Talk:Small interfering RNA

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shRNA are different from siRNA - sh stands for Short Hairpin, not just plain Short.

shRNA are synthesized as a single-stranded palindromial RNA fragments, short enough to constitute as an artificial siRNA.

There was a confusion between de two concepts. I've changed some sh by si. Llull 16:44, 25 March 2006 (UTC)

I have also deleted confusing description of siRNA as a "silencing RNA" User:Bavykinas

Please notice that there is no reference to the following section: RNAi induction using siRNAs or their biosynthetic precursors. Obviously the info was taken from particular study, I mean there should be the paper reference after This is done by the introduction of a loop between the two strands, thus producing a single transcript, which can be processed into a functional siRNA.--Vnatik (talk) 16:43, 22 September 2011 (UTC)

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Questions

that intend to enhance understanding the concepts of this article

• How does siRNA relate to Viroids? --Tomaschwutz (talk) 15:26, 20 November 2008 (UTC)

SiRNA targets viral matrix RNA and stops synthesis of viral proteins. User:Bavykinas

Perhaps it would be beneficial to explain the mechanism(s) used by Small interfering RNA to silence gene expression as mentioned on this page. I see that this page talks about siRNA being used for gene silencing but now how it accomplishes this feat.

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The Wikipedia entry has relevant information, however, there isn’t much information about the post-transcriptional gene silencing. There is information as to the discovery of it, but not much information on how exactly this process works. The page also doesn’t have a section on transposon silencing, which siRNA causes. This is also something that can be added. Lastly, there aren’t many images on the page, so we can contribute by adding images too.Shirleycaly (talk) 15:34, 21 October 2016 (UTC)

Peer Review and Responses during the educational assignment in Fall 2016

siRNA Peer Review 1[edit]

Ali F[edit]

The introduction to the article needs to be cleaned up. It’s not terribly inaccessible, but I would focus on making it simpler for the average individual. Furthermore, the sources listed are mainly primary sources: while this is good for establishing ethos, it limits the accessibility of the article further. This is further inhibited by the lack of new figures: the figures that are already in Wikipedia are OK, but you need more. In particular, a GIF or other animation of the process would be helpful. Overall, the content seems to be OK, but the presentation could be improved. The information presented is good, but presentation is important and can stand to be improved. -AMF2718 (talk) 19:01, 20 October 2016 (UTC)

Response: Thank you for pointing out the clutter in the introduction. We have organized the introduction, so the mechanism is simpler and easier to understand. We have also cited textbooks to incorporate secondary sources as well. Figures have also been added however was difficult due to the complexity of some parts of siRNA.

Jonathan K[edit]

The wikipedia page for siRNA is largely the same except for the addition of the sections named "siRNA post transcriptional gene silencing", "siRNA role in Transposon silencing", and "Intracellular Delivery". These 3 new subsections add about 6 more paragraphs of information; however, I do not see anymore citations added for this new information. Altogether, the wikipedia page still has quite a few references, which is good, except all the resources are from research journals. Research papers are a good source of information, but including other sources could be beneficial as well in order to give a more holistic, less biased view of the siRNA topic. Regarding the "siRNA post transcriptional gene silencing" subsection, the first 5 sentences are basically a rephrasing of the information from the introductory section. I did not see any new information, so it might be worth getting into the specifics right away. Since this section is about gene silencing after transcription, maybe it's worth prefacing this section with a statement about how transcription is not affected, which means a normal mRNA is produced. It may also be worth explaining the different parts of RISC such as the different proteins. The remainder of this section has a lot of good information, but the words "5' end", "3' end", "Argonaute", "endonucleolytic/endonucleases", and "ATP hydrolysis" should be linked to their respective wikipedia pages. For the "siRNA role in Transposon Silencing", instead of directing users to another page to view the image, try recreating and simplifying the image and posting it onto wikipedia. The words "transposon", "ping-pong method", and "RdRP" should be linked to their respective pages. Also, try explaining the ping-pong method because most users will not know what that is and how it is relevant. In the "Intracellular Delivery" subsection, there are a lot of words that should be linked because words like "cationic liposomes" and "transfection" will not be known by the common person. Also, you tell the reader that there are 4 techniques but only explain 3 techniques, not sure what that is about. The "Transfection" subsection seems to end abruptly, doesn't contain many details regarding the process, and it doesn't explain its advantages and disadvantages but merely states them. The "Electroporation" subsection is explained very well, but try explaining the advantages and try to give all the details so the reader doesn't have to put the pieces together. For instance, when explaining the higher probability of cell death, explain how this may occur from the loss of important molecules through the pores. The "Viral-mediated Delivery" subsection is a little more confusingly written than the last two subsections and it also needs links for many terms such as "shRNA" and "adenovirus". It is worth going back through this section and trying to simplify the ideas expressed. Overall, the edits have added a good amount of information but could be expressed in a little more detail. Try looking for a textbook or another source that explains the information, if possible. The figures on the page a very good at illustrating some of the concepts but your picture should be on the page rather than in a link. The linked picture is high-quality but seemed extremely confusing to follow. Try to make a simplified picture that only involves the important steps rather than all of the steps. I like what you have written, but there are a few wikipedia pages that contain bits and pieces of the information that you wrote about such as "Transposon Silencing". It may be worth googling each added topic to make sure that you aren't duplicating other wikipedia works. I noticed quite a few grammatical errors such as misplaced commas (or an absence of them) as well as tense changes within a sentence. This should be an easy fix if you all can quickly read the entire passage out loud and correct any inconsistencies. Liljk (talk) 21:36, 18 October 2016 (UTC)User:Liljk

Response: We have added more sources as suggested as well as linked the suggested words. The 4 techniques was a mistake. Explaining RISC seemed unproductive since it is explained in the RISC wiki page.

Adam N[edit]

The Small interfering RNA (siRNA) wikipedia page edits largely remain the same when compared to the original wikipedia page, which is fine because new original information has been added. Those new information specifically being the new section of "Intracellular Delivery" along with its' three sub paragraphs. I do think it's a little bit of a organization problem however, with the added "Intracellular Delivery" section and the original "Therapeutic applications and challenges" section. Within the application paragraph specifically, the issue of siRNA delivery in "off-targeting systems" is mentioned. Then moving on to the added section of "Intracellular Delivery" more challenges are mentioned such as "Transfection," "Electroporation," and "Viral-mediated Delivery." I would consider reorganizing the headings so that challenges with siRNA are grouped together and then can be divided up into sub paragraphs depending on the type of challenges expereinced. In addition, the small paragraph before the heading "Transfection" mentions that there are siRNA delivery challenges but only briefly goes over the types of challenges. "Transfection," "Electroporation," and "Viral-mediated Delivery" paragraphs spend more time focusing on their advantges rather than challenges. Specifically, "Electroporation" it talks about how the technique is very useful for cells that are difficult to transfect. Within the section of 'siRNA role in Transposon Silencing," you told readers to go to another page to the view the image. I would consider creating a an image and posting it within that section. That way readers are viewing it firsthand and hopefully understanding what is being said. In addition, because the "ping-pong methdod" is an important part of the paragraph, I think it would be wise to go into detail about the method that way readers understand the background information. The three added sections "Transfection," "Electroporation," and "Viral-mediated Delivery" all have references to research articles. Research papers are a great source of information and reference however, with any source of writing they do present a source of bias because research papers have and agenda. I would consider adding other sources such as science textbooks to get a balance of perspectives. All in all, the edits to the original page were well thought out and help balance the siRNA page out with pertinent information that a reader would find useful. I think with the edits suggested above and by other group members, the page will be really well done. A few last minute changes would be to link/cite a few advanced science terminology so readers can get easy access to what is being talked about instead of opening up a new page and having to search the term or phrase. -Adam Nehme Umichfratboy (talk) 18:38, 19 October 2016 (UTC)

Response: We have added detail to the Ping-Pong method as specified as well as looked at textbooks for references. We also linked more terms as suggested. While we appreciate your suggestion for reorganization of the intracellular delivery, we do not think there is enough info to insert a subheading.

Kolin K[edit]

Some additions have been made to the small interfering RNA (siRNA) Wikipedia page, all of which seem to be appropriate for this page. Some minor edits could be made to a few of the changes that are being purposed. Many of the edits that I have noticed are similar to the edits that my colleagues have pointed out. In addition to those edits, there were a few others that I have noted:

Regarding the "siRNA post transcriptional gene silencing" subsection, it would be beneficial to add links to some of the terms that were used. The terms that I noticed are exonuclease, endonuclease and exosome. Also, XRN1 is mentioned without any explanation. XRN1 should have a brief description and a link if one can be found. Additionally, many of the topics mentioned in this section are covered on the “RNA interference” Wikipedia page.

Regarding the "siRNA role in Transposon Silencing" subsection, links to the terms transposon and RNA-dependent RNA polymerases should be included. The last sentence regarding the “ping-pong” method could be revised, possibly deleted if a link is available for the previous mentioning of the method. A figure regarding the ping-pong method should be created under this section as well.

Regarding the "Intracellular Delivery" subsection, once again each of the terms under this section could use a link. The content included is specific to siRNA so linking the terms is the only edit I would make here. Moreover, figures for each of these terms would be beneficial to help visualize the different processes.

For the page as a whole, there is no individual picture of siRNA only a picture of the process that makes siRNA. A molecular picture of siRNA should be created and included in the main section. Additionally, there are sufficient references, however, as noted before, there are no non-journal references included. The changes that were made are essential for the understanding of siRNA. The group did a great job in introducing the different roles of siRNA and the length of each section that was added is sufficient for the topics covered. Once the minor edits that were introduced are made, this page will be complete. KKJK19 (talk) —Preceding undated comment added 23:33, 19 October 2016 (UTC)

Response: We linked the suggested terms and added figures as suggested.

Calia R[edit]

Overall the page could be more concise. It is written with many short repetitive sentences versus a single detailed sentence. A wiki page should be quick and to the point. It should also include an introduction before the specific details. A lot of this was from the original page versus the new information added but it is something that would improve the page greatly.

The introductory paragraph is confusing and does not introduce siRNA well. It is confusing to explain the mechanism before including the purpose of siRNA. Interference is mentioned but it is confusing as to what that actually means. Also, it was not mentioned that siRNA is non-coding RNA. Additionally, I read that although siRNA is almost always double stranded, it can be single stranded which you might want to include. Additionally a more concise version of the introductory paragraph would be: Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a type of RNA interference (RNAi) in which noncoding double-stranded RNA is cut into 20-25 base pair segments. It interferes with specific mRNA sequences complementary to the siRNA, typically to silence the gene. After entering the cell, the dsRNA binds to the protein complex Dicer which cuts the RNA into smaller fragments. Next a single strand is loaded into the RNA-induced Silencing Complex (RISC) which binds the siRNA to the mRNA through base pairing, destroying the mRNA, inhibiting translation and therefore protein production, silencing the gene. siRNA therapy can be error prone because although the antisense strand typically bind to RISC, the sense strand could also leading to incorrect targeting.

In the second paragraph of the page, it has already been mentioned that siRNA is a from of RNAi, it does not need to be mentioned again. The first sentence would be better phrased as: siRNA can function as an antiviral mechanism or influence the shape of the genome chromatin structure.

In section "RNAi induction using siRNAs or their biosynthetic precursors" the transient nature of siRNA is mentioned but not why it is transient. This should be explained. In section "RNA activation" dsRNA is mentioned but it is confusing, it all dsRNA being discussed or specifically the dsRNA of RNAi or siRNA? This could be better addressed. In section "siRNA post transcriptional gene silencing" a hyperlink to the wiki page for piwi would be helpful. In section "Innate immunity" a hyperlink to the page for PKR would be helpful. Also the addition of background information is important because mechanistic details such as PKR and retinoic acid are discussed but it is not clear as to what that means in terms of the big picture of siRNA.

In section "Off Targeting" it would be more professional to just cite the publications of the professor mentioned and talk more about their results rather than mentioning them specifically and the year. In section "Adaptive immune response" it is confusing what is meant by Plain RNAs. Also a hyperlink should be included for "immunogens" In section "Chemical modification in siRNAs" the two sentences in this section do not really add much additional information, not do they actually discuss specific chemical modifications made. This sentence could be included in another section and the heading could be deleted all together. In section "Therapeutic applications and challenges" the examples of the phase 1 clinical trials is poorly worded and it is confusing as to what this example adds to the explanation of siRNA. There needs to be more detail rather than just mentioning that RNAi has been a treatment method in the past. Possibly include benefits over other treatment options.

Finally, formatting wise, either capitalize the whole title or only capitalize the first word but just keep it consistent. Right now there are some of each. CAR15 (talk) 06:03, 20 October 2016 (UTC)

Response: We simplified the introduction and made suggested edits. We took out repeating information or made it more detailed to justify the repeat. The therapeutic application section is verified my wikipedia and we did not edit it.

Additional comments from the librarians[edit]

Your peers have mostly made the points that I would suggest. I'd add that you should double-check the "Intracellular delivery" section: its introduction asserts that there are four main techniques of siRNA delivery, but the following text gives only three. You should also include the ping-pong method paper as a reference at the point where you mention the technique, rather than calling it out as a link in the text at the end of the paragraph - the current wording is not in keeping with good Wikipedia writing practice. Finally, make sure that you've adequately linked your technical terms to existing Wikipedia articles on those topics. ScottMLibrary (talk) 15:24, 24 October 2016 (UTC)

Response: We checked the intracellular section as well and included the ping pong method paper as a reference. We also added links. SheaBayBay3 (talk) 20:35, 15 November 2016 (UTC)

siRNA

Never used for HIV. — Preceding unsigned comment added by 2A02:2149:8453:6D00:618E:99C7:F7FE:C82F (talk) 20:50, 18 November 2019 (UTC)

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