Talk:Histone-modifying enzymes

Wiki Education Foundation-supported course assignment

This article was the subject of a Wiki Education Foundation-supported course assignment, between 31 August 2021 and 9 December 2021. Further details are available on the course page. Student editor(s): Sctoves, Ed10005. Peer reviewers: Jonalektiar, Ristresso621, Chem455cr.

Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 23:30, 16 January 2022 (UTC)

The image

What data source/article was used to create the image ?

Why doesn't it include HDAC1-11 ? Rod57 (talk) 08:49, 28 October 2010 (UTC)

Peer review and responses during the educational assignment in Fall 2021

Histone-Modifying Enzymes Peer Review 1

First and foremost, you both did an excellent job expanding on the current histone-modifying enzyme wiki page and making a well-structured article! I really enjoyed your addition of tables, as it organized the various enzymes in an extremely clear and easy to understand way. I also appreciated the distinction you made between common and uncommon histone modifications, as it places these enzymes reactions in a broader context. Some of your sections say TBD, and I think they will also be excellent additions to your article when you complete them!

Here are some suggestions I have for your draft:

While your introduction is extremely thorough, it uses extremely jargon-heavy language right from the outset. I think this introduction would be much more accessible for the general public if you use simpler language, or define the terms you are using concisely.

I think your modifications sections would really benefit from the use of figures/images! Interactions like Acetylation and Methylation, and how these modifications interact with each other, can be pretty hard to conceptualize from the text alone. Adding a few images may help clarify some of your points. It would be especially useful for your Sumoylation section.

I noticed that you mentioned key residues that specific enzymes tend to target for O-GlcNAcylation, and I think this is information that could be worthwhile to add for your other sections too.

In your future applications section, you mention that "recent evidences show the importance of HDACs in regulation of lipid metabolism and other metabolic pathways playing role in the pathophysiology of metabolic disorders." How specifically are HDACs implicated in this regulation? And which specific metabolic disorders? While I don't think you need to go extremely in depth on this, providing a bit more information and context to support this claim could be useful.

Overall, this is a great first draft. I'm excited to read the final copy in a few weeks!

Chem455cr (talk) 03:09, 9 October 2021 (UTC)Chem455cr

Histone-Modifying Enzymes Peer Review 2

This is a great first draft of your wikipedia page! The structure makes the article much easier to follow and breaks up the information into manageable chunks. The tables are also a fantastic way to present the specifics of the modifications - it's much easier to follow than a paragraph. It's also clear that you have expanded a lot on what the modifications entail, which was lacking in the original page.

One of the main suggestions I have is to restructure the introduction and use language that is a bit more accessible to people who don't have a large science background. An image of chromatin (the beads on string model) and a label that the beads are the histones would make it easier to contextualize what the enzymes are doing. In the introduction, it might be helpful to explain what the histones are first, then proceed into the modifications and how they affect the conformation.

The sections for each modification include a large amount of detail while remaining easy to understand, however I would include a few more pieces of information either in the tables, paragraphs or both. Including an image for each modification to show the groups that are added or changed, a written version of the formula of the functional group, or adding links to the wiki page for those reactions or functional groups can make it easy to find more information without cluttering what you already have. This would be especially helpful for sumoylanation.

The only other thing I would include is what might cause some of these modifications - i.e. certain types of cell stress or damage - and how this might relate to epigenetics. Other than that, this is a great start! I'm really impressed by how easy it is to understand this page and am excited to see how it progresses!

Ristresso621 (talk) 03:41, 16 October 2021 (UTC)

Histone-Modifying Enzymes Peer Review 3

As my teammates have said, you guys did a great job expanding this article. Visually alone, the addition of tables and entire sections to break down the histone modification enzyme types and classes brings this article from a stepping stone to other articles to a valuable source of information on its own. It's clear that you've put a lot of work into this as a group, and I'm interested to see the end result.

A few minor edits:

Your first sentence should be a strong one which succinctly defines or describes your subject. As it is, while I think your introduction provides a lot of good information, it starts somewhat abruptly. I know that this was borrowed from the old article, so I think adding a more encapsulating first sentence would better provide context for the rest of the intro section.

Another fairly easy edit is adding images! I'm not sure how many Creative Commons images are out there about histone-modifying enzymes, but there are a lot of great resources out there to make your own, if need be. They would definitely help visualize and contextualize your descriptions of the more basic modifications.

I like the idea of a discovery section for sure, I'm looking forward to seeing that! There's probably a meta-analysis or two out there that could introduce this information in great detail, seems interesting!

Another fairly technical detail goes back to the intro and the concept that heterochromatin is inaccessible to transcription factors. Apparently (and I only know this from the heterochromatin Wikipedia page I read for our own project), this isn't as open and shut as we once thought. Changing the wording from "makes it inaccessible" to something like "makes it far less accessible" allows for expanding upon this later on in the page.

Again, your group did a fantastic job with this, and I'm excited to see how it turns out.

Jonalektiar (talk) 03:04, 17 October 2021 (UTC)

Catherine's feedback

Great work expanding this article! Your peers have provided lots of really good feedback here. I think you should briefly describe what writer and eraser enzymes are at some point - or see if there's already an article about that concept that you could link here. I want to echo what was previously suggested about providing more information about specific histone residues that are consistently modified. For example, there are a few lysine residues that are key for DNA accessibility. I don't know if the "Discovery" section is necessary because we are still actively learning more about histone modification and I'm sure each enzyme was discovered differently. Best of luck with the edits! Cawilhel (talk) 20:59, 17 October 2021 (UTC)

Nils comments

Great first draft, with lots of details already! Since this is an overview page over many enzymes and processes, make sure you continue to link to other Wikipedia entries.

Ngwalter (talk) — Preceding undated comment added 22:04, 17 October 2021 (UTC)

MLibrarian Feedback

Great extension of the article! A few comments:

1) Some typo I found in the 2nd paragraph of the Lead section "...enzymes that that add these functional groups are dubbed writers while enzymes that remove these functional"

2) I agree that Discovery section is not necessary

3) Please link to the preexisting Wiki article, e.g. on Histone deacetylases in Acetylation or on histone methyltransferases and histone demethylases (https://en.wikipedia.org/wiki/Demethylase#Histone_demethylation) in Methylation, or metabolic disorder in Future applications

4) I noticed that Table for Uncommon histone modifications has Citrullination and Proline isomerization which have no information associated with them. If this is yet unknown, I suggest removing it from the table and just have a sentence under the table listing this two additional ones and specifying that no information yet exists. MLibrarian (talk) 18:33, 20 October 2021 (UTC)

What we plan to do

1) Complete missing sections

2) Ubiquitination, Proline Isomerization, & Future Applications

3) Further simplify Introduction

4) Replace jargon-heavy language

5) Briefly describe what writer and eraser enzymes are

6) Continue to refine descriptions of particular modifications

7) Include key residues or histone targets

8) Add images of modifications & relevant functional groups

9) Continue to link other Wikipedia articles