 that over 80% of DNA in the human genome "serves some purpose, biochemically speaking".[2] This claim has, however been criticized by some in the genomics community.

No source. 184.153.187.119 (talk) 02:39, 15 October 2012 (UTC)


Now it seems the lead has been replaced with this:
"This conclusion however is strongly criticized by other scientists.[4][5]"
"other scientists" suggest criticism is widespread, when it looks like there is only a small handful of dissenters.
The ENCODE Project was researched by many more scientists than the 7 or 8 of article linked to. There are endless examples of biochemical function in diverse non-coding regions all throughout the scientific literature. This antiquated idea that most or any of the genome is still 'junk' seems to be much more of a Fringe view, and thus it is questionable whether their views hold any weight to be mentioned in the article. 184.153.187.119 (talk) 16:35, 24 February 2013 (UTC)
My impression is that there are large numbers of scientists who think that the ENCODE report overstated its results to some degree. They showed that over 80% of the genome is transcribed, but in the absence of evidence that the resulting RNA is biologically active, they didn't really show that all of this serves some purpose. Looie496 (talk) 16:51, 24 February 2013 (UTC)
See http://gbe.oxfordjournals.org/content/early/2013/02/20/gbe.evt028.short?rss=1 , full paper, free download, for a source QuentinUK (talk) 18:33, 24 February 2013 (UTC)
It seems that there are only a few scientists who disagree. I think the statement should be rephrased because it suggests wide-spread criticism when that's not the case. The criticism seems to come from the six scientists in the article above. ENCODE had 442 scientists working on the project. So how is a response from 6 scientists suddenly deserving of more weight? It certainly needs to be rephrased. --86.21.101.169 (talk) 14:30, 15 March 2014 (UTC)

Addition of Silencers[edit]

I added Silencers as a transcription factor site. I formatted it along with the other regulatory region sections. Clucaj (talk) 01:58, 26 April 2013 (UTC)

"Knowledgeable scientists" and lack of neutrality[edit]

My concern is with these excerpts from the article: "However, knowledgeable scientists have known for decades that many noncoding sequences are functional....No knowledgeable scientist ever said that all noncoding DNA was junk....The general consensus among knowledgeable scientists is that a large percentage of the human genome is junk DNA. Naturally, this junk DNA is all noncoding DNA but that does not mean that all noncoding DNA is junk."

The phrase "knowledgeable scientists" appears 3 times. Is it appropriate? What does that mean? I think this is meant to refer to an argument between certain scientists or factions of scientists. This approach seems to violate Wikipedia's neutrality principle

Also, consider especially the sentence "No knowledgeable scientist ever said that all noncoding DNA was junk." First, is that factually correct? I'm not sure about that. I believe some very esteemed research biologist have said that all or virtually all of noncoding DNA had no function. And, again, who are the "knowledgeable scientists" who've never said this, and who are the un-knowledgeable scientists who have said it? This needs to be made explicit, or the whole contentions issue should be dropped altogether.

And focus on this sentence from the article: "Naturally, this junk DNA is all noncoding DNA but that does not mean that all noncoding DNA is junk." This seems to be an argument that the writer is having with the Intelligent Design theorists. If the writer wants to add a section about how Intelligent Design promoters have used and/or abused the non-coding DNA issue to promote Intelligent Design and to attack mainstream scientific evolutionary theories, perhaps the writer should create a new section in the article to address that. As it is, I think this violates the neutrality principle of Wikipedia.Credidimus (talk) 02:58, 25 November 2013 (UTC)

It has been known for a long long time that there are almost always regions directly upstream from a start codon where transcription factors can bind. Those constitute functional noncoding DNA, and anybody who didn't know that would certainly not be a "knowledgeable scientist" in any meaningful sense at least regarding genetics. So I don't think the statements are inaccurate. But I agree that "knowledgeable scientist" is not a very good term. Looie496 (talk) 15:25, 15 March 2014 (UTC)

I totally agree with the lack of neutrality pointed out here. Don't just sweep this under the rug. Lehasa (talk) 14:16, 24 July 2014 (UTC)

Historical revisionism[edit]

There is a significant amount of bias and revisionsim in statements about junk DNA.

"Initially, a large proportion of noncoding DNA had no known biological function and was therefore sometimes referred to as "junk DNA", particularly in the lay press. However, it has been known for decades that many noncoding sequences are functional. "

  1. This was not "particularly in the lay press". I clearly remember scientific journals and biologists calling it junk DNA.
  2. Decades? too imprecise. I think this it ins only since 2000 that people have started to reevaluate the concept of Junk DNA.

"The term is used mainly in popular science and in a colloquial way in scientific publications and it has occasionally been suggested that its connotations may have delayed interest in the biological functions of noncoding DNA."

Again, this article is being revisionist and misleading. Back in the 1980s everyone believed that it was junk DNA and thus would not bother to really investigate it. There would be no research money for doing something like this. It is misleading to characterise this as something that non-scientists are doing to come up with a cute word that doesn't reflect the science community. It was indeed the term used by geneticists. Lehasa (talk) 14:14, 24 July 2014 (UTC)

Regarding your first point, "particularly in the lay press" and "I saw it one or more times in a journal" are not mutually exclusive. Decades is imprecise I agree, but the article cites (for example) this 1980 paper discusses a type of function for ncDNA, I expect 3.5 decades falls within most people's expectation for decades. I don't doubt the term "junk DNA" has in the past and continues to be used by geneticists. benmoore 18:50, 24 July 2014 (UTC)