Talk:Transposable element

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Transposons
i think the transposons in science section needs to be merged into the rest of the article. - Omegatron 04:53, Jul 12, 2004 (UTC)

Citations needed
I noticed the evolution section has many unsourced statements. Thinking a sweep through of the article to place some citations needed might be good.Dantose (talk) 23:10, 10 December 2015 (UTC)

Transposons and Retrotransposons
This article appears to have some confusion in description.

The leading paragraph distinguishes between "transposons" and "retrotransposons", highlighting difference in how they move from a position to another in DNA.


 * Transposons can move directly from one position to another within the genome, while retrotransposons have first to be transcribed to RNA and then back to DNA by reverse transcriptase.

The section "Types of transposons", however, states that the retrotransposon is a type of the transposon, leaving a question whether or not the retrotransposon should be regarded as a transposon.

Admittedly the section refers also to "Class II transposons" after "retrotransposons", and then readers may learn that what is called "transposons" in the leading paragraph should be taken as "Class II". But rewriting the description would make the article easier to read, I believe.--Toby (YebisYa) IQUEPPE 09:33, 2 May 2005 (UTC)

Not all DNA transposons use a "cut and paste" mechanism
For example, an E. coli transposable element, known as Tn1000 or gamma-delta transposes via a cointegrate structure which, after a process called resolution, results in a copy of the original element inserted in a new location.

--Phillip 01:58, 14 Jun 2005 (UTC)

Insertion element/sequence
After a quick search through this article and Wikipedia, I could not find discussion about insertion elements or insertion sequences. I would think this would be an important subject in the context of transposons, and it probably even deserves its own article. Am I correct in my conclusion that no such article/discussion exists or am I overlooking something?--GregRM 01:36, 1 December 2005 (UTC)
 * As far as I know there are no articles on prokaryotic insertion sequences yet, it'd be a great addition and would probably be best in its own article.--nixie 01:53, 1 December 2005 (UTC)
 * I started an article on insertion sequences. For the most part, my knowledge on the subject is limited to what I have read in a few textbooks and what I have learned in a few general classes.  Therefore, it would be great if people with more experience on the topic could expand the article, check for accuracy, etc.--GregRM 01:42, 12 January 2006 (UTC)

Class III
There seems to be a third class, consisting of transposons whose transposition mechanism is currently unknown (meaning that they will probably end up in Class I or II eventually). I may have misunderstood my GF's notes, of course. --Palnatoke 16:49, 26 January 2006 (UTC)
 * A long time ago I wrote on EvoWiki : Class III are Miniature Inverted-repeat Transposable Elements (MITEs): sequences of about 400 base pairs and 15 base pair inverted repeats that vary very little. They are found in their thousands in the genomes of both plants and animals (over 100,000 were found in the rice genome). MITEs are too small to encode any proteins. My reference was either Russel 2002 or Kimball's Biology Pages  or both. Joe D (t) 17:20, 26 January 2006 (UTC)

Is there any newer information concerning this topic? The german article still contains a section on MITEs, but I would like to have a more concrete source (something like a recently published paper...). Elatrin (talk) 21:26, 16 September 2008 (UTC)

Examples, especially Alu
Hello. In the examples listing, it is written that the Alu sequence is a big part of transposable elements in the human genome. I do not doubt this at all, several textbooks mention this as well - no problem with that. However had, it is also written this: "can be found between 300,000 and a million times in the human genome" and here I am confused. How can the number fluctuate as much? But the biggest problem, with this latter part, is that there is no source linked to this at all! So how can it be explained that there are either 300.000 or 1.000.000 copies of it in the human genome? The difference is huge - if Alu has 300 bp, then it means that a difference of 700.000 leads to 2.1 million more base pairs at maximum! Please, we need either an explanation, or a verifiable source for that claim. Otherwise, I would suggest to remove the latter part. The rest of that example seems fine, 300 bp length, and Alu being so often seen is fine. (PS: Actually, it may be useful to make a link from this to a page describing Alu in more detail, given that it is so often found in the human genome anyway.) EDIT: Sorry, my bad, there is already a link to the Alu page. However had my original claim still stands as it is, there needs to be a verifiyble source for the latter part. 84.112.136.52 (talk) 19:21, 15 October 2013 (UTC)

"Silencing of TEs" section
This section is useful but needs English and grammar help--it seems to have its own transposon :) at the end of its first sentence, acting like a transposon and destroying part of the meaning of the sentence. Something similar happens later, either in the last sentence or next-to-last.  I would take a stab at editing this section but my knowledge is very limited in biology.  This subtopic is important and should not be deleted, just repaired.LM6407 (talk) 02:50, 14 October 2014 (UTC)

"See also" section
I just added a "see also" section, but I wasn't sure about the policy on adding links that already appear in the article (e.g. I had considered adding P element, Transposons as a genetic tool, Retrotransposon, and Transposase). I could not find any definitive policy on this in the style guide after a limited search. If you think they are appropriate, let me know, and I can add them in.--GregRM 03:57, 29 January 2006 (UTC)
 * As a general guide, there is no reason to include links that appear in the article as a see also section, it duplicates existing information, and increases the lenght of the table of content and page for no real gain.--nixie 22:32, 29 January 2006 (UTC)

A Few things - title, content, and classification
I think the page itself should be renamed to mobile genetic elements, because the classes given in the section don't refer to classes of 'transposons,' but rather, transposable elements of DNA. Class I should be RNA-based elements (because class I are the elements that transpose via a RNA based intermediate, while class II are elements that transpose through a DNA intermediate), which includes retrotransposons and retroviruses (and telomerase which likely evolved from the RT in the LINEs?), as opposed to 'retrotransposons'. Similarly, Class II is also incorrectly named because it refers to DNA based transpositions, which includes the insertion elements also mentioned in this discussion, as well as transposons and phages. Also, as mentioned, DNA based elements can also use a copy and paste based mechanism. As well, the classification of the RNA-based elements is incorrect. It should be grouped into LTR and non-LTR elements. And in the non-LTR elements section, it's classified as SINE or LINE. That's the way they teach it nowadays anyway. Furthermore, both RNA and DNA-based elements can be classified based on whether they are autonomous or non-autonomous, that being whether they encode all the enzymes required for transposition (autonomous) or are still functional if the missing activities can be provided by other elements (the autonomous ones). This makes will clear confusion regarding SINEs and LINEs too since LINEs are autonomous, while SINEs are non-autonomous and depend on machinery encoded within SINEs, which is also reflected by their respective sizes (6-8 kb for LINEs; 100-300 bp for SINEs). --Alan C 06:15, 24 April 2006 (UTC)

Missing Prokaryotic Transposoable Elements
An entire prokaryotic transposon section is missing. Terms like composite transposons, inverted repeat sequence, simple transposons, target site duplication, replicative transposition, and conservative transposition should all be included in that section. --Matt E

Prokaryotic transposons
This edit seems to suggest that all prokaryotic transposons are insertion sequences. I was under the impression that insertion sequences only contained genes for their own transcription, which seems to contradict the articles' apparent claim that insertion sequences contain additional genes. Is this an issue of nomenclature or is this section wrong?--GregRM 21:25, 30 June 2006 (UTC)
 * Update: I tried to correct the description of insertion sequences. If you disagree, feel free to discuss here.--GregRM 01:17, 13 July 2006 (UTC)

Transposons Role in Evolution
Maybe someone more familiar with editing wiki can address this, but I believe there is siginificant evidence that transposons accelerated evolution "http://www.hhmi.org/cgi-bin/askascientist/highlight.pl?kw=&file=answers%2Fgenetics%2Fans_029.html"--192.147.58.6 (talk) 18:25, 11 January 2008 (UTC)

Here is another story about transposons entering mammals, teh hAT (hobo/Activator/Tam3) superfamily. Do we need a list of transposons? Graeme Bartlett (talk) 01:53, 23 October 2008 (UTC)

I think it is important to address the reasons why transposons exist in the first place and why they themselves developed to play a role in DNA modification. —Preceding unsigned comment added by 128.220.212.158 (talk • contribs) 15:54, 29 October 2008

80 years ago in cancer research
This unsourced assertion from 2007 that retroviruses were first identified 80 years ago in cancer research seems dubious to me. That would have been 1927, which was a l-o-n-g time ago in medical research. (Penicillin didn't start initial clinical trials for another three years, and it was another 15 years before it was marketed... and 17 years before it was readily available.)

If this seems as dubious to other editors as it does to me, then perhaps we should remove this sentence. WhatamIdoing (talk) 20:37, 20 November 2009 (UTC)

Ty elements redirection
Just a technical note: In an article, there are two functional links to Ty elements type. Ty5 redirects correctly, but Ty2 links to PKP class Ty2 locomotive. Sadly, I am not able to make Ty 1-5 pages, because my knowledge on this topic is rather limited. Is it possible to correct that redirection somehow? Thanks Faskal (talk) 19:47, 20 January 2010 (UTC)

Merge
I believe that mobile genetic elements = transposable genetic elements = transposable elements = transposons. Therefore I think that there should be one page that has one of the names I mentioned. This means this page and the page named 'mobile genetic elements' should be merged. --Zaluzar (talk) 13:32, 27 January 2010 (UTC)


 * Partly no, for instance "plasmids" and "integrons" can be described as "mobile genetic element" but they are not "transposable elements".
 * However, I am happy that you proposed to rename this page ;) Indeed, it would be much better to rename this "transposon" page into "transposable element". Indeed, the scientific community uses "transposable element" (abbreviated in "TE") and then distinguishes "class I TEs" (that move via an RNA intermediate, among those the LTR retro-transposons and the L1 LINEs), and "class II TEs" (that move via a DNA intermediate, among those the DNA transposons).
 * To see why "transposable element" should be used rather than "transposons", please have a look at this article: Biemont, C. A brief history of the status of transposable elements: from junk DNA to major players in evolution. Genetics 186, 1085-1093 (2010). Look also at this article: Wicker, T. et al. A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics 8, 973-982 (2007).
 * Therefore I propose to rename this "transposon" page into "transposable element", knowing that a redirect from "transposon" to "transposable element" will be automatically created. What do yo think?
 * Wfoolhill (talk) 04:10, 27 April 2011 (UTC)

More info
Probably too early for use in this article, but relevant:

http://www.sciencedaily.com/releases/2011/09/110906161634.htm

"Jumping Gene's Preferred Targets May Influence Genome Evolution"

-- -Jo3sampl (talk) 13:09, 8 September 2011 (UTC)

transpoviron
" they found an independent stretch of DNA inside Lentille virus that outnumbers the giant virus’s own DNA by as much as 14 times and can insert itself into the virus’s genome or stay outside of it. Mobile pieces of DNA have been found in giant viruses before, but Raoult saw this as a new type, one with similarities to the transposons that jump in and out of the genomes of living cells. The researchers dubbed the new mobile element a transpoviron."

http://www.the-scientist.com/?articles.view/articleNo/32840/title/A-Parasite-s-Parasites/

new discovery — Preceding unsigned comment added by Vmaldia (talk • contribs) 15:50, 16 October 2012 (UTC)

"TEs are more common than usually thought. "
This sentence is meaningless. How common are they usually thought to be? Who thinks they are not common? 87.102.44.18 (talk) 17:53, 8 January 2015 (UTC)

I deleted the sentence, since I agree with you. It didn't add any information.Ilikelifesciences (talk) 13:33, 1 September 2015 (UTC)

Reference cross check
I read over the information and cross referenced it with the sources. There are no gaps and everything is represented properly. -Neha Agnihotri

Section clarification needed
Hi the section Transposable element needs clarification. I don't understand the grammar. It was added in this edit. Invasive Spices (talk) 20:07, 3 August 2021 (UTC)

Positive effects
This article needs a positive effects section. There is a throwaway mention that many exist, in the middle of the section on negative effects! Cl ea n Co py talk 16:41, 27 November 2021 (UTC)

Disagreement in percentage of maize genome composed of TE
At the beginning of the section titled "Distribution", the maize genome is described as being 64% composed of TEs.

The first bullet point in the "Examples" section, the maize genome is described as being 85% TEs. — Preceding unsigned comment added by Lemmagene (talk • contribs) 00:27, 5 March 2022 (UTC)


 * Thanks for catching that. The 85% figure is based on a poorer-quality genome. The 64% figure comes from a more recent study using an improved sequencing technology. I replaced the 85% figure with 64% and added the appropriate reference. CatPath   meow at me  07:45, 5 March 2022 (UTC)

Transposon-related sequences
Most large eukaryotic genomes consist of large amounts of sequences that are the descendants of once active transposons that have acquired mutations, deletions, and insertions. These transposon-related sequences don't really qualify as transposons, per se, because they are fossil remnants. They are part of the non-functional portion of those genomes - often called junk DNA.

This important fact needs to be described and explained in this article. It is a significant part of the story on genome evolution and it relates to nearly neutral theory and the effect of population size on genome evolution. Genome42 (talk) 21:04, 7 March 2023 (UTC)