Talk:Gene silencing

Genes are regulated at either the transcriptional or post-transcriptional level.

why does post-transcriptional hyperlink to the article on translation?--Xiaou 09:19, 24 December 2005 (UTC)

How are transposons connected to gene silcening?

I really wonder how Transposons should posses a function in gene silencing? They are mobile genetic elements and I don't see a connection? Anyone else maybe? CU CoBli —Preceding unsigned comment added by 89.59.104.38 (talk) 13:09, 27 April 2008 (UTC)

Bit of a late reply, but no harm in me answering the question I suppose. Transposons can cause gene silencing when they're inserted into a gene, hence altering the DNA sequence of that gene. Proteins coded by this gene will then likely be non-functional and so the gene is 'silenced'. Ribrob (talk) 22:56, 15 January 2009 (UTC)

Article Improvement

Hello fellow Wikipedians! As part of our Molecular Biology course at Johns Hopkins University, Ileana and I will be working to improve this article.

Summary of our suggested improvements:

• Organize the article into the following categories: Introduction, gene silencing in the cell, and gene silencing in research.
• Expand on the introduction of gene silencing and touch on the different aspects associated with gene silencing, such as post-transcriptional gene silencing, transcriptional gene silencing, and the use of gene silencing in research.
• Discuss the mechanisms of gene silencing under the “Gene silencing in the cell” category. Also, discuss transcriptional gene silencing, post-transcriptional gene silencing, and meiotic gene silencing in detail.
• Discuss gene silencing techniques that are utilized in research experiments.
• Explore how gene silencing can be used to study disorders, such as neurodegenerative disorders, and produce therapeutics.

Any input or suggestions would be greatly appreciated! Thank you! - Agulati4 (talk) 03:30, 22 October 2013 (UTC)

Comments from hnagy2

The new organization for the article is spot-on, comprehensive and not too narrow. It's stylistically appealing and allows for ease of skimming. The breakdown for research techniques is a very useful section. I personally like how the ribozyme sub-section is written with a brief description of the different known motifs and the common elements of their catalytic mechanisms. A lot of information is condensed but made understandable. The image used is simple (not confusing or overwhelming with too much information) and appropriate. I'm interested in seeing how you summarize antisense oligos and RNA interference. It is shaping up to be a great sub-topic.

It's an interesting approach to break down gene silencing in research by disorder. The wide variety of disorders you have listed shows how powerful silencing techniques are. The section devoted to challenges in research is another useful one, not every Wiki article addresses issues in therapeutic approaches. There are so many related articles on Wikipedia that the section categorizing transcriptional, post-transcriptional and meiotic gene silencing is a practical way to tie them in with gene silencing in general. Maybe some text could be added to preface each grouping for common features or to give more context. Overall, this is a terrific start. The references are properly cited and used appropriately, including a wide range of published third-party articles. The tone is neutral, the language is understandable and the organization makes sense intuitively. If all subsections are filled in using the same standards this will be a top-notch article. — Preceding unsigned comment added by Hnagy2 (talk • contribs) 01:07, 4 November 2013 (UTC)

Thanks for the review! We will definitely work on adding more information to the transcriptional, post-transcriptional, and meiotic gene silencing sections. Please let us know if you have any other recommendations on how we can improve the article. Thanks! - Agulati4 (talk) 00:50, 6 November 2013 (UTC)

Review by Neelix

Hi all,

The improvements to this article are looking good so far. Here are some additional recommendations:

• Paragraphs should be made up of more than one sentence.
• All sections should contain paragraphical text.
• Avoid vague use of the word "this".
• A given wikilink should appear only once in the body text of an article.
• There should be no unsourced statements in the article.
• When referring to particular studies, specify the who/where/when.
• The word "use" is almost always preferable to the word "utilize".

Thanks for contributing to Wikipedia! Let me know if you have questions about the above. Neelix (talk) 01:43, 4 November 2013 (UTC)

Thanks for the review and the suggestions! We will definitely make the changes you suggested. I have already edited the wikilinks and changed the sentences that used "this" vaguely. I also went through and changed "utilize" to "use". Please let us know if you have any other recommendations on how we can improve the article. Thanks! - Agulati4 (talk) 01:10, 6 November 2013 (UTC)

Hi all,

I like what you've been doing with this article. Several issues I outlined above continue to linger; I would recommend reviewing the list I provided above. I hope you are having a good experience with Wikipedia.

Neelix (talk) 06:03, 26 November 2013 (UTC)

Thank you Neelix. We will continue to work on the suggestions you made above. - Agulati4 (talk) 00:31, 27 November 2013 (UTC)

Comments from Juanquina Thomas

The information added to this topic is very plentiful! I like the style of your content and its ability to flow from one subtopic to the other. You seemed to have simplified your information very well. I feel that it is very easy to read and does not contain too much science jargon for those people who are not scientists. I am not very sure of the font size and style of your content, especially under the heading 'Gene silencing in medical research'; however, I understand that this is not the final draft. There are a few things I would like to point out:

• The introduction paragraph does not contain any citations
• The start of the first two sentences in the introduction seem redundant.
• Is there a need for the parenthesis and quotation marks around "turned on" in the introduction paragraph?
• Under the topic 'Gene silencing techniques' it seems that the topics you listed (that are going to be discussed) are not actual techniques, but components used in gene silencing techniques (I could be mistaken. I am not an expert on this topic.)

Overall, I think this is going to result in a great article! It seems that there will be a substantial amount of information for any topic in relation to the main topic. You guys are going in a great direction with your jargon! I have not observed any plagiarism of information that has been cited. Great job guys. Keep up the good work!Juanquina Thomas (talk) 03:44, 6 November 2013 (UTC)

Thank you for the review! We are still in the process of going through the Introduction, but your tips will be extremely helpful as we clean it up! For the "Gene silencing research techniques" section, I believe you're correct. The title is a bit misleading. So, I have changed it to "Gene silencing methods used in research." Please let me know if you think that heading is more accurate to describe the methods of gene silencing used by researchers. Also, I'm not exactly sure what you mean by the font size and style of the content under the "Gene silencing in medical research" section. If you could expand on that, I would really appreciate it! Thanks! - Agulati4 (talk) 23:30, 11 November 2013 (UTC)

Comments from Galemu2

At first glance this article has an excellent outline. I think you have sections for all the necessary topics that should be discussed under this subject. I believe this article is on its way to becoming a great source of references for all readers. You also have lots of references, which is a good thing.

I have to work hard to find improvements for this article. One sticking point for me is that the lead section looks a little light. It may add substance if you summarize key parts of the article in the lead section. The second important aspect of a lead section is to establish noteworthiness, which you have done. Lead section does not need references according to the style guideline.

Additionally, you will improve article by including images. Scientific discussion is almost impossible without images. Furthermore, I think all scientific terms should be wikilinked the first time they appear in the article. This way a lay person can know the meaning of the term before continuation to the rest of the article. I really believe this article is on its way to becoming a B class or better Wikipedia article. Wish you much luck. Galemu2 (talk) 05:16, 19 November 2013 (UTC)

Thank you for your suggestions! Yes, I agree the lead section does look a bit light. I will add more details to it. Thanks for including the link to the lead section style guide. That will definitely be useful as I edit the lead section! I will also work on adding more images and making sure the scientific terms are appropriately wikilinked. Thanks again for the suggestions. They are much appreciated! - Agulati4 (talk) 22:58, 19 November 2013 (UTC)

Hello again Agulati4. You have done a great job improving this article from its previous state. I can see that you have added more references. I also can see you have been working on the lead section. I am eager to see what this article would look like after most sections have finished. Keep up the good work. Galemu2 (talk) 06:05, 7 December 2013 (UTC)

Thank you Galemu2! Please let us know if you have any other suggestions as to how we can further improve the article during this last week. We would truly appreciate any advice! - Agulati4 (talk) 05:18, 12 December 2013 (UTC)

Hello Agulati4. Hope all is well. I can see that you have worked hard on the "..medical research" section. This section is clearly relevant to gene silencing and you have made the correct choice on focusing on this. Hope you don't mind that I changed the image location in the "Hungtington’s disease" subsection. I think it would look better on the right. Hope you'll continue to work on this. Galemu2 (talk) 04:28, 14 December 2013 (UTC)

Hi Galemu2. That is perfectly fine! I wasn't sure which side it looked better on so I had put it on the left so that it would balance out with the other image that I had positioned on the left, but when I look at it now I think you are correct and it does look better on the right. Thank you for changing that! - Agulati4 (talk) 14:50, 14 December 2013 (UTC)

Comments from Madscientist2007

Dear Agulati4 and Opalite3579,

If I had to sum up the work you have done so far into one word, that word would be “Wow!” I must say that I am thoroughly impressed by how well researched and well written your article is thus far. I know that the same time and effort will be put into the remaining sections, along with the passion you both obviously have for this topic.

I took a page out the book of one of our fellow classmates who analyzed my group’s article during the first round of reviews, and went back to the earliest version of the “Gene Silencing” article I could find. This took me back to the end of October. I would have liked to have gone back to before you chose this article. With that aside, I must say that the contrast is amazing. In a few short weeks, the two of you have really transformed this article. Furthermore, I can only see this article getting better and better in the remaining weeks.

I read over the comments provided by my fellow reviewers from both the first and current review periods. In hindsight, this was a mistake as they basically covered all of my ideas! It is also obvious that you took great care to incorporate these ideas into your writing and presentation. Although it is needless to say at this point, I will say it anyway. I agree with the comments and suggestions put forth my fellow reviewers.

With that said, I am not sure as to how much more I can add. I did, however, do a quick search online and came across two areas of interest that I would like to propose here:

• I found at least a few articles that examine the possible connections between gene silencing and aging. Some of these pieces go a step further and examine as to how dietary restrictions such as caloric intake might play role in these connections.
• I came across the following comment on www.biology-online.org: “I have checked Wikipedia, but I still do not understand the differences between gene knockdown, gene knockout and gene silencing. Anyone please help me. Thanks.” This may be something that you might want to consider as a potential section or subsection. Should you chose to go in this direction, there is one reply to this request which might provide with you with a good jumping off point.

Your article is unfolding beautifully. There is a smooth, logical flow to it, which is greatly aided by your use of well-constructed, well placed transition sentences. Please keep this in mind as you fill in your remaining sections as these transitions help to keep an article from sounding disjointed. Overall, a job well done. I have no doubt that your work will continue to remain as such as the semester comes towards a close. I wish you both the best of luck and I greatly look forward to reading the finished product come mid-December.Madscientist2007 (talk) 17:22, 22 November 2013 (UTC)

Thank you so much for your suggestions! Also, thanks for directing me to the comment on the differences between gene knockdown, gene knockout, and gene silencing. This will be perfect information to include in the lead section of the article! We will also definitely try our best to incorporate the connections between gene silencing and aging. Thanks again for the suggestions! They are extremely helpful! - Agulati4 (talk) 23:52, 23 November 2013 (UTC)

I am glad that I could help! To make things a little bit easier, I went back and grabbed the link that will lead you to that comment and the given answer: http://www.biology-online.org/biology-forum/about6772.htm. I am sorry for not including that before. Good luck with everything! Madscientist2007 (talk) 01:05, 24 November 2013 (UTC)

Thank you for the link! That is extremely helpful! - Agulati4 (talk) 07:47, 24 November 2013 (UTC)

No problem! Madscientist2007 (talk) 15:31, 24 November 2013 (UTC)

The article looks great! You both have done such a wonderful job transforming this article. The best of luck to you both as we head into the final week. Madscientist2007 (talk) 22:44, 8 December 2013 (UTC)

Thank you Madscientist! Please let us know if you have any other suggestions as to how we can further improve the article during this last week. We would truly appreciate any advice. Good luck to you as well! - Agulati4 (talk) 05:20, 12 December 2013 (UTC)

You are quite welcome! I will certainly let you know if think of anything else.Madscientist2007 (talk) 20:41, 12 December 2013 (UTC)

Comments from Pozmi

Hi Group 84F! Your article was a great read. Here are a few comments:

Content Coverage: The writing style is helpful and clear, one example being the explanation of gene knockout vs. knockdown in the introduction. There is a diverse amount of information on the role of gene silencing in research and medical research. I also appreciate that you added some of the history and development of the study of gene silencing. For the section of gene silencing in cells, there's a good list of other relevant Wikipedia pages, which is a good feature to have retained from the original stub. Most of these topics (except for a few in the Transcriptional gene silencing section) have their own pages, so the content does not need to be repeated on this page. However, if I were to suggest the addition of any more prose content to the article, it would be in the "Gene silencing in cells" section. For example, a few sentences explaining the features of transcription vs. post-transcriptional vs. meiotic gene silencing. This way, the content of the specific articles wouldn't be repeated, but the user would have an overview of the differences between them.

Writing Organization: Good structuring of the sections and subsections. The content also seems to be evenly distributed, giving the article a balanced look. Dividing gene silencing by location in cells, research, and medical research also helps the user understand the role of gene silencing in different contexts.

Wikilinking: Good job in making diverse and specific wikilinks without repetition. Some more links that could be added are "genome" in the introduction and "RNAi". I see you've already wikilinked "RNA interference" but linking RNAi as well could emphasize the subject. One of the wikilinks is "Escherichia coli", which I believe should be italicized. I wasn't sure if it was form to put wikilinks into italics, but I've seen it done on this page as E.coli.

Illustrations: Nice work in providing your own image for the ribozymes section! Perhaps the RNA interference image could be shown a bit bigger, since it has a number of components and a long caption. To accomodate the large size, the image can be placed in the center under the text of the RNA interference section.

Referencing: Good use of providing citations throughout the article. You seem to have chosen reputable sources, and I appreciate the diversity between journal articles and textbooks. These references, along with the "External links" you provided give the reader some quality options in continuing their reserach on this topic. If you want to tighten the formatting of the references section, you can write

{{reflist|2}}

which presents references as two columns. My group's article shows an example of this.

Great development since the original stub and best of luck with the final contribution! Pinar --Pozmi (talk) 06:03, 7 December 2013 (UTC)

Hi Pinar! Thank you so much for your suggestions! We will definitely try to add more information to the Gene silencing in cells section. I will definitely wikilink RNAi and genome as well and will try to figure out how to make the Ribozyme image bigger. Also, great suggestion for the reference section! Thanks again for the suggestions. They are extremely helpful! Please let us know if there is anything else that we can do to improve the article! Thanks!- Agulati4 (talk) 05:09, 12 December 2013 (UTC)

Comments from Pdholak1

Hello! I am so impressed by your article, you guys have done a great job to cover all aspects of your topic. Here are some general comments about the page:

• Solid introduction, I especially like the concise explanation of the differences between knockout and knock down
• The list for gene silencing in cells has really great wikilinks...the ones that dont have a link you may consider either removing or adding a small description so that people can have at least a little information about those
• The two pictures in the research section provide good support to the content. You may consider adding a picture or two to the medical research section, maybe for the infectious disease part?
• Overall the writing is informative but easy to read.

Thanks, and good luck with the finishing touches! You guys are doing great. Pdholak1 (talk) 18:29, 8 December 2013 (UTC)

Thanks for the suggestions Pdholak! I am looking for more images to add, but I'm always a bit unsure of the licensing part. Hopefully I can find something on Wikipedia Commons that will enhance the article! I will definitely keep a look out for any words that are not wikilinked and try to explain them further. Thanks again for the suggestions! We truly appreciate it! - Agulati4 (talk) 05:13, 12 December 2013 (UTC)

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Why is CRISPR included in this page?

The article says "Gene silencing is considered a gene knockdown mechanism since the methods used to silence genes, such as RNAi, CRISPR, or siRNA, generally reduce the expression of a gene by at least 70% but do not completely eliminate it." However, I am not understanding why CRISPR is included in the discussion of reducing expression of a gene - RNAi and siRNA are mechanism that target mRNA and will therefore only reduce expression, whereas CRISPR works with Cas enzymes to cut DNA at a specific location. How does CRISPR only reduce expression? Can someone provide clarification? D Money 16 (talk) 02:07, 26 August 2020 (UTC)

Silencing can also be transcriptional e.g. methylation - in this case the transcript is produced at a lower level, as opposed to post-transcriptional silencing in which transcription occurs but the mRNA is degraded before translation into a product. I'm not sure if I agree, but the logic would be that CRISPR can also involve small mutations to prevent or reduce transcription, causing silencing rather than a "knockout" in a traditional sense. However... CRISPR can also be used to completely remove a gene! So I feel it's misleading.

Also, I don't know about the 70% figure... there are plenty of studies where gene silencing is able to completely prevent the expression of a gene, and there's no citation. An example I pulled at random: https://www.liebertpub.com/doi/abs/10.1089/154545703322617069

I don't have time to edit it properly but the introductory section definitely needs work... I'll add a citation needed tag at least. 167.179.189.213 (talk) 02:12, 23 September 2023 (UTC)

Transgene silencing

I'd like to suggest removal of transgene silencing as a "type" of silencing - or at least it should be in both TGS and PTGS categories. There's no evidence it involves unique silencing mechanisms, though how/why transgenes are targeted by silencing is still not fully understood. 167.179.189.213 (talk) 02:16, 23 September 2023 (UTC)