Talk:Gene desert

	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.Molecular BiologyWikipedia:WikiProject Molecular BiologyTemplate:WikiProject Molecular BiologyMolecular Biology
???	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 Low-importance).

Delete this article

This article is ridiculous. It conflicts with other articles such as Junk DNA and it contains no useful information that isn't covered better in other articles. I intend to delete it next week unless there are any objections. Genome42 (talk) 18:32, 20 July 2025 (UTC)[reply]

Same with the other articles, at least consider a WP:MERGE proposal and review the article to see if there are pieces that might be worth salvaging — 🪫Volatile ^{📲T | ⌨️C} 03:31, 22 July 2025 (UTC)[reply]

Also, just out of curiosity, how would you intend to delete this article? Through a blank and redirect WP:BLAR or deletion nomination? — 🪫Volatile ^{📲T | ⌨️C} 03:33, 22 July 2025 (UTC)[reply]

I would remove almost all of the content and replace it with a stub noting that the term "gene desert" is not commonly used by scientists these days. It used to refer to regions of a chromosome that are deficient in genes.

There's nothing in the article worth salvaging.

Do you object to this? If so, what are your scientific reasons for retaining information that's misleading, redundant and/or not relevant?

Are you knowledgeable about this subject or are you just making sure that Wikipedia policies are followed? Genome42 (talk) 17:00, 22 July 2025 (UTC)[reply]

This is a notable concept in genetics, backed by reliable sources. It is about the spatial organization of genes in genomes and also partially about what is contained in gene deserts. If there is information in the article that is incorrectly summarized, fixing that is a matter of editing, not deletion. Junk DNA says little about spatial organization and doesn't even mention gene deserts. The term, like junk DNA itself, is still used; there are 1,280 hits in GScholar for "gene desert" since 2021. I see no conflicts with junk DNA that could not be solved with editing. Keep the article and improve it. --{{u|Mark viking}} {Talk} 18:05, 22 July 2025 (UTC)[reply]

The term gene desert was hardly used in the scientific literature before 2000. Recently it has been used by a few people working on the human genome as a synonym for intergenic region. Both terms (gene desert and intergenic region) are pretty useless as scientific terms. We have known for 60 years that there are regulatory sequences located between genes so we hardly need to make a big mystery out of that by referring to regulatory sequences as gene deserts.

We've also known for just as long that our genome is full of junk DNA so it's not a surprise that some of this junk accumulates between genes. What's the point of referring to this junk DNA as a gene desert? I strongly suspect that people who use the term "gene desert" are trying to make a big deal out of the fact that there's more functional DNA than just coding regions. That's not news but whoever wrote this article says the following in the History section.

"Although the possibility of function in gene deserts was predicted as early as the 1960s, genetic identification tools were unable to uncover any specific characteristics of the long noncoding regions, other than that no coding occurred in those regions."

Really? I was a graduate student in the late 1960s and I certainly knew about non-coding genes (tRNA and ribosomal RNA), regulatory sequences, origins of replication, termination regions, and centromeres.

I suggest replacing the entire article by the following stub.

The term gene desert was rarely used in the 20th century. Recently, it has been used occasionally as a synonym for intergenic region, especially in mammalian chromosomes. About 55% of the human genome is intergenic but this includes large regions such as centromeres and telomeres. The regions between genes in a typical chromosome consist of regulatory sequences, origins of replication, scaffold attachment sites and considerable amounts of junk DNA. (See also non-coding DNA.)

Genome42 (talk) 18:35, 23 July 2025 (UTC)[reply]

No, you seem to be missing the point. Gene deserts are not just intergenic regions, they are particularly large intergenic regions. They comprise about a quarter of the human genome and are of interest in their own right. For example, A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival is a 2024 Nature Communications paper discussing the role of a gene desert in the context of regulation of a developmental gene. Spatial organization of the genome matters and gene deserts are a notable aspect of that organization. You may have known of various general aspects of noncoding regions back then, but you knew little about them in the context of gene deserts, because nobody did back then. To write a good encyclopedia article, digesting the current literature will produce a better result than relying on what you learned as the state of the art 60 years ago. As an aside, termination regions were not discovered until the 1970's, e.g., see Proudfoot's retrospective on the topic [1]. --{{u|Mark viking}} {Talk} 18:16, 24 July 2025 (UTC)[reply]

As an aside, I was referring to DNA replication replication terminator regions. Genome42 (talk) 16:35, 26 July 2025 (UTC)[reply]

I went to the UCSC genome browser and looked at the intergenic spaces between genes around the Shox2 genes on chromosome 3. The intergenic space between Shox2 and the nearest upstream gene is a bit bigger than that between some other genes in the region but not it's not an unusual distance to my eyes.

If you think there's something unusual going on here then maybe you should edit the article to make it clear. You could start by clearly defining how big an intergenic region has to be in order to qualify as a gene desert and then explain what you mean by saying that gene deserts occupy about 25% of the genome. Keep in mind that intergenic regions take up 55% of the genome and the average distance between genes should be about 68 kb.

It would also be very helpful to explain just how much of that intergenic region upstream of the Shox2 gene is functional and how much is junk.

If you are going to edit the article in order to preserve it, then make sure to delete derogatory remarks such as this sentence in the first paragraph of the introduction.

"Originally believed to contain inessential and "Junk DNA" due to their inability to create proteins, gene deserts have since been linked to several vital regulatory functions, including distal enhancing and conservatory inheritance."

Those of us who were around over 50 years ago were well aware of the fact that non-coding regulatory sequences existed between genes and well aware of the fact that the human genome was 90% junk but 10% functional. (1% coding and 9% non-coding but functional.) The idea that we were all too stupid to recognize functional non-coding DNA doesn't belong in a Wikipedia article. Genome42 (talk) 17:18, 26 July 2025 (UTC)[reply]

Please correct me if I'm wrong, but I also took a look at the regions upstream of Shox2. The first gene entry upstream was RP11-290K4.2, with gene class listed as non-coding. The first coding gene I identified, PQLC2L/SLC66A1LP, was roughly 496kb upstream. This is slightly lower than the 2024 paper's description, but is still 7 times longer than the average intergenic region of 68kb (as you have stated).

Regarding the 25% gene desert figure, I was able to trace the statement back to the 2001 Venter article "The Sequence of the Human Genome", stating that If we define a desert as a region .500 kbp without a gene, then we see that 605 Mbp, or about 20% of the genome, is in deserts. The same quote also offers a functional definition of gene desert (a region lacking protein-coding genes longer than 500kb). By that definition, the region upstream of Shox2 is a gene desert.

Do agree that the intro sentence should be reworded, it's much too vague and directly contradicts the first sentence in the History section, which agrees that in the 1960s, there was awareness that non-coding regions serve functional purposes.

For purposes of better organization, what is your opinion on condensing notable portions of the article down and migrating the material into Non-coding DNA, maybe under a section titled "Large non-coding regions"? Perhaps the same can be said of Intergenic region as well. Of course, all suggested names and merges are open to be workshopped and discussed. — 🪫Volatile ^{📲T | ⌨️C} 06:04, 27 July 2025 (UTC)[reply]

Here's what I think are the important points about gene deserts.

- They are some intergenic regions of large eukaryotic chromosomes that are bigger than 500 kb. These are called gene deserts. (I assume they don't exist in yeast, Drosophila, and bacteria.)

- About 90% of large eukaryotic chromosomes is junk DNA so these large intergenic regions consist mostly of junk DNA.

- Like all other intergenic regions, gene deserts also contain a small amount of conserved regulatory sequence.

- They may also contain other functional DNA elements.

I don't see anything in the History section that's worth keeping. It doesn't sound correct to me.

The section on Possible functions seems to be arguing that large intergenic regions are required for looping. That's the only speculative function that I see attributed to large intergenic regions but there's no explanation for why this explanation doesn't apply to shorter intergenic regions. The article mentions that Fugu seems to get along just fine with much smaller intergenic regions. I assume that there are a lot more gene deserts in lungfish genomes.

The section on Stable and variable gene deserts doesn't make any sense to me.

The section on Genetic diseases simply confirms that genetic diseases can be caused by mutations in functional non-coding DNA elements such as regulatory sequences. Unless I'm missing something, this has nothing to do with the fact that some intergenic regions are much larger than others. In fact, the section on "A caveat" seems to confirm that point. Genome42 (talk) 17:26, 27 July 2025 (UTC)[reply]

After taking a look through the article, I'm inclined to agree. This whole article itself is written like a review of research on gene deserts, and I don't see any portion of the history section that isn't better covered by the article on Junk DNA.

At best, the section on stable versus variable deserts probably only merit a paragraph. Though the Venter and Ovcharenko papers provide potentially useful information, we should refocus the section around the definition of stable vs unstable and why they're significant. Of course, if there is no real significance then that that section can be removed.

I'm not opposed to an outright removal of "possible functions" either. Wikipedia is not the place for speculation, the information should be included after scientific consensus is gained.

As for genetic diseases, the current section is really focused on the 8q24 gene. At best, most of this information is better suited for an article on the gene itself or the MYC promoter. At worst, the scope is so limiting we should remove it outright. — 🪫Volatile ^{📲T | ⌨️C} 22:47, 27 July 2025 (UTC)[reply]