Talk:RNA silencing

Wiki Education Foundation-supported course assignment

This article was the subject of a Wiki Education Foundation-supported course assignment, between 22 August 2019 and 4 December 2019. Further details are available on the course page. Student editor(s): Avultaggio. Peer reviewers: Kasarlo.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 07:39, 17 January 2022 (UTC)

Comments from Bmesido1

The lead section follows style guidelines though I would strengthen it more by also including piwi-interacting RNA in the lead paragraph. Cited sources accurately represent the contents mentioned in the article and the writing is clear without excessive jargon and without ambiguity. Each section matches well with the section heading and the content is well-structured and written from a neutral point of view.

I would suggest amending the heading "Applications" to "Therapeutic Applications." Also, the author(s) may wish to add short hairpin RNA (shRNA) to the article. Pfeffer et al. found that shRNA is a valuable tool in genetics for technological and therapeutic applications in RNA silencing and you may find their work relevant to your article. Pfeffer et al. looked at the use of synthesized shRNA that are processed to siRNA to stably inhibit gene expression.

Works Cited:

Pfeffer et al. (2005). RNA silencing. B.I.F. Futura. 20. Retrieved on 2 May 2013 from < http://www.rockefeller.edu/labheads/tuschl/Pfeffer,BImeeting05.pdf>. Bmesido1 (talk) 02:23, 3 May 2013 (UTC)

Thank you Bmesido1. This is very helpful. I agree with referring to piRNA in the leading paragraph and adding a description of shRNA. Thank you for the citation as well. I also agree with clarifying the Applications header, but may find a different descriptor than therapeutic because the applications are not all strictly related to the clinical/medical areas. Again, thank you for this very helpful feedback! Ppelletier (talk) 01:19, 7 May 2013 (UTC)

Comments from Awotawa1

Hi, guys. It really looks like you've put a great deal of effort into your article. Congratulations! I have a few observations and a few suggestions for improvement to list; however, the article is looking very good. I want to begin by saying that, overall, the text is well-written and flows well. I like that you've incorporated at least one image into your article. There may be some places in the article for you to add additional images if something seems appropriate and will add meaningful support to the text. Just be careful to maintain an encyclopedic tone throughout the article. There are a couple of instances in the article that the phrase "at least" is used in a manner that is not necessary. A non-scientist would have a difficult time getting through this article. It makes perfect sense to us because we hear and see these terms every day. There may be some opportunities within the article to make things a little simpler without feeling like you're "dumbing it down" too much. Under the piRNA section, you briefly mention rasiRNAs at the end, and then don't explain what they are. That just leaves the reader hanging. There is a LOT of overlap between this article and the RNA Interference article. I realize that you don't want to be redundant and repeat what the other article already states, but the section on biological functions is almost completely referring the reader to another article. Brainstorm and see if you can come up with some novel content in this section. Also, there are some sections near the end of the article, such as the research section that have no content. As for the subheading for open ended questions, you may want to consider changing that to Ongoing Research or something similar since it closely follows the section addressing recent and current research. I hope this is helpful. Great job so far! Awotawa1 (talk) 02:39, 3 May 2013 (UTC)

This is great feeback. Thank you for pointing out that rasiRNA needs to be fully developed elsewhere. I will attend to that. Using the phrase "at least" is a bad habit I have picked up working as a patent attorney and will edit appropriately. Great catch. I also agree that know that the majority of the content has been introduced, it is worth adding some explanatory/paraphrasing to make it more accessible to a non-scientist. Also, I am working on an illustration or two to include for that purpose as well. I am completing the unfinished sections this week also agree that Ongoing Research is a very good title. Again, many thanks for this very helpful and constructive feedback. I also agree we should avoid where possible referring the reader to a different page. To the extent we have overlapping subject matter we can adapt the explanation to the context in which we are discussing it. Martin, can you work on that in the biological functions section? Ppelletier (talk) 01:19, 7 May 2013 (UTC)

Unit 11 and 12

Martin, I am finalizing my new entries now. Also, I want to create a diagram and will do so today. My thought is that the best place to post it will most likely be in the "Mechanism" section. I will try to diagram something that complements the portions you have drafted and otherwise will incorporate some explanatory content. Ppelletier (talk) 14:42, 26 April 2013 (UTC)

Tiny details

By reading a little more of the article "Genetics of RNA Silencing", I believe that the terms Post-Transcriptional Gene Silencing and cosupression were just used first, before the use of the word RNAi (check iRNA in 3rd paragraph of Background). There really isn't any difference in the mechanisms, so I won't add anything to that part. I'll add a link to the RNAi sub-article about the more-in-depth RNAi mechanism description. MartinLubell (talk) 02:59, 26 April 2013 (UTC)

Groups of similar citations. (I'll take care of this once we are done.)

1. 6, 16 21, 29
2. 8, 38
3. 10, 19
4. 13, 15

MartinLubell (talk) 16:12, 25 April 2013 (UTC)

Hi Martin, I confess I did not consolidate the citations because I did not know how to do it. I assume it is by using the "Named References" feature. But I will do so going forward. Thank you for catching. Ppelletier (talk) 16:18, 25 April 2013 (UTC)

Google finds RNA Silencing right away!

Hello Pauline, It's probably obvious, but when you search for "RNA Silencing" with Google, our article shows up first. That's pretty cool! I think we should make sure that there exists the link to the RNAi article right away, which is considered one of the best Wikipedia articles. (I checked, we do have the link, but maybe we can bring the 2nd paragraph as the 2nd sentence of the 1st paragraph?) MartinLubell (talk) 16:00, 25 April 2013 (UTC)

Hi Martin, I agree. Prominent linking to that page is a priority. As well as throughout wherever appropriate. It is important for situating the topic. Ppelletier (talk) 16:16, 25 April 2013 (UTC)

Comments from tbrownc1

The article has a lot of good information and the amount of sources are great. The material reads smoothly and is easy to comprehend. The only thing that I suggest that the group may want to reorganize/change is the part of the article were there is an overview, introduction, and summary. A different title for these section may help the awkwardness (for lack of a better word). Maybe merge the "Overview" and "Introduction" and title it "Background". This would give the different types of RNAi's could have a section title. I also have to agree with Lauren on the "Biological Functions" section, more research should be done on this section or maybe try to incorporate it into another section within the article. Tbrownc1 (talk) 03:29, 12 April 2013 (UTC)

Thanks Tiara. I will be working on adding more to the biological section. The problem I've been having is that the RNAi article, that has already been written, and considered one of the best of Wikipedia, contains a lot, and I don't just want to repeat that. What I'm going to try to do is point out the biological parts of RNA silencing that are not included in the RNAi parts.

MartinLubell (talk) 15:37, 25 April 2013 (UTC)

After working on it for hours, I just decided to link to the sub-section of the RNAi article, because I would just be repeating the concepts, but using poorer wording. This way, I'm keeping it simple and not plagiarizing. Pauline, if you want to delete it completely, I would understand. MartinLubell (talk) 09:12, 26 April 2013 (UTC)

I agree with Tiara. I will merge the sub-headers into a single section. There is no reason to sub-divide further than that until we get into the substance of the article. Ppelletier (talk) 16:22, 25 April 2013 (UTC)

Comments from laurenwking

So I think overall this page is good. There is substantial information on the topic, but you don't lose focus. My only real issue is with the "summary" section. I think it needs a different name. Actually, if you just get rid of summary, that paragraph can stay under the introduction heading. Also, the first two paragraphs need to either be removed or incorporated into the rest of the page. They do not flow with the rest of the page and it seems disjointed. Finally, maybe expand a little more in the Biological Functions section; it seems light on information.Laurenwking (talk) 01:24, 12 April 2013 (UTC)

Thanks Lauren, I will be working on improving the biological part of it. As I explained to Tiara, my dilemma is differentiating the parts that are already included in the RNAi article, considered one of the best of Wikipedia.

Lauren, I just decided to link to the sub-section of the RNAi article, because I would just be repeating the concepts, but using poorer wording. MartinLubell (talk) 09:09, 26 April 2013 (UTC)

I will work on improving the flow of the first section. I agree it could be integrated more smoothly. Ppelletier (talk) 16:24, 25 April 2013 (UTC)

Hi guys, I think you did a great job reorganizing and adding to the article. I agree that linking the sub-sections was the way to go. As far as content, this page seems pretty complete to me (with the exception of the last two sections which I know you will fill in). Well done! Laurenwking (talk) 22:08, 1 May 2013 (UTC)

Hello Lauren, thanks for the compliments, Pauline deserves most of them! I'm still wondering if the "Wikipedia raters" will also think that linking the sub-sections is the way to go. For next week, I'll be working of the "Open ended questions" section. MartinLubell (talk) 03:18, 3 May 2013 (UTC)

Unit 9 - RNA Silencing Wikipedia article

Hello Pauline, in my sandbox, I wrote a rough draft of the mechanism of RNA Silencing, yeah, pretty bad, but anyway, I got something down, and I'll be continuing tomorrow with the biological functions. Once you've put up your stuff to the article (I'm assuming, or just in our group page?), I'll add my stuff. I don't want to overwrite your stuff or vice-versa : ) Good night, MartinLubell (talk) 04:58, 5 April 2013 (UTC)

Hello again, I just added my mechanism part on the article to see how it would go, and I think it went OK. I hope I didn't disturb your edit. If anything, you'll just overwrite mine, but I have a backup :) MartinLubell (talk) 05:26, 5 April 2013 (UTC)

Hello Martin, I am going to incorporate my content. I may also try to create an original diagram and upload it to the commons later today.Ppelletier (talk) 16:21, 5 April 2013 (UTC)

Hello Pauline, amazing job you've done, the number of references alone is incredible! MartinLubell (talk) 17:28, 5 April 2013 (UTC)

Hello Pauline, I added Prof. Ogg's quote 2nd paragraph. Feel free to move it around or integrate it in your overview. I like it at the beginning because it was something that I had a hard time understanding. "RNA silencing is a broader category than RNAi, and RNAi falls into the category of RNA silencing. However, having this distinction does not necessarily mean that everyone considers silencing and interference to be two separate entities. In much of the literature you will hear both terms used interchangeably." MartinLubell (talk) 19:32, 5 April 2013 (UTC)

Improvement of the Article

The following editors are currently dedicating time to improve this article.

• User:MartinLubell/sandbox
• User:Ppelletier/sandbox
• Team Talk Page - Group_81H

Ppelletier (talk) 17:26, 5 April 2013 (UTC)

General Comments

In general, a unique issue with this topic is its breadth and potential overlap with iRNA, which encompasses miRNA and siRNA. Each of these topics have a respective entry on Wikipedia. "RNA silencing" is construed here as broader, although it would be helpful to have feedback on this construction from the community. The Overview section is intended to address RNA silencing and how it has evolved over the years, whether there are any other types of RNA silencing in addition to miRNA and siRNA, and beginning to craft some distinctions to the extent this is helpful in understanding RNA silencing as a broad topic covering a variety of mechanistically related pathways for controlling gene expression involving small RNA.Ppelletier (talk) 17:26, 5 April 2013 (UTC)

Regroup all the terms RNA Silencing, DNA Silencing, RNAi, etc and link to the different Wikipedia articles or regroup all the different articles under one mixed title? MartinLubell (talk) 04:54, 14 March 2013 (UTC)

• Small interfering RNA
• Gene silencing

(Copied list from Gene silencing article)

Proposed Outline

Our proposed outline is as follows, again feedback is requested from the community:

1. General Overview
   1. Definitions (PP-Unit 9)
      1. RNA silencing
      2. RNAi
      3. miRNA
      4. siRNA
      5. rasiRNA
   2. Summary (PP-Unit 9)
      1. family of gene silencing effects
      2. post-transcriptional gene silencing (PTGS)
      3. general overview of RNA silencing
2. Molecular mechanisms (ML-Unit 9)
   1. Key players
   2. Mechanistic description
3. Biological functions (ML-Unit 9)
   1. Processes affected
   2. Manifestations
4. In-depth
   1. Laboratory techniques (PP-Unit 12)
   2. Medical implications (PP-Unit 12)
5. Recent discoveries (PP-Unit 12)
6. Open ended questions (PP-Unit 12)

Ppelletier (talk) 17:26, 5 April 2013 (UTC) Updates to outline. Ppelletier (talk) 03:09, 26 April 2013 (UTC)

Hey, I just wanted to drop by and say that this outline looks great! :) Keep up the fantastic work - I'll try to get a review done for you guys in the next few days. Keilana|^{Parlez ici} 14:49, 26 April 2013 (UTC)

Specific studies of gene silencing

There are several more terms related to specific topics of gene silencing:

Transcriptional Gene Silencing:

• Genomic Imprinting
• Paramutation
• Transposon silencing
• Transgene silencing
• Transcriptional gene silencing
• position effect
• RNA-directed DNA methylation

Post-transcriptional Gene Silencing:

• RNA interference
• Nonsense mediated decay

Meiotic gene silencing:

• Transvection
• Meiotic silencing of unpaired DNA

Cellular components of gene silencing:

• Histones
• Chromatin and heterochromatin
• MicroRNA
• siRNA
• dsRNA
• Dicer
• Transposons

Ribozymes, siRNA and antisense technologies such as Morpholino or PNA oligos are experimental approaches used to post-transcriptionally silence targeted genes of interest. — Preceding unsigned comment added by MartinLubell (talk • contribs) 05:21, 14 March 2013 (UTC)

Reverse order: Last subject in is at top!

It might be confusing in the long run, but the latest subjects are at the top. MartinLubell (talk) 03:26, 3 May 2013 (UTC)

RNA silence and RNA interference

These are two different things, with two separate articles, so I'm not sure why the lead sentence of the article implies that they are the same thing. Pariah24 (talk) 18:12, 14 December 2018 (UTC)

Indeed, it is confusing. As an RNAi researcher, I used them interchangeably and didn't know the distinction. The RNA interference article also doesn't link to this page, which doesn't help. It might help to put in a "Terminology" subheader under "Background" Strongyloides (talk) 21:32, 20 September 2021 (UTC)