Talk:RNA interference

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The subject of the 2006 Nobel Prize in Physiology or Medicine - absolutely should be an FA. – ClockworkSoul
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Contents

[edit] older entries

The article should explain which organisms use RNAi. All eukaryotes? Only eukaryotes? AxelBoldt 02:38, 12 February 2006 (UTC)

RNAi is due to a conserved mechanism in nematodes, insects, plants and mammals. These are the organisms I know of, not sure of others. Xanin 19:24, 17 April 2006 (UTC)

Removed Link Directory Spam Bioinformin

[edit] Knockout

I do not like the use of the word "knockout" to describe RNAi in this article:

RNAi has recently been applied as an experimental technique to "knockout" genes in model organisms for experimental analysis in determining the function of a gene.

RNAi is not knockout. I have only ever heard knockout used to describe permanent genetic modification. Knockdown is the term that is used for RNA interference universally. Peter Znamenskiy 19:18, 7 June 2006 (UTC)

Completely agree - knockdown is correct terminology Goldfinger820 03:57, 8 June 2006 (UTC)

You are absolutely correct. Nobody uses the word "knockout" to describe RNAi.

[edit] Merge

I was under the impression that RNAi, antisense RNA and miRNA too are all different things (with overlap of course). --Rajah 20:47, 27 June 2006 (UTC)

Here's a good reference showing the two are different: [1]. I don't mind if the articles are merged, I just think that it should be pointed out that antisense RNA and RNAi aren't necessarily the same thing. --Rajah 21:05, 27 June 2006 (UTC)

RNAi is a completely different biological pathway. Although the down stream mechanism of silencing in both antisense and RNAi involve sequence-specific post transcriptional targeting of mRNA for degradation, the celluar machinary used to trigger them are wholly disimillar —The preceding unsigned comment was added by 129.81.15.58 (talk • contribs) 14:14, 19 July 2006 (UTC)

[edit] rnaiconception.com

That is not an appropriate link for this page, and repeatedly restoring it without discussion is inappropriate as well. The link is to a personal advocacy site related to an obscure authorship dispute that is irrelevant to the general discussion of RNAi presented here, and the inclusion of only one disputant's opinion on the matter is a violation of the neutral point of view policy. To the anonymous user who has repeatedly inserted this link, please do not do so again, especially not without discussion. Opabinia regalis 23:48, 21 July 2006 (UTC)

I disagree. I think to call the site an "obscure authorship" dispute is dishonest. The author of "RNA interference page" credits and singles out Craig Mello and Andrew Fire as the discoverers of RNAi by name, and yet when a link is presented to the readers with the possibility that Craig Mello and Andrew Fire may have committed an intellectual fraud and thievery to credit themselves as the conceivers of RNAi (based on their own inconsistent stories of conception; the entire website is dedicated to what led Mello et al and Fire et al to the recognition that the key interfering agent mediating RNAi was/is indeed dsRNA molecule, not about authorship dispute as the editor claims), the readers should be allowed to read upon an alternative and factually disputed assertion detailed in the website. I think, ‘Mr. Editor’ should not deprive his readers of this 'controversy' or at the very least explain why he implicitly portray (by name) Craig Mello and Andy fire as the real co-discoverers of RNAi, if the page were dedicated to a "general" discussion of RNAi. Why leave out the thousands of other equally worthy scientists who ultimately contributed to the discovery of RNAi???? Mention their name too. Let me know if you need help with names. Plus who are you...more relevantly what makes you the self-proclaimed “RNA interference historian” in any case?—The preceding unsigned comment was added by Mussaali (talk • contribs) 20:32, 23 July 2006 mussa ali (UTC)

Thanks for coming to this page to discuss these changes. Mello and Fire are the commonly recognized discoverers of RNAi and claiming otherwise based on your personal analysis or involvement with the case violates Wikipedia policies on original research and verifiability. The dispute itself seems not to be covered by any independent and reliable source outside of your website, which I'm sure you understand is not admissible as a source due to your personal involvement. Until and unless the scientific community independently recognizes other individuals as key discoverers of RNAi, the accepted attribution should remain in the article.
Mello and Fire's labs were the two involved in the discovery, so it's not surprising that "credit" goes to them. Attribution that included every postdoc, grad student, and lab tech in either lab would be unwieldy and frankly unlikely, here or in the scientific literature. Opabinia regalis 01:14, 24 July 2006 (UTC)

Since you are the self styling RNAi historian, I think I am dying to know who you are. Are you friends of Mello and Fire? Have you done any work with RNAi before its conception. I agree with you a key recognition was published by mello and fire in 1998. And since you went to the trouble of highlighting that "historic eureka moment" any 'controvery' surrounding it is a fair game. Don't you think? Otherwise the self proclaimed historians would be having a field day and pushing a personal and biased history down everybody's throat as the true history. mussa ali

"Mello and Fire are the commonly recognized discoverers of RNAi"?? I think you should rephrase that to read as Craig and Andy are commonly extolled for having disclosed a key RNAi finding in their lab. Do you know that Craig Mello had stated publicly that he has “discarded” the original RNAi notebooks. That is a public record and verifiable. I bet in your eyes this is completely irrelevant! I will have more to say....later mussa ali—The preceding unsigned comment was added by Mussaali (talk • contribs).

I'm not an "RNAi historian", nor do I personally know Mello, Fire, or anyone else involved. I have worked a bit with RNAi in the past but don't at the moment. Also, I didn't originally add the text attributing the discovery to Mello and Fire, but since it is the accepted attribution I believe it should stay in the article. Notice that the article doesn't say anything about "eureka" moments; it only states that the two labs in collaboration were the first to notice (and publish about) dsRNA-mediated silencing in C. elegans - which is true regardless of who knew what earlier. mussa ali
Secondly, your personal experience of what did or did not occur at the time is not an acceptable source for this article, especially if your retelling has not been published outside of your website. has there been any external, third-party coverage of this inventorship dispute? As in, a news brief in a journal about the court case(s), or something to that effect?
(Off the subject, just FYI - you can sign your comments with four tildes (~~~~) and indent them by beginning each paragraph of your comment with a colon. Makes threaded discussions easier to read.) Opabinia regalis 06:35, 24 July 2006 (UTC)

Enough about the rnaiconception.com website issue…

Let’s look at your loose use of the word “noticed”. Since you weren’t there in either Mello’s or Fire’s lab, you do not have or ever had a first hand knowledge of who may have “noticed” it first. i.e., assuming by “noticed” you mean to infer “recognized” or “conceived.” (If you need a more direct Mello audio back up? Let me know…) mussa ali

More relevantly, (I am generously assuming that you have some RNAi background, and I encourage you to read my perspective on the competing RNAi-induction models), your use of the word “noticed” may be mechanistically flawed. Assuming Fire’s paradigm is correct, that is a dsRNA contaminant (unbeknownst to us at the time) was sufficently inducing RNAi in C. elegans, the first group to have “noticed” or observed dsRNA mediated interference in C. elegans was that of Dr. Kempheus group at Cornell in 1995. (For starters, You should hyperlink Cornell and Dr. Kempheus too). mussa ali

As such I think you should replace the word “noticed” with “reported”. mussa ali

Again you should let your readers know who you really are at least in terms of your scientific credentials and just as relevantly your affiliations(s)…..before you start deleting other people’s website with shameless pomposity. mussa ali—The preceding unsigned comment was added by Mussaali (talk • contribs).

My personal opinion is that the RNAi Wikipedia page reads more like a promotional advertisement for University of Massachusetts and the Carnegie Institution of Washington masquerading as the brief history of RNAi. You should do much better ... Mr. Historian. —The preceding unsigned comment was added by 209.16.74.251 (talk • contribs). mussa ali
FYI, and if you ever noticed, almost everything on the rnaiconception website (http://www.rnaiconception.com/inventionofrnai-2006.pdf) is supported by published documents and extensive third-party corroborations. In fact I invite or challenge you to read it thoroughly and critique it. Do not be afraid to ask me any questions you may have. Again, my gut tells me you are a spokesperson for Mello and company masquerading as an HISTORIAN. Who are you... since you are the historian, editor, site manager etc who are you???? —The preceding unsigned comment was added by 70.183.113.24 (talk • contribs). mussa ali
Since this is starting to get petty is anyone going to acknowledge plant science contributions to all this? I suppose it is possible that all the C. elegans researchers reinvented the wheel. But who cares when the proof of concept was already known? David D. (Talk) 20:27, 24 July 2006 (UTC)
David D. That is actually a very interesting point. But, I just need to finish off this RNAi historian's/expert's pompous viewpoint that is patently flawed. I agree the conversation has gone petty.—The preceding unsigned comment was added by Mussaali (talk • contribs).

It is time to remind the people posting here to be WP:CIVIL. Personal attacks are never appropriate.TedTalk/Contributions 00:10, 25 July 2006 (UTC)

Well, this has exploded since I was here last. Mussa, your point about the usage of "noticed" is fair, and it's been clarified. How it can be an ad, though, is beyond me - Mello, Fire, UMass, and the Carnegie Institution collectively get one mention in one sentence at the end of a section that is primarily about plants. Opabinia regalis 00:57, 25 July 2006 (UTC)

Although I have many issues with the website, I thank you for fixing one of its major flaws. Appreciate it. —The preceding unsigned comment was added by Mussaali (talk • contribs) 21:58, 24 July 2006 (UTC)

By way of closing, and assuming that the editor of this page has no ulterior motive(s) and or is not (or has ever been) C&A's friend and was not engaging in a tacit C&A promotional exercise, I want to apologize for some of the comments I have made. I think I may have gone a bit overboard. I also would like to commend the editor for the significant changes that have been made to the original version of this page, which was the genesis of my contentions.

I can't speak for the other contributors to this article, but I don't know and have no connection with any of the people involved. I'm glad this was resolved and I'm sure you could make valuable contributions to this and related articles if you decided to stick around. Opabinia regalis 04:12, 17 August 2006 (UTC)

Mussaali I have removed the conversation on this page that had nothing to do with RNAi. If you feel the need to continue this conversation please continue on Opabinia regalis' talk page. David D. (Talk) 02:51, 30 September 2006 (UTC)

This is a note to ‘Ted’ and ‘O. Regalis’: I have heard it through the grapevine that you guys are unrelentingly impugning me and letting your comments--which in my opinion reads more like a poorly scripted hate speech than a truly scientific analysis of RNAi and how it was discovered--appear prominently when one googles mussa; keep on spewing. O.R: you may have a point when you indicated that I may have not included (at www.rnaiconception.com) what the other side may be saying by way of response; so I will include documents which reflect the other side’s stand: which really is stonewall, stonewall and further stonewall. I have also included a downloadable conception audio link.

At the end of the day, the truth will perdure. Given the convoluted history of RNAi....just remember guys that the Fire-Mello published work is worthy of note because of the key Recognition --and validation of such ---that dsRNA is the key molecule mediating RNAi.

[edit] Question

"RNAi is distinct from other gene silencing phenomena in that silencing can spread from cell to cell and generate heritable phenotypes in first generation progeny when used in Caenorhabditis elegans." This sentence is in the introduction. There is nothing relating to this sentence in the main text so we need a section on the systemic nature of RNAi silencing. But first, what are the "other gene silencing phenomena" being referred to here? I assume X-inactivation, imprinting and heterochromatin. Or is it something else? David D. (Talk) 06:17, 26 July 2006 (UTC)

I added a brief mention of the organisms in which RNAi is and is not systemic, but I'm not convinced the lead is really clear. I also think that, after splitting up the overview section, the new section order is a little out of whack. What do you think? Opabinia regalis 00:55, 29 July 2006 (UTC)

[edit] Request for addition of other organisms

Specifically, Trypanosoma cruzi, in which (I've been told) "post-transcriptional gene silencing" was about as thoroughly charactertized at the time of the Fire/Mello paper as it was in pentunias and worms. Probably deserves mention under Cellular Mechanism and History.Og0709 13:28, 2 October 2006 (UTC)

[edit] Removal of inappropriate addition

I have removed the following text that had been recently added by Xuanwu, since it is an inappropriate and subjective editorialization:

"Mello and Fire's research was directly based on the work of a team lead by two Indian scientists, Dr. Utpal Bhadra and Manika Pal Bhadra. Together with a third researcher, Dr. Jim Birchler, they described gene silencing in animals in a Cell article published in 1997, a year before Fire and Mello's landmark paper.[3] According to Dr. Bhadra, "The work of Andrew and Craig is based on the research of my team from University of Missouri." [4]"

The Bhadra et al. 1997 Cell paper makes an interesting demonstration in an animal system (Drosophila) of the phenomenon of cosuppression, as it was known at the time, albeit without providing much mechanistic insight into the process responsible. This phenomenon had previously been observed only in plants and fungi, but although Bhadra et al. showed that it existed in animals, the phenomenon remained puzzling and unexplained.

The real breakthrough in this field was provided by Fire and Mello in their 1998 Nature paper. Working in C. elegans, they made the crucial demonstrations that (1) gene silencing depended on duplex RNA containing sense and antisense strands homologous to the target mRNA; (2) gene silencing mediated by dsRNA was specific and could be used as a general tool for gene silencing; (3) dsRNA-mediated gene silencing appeared to be catalytic, suggesting the existence of an endogenous enzymatic mechanism for this process.

The work of Fire and Mello was performed in an entirely different system from that of Bhadra et al. and was really entirely unrelated, other than the fact that the effect described by Bhadra et al. may have had a similar basis. In fact, the Fire and Mello paper was a direct extension of several earleir papers on RNA-mediated gene silncing from Fire's group. If the Bhadra et al. observations were indeed a manifestation of RNAi, their data suggesting a dependence on polycomb group proteins is curious, since their is no known role for this protein family in RNAi. Ve ri tas 06:31, 5 October 2006 (UTC)Ve ri tas

I'll start by saying I have no personal stake in whether the references I added remain. I added them because they meet the criteria for inclusion in Wiki: 1) they are from reliable sources, 2) the statements in terms of Bhadra's work in RNAi are conclusions made by secondary sources (so they're not original research), and 3) and they're relevant to the topic at hand (RNAi history). Since my lines were summaries of what had been published in those newspapers, they were not editorializations.
I understand your points for disagreeing with what the newspapers said. However, I have to ask: do you have an article that you can cite that says what you said above? Remember, a Wiki editor's own analysis of a conclusion's worth is original research and not usable in Wiki. What I entered presented analyses from third parties (the two newspapers) that say Bhadra inspired Mello and Fire. In order to refute it, you must provide a counter viewpoint from a secondary source. In other words, even if you've read the research papers in question (and I think you have), you can't use your own analysis as a reason to remove it. This is similar to Wiki articles on historical and political topics: a Wiki editor can't (or at least, shouldn't) delete a conclusion published in a reliable source when it's been added to the article, but they can cite a reference that disagrees with it and state, "while some say A, others say B for these reasons."
As I said, I agree with your analysis of their work, but you can't remove accounts written by other people based solely on your analysis. It doesn't agree with Wiki policies. Here's what can be done to resolve the situation in accords with Wiki guidelines: I'll add the Bhadra stuff back in, since it's at the least a noteworthy claim that's been carried in multiple news sources. You need to find a secondary source (a newspaper, science journal, something that meets WP:RS) that basically states what you just said above and then modify what I wrote to read something like, "However, while Bhadra's paper mentions gene silencing in animals, the mechanism and explanation for this silencing was detailed by Mello and Fire."
I don't think you can say the research is unrelated, though, since Fire has been quoted as saying his research was based on Bhadra's (both articles I cited mention this). But certainly explaining the difference in what Bhadra did and what Mello and Fire did is important. It's just that Wiki's guidelines have to be adhered to while doing so. Thanks for helping! Xuanwu 18:17, 5 October 2006 (UTC)
I would classify Indian newspapers as at best marginally reliable sources for the origins of scientific discoveries. I've moved this stuff to the history section pending further review; it certainly doesn't belong in the first paragraph of the first section, and I wonder about the true relevance of their data. (I am also wondering why you would think sourced material cannot be removed once added; irrelevant material can always be moved or excised.) Opabinia regalis 04:41, 6 October 2006 (UTC)
I just noticed this material had also been added to Mello and Fire's biography pages, where it is clearly irrelevant. Let's at least keep this confined to this page. Opabinia regalis 04:45, 6 October 2006 (UTC)
I wholeheartedly agree that circumspection is in order when Inidan newspapers are adduced as primary sources, and I still maintain that the cited material is of very questionable relevance, since it represents one investigator's subjective opinion. It is inaccurate to contend that "Fire has been quoted as saying his research was based on Bhadra's (both articles I cited mention this)." The second- or third-hand accounts of Fire's communication to Bhadra, as presented in the Indian newspaper sources cited by Xuanwu, variably read as follows: "Though I and Craig Mello won the prize, there were many more who worked in this field with us. You are also a part of that research work," or "While we got the Nobel Prize, there are a lot of giant discoveries and you are part of that." Even if these quotes are accurate, they merely acknowledge that Fire and Bhadra work in the same field, and they do not suggest that Fire's work was in any way based on Bhadra's. If you actually read the Fire et al. and Bhadra et al. papers, you will see that they are really quite unrelated in system and approach. Moreover, if you look at the 1996 Nature paper from Fire and Mello (Seydoux et al., Nature 382: 713), you will see that the work that directly led to their discovery of RNAi was already ongoing well before the Bhadra et al. (1997) study was published. Finally, if you want a published secondary source regarding the appropriate place of the Bhadra et al. work in the larger context of RNA interference, I refer you to two excellent reviews by authorities in the field: Sharp, P.A., 2001, Genes Dev. 15: 485; Hannon, G.J., 2002, Nature 418: 244. Both of these authors unambiguously credit Fire and Mello with the discovery of RNA interference. The Bhadra et al. paper is ascribed a fairly marginal role, since the basis of the effect that they describe remains obscure. Indeed, Hannon notes in direct reference to this study, "In a few cases, silencing has been correlated with integration of transgenes as complex arrays that can produce dsRNA directly, although silencing can also be triggered by the presence of single-copy or dispersed elements. What remains a mystery is how, and indeed whether, such elements produce the dsRNA silencing trigger that has become a hallmark of RNAi." Q.E.D. Ve ri tas 07:25, 6 October 2006 (UTC)Ve ri tas
I'm glad you found that information. Please add it to the article, then, to counter the claims made by the sources I added. Also, I didn't say sourced material couldn't be removed when added. But the material is relevant since it's an account of RNAi history. Rather than deleting that account (which would be like saying it doesn't exist), the account offered by the papers should be mentioned and then refuted. Again, this is in keeping with how other articles handle matters like this where there are points of contention, such as those on Taiwan. And, again, remember that I agree with your point about Bhadra's work being marginal, so you don't need to convince me. My point is about how the topic is handled in the article so that it follows Wiki guidelines. When recounting history, encyclopedias will often mention several different published versions of how a scientific discovery was made (such as those claiming a particular country made the discovery first) and then mention how these versions have been judged by experts in the field (pointing to an article that pokes a whole in the nationalist account's timeline) and letting the reader make up their own mind. That's what we should do here. Xuanwu 16:27, 6 October 2006 (UTC)
That is a problem with Nobel Prizes today. There are very very few actual discoveries that are entirely independently made. Who can't come up with a dozen names of individuals who contributed (significantly) to the process -- not the least of which is the plant research which is normally ignored for the Nobel Prize. As soon as the furor over the Nobel Prize dies down, then it can be rewritten to talk about actual science. The attempts to latch onto a part of the "Nobel Prize Glory" is sad, but at least we didn't embarrass ourselves like the Chemistry prize this year. TedTalk/Contributions 17:38, 6 October 2006 (UTC)

[edit] Add piRNA

We should add a paragraph of piRNA and rasiRNA,because it is RNA silencing just a different means. It seems to be germline specific, but it is significant. GetAgrippa 20:19, 7 October 2006 (UTC)

[edit] No mention of Peter Waterhouse?

Not a word, in the main text or the reference list? Odd. Tony 17:15, 10 October 2006 (UTC)

I agree his work should be mentioned but there are many contributors to this body of work, so it is not surprising that many are not mentioned. While we are at it David Baulcombe was the first to indentify the 24nt ds RNA molecules. Flavell proposed a dsRNA model from aberrant transcripts for silencing in 1997. Neither of those are mentioned from a brief skip red of the references. David D. (Talk) 17:24, 10 October 2006 (UTC)
Metzlaff, M., O'Dell, M., Cluster, P.D. and Flavell, R.B. (1997) RNA-mediated RNA degradation and chalcone synthase A silencing in petunia. Cell, 88, 845–854.
Hamilton, J.A. and Baulcombe, D.C. (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science, 286, 950–952.

[edit] Nobel lectures

Fire and Mello will give their Nobel lectures on December 8. --JWSchmidt 15:50, 2 December 2006 (UTC)

In his nobel lecture, Andrew Fire seemed very comfortable using the term "RNA interference" for all of the different mechanisms for inhibition of gene expression that can be triggered by double stranded RNA, including mechanisms at the level of transcription control. --JWSchmidt 21:31, 12 December 2006 (UTC)

[edit] relationship between miRNA and RNAi

Can the article's first paragraph be more clear about the definition of RNAi and the relationship between miRNA and RNAi? "RNAi is mediated by the same cellular machinery that processes microRNA, small RNA molecules involved in large-scale gene regulation in the cell." What does "machinery that processes microRNA" mean? Is the intent to make reference to Dicer and the processing of pre-miRNA? Is the intent to make reference to the involvement of the RISC complex in the mRNA-degrading action of a RISC complex nuclease that can be targeted either by siRNA or miRNA?

It seems like there might be two different views about how RNA interference should be defined. According to this article, "RNA interference (RNAi) is a posttranscriptional gene silencing mechanism in eukaryotes, which can be triggered by small RNA molecules such as microRNA (miRNA) and small interfering RNA (siRNA)." A broad definition of RNA interference would just say that it involves double-stranded RNA, not specifically siRNA. This other article uses "posttranscriptional silencing" as a general term, and lists RNA interference as one mechanism, saying: "A hallmark of RNAi is the presence of small interfering RNAs". They try to distinguish multiple mechanisms by which microRNA can act in posttranscriptional silencing, only one of which involves RNA-dependent RNA polymerase and the production of siRNA from miRNA. So is RISC complex-mediated mRNA destruction called RNA interference even if siRNA is not involved, but only the double-stranded RNA of pre-miRNA hairpins?
--JWSchmidt 18:27, 2 December 2006 (UTC)

About a month ago, I got about a third of the way through an attempt to make this article and miRNA more consistent with each other, but got distracted and never really finished. The informal usage I'm familiar with restricts "RNA interference" to gene silencing that is the result of siRNA, most generally when artifically induced. I think a brief section on variations in nomenclauture in the literature might be in order, especially since there were so many names given to related phenomena before the mechanism was identified. Opabinia regalis 00:46, 3 December 2006 (UTC)

I just read the Wikipedia article on Dicer, which says, "Dicer is an RNAse III nuclease that cleaves double-stranded RNA (dsRNA) and pre-microRNA (miRNA) into short double-stranded RNA fragments called small interfering RNA (siRNA)". Does Dicer-mediated processing of pre-microRNA result in the production of siRNA or miRNA?

The Wikipedia Dicer article cites

Macrae IJ, Zhou K, Li F, Repic A, Brooks AN, Cande WZ, Adams PD, Doudna JA. (2006). Structural basis for double-stranded RNA processing by Dicer. Science 311(5758):195-8.

Which says, "Dicer first processes input dsRNA into small fragments called short interfering RNAs (siRNAs), or microRNAs (miRNA), which are the hallmark of RNAi." This seems to be another broad definition of RNAi that goes beyond a requirement siRNA.
--JWSchmidt 03:03, 3 December 2006 (UTC)

The article on microRNA starts out by saying, "Mature miRNA molecules are complementary to regions in one or more messenger RNA (mRNA) molecules, which they target for degradation." Later the article says, "The annealing of the miRNA to the mRNA then inhibits protein translation, but sometimes facilitates cleavage of the mRNA. This is thought to be the primary mode of action of plant miRNAs. In such cases, the formation of the double-stranded RNA through the binding of the miRNA triggers the degradation of the mRNA transcript through a process similar to RNA interference (RNAi), though in other cases it is believed that the miRNA complex blocks the protein translation machinery or otherwise prevents protein translation without causing the mRNA to be degraded."

A recent article in PLoS Biology talks about miRNA-mediated RNA interference and says, "Although RNAi has commonly been associated with siRNAs, this process is largely mediated in plants by miRNAs," and, "miRNAs can behave like siRNAs and induce mRNA cleavage when the miRNA sequence is completely complementary to a target mRNA". However, this paper describes a different miRNA-containing RISC complex that blocks translation by another mechanism: "RCK/p54 is the effector molecule in miRISC that represses translation and that the specificity of this repression is dictated by the sequence of miRNA binding to complementary sites in the 3′ UTR of the target mRNA." (see their figure 8). They favor a broad definition of RNAi, "RNA interference (RNAi), an evolutionarily conserved process whereby double-stranded RNA induces the sequence-specific degradation of homologous mRNA," and they say, "Endogenously, RNA interference triggers are created from small noncoding RNAs called microRNAs (miRNAs)".
--JWSchmidt 04:01, 3 December 2006 (UTC)

Sounds like we should use the broader definition then. No objections. IIRC I wrote or rewrote both Dicer and the material you mention in miRNA, so I apologize for being inconsistent :) This is a fast-moving field and I am probably well out of date. Opabinia regalis 05:58, 3 December 2006 (UTC)
The literature for this rapidly advancing research topic area reads like the reports from a group of blind people exploring an elephant. I hope that the Nobel prize will encourage someone to step back, take a look at the whole picture and write a great review article. The majority of people who are publishing articles about RNAi are trying to use it as a laboratory tool and those folks seem to have a rather simplified view of RNAi. The relatively few labs that are studying the details of the endogenous RNAi processes keep reminding everyone that there is still much to learn. I think the Wikipedia Argonaute article needs an adjustment; it seems too centered on siRNA. "In some cases, including Caenorhabditis elegans, distinct Argonaute proteins function in conjunction with siRNAs and microRNAs, respectively. In other animals, the same Argonaute can function with both siRNAs and microRNAs" (source). The authors of that article suggest a very broad definition of RNAi, "a variety of transcriptional and post-transcriptional gene-silencing processes that are collectively referred to as RNA-mediated interference". I just re-worked the introduction to RNA interference and tried using a definition of RNAi that is limited to post-transcriptional gene-silencing by targeted RNA destruction guided by either siRNA or miRNA. Maybe even that definition is too narrow. --JWSchmidt 16:56, 3 December 2006 (UTC)

Recent nature review paper introduce RNA interference like this: "RNA interference (RNAi) is an evolutionarily conserved phenomenon that involves dsRNA molecules. Small interfering RNAs (siRNAs) and microRNAs (miRNAs) are non-coding RNAs that are generated by a class of RNase III ribonucleases (specifically, Dicer and Drosha). These small RNAs are incorporated into the RNA-induced silencing complex (RISC), which mediates the RNAi process." (Nat Rev Mol Cell Biol. 2006 Dec;7(12):919-31.)Sangak 19:17, 3 December 2006 (UTC)

[edit] Broad definition of RNAi

After listening to the Noble Prize lectures, I have updated the introduction of the article to use the broad definition of RNA interference which includes gene regulation at both transcriptional and post-transcriptional levels. --JWSchmidt 21:43, 12 December 2006 (UTC)

[edit] GA on hold

As a biochemist myself, I say we have here a stupendous article, as far as content and writing style are concerned. The only things keeping me from passing it to GA are:

  • The left-aligned image displayed in front of a right-aligned image, that squeezes the text body in between. The best thing is to move the left image to another place;
  • If possible, try to summarize even more the left-aligned image's caption;
  • The first occurrence of "GW bodies" is not wikilinked, as opposed to the second one; invert this so that people can understand what it is the first time they read it.

— Parutakupiu talk || contribs 03:14, 1 February 2007 (UTC)

Working fast I see :) I forgot one thing and I'll advice on one of the fresh changes:
  • Don't specify a "size" for the thumb images because that can work bad for some users whose display preferences are different from yours;
We need to specify this for the first diagram, otherwise it is unreadable, removed from the others.
You did well. In cases like diagrams this recommendation can be ignored ;) Parutakupiu talk || contribs 18:59, 2 February 2007 (UTC)
  • If you want to number the images with "Figure #", it's better to either number all or none; IMO, don't number at all, since you don't have any references along the article specifying this or that image in particular.
Done.
  • The "GW bodies" occurrence I mentioned wasn't the one on the journal reference but on the text body;
Done.
— Parutakupiu talk || contribs 03:35, 1 February 2007 (UTC)
Thanks for the review. TimVickers 16:54, 2 February 2007 (UTC)

Thumbs up! Great job, you have yourselves another GA. Congratulations! Parutakupiu talk || contribs 18:59, 2 February 2007 (UTC)

[edit] New articles

This is an area of intense interest and rapid growth. I noted two new RNAi related articles in my Jan. Science: Distinct Populations of Primary and Secondary Effectors During RNAi in C. elegans Julia Pak and Andrew Fire Science 12 January 2007: 241-244.

Secondary siRNAs Result from Unprimed RNA Synthesis and Form a Distinct Class Titia Sijen, Florian A. Steiner, Karen L. Thijssen, and Ronald H. A. Plasterk Science 12 January 2007: 244-247. GetAgrippa 04:28, 1 February 2007 (UTC)

[edit] Plant and animal differences

I think that the figure in this article might be a good addition. --Peta 01:23, 15 February 2007 (UTC)

  • It's probably better than the current lead image since it shows where the various processes happen.--Peta 01:32, 15 February 2007 (UTC)
Thanks. I like the way this one is organized better. Since BMC doesn't explicitly refer the creative commons licenses in the open-access statement, though, I'm not sure how to tag this. Opabinia regalis 01:47, 15 February 2007 (UTC)
It's there on the page: this is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0). This is considered a free license for the commons. --Peta 01:49, 15 February 2007 (UTC)
Well, I'm unobservant then ;) I was looking in the linked open-access charter. Appearing imminently. Opabinia regalis 02:04, 15 February 2007 (UTC)
Neat, should this stub on P-bodies be linked somewhere?--Peta 02:34, 15 February 2007 (UTC)
It is, but they're called GW bodies in the text. I guess that should be changed to match the image. Opabinia regalis 02:36, 15 February 2007 (UTC)
On second thought, I think I like it better in the variations section - that way it comes after the introduction of all the proteins that are labeled in it, and is located in the text with the discussion of P-bodies/GW-bodies. The existing lead image also explicitly includes siRNA production, which I think is important to show early on. Opabinia regalis 02:36, 15 February 2007 (UTC)
I think it works well where you have put it. On a different note I think that the cellular mechanism section could use a little introduction before it plunges into taking about cleavage. I think 2-3 sentences explaining that the process occurs in the cytoplasm; and that miRNAs have to be actively shifted from the nucleus, and siRNAs imported into a cell to be processed this way. Where things happen in cells is pretty important to understanding the process.--Peta 03:26, 15 February 2007 (UTC)
A little copy-editing note: "Dicer" is not capitalized consistently. –Outriggr § 04:30, 15 February 2007 (UTC)
Thanks, I think I got them all now. It used to be consistently capitalized in the literature and now is varied - a lot of papers seem to use Dicer for the original protein and dicer for all homologs, bu that's probably not a sustainable distinction. Opabinia regalis 04:59, 15 February 2007 (UTC)

[edit] Slight re-write of lead?

Hi, the present lead seems kind of daunting for non-experts, since it relies on knowledge that many people won't be familiar with. I at least had a little trouble following it, although maybe that's just me. :( Perhaps we could replace it with something written at a slightly lower level? Here's an initial draft

RNA interference (also called "RNA-mediated interference", abbreviated RNAi) is a mechanism for inhibiting gene expression in which the messenger RNA (mRNA) for a specific gene or set of genes is digested, preventing it from being translated in the corresponding protein(s). The RNAi mechanism is thought to have evolved early in the history of life and is substantially the same, i.e., conserved, in most eukaryotic organisms. RNAi serves as a form of innate immunity against viruses, and also plays major roles in regulating development and genome maintenance.
The central ribonuclease of the RNAi pathway is the argonaute protein, which is part of a multi-protein complex called RISC. To be activated, the complex must be first "armed" with a single strand of RNA, typically 20-25 nucleotides long; the argonaute protein digests only mRNA that can hybridize with this guide strand. This allows RNAi to suppress specific genes independently of one another; yet it is also a very general system, since the RISC complex may bind nearly any guide strand. The various guide strands are produced by the digestion of ’’double-stranded’’ RNA (dsRNA); the resulting fragments are known as small interfering RNA (siRNA) when derived from foreign genetic material and as microRNA (miRNA) when derived from the cell's own genome.
RNAi is an effective method for post-transcriptional gene silencing, making it a valuable in vivo laboratory research tool, both in cell culture and in living organisms. For example, synthetic dsRNA may be introduced into cells to induce RNAi suppression of the encoded genes. RNAi may also be used for large-scale screens that systematically shut down each gene in the cell, which can help identify the components necessary for a particular cellular process or an event such as cell division. RNAi is also a promising therapy in human disease, such as...(please fill me in)
RNAi has been particularly well-studied in certain animals such as Caenorhabditis elegans and Drosophila melanogaster, and in plants such as Arabidopsis thaliana. The earliest signs of RNAi were observed by plant biologists, who described post transcriptional gene silencing and noted that genes could be suppressed by antisense RNA [1], but also by sense RNA. The key role of double-stranded RNA in RNAi was discovered in 1998[2] by Andrew Fire and Craig C. Mello in the nematode worm C. elegans;[3] for this work, they shared the 2006 Nobel Prize in Physiology or Medicine.

Please let me know whether you like this version of the lead. Feel free to tinker with it as well. We should wait for Opabinia regalis before doing any substitutions in the main article, though.

Oh, btw, we also might want a reference for the "human disease" sentence. Is it mainly good for viral diseases, or has it been used effectively for bacteria and parasites, too? I haven't looked into it yet.

Hoping that this is useful, Willow 12:03, 15 February 2007 (UTC)

  • I think your version is a bit more to the point; a few points (1) it fails to mention dicer (2) I would remove the speculation about its promise for medicine, maybe replacing it with something like "RNAi is being used to develop treatments for human disease and (something about biotech applications) (3) there are a few things in the last pargraph that need reworking like " but also by sense RNA" (who?) and "The earliest signs of RNAi" (weird phrasing, doesn't really say what it means by this).--Peta 23:20, 15 February 2007 (UTC)
I tried to simplify a bit, and describe the major points earlier; what do you think? Willow, the problem with your first sentence is that it doesn't really reflect current usage; see the above discussions about 'broad' vs 'narrow' definitions. The term 'RNAi' now generally refers to RNA-induced downregulation, which isn't necessarily via mRNA degradation. The medicine/biotech sentence is mostly just a pointer to that section; especially in medical applications, people have been talking (over-)excitedly about this for years ('antisense therapy' was certainly proposed before RNAi was discovered) and it's been mostly vaporware till recently. To answer the disease question, it's viruses that are talked about from an 'immune' standpoint, but a lot of the real excitement is in suppressing overexpressed genes in cancer cells. It could be used against other pathogens indirectly, if there were some gene that could be suppressed to bolster the immune response (or, I suppose, if the pathogen would take up the dsRNA delivered to the patient). Opabinia regalis 02:52, 16 February 2007 (UTC)

[edit] Conditional RNA interference

Should there be an article created about it? This article is well researched so I assumed that there was a purpouses on excluding conditional RNA interference. The article touch it from what is implied, but without really covering the subject as it should. Fad (ix) 18:35, 18 February 2007 (UTC)

There's only so much that will fit in one article ;) I added a very short sentence on techniques used in mammalian systems, including conditional RNAi using lentiviral vectors, but if you want to create a separate article, that would be great. Opabinia regalis 04:57, 19 February 2007 (UTC)
This article should not be addressing conditional RNA interference. That would be like the genetic recombination article addressing conditonal knockouts. it would be much more useful in some sort of techniques article. David D. (Talk) 05:17, 19 February 2007 (UTC)
I would have believed that conditional knockout could be at least cited in the genetic recombination article. But I gess given the size of those articles, it is better off. Opabinian regalis, I have followed the history of this article, you have really done an impressive job. Fad (ix) 06:19, 19 February 2007 (UTC)
Thanks ;) I think a sentence on techniques in mammals fit well, since there was already previous discussion of techniques in C. elegans. But an article on conditional RNAi, or on RNAi techniques in general, wouldn't be a bad thing. Opabinia regalis 08:28, 19 February 2007 (UTC)

[edit] Paragraph in intro

The selective and robust effect of RNAi on gene expression makes it a valuable research tool, both in cell culture and in living organisms; synthetic dsRNA introduced into cells can induce suppression of specific genes of interest. RNAi may also be used for large-scale screens that systematically shut down each gene in the cell, which can help identify the components necessary for a particular cellular process or an event such as cell division. The RNAi pathway has been particularly well-studied in certain model organisms such as the nematode worm Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the flowering plant Arabidopsis thaliana. Exploitation of the pathway is also a promising tool in biotechnology and medicine.

At first it appears as if this paragraph is about the various applications of RNAi as a tool: to study the function of specific genes, to perform large-scale screens, to study cellular processes, and in biotech and medicine. But then there is one sentence in the middle that doesn't fit the paragraph's general theme: it tells us that the RNAi pathway has been particularly well studied in model organisms. This sentence is about our knowledge of the RNAi pathway, not about its applications. Further, the last sentence uses "also", implying that the last two sentences somehow talk about the same, but they don't.

I propose that the sentence "The RNAi pathway has been particularly well-studied in certain model organisms such as the nematode worm Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the flowering plant Arabidopsis thaliana." be moved from the paragraph about RNAi's applications to a section that describes its discovery and study. AxelBoldt 17:00, 4 March 2007 (UTC)

I see your point, though I'm not sure it's really unclear; much of the reason RNAi is well-studied in these organisms is that they are the ones in which it is easy to use as a tool (of course, this goes the other way around too; it's easy to use RNAi because the behavior of the pathway is relatively well understood in these organisms...). But the lead definitely doesn't need to get any longer. I tried just moving the 'well studied' sentence to the end of the second paragraph that describes the pathway, which I think fits well with the subsequent text elaborating on the biochemistry, most of which was discovered in these organisms. What do you think? Opabinia regalis 18:00, 4 March 2007 (UTC)
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