Talk:DNA repair protein XRCC4

message: 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)
thread_title:  Some ideas for improving the Wikipedia page for XRCC4 

message: 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 information was correct for PRKDC and was taken from:
: 
: While a little sloppy, gene and protein names are sometimes interchanged as in the OMIM entry linked above. It would have been more proper for the displayed link to be DNA-PKcs instead of PRKDC but both link to the same article whose subject matter is about the enzyme and the gene encoding that enzyme. Boghog (talk) 20:23, 29 April 2013 (UTC)
replies: text: This has now been done. Jgould1400 (talk) 03:39, 25 April 2013 (UTC)
thread_title: Comments from Binhtruong (Responses in Italics)

message: 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):
* The first sentence in the lead is a little too hard for a layman to understand.  Could you simplify the language a bit?  For example, you wrote, "... during NHEJ", which, when I first read it, made it sound as if the DNA breaks occur during some process called NHEJ.  It is not clear that NHEJ is part of the process of the repair.
I will try to re-word the first sentence and maybe break it up into two sentences.
* This is a generally suggestions for the lead:  could you try to simplify the language?
* In the lead, you use the word "polymorphism" to refer to a gene, and link to the polymorphism article.  But in that article, they say, "This usage is not discussed in this article."  Could you use a different term?
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.
: Because someone else added this material is not, in itself, a valid reason for its removal. Of course, if the material is not relevant it should be removed or if it is poorly written, it should be edited. To reiterate, the material was added in an attempt to provide information specific to XRCC4 in the lead.  Boghog (talk) 19:05, 1 May 2013 (UTC)
replies: text:  Hi Klortho.  Thank you for taking the time to discuss this page by phone; and, separately, thank you for your assistance in restoring the portions that you wanted restored.  Revisions are underway that will address additional points that you have raised. (See especially the recent revisions by my teammate, Cdunca).  Please let us know if you have any further comments or questions.Jgould1400 (talk) 02:51, 24 April 2013 (UTC)

text: It seems that the infobox was removed by User:Boghog, please disregard those comments. I'll ask him about that.  Klortho (talk) 19:12, 21 April 2013 (UTC)
replies: text:  Actually, another correction.  The infobox I was talking about was the one that's now under the "Structure" section, and it is still in the article.  I was going quickly, and hadn't noticed that it was moved instead of deleted.  Sorry for the confusion!  Klortho (talk) 19:32, 21 April 2013 (UTC)
replies: text:  Sorry.  I didn't realize that this article was the subject of a course assignment.  I will hold off on further edits until the course is done.  Please note that the PBB controls and templates are no longer used by User:ProteinBoxBot to maintain Gene Wiki articles and hence are deprecated (see for example this discussion).  I therefore removed the controls to reduce the clutter.  The original  template (and graphic) was for the N-terminal domain of the XRCC1 protein.  This domain is not contained in the XRCC4 protein.  I therefore made the appropriate correction in this edit.  I also moved the pfam box to the structure section which I believe is an appropriate section to place this box. Boghog (talk) 19:53, 21 April 2013 (UTC)
replies: text:  Thanks, and thanks again for the explanation about the infoboxes.  Klortho (talk) 16:43, 22 April 2013 (UTC)
thread_title:  Review from Klortho (Responses in Italics) 

message: 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:
* In humans the X-ray repair cross-complementing protein 4 is encoded by the XRCC4 gene.  In addition to humans, the XRCC4 protein is also expressed in many other metazoans, fungi and in plants. (ref:  which in turn cites )
A dead simple explanation why it is important:
* Certain mutations in the XRCC4 gene are associated with an increased risk of cancer. (ref: )
A simple description of the composition of the NHEJ complex with wiki links to the other component of the complex:
* The NHEJ enzymatic complex includes XRCC4 (this protein), DNA ligase IV (LIG4), a DNA end-binding Ku70 / Ku80 heterodimer and a kinase subunit DNA-PKcs. (ref: )
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.,  DNA-PKcs).  Boghog (talk) 20:54, 24 April 2013 (UTC)
thread_title:  External review 

message: 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)
replies: text: I have made what I thought were a few constructive suggestions above that were not taken into account.  Hence I hope you don't mind that I have now included them in the article with these edits.  Keep in mind that it is important to include appropriate links to Wikipedia articles.  This article does not exist in isolation.  Also please keep in mind that the lead to an article is not just an introduction.  It also should summarize the important points in the article.  Finally it is important not just to interact with classmates, instructors, and ambassadors when editing a Wikipedia article as part of a class assignment. It is also important to interact with other editors. Boghog (talk) 20:46, 29 April 2013 (UTC)
replies: text: Thank you for taking the time to review and edit our article.  The article is not yet completed and work to be added or editing is still an ongoing process until next week (unit 14), which is the last week of class and the last major contribution to the project will be made.  I just added the "Structure" subsection under "Properties" this morning and was going to add the links tonight.  I agree that the lead section is also a summary of the whole article and wanted to add one more sentence at the end in regards to DNA damage leading to different types of cancers.  Thank you. Cdunca12 00:51, 30 April 2013 (UTC)
thread_title:  Progress Report for Units 11-12 

message: 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:
* <recommended UniProt name> is a protein that in humans is encoded by the <approved HUGO gene symbol> gene.
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:
* DNA repair protein XRCC4 also known as X-ray repair cross-complementing protein 4 is a protein that in humans is encoded by the XRCC4 gene.
:: I will clarify to see which protein name is the correct one in humans.  I may make this modification.
::: The name I suggested above is taken from  which specifically refers to the human variant [and is identical to mouse (), slime mold () and most other species except for the capitalization of XRCC4 which follows the standard convention, human – all caps, other mammals – only first letter capitalized, non-mammals – lower case], Boghog (talk) 06:59, 6 May 2013 (UTC)
replies: text:  I think the lead suffices in the summarization of the article.  It has a basic background of DNA damage and DSBs, protein mechanism, and mutations in XRCC4.  I may add one more sentence about different mutations leading to cancers in the last sentence. Cdunca12 05:51, 6 May 2013 (UTC)
replies: text:  The current lead contains too much introduction to the NHEJ pathway and not enough summary of information specific to XRCC4.  As the article is expanded, the lead will require periodic editing so that it reflects the contents of the article. Boghog (talk) 06:59, 6 May 2013 (UTC)
replies: text: What specific sections do you want to see better represented in the lead? I would say Pathology and maybe a little bit more about post-translational modifications. Thoughts? Keilana|Parlez ici 21:30, 9 May 2013 (UTC)
replies: text:  I agree pathology should more prominently mentioned in the lead, particularity its use as a biomarker. I also note parenthetically that the subsection on potential role in therapeutics needs some work.  XRCC4 SNPs mentioned in the first part of this section are effectively biomarkers.  The rest of this section is a bit fuzzy.  Drugs that specifically inhibit XRCC4 theoretically might be useful in cancer treatment but we would need a reliable source to document this proposed use.  Boghog (talk) 22:08, 9 May 2013 (UTC)
replies: text:  A bunch of revisions were just made by me in an effort to address BogHog's comments regarding the pathology section. Jgould1400 (talk) 07:56, 16 May 2013 (UTC)
thread_title:  Article title and first sentence (Responses in bold and Italics) 

message: 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.
: Adding one or two additional sentences about the XRCC4 protein to the lead is not going to cut it.  The four paragraphs of the lead should focus on the XRCC4 gene/protein and not the NHEJ pathway. The longest paragraph in the current lead (paragraph #2) doesn't even mention XRCC4. Furthermore the section in this article on double strand breaks really should be merged into the double strand breaks section of the DNA repair article. Boghog (talk) 19:40, 7 May 2013 (UTC)
replies: text: A more detailed explanation was already provided below. Also why am I being referred to in the third person plural? ;-) Boghog (talk) 20:12, 7 May 2013 (UTC)

text: Just a clarification and some history about the "human XRCC4 gene contains 8 exons ..." sentence.  This sentence was first added to the article by me in February 2008 to provide seed material that could later be expanded by other editors.  This material was copied from Entrez.  Because this material is in the public domain (see ), including it in a Wikipedia article is considered fair use as long as proper attribution is included (citation).  I have restored this sentence twice after it has been deleted, first to the lead, and then to the gene section because it describes basic facts about the XRCC4 gene that should be mentioned somewhere in this article.  By all means, please edit the sentence to improve its clarity and expand on it. That was and still is the intention of including this seed material.   Boghog (talk) 07:41, 1 May 2013 (UTC)
replies: text:  Thanks for the clarification, Boghog. I went ahead and made it two sentences but I'll leave it up to my classmates if they'd like to expand that section. Aluquette (talk) 23:30, 1 May 2013 (UTC)
replies: text:  And thanks for your edit, Aluquette.  That looks great. Boghog (talk) 14:33, 4 May 2013 (UTC)
replies: text:  Thanks for editing this portion.  I will add more information to the Gene and Protein subsection and will combine this as well.  Cdunca12 06:03, 6 May 2013 (UTC)
thread_title:  Comments from Aluquette (Responses in Bold and Italics) 

message: 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)
thread_title:  Proposal for downsizing / migration