Talk:RNA interference

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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

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.

Andrew Fire's paper "RNA as a target of double-stranded RNA-mediated genetic interference in Caenorhabditis elegans" specifically says "knock-out" in the introduction.

this term is not universally used - "knockdown" more accurately describes the process. "Knockout" implies that gene expression has been completely abolished (in RNAi it normally isn't completely). "Knockout" is better suited to describe complete genetic removal of expression normally via transgenics Goldfinger820 03:07, 16 May 2007 (UTC)

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 —Preceding unsigned comment added by 129.81.15.58 (talk • contribs) 14:14, 19 July 2006

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?—Preceding unsigned comment added by Mussaali (talk • contribs) 20:32, 23 July 2006 mussa ali

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—Preceding unsigned comment 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—Preceding unsigned comment 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. —Preceding unsigned comment 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???? —Preceding unsigned comment 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.—Preceding unsigned comment added by Mussaali (talk • contribs)

It is time to remind the people posting here to be WP:CIVIL. Personal attacks are never appropriate.Ted^Talk/_{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. —Preceding unsigned comment added by Mussaali (talk • contribs) 21:58, 24 July 2006

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.

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)

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)

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. Ted^Talk/_{Contributions} 17:38, 6 October 2006 (UTC)

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)

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.

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)

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)

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)

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)

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)

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)

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, but also by sense RNA. The key role of double-stranded RNA in RNAi was discovered in 1998 by Andrew Fire and Craig C. Mello in the nematode worm C. elegans; 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)

I found the introduction incredibly daunting. Not very useful for non-experts. —Preceding unsigned comment added by 98.169.69.1 (talk) 05:49, 16 December 2008 (UTC)

References

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)

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)

Misspelling in figure

The figure "Illustration of the major differences between plant and animal gene silencing" misspells "asymmetric". I believe under the image's licence we are OK to modify the spelling in the figure, if anyone wants to have a go. Crana 21:12, 4 May 2007 (UTC)

I must be missing something... The image appears to have 'asymmetric' spelled 'asymmetric' - i.e. correctly. Am I completely blind? -- MarcoTolo 03:07, 5 May 2007 (UTC)

You're right, it is correct. Weird. I know I wasn't making it up, because the original image [2] has the misspelling. Maybe I looked at the original image and thought I was looking at the WP one? Sorry. Crana 18:36, 5 May 2007 (UTC)

No, you're not going mad. Your original comment was correct. I saw your comment an then corrected the version in commons. Sorry for the confusion. David D. (Talk) 17:53, 7 May 2007 (UTC)

free image

I just uploaded an elegant, simple diagram of RNAi from PLoS to the commons here. Have a look if you're interested. Calliopejen1 16:55, 5 August 2007 (UTC)

siRNA

In the intro it stated that siRNA only derived from exogeneous sources. This isn't true, it derives from the dsRNA of the same cell, it implies that only humans create siRNA or atleast only other cells create the siRNA that a particular cell requires. I've changed it but i'm not certain if the terminology is correct. All i know is that its more accurate than before. I was surprised to find such an error in the introduction of a featured article to be honest. Perhaps there are other mistakes as I have neither studied this article nor know enough about RNAi to comment. But a check through should definately be required as a featured article suggests that almost everything it contains is correct which doesn't seem to be the case. —Preceding unsigned comment added by 86.133.236.247 (talk) 12:04, 23 October 2007 (UTC)

gobblygook

I find it astonishing that this article made it to FA with an intro that is extremely difficult for this failed physicist to decipher. It consists of a string of equally indecipherable terms and never explains what is happening inside the cell. If we going to be talking about interference, it's vital that we say what is being interfered with, in terms that don't require lookups in other articles. This needs to be fixed. A link to the gene expression article is simply not good enough, especially considering that that article is in a sorry state. Maury (talk) 17:42, 21 November 2007 (UTC)

Here is the opening sentence:

RNA interference (also called "RNA-mediated interference", abbreviated RNAi) is a mechanism for RNA-guided regulation of gene expression in which double-stranded ribonucleic acid inhibits the expression of genes with complementary nucleotide sequences.

It clearly defines interference as "double stranded ribonucleic acid inhibits the expression of genes". How else could this be expressed to make it more accessible? The phrase gene expression seems pretty obvious. Is this really gobbledygook? If every term has to be defined such as gene and expression you will end up with an equally uniterpretable article since it will have no flow whatsoever. David D. (Talk) 20:13, 23 November 2007 (UTC)

I tweaked the first paragraph a bit. Tim Vickers (talk) 20:47, 23 November 2007 (UTC)

It's slightly better now, but I think it still needs work. To answer David's question, here is one way...

In eukaryotic cells cells, those containing a nucleus, cellular machinery outside of the nucleus produces proteins following instructions stored in the nucleus's genetic material. The overall process is known as gene expression. The instructions for building the proteins are normally communicated through short strands of nucleic acid known as mRNA. mRNA is not the only source of RNA material in the cell, however, viruses and other processes can cause the cellular machinery to produce proteins that are not part of the genetic material, sometimes to the detriment of the organism as a whole.

RNA interference (RNAi) is a mechanism that interferes with the gene expression process in order to control the production of certain proteins. Key to the workings of the RNAi process is small interfering RNA (siRNA), short strands of RNA that have complementary nucleotide sequences to a targeted mRNA strand. The mRNA in question is typically a portion of a longer sequence of long double-stranded RNA (dsRNA), often foreign to the cell. The siRNA "primes" a mechanism within the RNAi pathway that finds the strands of targeted mRNA and "cleaves" then, breaking them down into smaller portions that no longer code properly into a protein. As the RNAi is conserved in most eukaryotic organisms, the pathway may have evolved as a form of innate immunity against viruses and transposons, and also plays a major role in regulating development and genome maintenance.

I believe this clearly states what RNAi does, in context of the overall picture, and does not fall prey to having "no flow whatsoever". YMMV. Maury (talk) 23:51, 24 November 2007 (UTC)

Ironically, I now find this confusing. :) I'll think about a rewrite following your concept however I'm not sure a description of the central dogma at the start of all these articles is the best approach. Gene expression is the least of the worries with respect to technical language in this article. I think there comes a point where we have to assume that readers are familiar with the biological language. And we have to expect that those who are not can use a glossary. Just above we discuss mRNA and protein, we don't describe them as string a string of amino acids or mRNA as a string of nucleotides. What is a nucleus? We have also thrown in transposon and genomes into the mix. Why are these all more approachable than gene exression? It's hard for me to tell since I'm so familiar with the terminology. David D. (Talk) 05:06, 26 November 2007 (UTC)

I think there comes a point where we have to assume that readers are familiar with the biological language.

NO NO NO NO NO! Geez, this is my biggest gripe about most of the technical articles on the wiki; they're written by (insert field here) nerds for (insert same field here) nerds. To anyone not intimately aware of the terminology, it's all unreadable technobabble. Forcing the reader to scour other articles, as I was forced to, to explain something that's a small para long is just torture.

This problem is endemic to science writing, not just here, but everywhere. But at least here we can fix it. So lets start right here. Maury (talk) 23:08, 26 November 2007 (UTC)

Well how do you propose we define every term. Biology is full of terminology. In these articles practically every sentence has two words that need to be defined. Where do we draw the line? Worse, one laypersons gobblydygook is meaningful to another layperson, so which is the subset of terms that are most important with respect to being defined? Above, you clearly do not think it is important to define nucleus, protein or nucleic acid, but why? Are these not further examples of terminology? The key is who is the audience, your assumption is that all articles need to be aimed at the laypeson. Here I would disagree, we need a spectrum from simple to more complex articles. This happens to be one of the more complex ones both conceptually and from a terminology perspective. There are two potential solutions to this issue. One is start a companion article called Introduction to RNA interference, similar to the way the Introduction to evolution relates to the evolution article. Or to write an article for RNA intererence at simple.wikipedia.org. There are many undergraduate and graduate level biologists that will appreciate this particular article. It would be a shame to rewrite the whole thing so it would be less useful at that level. David D. (Talk) 00:10, 27 November 2007 (UTC)

No, that isn't sensible. Basic articles deal with the basic terms, there is no advantage in repeating this simple information in articles on other, more complicated topics. That would be completely redundant. You just don't need to define molecules, proteins or enzymes in an article on methylenetetrahydrofolate reductase or serpins. Tim Vickers (talk) 23:12, 26 November 2007 (UTC)

umm, obviously we're not talking about explaining "proteins", as is clearly demonstrated in the proposed version above. We're talking about clearly defining what RNAi is. Understanding how RNAi works in relation to gene expression suggests some explanation of what gene expression is is definitely required. Instead of arguing the point, which may or may not be explained well, argue the text. Maury (talk) 00:06, 27 November 2007 (UTC)

I wrote above before seeing this but to continue here. I'm not sure I understand, you seem to be worried about the whole terminology issue, which is a valid point, but why only with respect to gene expression? David D. (Talk) 00:10, 27 November 2007 (UTC)

No time to complete this now. Here is a start:

RNA interference (RNAi) is a mechanism that inhibts gene expression by causing the degradation of specific RNA molecules or inhibits the transcription of specific genes. The targets are often RNA from viruses and transposons, although it also plays a role in regulating development and genome maintenance. Key to the RNAi processes are small interfering RNA strands (siRNA), that have complementary nucleotide sequences to a targeted RNA strand. The RNA in question is typically targeted due to a double-stranded RNA (dsRNA) version of the sequence that is formed in the cell.

(undent) That is much better. I would recommend adding in " likely a form of innate immune response" after the word transposon. I am also confused by the last sentence, which is not how I understand it to work. See if this is more accurate:

RNA interference (RNAi) is a mechanism that inhibts gene expression by causing the degradation of specific RNA molecules or inhibiting the transcription of specific genes. The targets are often RNA from viruses and transposons, likely as a form of innate immune response, although it also plays a role in regulating development and genome maintenance. Key to the RNAi processes are small interfering RNA strands (siRNA), that have complementary nucleotide sequences to a targeted RNA strand. The targeted RNA is typically a small portion of a larger double-stranded RNA (dsRNA) version of the sequence that is formed in the cell.

Maury 22:40, 30 November 2007 (UTC)

I had already changed above, deciding to move the double stranded section to the following paragraph. i think above was a half finished thought on my behalf. I just added back the innate immunity. See the opening two paragraph in the article now. David D. (Talk) 23:10, 30 November 2007 (UTC)

It is looking a lot btter than it was, but we could probably make it even simpler, at least in the lead - I'm one of those people who likes things to be understandable by intelligent 14 year olds, if possible, and I think it is possible in this case. Adam Cuerden ^talk 23:33, 30 November 2007 (UTC)°

Adding "likely as a form of innate immune response" is only confusing IMO, it already says it defends against viruses. I can't figure out what the last sentence is supposed to mean. Narayanese 23:51, 30 November 2007 (UTC)

I still find this very difficult. Is this version better?:

"RNA interference (RNAi) is a mechanism that inhibits gene expression by causing the degradation of specific RNA molecules or hindering the transcription of specific genes. RNAi targets include RNA from viruses and transposons (probably as a form of innate immune response), and also plays a role in regulating development and genome maintenance. Small interfering RNA strands (siRNA) are key to the RNAi process, and have complementary nucleotide sequences to the targeted RNA strand. Specific RNAi pathway proteins are guided by the siRNA to the targeted messenger RNA (mRNA), where they "cleave" the target, breaking it down into smaller portions that can no longer be translated into protein. A type of RNA transcribed from the genome itself, microRNA (miRNA), works in the same way." DrKiernan (talk) 14:57, 11 January 2008 (UTC)

Looks good. I just added it to the article. You can do those kinds of edits yourself too, I don't think edits that attempt to clarify would be regarded as controversial. David D. (Talk) 17:06, 11 January 2008 (UTC)

Superb article

This is a superb, outstanding article, the best on the web. My congratulations to all editor.--GrahamColm^Talk 21:50, 10 February 2008 (UTC)

I don't quite understand how to do the editing nor do I have the time but could someone please add the following ORIGINAL reference to the section for Upregulation of Genes? The current reference is #74. Here is a link to the original paper published on this topic as the current reference is only a review: http://www.pnas.org/cgi/content/abstract/0607015103v1 Thanks Racheloser (talk) 02:46, 21 February 2008 (UTC)

What's wrong with review articles? But since the article you mentioned is free I it doesn't hurt to include it, plus it is better in terms of detail than the nature news. It doesn't mention their miRNA findings though. Narayanese (talk) 21:25, 21 February 2008 (UTC)

Lead picture

Did I get it all right? I've been taught it is viral RNA-dependent RNA polymerase that makes dsRNA from a ssRNA and starts RNAi, but the presence of endogenous RdRPs in RNAi makes it a little confusing. Narayanese (talk) 20:37, 18 March 2008 (UTC)

In plants and drosophila it is the endogenous RDRP that is important for amplification of the siRNA's. Mutants in those genes are less effective in silencing. Mammals do not have the activity. David D. (Talk) 03:28, 19 March 2008 (UTC)

Ah, so that endogenous RdRP has a limited role after all. Thanks. Narayanese (talk) 09:22, 19 March 2008 (UTC)

What about parasitic flatworms?

The article seems to lack any information about the work done on three species of trematode. Donek (talk) 22:42, 2 November 2008 (UTC)

Cellular Mechanism

The "dsRNA cleavage" section confuses me. Paragraph 1 says that dsRNA activates dicer to cleave it, then they are broken into single strands and, finally, the siRNAs are incorporated into RISC. Paragraph 2 seems to start at the beginning again describing how an effector protein detects the dsRNA and then the effector protein stimulates dicer to cleave the dsRNA and that both the effector protein and dicer present the siRNAs to RISC. Have I misunderstood this or is there a problem with the section? Donek (talk) 16:26, 18 November 2008 (UTC)

RNA silencing

What is the difference between RNA silencing and RNA interference. Is it just that RNA silencing is in plants, and RNA interference is in animals, or is there more to it than that? If so, shouldn't the pages be merged? SiameseTurtle (talk) 19:07, 19 December 2008 (UTC)

undefined term

In the second paragraph, the term dsRNA is used without prior definition. thanks. —Preceding unsigned comment added by 128.249.96.253 (talk) 18:32, 23 January 2009 (UTC)

Merge with post transcriptional gene silencing

My understanding is that post transcriptional gene silencing (PTGS) originally referred to gene silencing effects in plants. This turned out to be a result of RNA interference and now PTGS rather describes the effects of RNA interference. I think this is already well covered in the lead paragraph and History and discovery sections; so I suggest PTGS should just redirect to RNA interference. Any problems with this? Ribrob (talk) 16:25, 11 April 2009 (UTC)

RNAi is the same as PTGS, RNA silencing, and Quelling in fungi. I also agree with a merger, but only if this article is developed to include information about the systems in all organisms. This article focusses too much on animal systems. Similarities and differences between the systems need to be highlighted. SiameseTurtle (talk) 18:56, 11 April 2009 (UTC)

new research

"The relevance of observations from fission yeast mating-type regions and centromeres to mammals is not clear, as heterochromatin maintenance in mammalian cells may be independent of the components of the RNAi pathway.[45]" a paper i have been reading published 2009 suggests that heterochromatin maintenance in yeast might be independent of RNAi as well... is an small update needed?

Alexander Kagansky, Hernan Diego Folco, Ricardo Almeida, Alison L. Pidoux, Abdelhalim Boukaba, Femke Simmer, Takeshi Urano, Georgina L. Hamilton, Robin C. Allshire (2009) Synthetic Heterochromatin Bypasses RNAi and Centromeric Repeats to Establish Functional Centromeres, Science 324, 1716 —Preceding unsigned comment added by X CheshireCat x (talk • contribs) 16:16, 15 December 2009 (UTC)

I have not read the paper but I'm not sure that the fact that synthetic centromeres don't require RNAi does not negate the fact that real centromeres in yeast do use, and require, a functional RNAi process to maintain their heterochromatin. David D. (Talk) 16:28, 15 December 2009 (UTC)

CSIRO in Australia Invented RNAi in 1995

PATENTLY, A BATTLE FOR GENETICS' NEXT BIG THING

Who invented hairpin gene silencing? It's literally a $64 million question, as the claimants to one of the most valuable biotechnology patents of the past decade begin skirmishing over its ownership.

Hairpin gene silencing, also known as RNA interference (RNAi), is a simple, quick, but exquisitely precise way of exploring gene function in higher organisms - it can be applied to switching off genes in plants, animals, insects, or any other higher organism. Changes in the organism then provide cues the function of the silenced gene.

There are four contenders: CSIRO Plant Industry, the multinational life science company Syngenta (UK), the Carnegie Institute in the US, and a partnership involving small Queensland-based biotechnology company Benitec Australia and the Queensland Department of Primary Industries (QDPI).

CSIRO lays claim to having discovered hairpin gene silencing in 1994; CSIRO Plant Industry molecular geneticist Dr Peter Waterhouse performed the first successful gene-silencing experiment in a plant - tobacco - in 1995. CSIRO's claim rests on its belief that Waterhouse's experiment was also the first demonstration of this novel method of gene silencing in any organism.

But CSIRO delayed lodging its patent until April 1998; the Benitec/QDPI partnership and Syngenta filed in March 1998. In the intervening period, the Carnegie Institute and Syngenta filed their applications - Carnegie filed on the basis of demonstrating hairpin gene silencing in the nematode Caenorhabditis elegans.

Dr Rob Defeyter, a member of Waterhouse's team, and now IP manager for Plant Industry, said the division prepared a draft patent in 1995, but delayed filing while it conducted further research.

"Our laboratory notebooks confirm we continued our research between 1995 and 1998, mainly to confirm our data, extend the technique, and find out how broadly applicable it might be," Defeyter said.

Benitec's claim is based on work done by former Plant Industry geneticist Dr Mick Graham, who worked with Waterhouse until 1995 before joining QDPI.

Graham was the first to demonstrated successful dsRNA silencing in mammalian cells, and the Benitec/QDPI alliance was the first to file a patent on the technique, in March 1998. The question of ownership is complicated by different views of what constitutes priority. Defeyter said patent offices in most countries, including Australia, based priority on the filing date, but the US Patent Office bases priority on the date of invention - even if the patent application is not lodged until later.

Yesterday CSIRO announced it was releasing the high-throughput gene silencing vectors it has developed for its own work in plants, or free use by any not-for-profit research organisation.

Today, Benitec announced a collaborative agreement with US biotechnology company Tranzyme, in North Carolina, to develop and market its own high- throughput gene-silencing and gene-delivery technologies.

In their joint press release, the companies said the combination of Benitec's High Throughput (HTP) gene silencing technology announced on January 7, 2003, with Tranzyme's industry-proven gene delivery and expression technology, would "offer customers a revolutionary means of producing gene 'knockdowns' quickly and efficiently.

"The combined technologies will be ideal for both in vitro and in vivo applications," it said. "The collaboration will target the pharmaceutical industry and will fast-track the discovery and validation of drug targets." The companies will share revenues, as well as developing their own proprietary targets using the combined technology for future joint commercialisation.

CSIRO's press release yesterday said its gene vectors can be used to identify the function of thousands of genes quickly and accurately, and predicted the technology would promote "major advances in biotechnology and agriculture".

Plant Industry Chief Dr Jim Peacock said, "Scientists can now accurately and rapidly identify the function of single genes or specific groups of genes from tens of thousands of genes in an organism." "As well as the speed of analysis, these vectors provide nearly 100 per cent efficiency in 'switching off' any gene under investigation. This means the effect of a gene in an organism can be determined confidently, and once its function is known we can decide how to use this information." Harbinger of attack Waterhouse's original 1995 experiment confirmed the existence of plant cells of an ancient mechanism, perhaps evolved as a defence against viruses, that detects the presence of double-stranded RNA molecules - a harbinger of viral attack.

When viruses infect living cells, they produce a double-stranded RNA (dsRNA) copy of their genetic blueprints as a prelude to mass-replicating new virus particles.

The anti-viral mechanism detects the dsRNA genetic blueprint, and by an as yet unidentified mechanism, cleaves it into useless fragments, halting the virus replication before it can begin. It is now clear that the cells of higher organisms use the same dsRNA technique to regulate their own gene activity, by producing 'mirror image' messenger RNAs that bind to the active gene's messenger RNA, forming a dsRNA complex - which is then degraded.

The 'knockdown' technique differs from the knockout technique used to silence genes in rodents, in that the DNA code of the original gene is left unaltered - the silencing is performed at the gene-transcription stage.

CSIRO's vectors, which carry names like 'Hannibal', 'Kannibal' and 'Hellsgate' are essentially plug-and-play gene cassettes into which geneticists can insert DNA sequences copied from the many messenger RNAs of active genes in living cells.

The gene sequence, and the complementary DNA code from the non-gene strand, are joined end-to-end, separated by a small sequence that forms a hinge.

When the vector inserts the gene construct into living cells, the transgene produces messenger RNAs that spontaneously fold back on themselves, by complementary base-pairing, forming a hairpin shape.

The resulting dsRNA molecule is then detected by the cell, and destroyed - an event that also programs the anti-viral mechanism to destroy the 'real' mRNAs from the targeted gene.

'The third great revolution' Benitec's director of research and technology, Ken Reed, said yesterday the company was confident of its patent position - "It's a great position to have. Mick Graham was the first, by two and a half years, to demonstrate its efficacy in animal cells.

"It's the third revolution in biotechnology - first there was recombinant DNA technology, then PCR, and now RNA interference," he said "We knew as soon as the world woke up to the fact that it could be used in mammalian cells, there would be the most massive brawl in relation to ownership of the patent.

"In recent years, once companies realized its value, everyone has been trawling back through their research in the early 1990s for anything that might allow them to claim priority. It's bigger than Ben Hur."

Source: http://www.gene.ch/genet/2003/Mar/msg00029.html

Finally, one needs to ask the question as to why, the C.S.I.R.O., the Q.D.P.I. and the Australian company Benitec dominate the RNAi patent landscape if they were simply contributors - remember with the USPTO works on 'first-to-invent' and not 'first-to-file basis.' Undoubtedly, Mello and Fire are great scientists, but the history and discovery section of this article is so narrow in its point of view that a better title might be - 'the life and times of Mello and Fire.'

http://www.pi.csiro.au/RNAi/ HairpinRNAi – a CSIRO invention In 1995, CSIRO was first to recognise the role of double-stranded RNA as the trigger for gene silencing, now popularly known as “RNA Interference” or “RNAi”. When a plant with an antisense construct directed against a virus sequence was crossed with a plant containing a sense construct against the same sequence, only the progeny that acquired both sense and antisense constructs were immune to virus infection (Waterhouse et al., 1998). The key CSIRO invention was a construct with linked sense and antisense or inverted repeat sequences (Figure 1). When transcribed, a self complementary RNA is produced that forms a ‘hairpin’ structure by folding back on itself (Waterhouse et al., 1998). Hairpin RNA with a double-stranded ‘stem’ is a more effective trigger of RNAi than separate sense plus antisense RNAs (Figure 2). This was proved by using constructs containing sequences from a reporter gene (GUS) and a viral gene (Potato Virus Y).

Rodney214 (talk) 13:30, 20 January 2011 (UTC)

Systemic spread

The lead contains:

"This process is known to spread systemically throughout the organism despite initially limited molar concentrations of siRNA."

The text suggests that this applies to all organisms. Is this correct? It appears to be true for plants and Drosophila. I've qualified the statement by adding "In some organisms ..." Aa77zz (talk) 11:38, 25 November 2011 (UTC)

Merck and RNAi: History Q

Especially for the keepers of the history sections: I attended an RNAi symposium in Cambridge in the early 2000s and at least one speaker mentioned that the first RNAi experiment that he was aware of was at Merck in the 1960s(?) or 1970s(?). (The same speaker also mentioned the more well known petunia experiments from the 1990s.) The Merck guys injected RNA into organisms (plants? mice? rats?) and ... I forget what effect they saw. Was anybody else at that symposium besides me? Does anyone have details of the Merck experiment and result? Please excuse the sketchiness of this contribution.AdderUser (talk) 18:18, 16 September 2014 (UTC)

Assessment comment

The comment(s) below were originally left at Talk:RNA interference/Comments, and are posted here for posterity. Following several discussions in past years, these subpages are now deprecated. The comments may be irrelevant or outdated; if so, please feel free to remove this section.

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

Last edited at 06:48, 3 October 2006 (UTC). Substituted at 03:45, 30 April 2016 (UTC)

Additions regarding RNAi mechanism and therapeutic approaches

First, I am delighted to find out that the article published on one of my most interesting fields is "featured"! In fact, it is truly well structured: clear table of contents and understandable leading overview. I also appreciate the quality of figures and the citation of key references of the main contributions to the RNAi discoveries.

Yet, I would like to point some lacunae: 1. Regarding the figure of the petunias, its reference must be Napoli & Jorgensen (i.e. 162 not 160). And it's important to mention their names in the text. 2. Regarding the first sentence of the article, you saved yourselves by using the diplomatic adverb "typically". Despite this diplomacy, the sentence is still wrong: if the the gene expression (i.e. transcription into mRNA) is inhibited, then there is no more mRNA (upstream) to be destructed. Therefore, to play it safe and cover all possible mechanisms of RNAi, I suggest to rephrase the first sentence as follows: "RNA interference (RNAi) is a biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules". This definition covers the possible actions of RNAi: in the nucleus before exit of mRNA to the cytoplasm, cleavage by RISC or blocking the access of ribosomes. 3. I would suggest to add an illustration of the experiment of Mello & Fire, which was central in the RNAi history, instead of simply showing a photo of C. elegans. 4. As for the mechanism of gene silencing, you missed a very crucial step: both miRNA and siRNA have two strands, sense and antisense. So, the major step before destruction by RISC is retaining the antisense and discarding the sense. RLC (RISC-Loading Complex) achieves this selection. 5. Mentioning "Argonaute" as the cleaving protein is braod; let's be more specific: its Argonaute 2 (Ago2)! Then, why was it named argonaute? I'm always interested in knowing and informing the readers about the nomenclatures and etymologies. 6. I would suggest to add some more therapeutic applications of RNAi beside viruses and cancer. By the way, either subtitle "viruses" and "cancers", or "antiviral" and "anti-cancerous", or "virology" and "oncology"! 7. I suggest adding a section about the delivery vehicles of RNAi.

Congratulations again for the quality of the article, especially on the level of organization! I'm available to participate in editing the article upon responses to my present evaluation. Thanks! Oucèma — Preceding unsigned comment added by AboulOus (talk • contribs) 03:24, 28 October 2016 (UTC)

@AboulOus: Thanks for posting your thoughts! I was one of the people who brought this to "featured" status, and most of that work was done in 2006, with a push to get it up to scratch after the Nobel was announced, leading to an FA nomination in early 2007. Obviously there have been updates since, but other than a brief review in 2008 I don't think anyone has really systematically gone through to make sure everything is current and polish it up again. Sounds like you know the topic well, so go right ahead! You can post at the MCB or medicine project talk pages if you need help or want more feedback. Opabinia regalis (talk) 04:12, 28 October 2016 (UTC)

miRNAs epigenetically altered????

Hi. A quote from the article: "For instance, in gastrointestinal cancers, nine miRNAs have been identified as epigenetically altered and effective in down regulating DNA repair enzymes." I believe that is an incorrect statement. I believe the correct statement should be: "For instance, in gastrointestinal cancers, nine miRNA genes have been identified as epigenetically altered and thus cause effective down regulation of DNA repair enzymes". Am I mising something? I haven't read the reference and citations from it in excruciating detail, but I don't believe the miRNAs themselves are modified. Small point at the fringe of my knowledge, so I haven't made the change unless I get input. Thanks, DennisPietras (talk) 13:23, 18 January 2017 (UTC)

Translation

@2604:2D80:4000:810C:2DF0:7F05:D8D0:9126: Seriously, do you understand the process of translation and how it differs from transcription? If you think you know something that I don't, please explain it here. DennisPietras (talk) 20:19, 24 January 2017 (UTC)

Regulatory RNA is not only RNAi

I think that this page is quite good on RNAi but what concerns me is that "Regulatory RNA" sends me to this page. RNA inhibition using the miRNAs is only one of the presently known kinds of RNA regulator-based systems that regulate gene expression at various levels. miRNAs are usually but not always inhibitory of gene expression, acting post-transcriptionally by activating the degradation of mRNAs that match the miRNA, true.

But there are other kinds of RNA that shut down transcription of blocks of chromatin, for example the Xist and Tsix and related molecules involved in X-inactivation for dosage compensation. Those are long noncoding RNAs (lncRNAs). The chromosome-wide inactivation of genes for transcription occurs via recruiting of polycomb complex. It's an epigenetic regulator of inactive chromatin state.

Enhancer RNAs might turn out to be a subset of the lncRNAs but some of them may be much shorter than the 200bp cutoff; in my view we haven't worked out enough systems regulated by enhancer RNAs to know. But they involve regulation of one or a few genes controlled by the enhancer that is transcribed, not multi-gene blocks of chromatin. I am planning to write an article for Wikipedia briefly summarizing the types of Regulatory RNA. It will connect to this article and the other relevant ones so that the strange cross reference won't have to occur. Please let me know if this sounds counterproductive to you.LLMHoopes (talk) 10:03, 6 August 2018 (UTC)

@LLMHoopes: Long-delayed reaction, but eeek, you're right, regulatory RNA really shouldn't redirect here. Did you ever get around to writing that more general article (maybe under another title)? Opabinia regalis (talk) 22:50, 29 December 2018 (UTC)