This article is rated B-class on Wikipedia's content assessment scale. It is of interest to the following WikiProjects: | ||||||||||||||
|
Regarding ways to improve the Wikipedia page for XRCC4, there is much work to be done since the current Wikipedia article for XRCC4 is still only a stub article. It contains a very simple lead section and only a few other sections. Moreover, each section only covers the most basic scientific background with much of the most important content missing. The current stub has two images of the protein but an image of the mechanism for non-homologous end joining with other proteins involved should also be included. Furthermore, the information from section to section is not cohesive and the article was most likely written as a mere starting off point.
Based on Unit 5's "Style Guide and for Gene and Protein Articles", it should include more background information in the lead section (instead of just one sentence) and establish why the topic is notable. The lead should cover a sufficient amount of information on XRCC4 so the reader can obtain a relatively thorough understanding on the topic, while providing enough detail to encourage the reader to delve deeper by reading specific sections in the remainder of the article. For example, the lead should specify the importance of having the NHEJ mechanism to rescue DSB that are generated prior to DNA replication, the cascading effect of proteins Ku70/80, DNA-PKcs and Artemis, and how XRCC4 acts in concert with Cer-XLF and Ligase IV to form a complex in order to repair the DSB, and explain the detrimental effects of having mutations in XRCC4 and these proteins touching on the diseases that result. It should also include a Gene and Protein section with fundamental information such as the chromosomal location of the gene, exons, protein splice variants and structure and domains (including images). For the Function section, it would be important to explain what DNA damage is, the different types, repair mechanisms, and what would happen if these damages are not repaired, especially for DSB that require NHEJ for repair (why pre-replicative DSB are the most damaging). This will help the reader put XRCC4 and NHEJ into a clearer context. Very specific details of the mechanism of the protein which highlight the structure of the binding site of XRCC4 and how it complexes with Cer-XLF and Lig IV, as well as binding or catalytic sites of the other proteins, and the mechanism of NHEJ. The regulation of XRCC4's gene expression. its location in the nucleus of the cell, and how its interaction in the cell can be visualized. The pathology section can cover known mutations and diseases they cause, the clinical significance of understanding potential drug targets, and ways to reduce DSB's. Experimental techniques section can cover current methods or technologies being used for studying protein homology and to discover or validate new mutations in the Xrcc4 gene and its regulatory sequences and how these findings can help to create more effective companion diagnostics and therapeutics. To make it really complete, a history section on who discovered the protein. Furthermore, there are many recent publications regarding XRCC4 that have not been taken into account or otherwise cited. Taking the above parameters into consideration combining with citing excellent peer-reviewed references in an accurate and original way should bring this article into an excellent article. Jgould1400 (talk) 04:16, 14 March 2013 (UTC) Cdunca12 22:12, 17 March 2013 (UTC)
This article seems like its heading in the right direction and has improved tremendously. With that being said, here are some feedbacks you might consider for your next contribution.
1) Correction in lead section: PRKDC is a gene and not a kinase subunit. I believe article is referring to the enzyme subunit DNA-PKcs, which is encoded by the PRKDC gene referenced in first citation.
The information was wrong for PRKDC. An editor had added paragraphs two and three in the lead section and they need to be re-edited. The wording was also awkward. I have already changed this.
"The core NHEJ machinery includes XRCC4, DNA ligase IV (LIG4; 601837), and the DNA-dependent protein kinase complex, which consists of the DNA end-binding Ku70 (G22P1; 152690)/Ku80 (XRCC5; 194364) heterodimer and the catalytic subunit PRKDC (600899)."
2) Illustrations of graphs are difficult to follow since there is no text reference. Perhaps remove the graphs completely or provide a thorough explanation for its purpose.
These graphs were a part of the original article and have been omitted.
3) There is too much emphasis on causes for double stranded breaks. I believe briefly mentioning and describing it would suffice. There is already a wiki page reference for DSBs so no need to elaborate too much on it.
Although this section is relatively long, the content is very important in establishing notability and helps the reader understand how DSB can be lethal without NHEJ. I may shorten it just a bit.
4) Role in DSB repair section seems to already describe the mechanism behind XRCC4, thus perhaps merging this section with the mechanism section.
Yes - I have removed the second paragraph and removed the mechanism section and just changed the section name for Role in DSB repair to “mechanism”.
5) The Interaction section needs more information or seems repetitive since XRCC4 has already been mentioned to interact with ligase IV in previous sections.
Once I add new information in the structure section which will cover binding sites and interactions with other proteins, we may remove this section.
6) Anti-XRCC4 antibodies are thoroughly described but have no relevant information on its purpose. Perhaps article can describe how these antibodies are utilized.
7) Additional content is needed on the structure of XRCC4 and post-translational modification.
I will be adding this in the next couple of days.
8) Subsections under Pathology category seems out of place. Perhaps create another section for XRCC4s role in therapeutics and its contribution to scientific discovery. In addition, more content is needed for some of the pathologies described. Additional content and references have been added in several places.Jgould1400 (talk) 04:15, 26 April 2013 (UTC) Thank you for all of your input and taking the time to review our article!
Good luck! Binhtruong (talk) 00:03, 9 April 2013 (UTC) Cdunca12 05:01, 24 April 2013 (UTC)
I agree. An editor came in and added this paragraph. I have already removed both the second and third paragraphs and added three new paragraphs which summarizes the article in concise way and addes better notability.
The last sentence in the second paragraph mentions the importance of NHEJ in preventing losses of long chromosomal regions.
I can add one more sentence to mention a couple of specific cancer-related diseases that Jim has elaborated on further into the article.
I have moved the structure section after the background on DSB. I think it makes more sense to have this background first before going into the protein structure and mechanism more in-depth.
The interactions section may be extraneous as the information is repeating parts of the Mechanism section.
Yes – that is what I have in mind.
The mechanism of NHEJ is very important and XRCC4 plays a major role, so it should have its own section.
I think Jim may have just added this summary. It looks good. Yes, this has now been done. Thanks for your comments. Jgould1400 (talk) 03:43, 25 April 2013 (UTC)
"Do you mean the RNA expression pattern? This is the expression pattern in different tissues. I think it gives an idea of the types of DNA damage or in this case, DSB, that occur in the cells of different tissues and that NHEJ is being used to repair this damage. It needs an explanation. If you click on the image to enlarge it, it will be more clear."
Yes, I was referring to that image and could understand what it was entailing. I just thought it was a bit of a headache haha, but it definitely shouldn't stand alone. I didn't see that you had mentioned the XRCC4 gene expression pattern in the article or made reference to the variable expression in different tissues when I made this comment. Maybe adding a bit of that info would suffice? Jmudukes88 (talk) 01:16, 28 April 2013 (UTC)
''I will consider where in the article I would include this. I may include a simple explanation in a new subsection.
Thanks
The links are relevant to the subject matter and will help the reader understand the overall information better. Can you specifically mention which words are considered jargon? I tried to describe the information in a very clear but descriptive manner as mechanisms are difficult to understand. I wanted to add different types of DNA damage, but was concerned about the length of this section.
I was actually referring to all of the text that is now under the "Sources of DNA Damage" subsection. I like how it stands now because of the organization within the larger section, plus you have linked those words that seemed moderate-to-heavy in jargon (ROS, singlet oxygen, etc.). The linking caused the text to standout and makes it clearer to read upon first glance, plus easier to find info on the material for the casual user of Wiki. Nice work! Jmudukes88 (talk) 01:16, 28 April 2013 (UTC)
Thanks! I think it does flow much nicer now and the links provide clear resources to obtain more background info on it. Cdunca12 05:18, 6 May 2013 (UTC)
Thanks – I’ve corrected this.
I have re-organized this section and just made one “Mechanism” section, and removed the two extraneous paragraphs from the original article. They repeated what I included in this mechanism section.
Let me consider the step-wise list. I actually thought the steps require more details about how the binding sites interact, very specifically. I didn’t really want to take away the consistency of the paragraph format, but I understand your point.
We will consider this. Jim, what do you think? I've left the structure as is; I think it flows nicely.Jgould1400 (talk) 04:09, 26 April 2013 (UTC)
Overall, I think the all the sections follow the guidelines such as the leads section (there are improvements mentioned in my comments/list). The writing is clear, but harder to understand only because of the nature of XRCC4, rather than the writing. I made all of my comments on how to clear up some of that technical jargon and I think they would help by making the activity in a stepwise fashion. The sections work in harmony with the proceeding content, but as you can see in the list above, I believe there could be great re-structuring/organizing of those sections. Luckily, we have some time to do this whether you choose to or not! The references that I checked hold accurate citations without material that is directly copied.
In regards to numbers 6 of my comments, I wanted to give sight to an area where you can find more substance to add in your section, "Structure". Your reference, Crystal structure of the Xrcc4 DNA repair protein and implications for end joining, is actually ripe w/ more content for the Wiki. Just looking through the references you can find other articles to find content on structure (related to function) as well. For example, the study mentions that the C-terminal stalk of XRCC4 interacts with DNA ligase IV suggesting a possible method for ligase coupling to DNA. Jmudukes88 (talk) 02:22, 12 April 2013 (UTC)
Yes- this is exactly what I have in mind in terms of structure. I will be adding new information in this section in the next couple of days. Thank you very much for taking the time to review our article. Cdunca12 05:21, 24 April 2013 (UTC)
First, I read through the reviews of your classmates above, and I think they are great, and have a lot of very useful suggestions. I would add a few of my own comments/suggestions (I did this quickly, so there might be some overlap with the suggestions from your classmates):
I will try to re-word the first sentence and maybe break it up into two sentences.
I have removed the second and third paragraphs in the lead as another editor came in and inserted them. I have added three new paragraphs which concisely describes DNA damage, DSB, the basic mechanism of NHEJ, and mutations in XRCC4.
Exogenous means environmental or external, and endogenous means internally and naturally derived from cellular metabolism.
I will elaborate a bit on this. If there are key proteins that are not translated and aren't available for certain functions as a result of the loss of that specific region of the chromosome, then the cell will be targeted for apoptosis.
No one removed this. I'm not sure what this is.
I put this section in as a place holder. I have not had the opportunity to do the research yet but will by unit 14 for my last contribution.
Thank you for all your input and help! Cdunca12 05:44, 24 April 2013 (UTC)
..
Klortho (talk) 13:58, 21 April 2013 (UTC)
Overall, there are tremendous improvements in the article. I do have a couple of suggestions however.
The subject of this article is the XRCC4 gene/protein that is involved in the NHEJ pathway of DBS repair and not the NHEJ pathway per se. This is a subtle but important point. A brief introduction to NHEJ pathway and DBS repair is appropriate, but shouldn't overwhelm information specific to the XRCC4 protein. One should refer to the background articles, but not attempt to fully duplicate the information already contained in these other articles.
Per WP:LEAD, the beginning of the article should define the scope of the article (XRCC4 gene/protein), provide a very brief introduction to the topic and why it is important and also summarize the main points of the article. The lead should also be written in way that it can be understood by a wide audience. The current lead lacks some fundamental information about XRCC4, for example species distribution:
A dead simple explanation why it is important:
A simple description of the composition of the NHEJ complex with wiki links to the other component of the complex:
The details of the mechanism are way too technical to be included in the lead.
Also in response to the above comment: "The information was wrong for PRKDC." The information is correct since the PRKDC article is about both the gene and the kinase encoded by the gene, although it was not as clear as it could be and can easily be fixed with a piped link (i.e., [[PRKDC | DNA-PKcs]]). Boghog (talk) 20:54, 24 April 2013 (UTC)
A very substantial amount of new material was added since our last progress report, including the new section on "History and Identification of the XRCC4 Gene", the new section on "Anti-XRCC4 Antibodies", and the new subsection on "Endometriosis Susceptibility" that was added to the Pathology section; and in addition, information and content was consolidated in several locations and many references were added. We have also considered the various comments we received and have made revisions and additions where appropriate. Jgould1400 (talk) 03:57, 26 April 2013 (UTC)
Per WP:LEAD, "The lead should define the topic and summarize the body of the article with appropriate weight.". Furthermore the lead should ideally define the topic (i.e., scope) of the article in the first sentence in a drop dead simple manner that can be understood by a wide audience.
As discussed here and here, we have tried to make clear that these Gene Wiki articles are not only about the human gene/protein, but also orthologs that exist in other species. The wording that was reached through consensus is perhaps a little awkward, but it is both accurate and concise:
The "that" in the above sentence is non-limiting implying that the protein (and gene) exists in other species besides human.
Hence I suggest that this article be renamed after the protein (DNA repair protein XRCC4) and the first sentence be changed to:
In the current version of the article, the XRCC4 gene is first mentioned in the last paragraph of the lead. I believe it should be included in the first sentence of the first paragraph. Thoughts? Boghog (talk) 21:25, 29 April 2013 (UTC)
Overall I am really impressed with your article! It looks like you’ve significantly improved it. I know we only have a week of class left so I’ll try to be brief with my suggestions.
I think the lead could use a little more info on the XRCC4 protein itself. After reading the lead it feels like the focus is on DNA repair and not XRCC4.
The lead isn't supposed to contain more than four paragraphs. The original lead I created was too long and ended being my main section. I will consider adding one or two sentences for XRCC4 properties.
I see some of the other reviewers have already suggested reducing the amount of info on DSB and the repair pathways… I know you spent a lot of time writing so if you consider reducing these areas perhaps you could move that content to other articles on Wikipedia (like DNA repair). Just a thought.
I know it seems long, but this section really helps the reader understand why NHEJ is important before they can understand XRCC4 and why this protein is critical in NHEJ. I will be adding more information in the Properties section of the protein, so it will be more complete.
The structure section is very detailed but I think it would be really helpful if there was a visual like the one at the top to look at while reading it. Without a visual it’s hard to picture what you’re talking about. Maybe you could move the structure section to right after the lead so it’s closer to the picture or find another picture to put with the structure section.
Good point. I am working on finding a more detailed image right now. I don't think I will move the Structure section as it falls under Properties.
This sentence was mentioned in previous reviews (and sounds like it wasn’t written by you?) “The human XRCC4 gene contains 8 exons, and alternative transcription initiation and alternative splicing generates several transcript variants.” I think it would read easier if it were two separate sentences – “The human XRCC4 gene contains 8 exons. Alternative transcription initiation and alternative splicing generates several transcript variants.” And if you have time, maybe say a little bit about the variants (do they serve different purposes, etc).
This sentence was originally a part of the lead before we started editing. I removed it and it was added back in again by editors. I will add more info in the Gene and Protein section.
Hope my suggestions help! Aluquette (talk) 00:48, 1 May 2013 (UTC)
Yes - they certainly helped. Thank you for taking the time to review our article. Cdunca12 06:03, 6 May 2013 (UTC)
This article really seems to have been tremendously improved.I think the citations are appropriate and correct. The content has a very nice flow and all sections have ample information. All of the improvements suggested, and followed, by other editors have really added to the overall quality of the article.
I am in agreement with Aluquette regarding the addition of a visual aid to the structure section if one can be located but I know this can be difficult. I think that the DSB information in the introduction is fairly extensive but I do not know that it distracts from the article all that much. I also believe that it may be necessary for explaining the importance of XRCC4. The only other suggestion that I would offer would be to move the history and identification section to the top of the article underneath of the introduction. This may help pull attention back to XRCC4 and then get back into the DSB information.
Great work so far!!Er1cah0p3 (talk) 00:20, 2 May 2013 (UTC)
Sections "Double-stranded breaks" and "Mechanism", while expertly written, seem to me to contain way too much detail for an article about a specific protein in NHEJ pathway. I propose the following:
1) Use these sections to improve the DNA Damage Repair article ("Double-strand break" section). Alternatively, DSB section could also be expanded into an article on its own. This will help people who happen to learn about DSB from Xlf, Shieldin, Ku80 or other linked articles.
2) Reduce these sections to what's relevant here (a few sentences of intro), while expanding on the particular role of Xrcc4 (neither DSB nor VDJ sections even mention it).
Loard (talk) 06:55, 13 December 2019 (UTC)