Talk:Epitranscriptome

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Material from RNA modification

Almost the entire RNA modification article was copied here, without attribution unfortunately, and without any explanation to tie it into this article. (As well as leaving reference errors when the full references were left behind.) I have added two sources to the further reading section and I am replacing the copied material with See also. It would be better to write the article from sources rather than pasting related material into this one. StarryGrandma (talk) 19:04, 13 April 2016 (UTC)

We plan to edit a lot of the page and add a lot of new content.

--Amhammoud5 (talk) 18:09, 13 October 2016 (UTC)

Epitranscriptomics Peer Review #1[edit] Is the paragraph describing epitranscriptomics going to be the introduction? I would move that to the top (if you aren't already planning to do so). What you have written seems like a really good way to explain this to the general public. Many people learn about epigenetics in basic science courses, so this is a good analogy. I love the details provided in the HNRNPC binding mechanism with m6A. Perhaps a figure would be great to show how the m6A is facilitating this.

It looks like the article goes right into pseudo-seq in the same section as m6A. Is that all supposed to be one section regarding examples of multiple modified nucleobases or are they meant to be in different sections? The level of detail is great, though. I would definitely include a figure with the techniques section to give people an idea of what some of those techniques might look like.

Also, I'm sure this is already obvious to you, but there are a lot of terms used like the different types of RNA and epigenetics that have their own wiki page so you will want to make sure and link those pages. It appears as though you have 5 sources. But, they are all journal sources. There is a slide from the wikipedia lecture that talks about using different types of sources rather than just journal ones. Maybe including a few sources from secondary literature would be good. The other thing I would pay attention to is grammar. But, since this is a draft I assume you aren't really worried about that yet. I think the length appears appropriate for most of it. Although, expanding the section on techniques might be helpful to elaborate for the non-scientist reader.

Here is a review I found that could work as a secondary source. It’s got interviews with experts in the field on developments in the area of RNA modifications. It gives a little bit of the history behind the development of detection techniques for m6A. It mentions the eraser, writer, and reader proteins. Maybe you can use it to expand the section talking about techniques.[1]

~Brian Hardaway (talk) 00:06, 19 October 2016 (UTC)

Epitranscriptomics Peer Review #2[edit] To begin, I think that overall, the authors provided a large amount of deep, and insightful information on the subject. You provide details many of the topics related to N6-methyladenosine (m6A) on Alternative Splicing, and I can tell that you all read into your subject thoroughly before summarizing papers for the purpose of creating this content. Below is my feedback, and review of your current content, which I think will allow you to improve your Wikipedia page even further going forward.

My first suggestion would be to work out the organization and structure of your overall Wikipedia page. Currently there are no titles, and it made transitioning between subjects quite challenging, and often confusing. I would add an intro section, and then divide up the Wikipedia page into sections such as “RNA Stem Loop Formation”, “HNRNPC Binding Site”, “RNA modification classes”, “Epitranscriptomic”, and “Engineered RNA Modification Techniques”. These are just suggestions, but having these in place would really allow the reader to sort out the content while reading through the article, and would allow readers for specific information to easily find the content they desire. Next, I would recommend adding more context and overview to the current content on your page. It seemed as if you jumped right into the discussion on “eraser” and “reader”, without a real overview of what N6-methyladenosine (m6A) on Alternative Splicing really means, who discovered it, and at a high level, what it functionality really is.

For your discussion on m6A and its relationship with HNRNPC, I think this would be a great area to add a detailed figure on the overall chemical changes and “switch” effect that you talk about in your mechanistic summary. A detailed figure here would help visualize the role of m6A modification on the HNRNPC region, and changes to the looped structure.

In your discussion of pseudouridylation in yeast and humans, I think it would be great to add content about the implications and relevancy of the discoveries found through the “process that utilizes a single-nucleotide-resolution method for pseudouridine identification”. Specifically, in the paragraph that begins with “There are more than 100 classes of RNA modifications….” I would include relevancy of the findings that you present. The last sentence of this paragraph begins to describe this, but adding content on the implications and relevancy will make the Wikipedia article less data heavy, and more balanced in answering the “so what" question of this Wikipedia article.

In your discussion about Epitranscriptomics, I would delete the definition of epigenetics that you include, as this isn’t as relevant to your topic. Instead, just link to the epigenetics page in case people need a refresher on the definition. Your paragraph about starting with “the relative youth of this field means there is still much progress...” is a great example of how context can be added to your Wikipedia page, and will provide more exciting, and beneficial reading for viewers.

Finally, in your section about engineered RNA modification techniques, it would be great for you to expand upon the medical techniques that this process has application for. Overall, I believe you need to reach your minimum of 5 added sources, so I would look for additional papers to do so. With this, I would also look at linking content and keywords to their respective wikipedia articles throughout your article (see my example of epigenetics).

~Ryan Boyd (talk) 18:38, 19 October 2016 (UTC)

Epitranscriptomics Peer Review #3[edit] To Group #5:

I think you guys have a good start but really need to organize your materials more clearly. Personally, I found it difficult to follow through and often had to go back and read again, so make sure to work on creating smoother transitions. For starters, I’m assuming that the introductory section is the paragraph that starts out as: “Epitranscriptomics describes an aspect of molecular genetics…” Move this to the top of the page, not the middle, but content-wise, I think it was very well-written and accessible for non-experts. Good job!

Also, I thought that the highlighted examples and lengths of each sections were fine, but could definitely utilize a visual aid to help the readers better understand specifically what you’re referring to (i.e. HNRNPC binding mechanism). Even though you do explain it pretty well in text form, a figure would definitely help, and you do need to add at least one original figure for the final draft.

Finally, you guys (or the first group member who did the top portion of the draft) did link terms/concepts to their respective Wikipedia pages for further reference, but the other group members did not, so make sure to do that as well! Also, it seems like that all 5 of your references are from review articles, so make sure to try and utilize different types of sources. And lastly, refer to “Wikipedia Editing Basics” Power Point, especially slides #33&34 on inserting references/citations. I did see an attempt, throughout the sections to cite your sources, but it was not done properly.

Overall, I think that you guys have a good draft content-wise, but need to work on adding a figure, and improving on organization/clarity. Right now, the page is a little messy and needs to be cleaned-up. Make sure to create subheadings (refer to slide #32 on the same Power Point mentioned above if you need help), separate your sections clearly (i.e. HNRNPC binding site, RNA stem loop formation, etc.), link references appropriately, and to review for grammar mistakes (I noticed a couple here and there)!

Thanks, Daniel Choi Danchoii (talk) 07:06, 20 October 2016 (UTC)

Epitranscriptomics Peer Review #4[edit] Overall, I think the most important things you guys need to work on are organization and clarity. The materials the article present are great, especially your elaboration on m6A and pseudo-seq, but they need to be much more structured since it is a little difficult to follow the article and understand when you guys are talking about which topic or moving on to something else. My suggestion is that you start the article with the introductory paragraph talking about the general term epitranscriptomics, then divide the contents into separate sections with titles like “examples,” or “classes of modifications.”

The highlighted examples and the length of the contents both seem reasonable, but I feel as if it would be hard to tell unless they are organized into different sections and information is listed in a more coherent order. Also, you guys have a lot of terms and concepts that should be linked to other pages for reference. I'm sure you guys meant to work on it later since this is just a draft.

I saw that one of the links in the reference paragraph leads to a website with a figure, I wasn’t sure if you guys wanted to include that figure or recreate your own version of it, but you should include figures with some of your contents, which would make organizing all the information you have much easier. The references also need to be separated (obviously) under a section titled “references” and numbered for clarity, because it was hard to distinguish the different sources in the paragraph you have at present. I am not sure if you guys do meet the five minimum requirement, but if I didn’t misread any of the sources, they are all journals. You could look into some non-journal sources when finding any additional material.

You guys are getting there, keep up the good work! Kjihyun (talk) 14:25, 20 October 2016 (UTC)Jihyun Kim

Epitranscriptomics Peer Review #5[edit] In terms of content, I would like to say that the information you have added to the sandbox so far is fantastic, descriptive, and interesting. Length-wise, I think that you guys have added enough original information (while sounding well-informed) to revise the existing epitranscriptomics page since the existing page contains barely anything. I think what's left to make extensive changes are some technicalities of the sandbox.

One thing was that your group's sandbox visually seems very unpolished and visually unattractive. You guys need to add some headers and organize the paragraphs. Each of the paragraphs by themselves were well-oriented but the organization between the paragraphs seems scattered. The existing introductory section is randomly placed in the middle, and one of your references is smack-dab right it the middle of the draft (not to the mention wrong format). I would like to add that it was difficult to trace your sources to specific articles that you cited since you did not add in-text citations. Sentences like "Research has shown however that in yeast pseudouridines are quite scarce." lacks an imperative citation that should come right after (where did you hear that yeast pseudouridines are quite scarce?). Also, I wanted to say that the sentence "Paper looks at pseudouridylation in yeast and human RNAs using psudo-seq" seems very un-Wikipedia style, not to mention the lack of "what" paper you are talking about. Instead of "paper looks at," you can say (more professionally) "a certain research study investigates [...]." I know this may sound meticulous and annoying, but all of these subtleties should be taken account of. With Wikipedia being one of the most forefront go-to Internet resources on the Web, the visuals for your draft could be as important as the content themselves.

Also, be sure to check your grammar. The following sentence, "Stem Loops occur was single-stranded RNA Watson-Crick complementary base pairs within the strand forming an unpaired end or loop," is ungrammatical.

It seems clear that you guys haven't added any figures yet; I would advise to add a graphic diagram that can highlight one of your draft's examples. For example, you guys can add a diagram that highlight the m6a effects on splicing and pathways that it triggers. This would be visually very helpful to readers who will visit your Wikipedia page for a quick reference or quick summary.

It seems that you have around 5 sources total which reaches the minimum. However, I would add just a bit more just to be safe!

Overall, content-wise you guys are on track; there is nothing that needs to be added/taken away (I personally am not informed on this topic well enough either). If you guys could just visually make your draft more organized and easy to guide, the draft will definitely be already Wikipedia-worthy!

Thanks, David

Supremichigan1995 (talk) 19:50, 20 October 2016 (UTC)

Additional comments from the librarians[edit] I agree with your peers' comments that some organization and structure are much needed here - it's really difficult to follow this text as it's currently presented. There are segments of text that are clearly meant to be headers (no punctuation on verb clauses), but they're not distinguished from the main text in any meaningful way. This is what the Heading features are for. The text also needs some copyediting for spelling and grammar; I'd suggest having group members take turns rereading and correcting specific paragraphs. Are you planning to keep the existing introduction to the article in your revision? Finally, don't forget to connect your technical terms to their existing Wikipedia articles. ScottMLibrary (talk) 15:57, 21 October 2016 (UTC)

Jump up ^ http://www.nature.com.proxy.lib.umich.edu/nrg/journal/v17/n6/pdf/nrg.2016.47.pdf — Preceding unsigned comment added by Sungyeob (talk • contribs) 04:06, 17 November 2016 (UTC)

Wiki Education assignment: Developmental and Molecular Biology Spring 2024

This article was the subject of a Wiki Education Foundation-supported course assignment, between 8 January 2024 and 24 April 2024. Further details are available on the course page. Student editor(s): MoRinaldi11 (article contribs).

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