Talk:Retrotransposon

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Statistics

Because this area is still developing, estimates for various statistics are likely to change. Right now, I'm adding {{fact}} for all statistics. I don't dispute them, but I do think it is important to cite them. Later, I'll fill in when I can easily find numbers, but I fully expect them to be out-of-date and encourage you to find better ones (along with their citation). — Preceding unsigned comment added by TedE (talk • contribs) 18:57, 22 April 2006 (UTC)[reply]

Source for statement?

"This translates to millions of elements, so that on average, every gene in our genome contains around 3 retrotransposons."

This statement doesn't make sense as written, and lacks a source. Anyone have an idea where it came from? Agathman (talk) 16:54, 3 April 2008 (UTC)[reply]

Difference between Retrotransposon#LTR_retrotransposons and endogenous retrovirus?

I've heard a version where retrotransposons containing LTR and endogenous retroviruses are one and the same thing. Personally I can't see the difference. I would appreciate if somebody make the difference clear in the text, or write that they are the same thing.Mortsggah 07:47, 7 April 2007 (UTC)[reply]

I think retroviruses are active while LTR Retrotransposons look more like 'dead' retroviruses that arnt actively jumping around Inoesomestuff (talk) 23:50, 6 April 2009 (UTC)[reply]

Retroposon

LINEs are not "LTR-retrotransposons"- this is a misconception brought on from one researcher being too incompetent to properly review the literature about his own field of study- then people repeating it because this particular researcher was arrogant enough for other people to believe him. Anyone who continues this misconception should be shot. —Preceding unsigned comment added by 153.90.236.124 (talk) 19:52, 2 November 2007 (UTC)[reply]

currently there is no article on LINEs on wikipedia. Someone knowledgeable should add a section back in. The section got deleted on 10 October 2008 by 132.216.66.53 Inoesomestuff (talk) 21:26, 22 April 2009 (UTC)[reply]

i love retrotransposons —Preceding unsigned comment added by 81.155.75.129 (talk) 18:36, 4 January 2008 (UTC)[reply]

portion of the human genome composed of retrotransposons

I'm reading here that roughly 17 percent of the human genome is composed of retrotransposons, not 42%. Can someone check me on this?

Source: Purves et al. Life: the science of Biology. Sinauer Associates, Sunderland, MA 2004.

Greenchilefrog 17:30, 8 April 2007 (UTC)[reply]

The Lander et al. (2001) reference cited by this article claims that "about half of the human genome derives from transposable elements". Specifically, [figure 17] in this publication indicates that the actual fraction is 45%, and "DNA transposable fossils" contribute 3% toward that figure. This substantiates the 42% retrotransposon fraction.

SteveChervitzTrutane 01:56, 17 May 2007 (UTC)[reply]

The 17% figure comes from the portion of the genome composed of LINE-1 retroelements, the reverse transcriptase/endonuclease protein of which is responsible for the retrotransposition of the non-autonomous classes (Alu, SVA) which are responsible for another large portion of the genome. In combination the figure is probably something like 42%. 69.139.19.169 02:27, 24 October 2007 (UTC)[reply]

There are several families of transposable repetitive elements. This article collectively calls them retrotransposons, and indeed several scientific articles agree with this definition. Searching a bit deeper, however, one finds a much more comprehensive and clarifying classification of these elements, whereby retrotransposons are only one class of them. According to this classification, proposed numerous times by scientists Brosius (an expert on the matter) and Stephen Gould, and followed by many other scientists specialized in this subject, all these elements are collectively referred to as retronuons. I am considering a thorough revision of this wikipedia article. I have made extensive research of the subject and the article seems to me very superficial and inaccurate. I won't do this until after a couple of months so that I finish my research and if someone has an objection to this s/he can say so here; I understand that wikipedia articles are not only for "specialized" people, so its articles must sometimes be written in a way that seems inaccurate to the "specialists". What I mean is that if someone objects my revision, then I won't go ahead. —Preceding unsigned comment added by Enkostek (talk • contribs) 13:17, 12 June 2010 (UTC)[reply]

LINE and SINE acronyms

In the edit history of this article, the acronym expansion of LINE and SINE has alternated between "Long (Short) INterspersed Elements" and "Long (Short) Interspersed Nuclear Elements". Either form is reasonable. I have a feeling that the "Nuclear" option may well be a later formation (a partial Backronym) by the tidy-minded (since in this context "nuclear" adds no useful information to the description). Can anyone cite appropriate primary sources to establish priority between these forms (i.e. which was used / published first)? FredV (talk) 07:57, 10 June 2011 (UTC)[reply]

Interesting question, I merely replaced the nuclear following an IP edit without giving it much thought. A crude pubmed search gives 1144 in favour of Interspersed elements and 277 for Interspersed nuclear elements (I don't think that its usage should be wholly dictated by which was published first). Nuclear may well be a later addition; I confess that when I replaced it, I missed the IN in interspersed Jebus989 ^✰ 10:28, 10 June 2011 (UTC)[reply]

I agree with you on usage - if the majority of the expert community involved has changed their standard usage, that is what Wiki should follow (perhaps noting the historical version as an alternative.) However, like you I found significant current usage of both forms, as well as occasion usage of "Nucleotide" for the N (and also L / S INterspersed DNA Elements - with the DNA presumably suppressed from the acronym). As a non-professional in this field, I will leave it to others to decide what the article should record, though I personally would prefer at least recognition of both principal forms. FredV (talk) 10:41, 10 June 2011 (UTC)[reply]

I am not sure how to go about this explanation, however as a researcher in this field, over the years I have come to be dismayed by the people who have been misinformed about the nomenclature of these repetitive elements. The first characterization of these elements was of SINEs. Upon their discovery, they were named "Short INterspersed Elements" (with no nuclear). When LINEs were discovered, they were named in the same style "Long INterspersed Elements". The insertion of the word "nuclear" into the name of the elements came from one researcher who published out of his original field of expertise and has (unfortunately) caught on with a small number of people who are writing papers in this ever-expanding field. In fact, the majority of the labs that are considered the experts in the field of human mobile elements (Haig Kazazian and Jef Boeke at Johns Hopkins, John Moran at U. Michigan - Ann Arbor, Prescott Deininger at Tulane, and Mark Batzer at LSU) will all agree that the acronyms S/LINE stand for Short/Long INterspersed Element. I hope this clarifies this some. — Preceding unsigned comment added by 129.81.183.235 (talk) 13:47, 10 June 2011 (UTC)[reply]

Not that I think it has any real relevance to the content of the article, but in fact, the names LINE and SINE began with the discovery of SINEs and their naming by Maxine Singer. She called these short interspersed repeats "short interspersed elements (SINEs)". Later, longer stretches of repeats were discovered and they were called "LINEs" to match the naming paradigm of the SINE world. In fact, the name "LINE" came before the name "long interspersed element". Recently people have added the word nuclear to both names to make the acronyms make more "sense". — Preceding unsigned comment added by 67.86.38.170 (talk) 16:06, 29 December 2012 (UTC)[reply]

I absolutely agree about the origin of the acronyms, however I disagree that the addition of the nuclear makes more "sense". While it may make the acronym itself seem like it makes more sense, it convoludes the biology of the retrotransposons with an implication of something "nuclear". — Preceding unsigned comment added by 129.81.247.101 (talk) 21:07, 23 May 2013 (UTC)[reply]

Edit Request

Can someone replace the word "recently" with dates? The word "recently" is used repeatedly throughout this article. Anyone with any sense should realize (especially given that the last addition/edit to this talk page was in 2013 and it's now 2016) that the word "recently" has no place in an encylcopedian's vocabulary. How can a reader possibly know when that particular sentence was written?? Obviously, we can't. Also, I am changing the clause "99.9% of which is no longer capable of mobilization" found in the LINEs section to "99.9% of which is no longer capable of retrotransposition, considered 'dead'" based on that language in the reference given, and the fact that "mobilization" has no clear meaning here.Abitslow (talk) 17:52, 23 March 2016 (UTC)[reply]

LINE vs. L1

The section on LINEs states them as "comprising 17% of the human genome (99.9% of which is no longer capable of retrotransposition, and therefore considered "dead" or inactive)". First, this is ambiguous. What is the antecedent of the word "which" here? The human genome or the LINEs? More importantly, according to the sources, the 17% (repeated later in the section) and the 99.9% are specifically for L1 elements. Our Long interspersed nuclear element article gives 21% for the combined contribution of L1, L2 and L3 elements to the human genome, and if I understand the literature correctly, fully 100% of L2 and L3 elements are not retrotransposition-competent. --Lambiam 08:33, 17 March 2018 (UTC)[reply]

Section on replicative transposition is a fragment

There's a section that contains only a sentence fragment and no citation, as follows:

Replicative transposition

Using Tn3 plasmid as a model

This was introduced in April in a series of edits by User:Pizzanotsinkships. I don't know if it should be expanded or removed - I've tagged it. Fences&Windows 12:03, 6 October 2020 (UTC)[reply]

Volition on the molecular scale??

In LNEs "ensures LINEs can be copied into whichever location it decides to insert itself into." Not my area so I don't know how the point of insertion arises, but I do not accept a decision has been taken by the not-a-virus involved. Midgley (talk) 01:38, 28 December 2020 (UTC)[reply]

I really don't like much the wording either, but "decision" does not necessarily imply volition, being somewhat of an anthropomorphic or zoomorphic figure of speech for processes where one agent or system proceeds in a non-random manner according to internal variables. Whenever possible I'd rather have wordings that are as succinct as possible while avoiding such figures of speech, though. Unfortunately it's not always very easy to find such alternative, it's easy to end up more prolix and maybe even pedantic. 45.167.98.146 (talk) 07:17, 5 April 2024 (UTC)[reply]

Regarding the speed of retrotransposon amplification in number

The article states "retrotransposons amplify in number quickly, composing 40% of the human genome." This proportion of the human genome mentioned following the "it's quick" statement doesn't really provide any kind of reference to measure how "quickly" it happens. It can be the case that most retrotransposos in the "human genome" are inherited from a common ancestor with other apes, all primates, or even further back. Maybe quick if compared to fish-to-human evolution, but not for non-bat-mammal-to-bat evolution, I guess. If most retrotransposons in the "human genome" are indeed not exclusively human, one could well also make the statement, "retrotransposons are slow to grow in number, most retrotransposons in a species are inherited from distant ancestors, and shared by several related species, in quite similar numbers." If those are mostly exclusively human, though, then that's perhaps close to what the common person would think as "quickly" in evolutionary scales, then it would be interesting perhaps to have a list of some time estimates for different retrotransposon amplifications in human populations. 45.167.98.146 (talk) 07:07, 5 April 2024 (UTC)[reply]

Yes, this statement doesn't bear too much sense, I'll edit it out later. Blosum62 (talk) 14:14, 3 May 2024 (UTC)[reply]

Empty Role in biotechnology section

There's this empty section that was apparently created in 2021. Being in the field for some years I've never heard of plans to use LTR retrotransposons in biotechnology, unlike DNA transposons which have been used for decades. I propose to delete the section altogether. Blosum62 (talk) 14:17, 3 May 2024 (UTC)[reply]

Cite spam in the intro

The introduction contains weird paragraph on piRNA pathway, which makes little sense in the context and referring twice to a paper that has little significance to the subject. Examining other edits by the user (this paragraph was added on February 5th, 2022) I found that their edits mostly comprise of adding citations by the same authors. I'm removing this paragraph altogether, but maybe it would be nice to add a section about host defense against retrotransposons which would include piRNA pathway and KRAB-Zinc finger proteins. Blosum62 (talk) 14:31, 3 May 2024 (UTC)[reply]