# Talk:Gene

Transcluded from Talk:Gene/Review
To WP:MCB, WP:GEN, WP:BIOL and WP:EB
The gene article gets 50,000 views per month but has been de-listed as a featured article since 2006. Given the success of the recent blitz on the enzyme article, I thought I'd suggest spending a couple of weeks seeing if we can get it up to a higher standard. I'm going to start with updating some of the images. If you'd like to help out on the article, it'd be great to see you there. T.Shafee(Evo﹠Evo)talk 09:49, 31 March 2015 (UTC)

It appears the main reason gene was delisted as a GA was sourcing (see Talk:Gene/GA1).  The following free textbook is probably sufficient to document most basic facts about genes:
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular Biology of the Cell (Fourth ed.). New York: Garland Science. ISBN 978-0-8153-3218-3.
a second one is even more relevant, but unfortunately not freely accessed:
Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R (2013). Molecular Biology of the Gene (7th ed.). Benjamin Cummings. ISBN 978-0-321-90537-6.
I will start working on this as I find time. Boghog (talk) 17:58, 31 March 2015 (UTC)
Thanks for the prompt on this! I see I did do some work here back in the day, but not enough. Looks like a typical large-but-untended wiki article - bloated up with random factoids with no attention to the flow of the article. I'm pretty busy for this week and out of town next week, but I'll try to give it some attention. Opabinia regalis (talk) 19:19, 31 March 2015 (UTC)
I'll probably go through and make all the necessary MOS tweaks for FA status to the article within the next week. Too preoccupied with other articles at the moment to make any substantive content/reference changes though. Seppi333 (Insert 2¢ | Maintained) 03:24, 1 April 2015 (UTC)


### Glossary
Snooping around I encountered Template:Genetics glossary, I don't know it's backstory, but it is a rather cleaver idea for a template in my opinion. I partially reckon it might go well under the first image in place or the second image depicting DNA, which conceptually is a tangent. I am not sure, hence my asking. --Squidonius (talk) 21:47, 1 April 2015 (UTC)

Including a glossary could be useful, but I think it should be concise and tailored specifically for this article.  Currently {{Genetics glossary}} contains 22 entries and some of the definitions are quite lengthy.  A shorter glossary, closer to the size of {{Transcription factor glossary}} or {{Restriction enzyme glossary}}, IMHO would be more effective.  Another option is to transclude the {{Genetics sidebar}} which in turn links to {{Genetics glossary}}. Boghog (talk) 06:38, 2 April 2015 (UTC)
...could also just transclude a collapsed version - provides the full set of terms and takes up little space. If people need a glossary, they can expand it. Glossaries probably shouldn't be expanded by default unless there's a lot of free space along the right side of the page between level 2 sections (i.e., horizontal line breaks), since images and tables should take precedence. Seppi333 (Insert 2¢ | Maintained) 07:25, 2 April 2015 (UTC)
Collapsed or not collapsed, {{Genetics glossary}} is still way too long. Glossaries should be restricted to key terms with short definitions that can quickly be scanned while reading the rest of the article.  IMHO, a long glossary defeats its purpose.  Furthermore an uncollapsed glossary is more likely be read and if kept short, no need to collapse. Boghog (talk) 08:30, 2 April 2015 (UTC)
Fair enough.  Might as well make a new one since it's not referenced anyway; imo, glossaries should cite sources, preferably another glossary, because it's article content. Seppi333 (Insert 2¢ | Maintained) 08:39, 2 April 2015 (UTC)
Hmm, apparently I added a bunch of stuff to that template awhile back, but don't remember it at all. It appears to be a subset of the article genetics glossary. (I'm not really sure we need both.) I agree that the template is way too long, and as constructed is hard to ctrl-F for a term.
I suggest just linking to the MBC glossary as a "reference". I would consider this kind of thing as a summary analogous to the lead paragraphs; no need for a clutter of little blue numbers. Opabinia regalis (talk) 21:47, 2 April 2015 (UTC)


### References
I'm planning on adding some more Molecular Biology of the Cell references to the article using {{rp}} to specify chapter sections. I went to the MBOC 4th ed. online page but I can find no way of searching by page number, chapter, section or anything else. Any ideas on how to specify specific sections as is possible for Biochemistry 5th ed. online? Alternatively, maybe there's a more easily refernced online textbook for general citations. T.Shafee(Evo﹠Evo)talk 11:30, 20 April 2015 (UTC)

I had the same train of thought here on the regular talk page. How about something like this? Uses {{sfn}} to include links to individual sections as notes. Of course, now they're separate from the rest of the references, but maybe it's not a bad idea to distinguish 'basic stuff you can find in a textbook' from 'specific results you need to consult the literature for'. Opabinia regalis (talk) 06:09, 21 April 2015 (UTC)
You're right, I missed that. I agree that it's actually a good way to format it. Having a separate list that indicates the significance of the references is useful. T.Shafee(Evo﹠Evo)talk 08:06, 21 April 2015 (UTC)
I am not a big fan of {{sfn}} templates.  They are more complicated and harder to maintain. Plus they don't directly address the problem of searching Molecular Biology of the Cell.  What seems to work is to search for the chapter or subchapter titles in quotes.  For example search for "DNA and Chromosomes" provides a link to the introduction of chapter 4.  Then one can reference the chapter or subchapter number with {{rp}}. I am busy this week but should have more time this weekend to work on this. Boghog (talk) 12:21, 21 April 2015 (UTC)
I mis-described my own suggestion; it's actually {{efn}} (not that that's better). I like your method better from an aesthetic and maintenance point of view, but the problem is that giving a reader a reference to "chapter 4" is less useful if there's no obvious way to get to chapter 4 from the book's table of contents page. I don't see a way to provide separate links for each chapter/section without splitting up the references in the reference list. We could use {{rp}} like this, but I think the links police won't like that. Opabinia regalis (talk) 18:03, 21 April 2015 (UTC)
OK, I now see what you mean.  The choice is between {{efn}} and in-line external links and {{efn}} is the lesser of two evils. One other possibility is to append the chapter external links to the citation:
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). Molecular Biology of the Cell (Fourth ed.). New York: Garland Science. ISBN 978-0-8153-3218-3. Chapter 4: DNA and Chromosomes; Chapter 7: Control of Gene Expression; Chapter 7.1: An Overview of Gene Control; Chapter 7.2: DNA-Binding Motifs in Gene Regulatory Proteins; Chapter 7.3: How Genetic Switches Work
or have separate citations for each chapter where only the |chapter= and |chapterurl= parameters differ:
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). "Chapter 7: Control of Gene Expression". Molecular Biology of the Cell (Fourth ed.). New York: Garland Science. ISBN 978-0-8153-3218-3. {{cite book}}: External link in |chapterurl= (help); Unknown parameter |chapterurl= ignored (|chapter-url= suggested) (help)
Boghog (talk) 18:47, 21 April 2015 (UTC)
My first reaction to your 'appended links' idea was that we shouldn't create our own linked pseudo-TOC given the publisher's apparent desire not to have a linked TOC hosted by the organization they actually licensed the content to. But all the other ideas do essentially the same thing, so that's a bit silly. I think I like that idea in combination with {{rp}} chapter labels best, as it's least intrusive in the text, makes clear how many citations go to a general reference, and doesn't require a separate list or potentially fragile formatting. Opabinia regalis (talk) 20:49, 21 April 2015 (UTC)
 I've not done much non-standard reference citation so I'll wait until you've done a couple so that I can see the format in context before doing any more. The ones I added yesterday shouldn't be too difficult to reformat. T.Shafee(Evo﹠Evo)talk 12:24, 22 April 2015 (UTC)
You're the one currently doing the work, so I think that means you get to decide :) Opabinia regalis (talk) 19:01, 22 April 2015 (UTC)


### MBOC references
Article
Genes are numerous and useful
References

So {{rp}} labels the chapter number but does not provide any easy link to the actual information. Therefore it's combined with a list of chapter links. the benefit is that the {{rp}} template is relatively easy to maintain and the list of chapter links doesn't require maintainance and places all the MBOC links together. As stated above, there's basically no way to avoid linking individually to chapters if we want to cite MBOC. I'll finish building the chapter list over the next couple of days. T.Shafee(Evo﹠Evo)talk 01:29, 27 April 2015 (UTC)

I've finished adding MBOC references up to section 3 (gene expression). Also, whoever originally wrote the gene expression section of the article really liked semicolons! T.Shafee(Evo﹠Evo)talk 10:51, 27 April 2015 (UTC)
Looks great, I like the collapsible box! I can't find it at the moment, though - IIRC there is somewhere an agreement not to use collapsed boxes for references for accessibility reasons. I don't see it in WP:ACCESSIBILITY so I could be misremembering, and since the box contains links and not the reference note itself, it's probably fine. Just wanted to mention it in case someone recognized the issue. Opabinia regalis (talk) 07:50, 28 April 2015 (UTC)
@Opabinia regalis and Evolution and evolvability: The guideline is MOS:COLLAPSE, which states "...boxes that toggle text display between hide and show, should not conceal article content, including reference lists ... When scrolling lists or collapsible content are used, take care that the content will still be accessible on devices that do not support JavaScript or CSS."  I checked this article on my phone, a mid-2011 model, and that entire box just doesn't appear at all using the default mobile view.  I tried setting the template parameter expand=true so the box is expanded by default but that made no difference.  Maybe better to change to a bulleted or indented list? Adrian J. Hunter(talk•contribs) 10:50, 30 June 2015 (UTC)
@Adrian J. Hunter: Well spotted - It's really irritating when templates don't work properly on mobiles! I've changed the MBOC list to be wrapped in {{Hidden begin}} + {{Hidden end}}, which renders properly on phones (default expanded). T.Shafee(Evo﹠Evo)talk 12:31, 30 June 2015 (UTC)
Yep, that works – thanks! Adrian J. Hunter(talk•contribs) 13:23, 30 June 2015 (UTC)

I request a volunteer to review a proposed reference to own research. Details below. Note: a similar request was already created in 2021 and was approved by a volunteer. The original version was later removed by @MrOllie in 2024 citing spam. I request a re-review of the proposed changes. This version moves the text to Transcription section and adds additional information on factors beyond the sequence elements of the immediate CPA machinery that could be involved in human gene end definition.
Proposed change is at the end of this paragraph:
In prokaryotes, transcription occurs in the cytoplasm; for very long transcripts, translation may begin at the 5' end of the RNA while the 3' end is still being transcribed. In eukaryotes, transcription occurs in the nucleus, where the cell's DNA is stored. The RNA molecule produced by the polymerase is known as the primary transcript and undergoes post-transcriptional modifications before being exported to the cytoplasm for translation. One of the modifications performed is the splicing of introns which are sequences in the transcribed region that do not encode a protein. Alternative splicing mechanisms can result in mature transcripts from the same gene having different sequences and thus coding for different proteins. This is a major form of regulation in eukaryotic cells and also occurs in some prokaryotes. [CITATION PROPOSED HERE]
I am requesting a reference to a recent paper from our lab - https://pmc.ncbi.nlm.nih.gov/articles/PMC10072996/
Wikipedia guidelines suggest citing review papers first, however, this is the first study that assesses whether known sequence elements are sufficient to predict human gene ends. We found that known elements can only explain half of all human gene ends. This project was aimed at answering fundamental questions of human gene definition. The results are significant, highlight the magnitude of missing information in the current understanding of processes human cells utilize to locate their genes, and propose likely candidates for further investigation in relation to gene transcription. Therefore, this study is a relevant source on the subject.
To justify expert knowledge - this paper comes from Hughes lab at the University of Toronto. Dr. Timothy R Hughes is a John W. Billes Chair of Medical Research and Canada Research Chair in Decoding Gene Regulation, one of the most cited Canadian researchers. Aleksei Shkurin (talk) 22:44, 21 April 2025 (UTC)

Wikipedia is not a place to publicize brand new results. We wait for review papers because we want to see if the field at large considers the new finding important enough to write about (or not). That is what your attempts to force this into Wikipedia are not accounting for. MrOllie (talk) 23:26, 21 April 2025 (UTC)
That's what the peer-review process is for. This article has been reviewed, published, and since then it's been cited. You have a dedicated process for self-citation for scenarios like this, which is what we are following Aleksei Shkurin (talk) 23:52, 21 April 2025 (UTC)
And part of that dedicated process is that volunteers (like myself) comment on such things. Thanks for using the talk page instead of reverting again, but simply using the process does not guarantee that others will agree that your paper should be cited in the article. In this case I disagree - Wikipedia is not an indiscriminate collection of every peer-reviewed paper that has been published. MrOllie (talk) 23:55, 21 April 2025 (UTC)
Agree to disagree. I am looking for a second opinion on this edit. The research comes from a reputable lab, provides valuable insight into human gene regulation and would be a useful read for people looking to understand gene transcription. It was previously approved by another volunteer and successfully published. So far you are the only one committed to not letting it get through, @MrOllie Aleksei Shkurin (talk) 00:01, 22 April 2025 (UTC)
I am very familiar with the work coming out of Tim Hughes' lab. The validity of the work is not in question.
This is an article about "Gene." It is not an article about gene expression and it is not an article about transcription. There are other Wikipedia articles devoted to those topics. We should be trying hard not to duplicate material on Wikipedia, not only because of duplication but because, given the nature of editors, duplicate articles tend to conflict with each other. I think we should delete the entire section on gene expression and just leave a link to other Wikipedia articles.
But even if we were to keep that section if needs editing. The section on transcription only refers to the transcription of protein-coding genes even though there are other kinds of genes that are transcribed. With respect to polyadenylation and the termination of transcription of human protein-coding genes, the important point is that it is sloppy and run-on transcription is common as noted by earlier work from the labs of Ben Blencowe and Tim Hughes (van Bakel et al., 2010). The proposed edit is far too complex, too narrowly focused (human), and too speculative for Wikipedia. (It also doesn't belong in this article.) Genome42 (talk) 19:15, 22 April 2025 (UTC)
Yes that's a better answer. I can move it and rewrite the conclusions of the study to fit the context of the transcription page, although could you clarify what you mean by "too complex" and "too speculative"? Aleksei Shkurin (talk) 20:12, 22 April 2025 (UTC)
It seems likely that transcription termination and polyadenylation are triggered by relatively simple sequences at the end of mammalian protein-coding genes. However, the process is sloppy and error-prone so there are often longer transcripts that can be detected due to run-on.
Your model suggests that the process is actually much more complicated and that termination is still precisely controlled - it's just that we don't know all the features that determine when the transcript will end. That's why your edit mentioned "Additional regulatory factors may include microRNA binding, protein-protein interactions involving RNA polymerase II and associated CPA machinery, nuclear export factors, RNA processing steps such as mRNA capping and splicing, as well as long-range sequence features in the terminal exon."
That's what I meant by saying that your explanation is too complex and too speculative. We don't know whether sloppiness is the correct explanation but we also don't know whether an unknown precise mechanism accounts for the data. Best to avoid this controversy.
It's the same issue that comes up with intron processing. You come from a lab that believes that most unusually processed transcripts are due to genuine alternative splicing that's specifically determined by splicing factors. I think that sloppy error-prone splicing is the best explanation for almost all of those rare, non-conserved, rapidly degraded transcripts. Genome42 (talk) 16:11, 23 April 2025 (UTC)
@Genome42 thank you again for the thoughtful response. Appreciate you actually digging into the subject. Let me expand on the design of the study and which definitive conclusions we draw from it that I want to share on Wiki.
You’re absolutely right that transcription termination is often noisy, and sloppiness likely explains longer-than-expected transcripts and some of the random misfires. But this study addresses a different question: not why transcripts run long, but why aren’t there more shorter transcripts - specifically, why many high-scoring cryptic CPA sites that appear biophysically valid are not used at all.
To do this, we deliberately avoided black-box models like CNNs or RNNs. Instead, we constructed a biophysical simulation of CPA machinery using known RNA-binding protein motifs and interpretable models like logistic regression. This allowed us to test the sufficiency of known CPA sequence features in a way that mirrors the actual protein-binding landscape. This way instead of having sequence (which can have noise and evolutionary left-overs) drive the predictive power, we use protein binding likelihood of known CPA RBPs.
The result is surprisingly clear: in ~39% of human genes, cryptic sites score higher than the actual CPA site, and yet they’re not used. Not as CPA sites, not as APA sites, both of which have extensive research behind them, particularly by Bin Tian who was the chair of the defence committee for this project. We then tested all known human RBPs, including U1 sites, as additional features to attempt to differentiate CPA sites from cryptic CPA sites and thus infer possible supporting RBPs and found minimal explanatory power. While it’s absolutely possible that unmodelled factors (e.g. chromatin, unknown RBPs, structural elements, etc) play a role, the main takeaway is that known sequence features alone are not sufficient to definitively explain CPA site selection.
Initially, I did include a list of possible mechanisms as food for thought, but I agree that those examples are speculative and could be removed. That said, I believe it’s important that readers come away with the understanding that our current mechanistic knowledge is incomplete. Wikipedia is often where researchers, students, and educators begin forming their mental model of a process, and why I believe this deserves a brief mention.
How about a concise, non-speculative sentence in the Transcription / Termination section such as:
“While most polyadenylation occurs at canonical sites defined by known sequence motifs, recent modeling has shown that these motifs alone are insufficient to explain observed CPA site usage genome-wide, suggesting that additional regulatory mechanisms remain unidentified.[ref]”
Happy to revise wording as needed! Aleksei Shkurin (talk) 00:51, 24 April 2025 (UTC)

The redirect Ras v12 has been listed at redirects for discussion to determine whether its use and function meets the redirect guidelines. Readers of this page are welcome to comment on this redirect at Wikipedia:Redirects for discussion/Log/2025 September 19 § Ras v12 until a consensus is reached.  1234qwer1234qwer4 13:32, 19 September 2025 (UTC)

The redirect Big gene has been listed at redirects for discussion to determine whether its use and function meets the redirect guidelines. Readers of this page are welcome to comment on this redirect at Wikipedia:Redirects for discussion/Log/2025 September 19 § Big gene until a consensus is reached.  1234qwer1234qwer4 13:36, 19 September 2025 (UTC)