Talk:Conserved non-coding sequence

This article is rated C-class on Wikipedia's content assessment scale. It is of interest to the following WikiProjects:

Molecular Biology: Genetics / MCB / COMPBIO This article is within the scope of WikiProject Molecular Biology, a collaborative effort to improve the coverage of molecular biology on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks. ??? This article has not yet received a rating on the project's importance scale. This article is supported by the Genetics task force (assessed as High-importance). This article is supported by the Molecular and Cell Biology task force (assessed as Mid-importance). This article is supported by the Computational Biology task force (assessed as Mid-importance).

Delete this article

Latest comment: 30 days ago15 comments4 people in discussion

There is nothing in this article that isn't covered in Non-coding DNA and other articles. I intend to delete it in one week unless there are objections. Genome42 (talk) 18:24, 20 July 2025 (UTC)Reply

Formally, the easiest process for this is to consider it a WP:MERGE, move any useful info to non-coding DNA (your post suggests there's nothing worth moving; I haven't looked into it) and redirect this article there. That has the additional benefit of leaving the contents of this article publicly viewable in the page history if anyone wants to go back and try to salvage something. I agree that conserved non-coding sequence is probably not a great article topic. Ajpolino (talk) 14:57, 21 July 2025 (UTC)Reply

Agreed, should consider opening a merge proposal and determining whether there's information that is not covered in Non-coding DNA that should be transferred — 🪫Volatile ^{📲T | ⌨️C} 03:29, 22 July 2025 (UTC)Reply

The only important part of a merge proposal is the discussion on this page so let's consider this a merge proposal. I propose to delete everything and leave a stub with links to other articles. Here's the stub.

Coding DNA accounts for a large proportion of bacterial genomes but only a small proportion of most eukaryotic genomes, especially those that contain large amounts of junk DNA. There are many functional elements that are not coding sequences and, as expected, those functional elements are conserved. (See Non-coding DNA.)

Genome42 (talk) 18:52, 23 July 2025 (UTC)Reply

That's not really how we do things here. If you don't think there should be a separate encyclopedia article for "conserved non-coding sequence" (which I agree with), then we should either delete this page per your original proposal, or have this page redirect an interested reader to a more appropriate topic (e.g. non-coding DNA). At that page, the reader would learn precisely what you're attempting to communicate in your proposed short paragraph. Ajpolino (talk) 22:43, 23 July 2025 (UTC)Reply

I'm happy to delete the entire article and redirect to Non-coding DNA. My only concern is that this will trigger a response from numerous editors who will tell me that that's not how we do things here.

I'll wait a few days then make the change. Genome42 (talk) 16:11, 24 July 2025 (UTC)Reply

Sure, the process is outlined at WP:BLAR. Ajpolino (talk) 20:15, 24 July 2025 (UTC)Reply

I object to a blank and redirect for this topic. How well noncoding DNA elements are conserved, across types and across species, and the noncoding elements that are found to be CNEs, is a notable topic. Non-coding DNA doesn't even mention conservation, except to point to this article for more information on the topic. I think this is fine as a standalone topic as evidenced by refs below. Merging in all the content related to conservation and evolution of noncoding elements is also a possibility; although it looks like the Non-coding DNA editors have at some point already decided this content is better as separate article. But blanking simply gets rid of reliably sourced material that is not in the target article. Here are some recent reliable sources that talk about CNEs that show CNEs are a topic unto themselves: [1], [2], [3]. And here is a paper about dbCNS, a database of CNEs [4]. --{{u|Mark viking}} {Talk} 20:44, 24 July 2025 (UTC)Reply

Read the introduction. It defines conserved non-coding sequences as regulatory sequences and transcription factor binding sites. There's no mention of conserved non-coding elements (CNEs) but there is a section on "Untraconserved regions." I agree that there should be an article on CNEs but not this one.

Other than ultraconserved regions, what other material in this article isn't covered just as well in another article? Regulatory sequences? Transposable elements? Pseudogenes? Introns? UTRs? Genome42 (talk) 22:27, 24 July 2025 (UTC)Reply

In that case, let's open discussion on what should be contained in the ideal article on CNEs and adjust or delete sections accordingly. Maybe shift focus away from where CNEs are located (which the article's organization emphasizes) towards their significance and functions/applications. In particular, the lead mentions comparative genomics, which could be one avenue of approach — 🪫Volatile ^{📲T | ⌨️C} 06:19, 27 July 2025 (UTC)Reply

Are you suggesting that we rename the article to "Conserved non-coding elements (CNEs)" and confine the material to a discussion about ultraconserved non-coding regions? Here's a definition from Polychronopoulos et al. (2017).

"Comparative genomics has revealed a class of non-protein-coding genomic sequences that display an extraordinary degree of conservation between two or more organisms, regularly exceeding that found within protein-coding exons. These elements, collectively referred to as conserved non-coding elements (CNEs) ..." Genome42 (talk) 19:51, 27 July 2025 (UTC)Reply

Sounds like a great start, ultraconserved non-coding regions being one potential section. Perhaps the sources provided by Mark Viking may reveal another section that's appropriate for the article, but time will need to be spent to review the information — 🪫Volatile ^{📲T | ⌨️C} 22:24, 27 July 2025 (UTC)Reply

You aren't being very clear. Are you suggesting that we keep the information on Introns, Untranslated regions, Transposable elements, Pseudogenes, etc. but simply expand the section on ultraconserved sequences?

Or are you suggesting a separate article on CNE's (ultraconserved elements)?

If there's strong objection to blanking this article on conserved non-coding sequence then should we add sections on the really important conserved non-coding DNA such as: centromeres, telomeres, SARs, non-coding genes, regulatory sequences, and origins of replication? All of those are covered in Non-coding DNA. Genome42 (talk) 14:52, 28 July 2025 (UTC)Reply

Keep in mind that the underlying issue here is the completely arbitrary distinction between coding DNA and non-coding DNA. It's based on the idea that at one time scientists thought that all functional DNA elements were located in coding DNA. That hasn't been true for 60 years.

This is why we have so many papers in the scientific literature proclaiming to have discovered some new functional DNA element in non-coding DNA as though that's a revolutionary thought.

We could just as easily divide the genome into centromeres and non-centromeres and write an article on conserved non-centromeric DNA as if that was something worthwhile. Genome42 (talk) 15:07, 28 July 2025 (UTC)Reply

I'm going off your comment that "there should be an article on CNEs" here. So yes, I'm agreeing that we remove the redundant info on Introns and untranslated regions and expand the section on ultraconserved sequences, with the idea of ultimately improving this article to host comprehensive coverage on CNEs (with a rename if needed). — 🪫Volatile ^{📲T | ⌨️C} 19:00, 28 July 2025 (UTC)Reply