Talk:De novo gene birth

Disambig

Should I put a 'not to be confused' link on here? This post might be confusing in regards to de novo variant of a known gene. Poeticfeelings (talk) 17:20, 10 June 2019 (UTC)

@Poeticfeelings: Do you mean as in mutations within a population causing new polymorphisms, or the discovery of new gene sequences by genome/transcriptome sequencing? I must admit I've not come across the term 'de novo variant' very often, but that might just be me. T.Shafee(Evo&Evo)^talk 12:13, 2 July 2019 (UTC)

I think a disambig could be useful here. In clinical genetics, practitioners do speak of de novo mutations or de novo variants. --{{u|Mark viking}} {Talk} 19:56, 10 July 2019 (UTC)

Ah, that makes sense, as in genetic disorder by germline mutation rather than by inheritance. Is there a section of an exiting article that could be pointed to by a 'not to be confused' template? Currently De novo mutation redirects to Mutation#By_inheritance, but I feel it doesn't quite make sense without the clinical relevance pointed out. Perhaps Germline_mutation#When_Mutagenesis_Occurs would make more sense, though it'd need to be updated a bit, since the term de novo muation just appears in the lead but links back to the mutation page without. T.Shafee(Evo&Evo)^talk 00:13, 11 July 2019 (UTC)

That's right, clinical de novo means a germline mutation. I agree that Germline_mutation is the better target for De novo mutation. In my reading, the lead is a bit clearer than the When_Mutagenesis_Occurs section and mentions the clinical relevance in the last sentence. As a quick definition of the term, the lead might be good enough, but agreed, de novo should be explained in the body of article, too. Identifying the clinical concept of de novo with a germline mutation is common, but a bit of a lie, as genetics tests are typically done on blood or saliva and the mutation in the germ cells is simply assumed. Problematic when mosaicism is encountered. --{{u|Mark viking}} {Talk} 00:38, 11 July 2019 (UTC)

free use creation off wiki

Per explanation at Template:Did_you_know_nominations/De_novo_gene_birth this article was created at https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1008160 under CC BY 4.0. --valereee (talk) 15:00, 10 July 2019 (UTC)

Good article?

I think it can be a good article 2001:EE0:4141:1832:45DD:112C:3480:9942 (talk) 00:12, 12 July 2019 (UTC)

Still too technical

The lead needs a crisp definition of How a de novo gene operates. 72.141.106.240 (talk) 15:12, 12 July 2019 (UTC)

NPOV concerns

@Joannamasel:'s careful attention to the article is much appreciated, but some of the edits she has made seem to be in violation of Wikipedia’s NPOV criteria. Dr. Masel is herself the originator and primary proponent of the preadaptation model, and has made some edits that present this model as fact rather than opinion. The major difference between the preadaptation and the proto-gene models is essentially philosophical in nature: the preadaptation model posits a binary genome composed exclusively of genic and non-genic sequences, while the proto-gene model proposes that the genome is a continuum, with ORFs residing on a spectrum that ranges from non-genic to genic. There is ongoing debate in the literature regarding the two models. This is the rule for discussing debated topics on Wikipedia:

• Avoid stating seriously contested assertions as facts. If different reliable sources make conflicting assertions about a matter, treat these assertions as opinions rather than facts, and do not present them as direct statements.

Although I am not an experienced Wikipedian, I am doing my best to interpret these guidelines and to help make the article as useful and balanced as possible. I have therefore rewritten some of these edits to include opposing viewpoints and better indicate that there is a lack of consensus on these points. In accordance with NPOV guidelines, I have generally avoided removing edits and have instead modified or built on them; to avoid violating WP:OR policy, I have stuck to statements that are directly supported by the given references. If a third party with more Wikipedia experience would be willing to confirm that these edits were done properly, it would be appreciated. — Preceding unsigned comment added by Jogmiez (talk • contribs) 17:28, 23 July 2019 (UTC)

Note: The edits mentioned in the above comment are diff set 1 (by Joannamasel) and diff set 2 (by Jogmiez). I was involved with this article at PLOS Genetics (as handling editor), so I'll avoid editing any contested wording to prevent any possible perception that PLOS is trying to control content. However I can help out with general clarity based on the consensus here. T.Shafee(Evo&Evo)^talk 02:45, 24 July 2019 (UTC) - Corrected per comment below. T.Shafee(Evo&Evo)^talk 03:02, 27 July 2019 (UTC)

I guess you meant diff set 1 and diff set 2. Adrian J. Hunter^{(talk•contribs)} 11:34, 26 July 2019 (UTC)

Hopefully we can have a good back and forth of edits between two scientists both active in the field here, with the resulting text as neutral as possible, and far more neutral than either party could achieve on their own. I think this process can be wikipedia at its best! I agree that wherever there is disagreement in the primary literature, the best thing to do is give both sides, so let's indeed proceed on that principle. In some cases, careful use of citations might be enough to establish one view as majority and the other as significant minority - we'll see, but in any case both sides. Academic and personal travel limits my ability to make those edits right now, I'll have a go but not sure how far I'll get, if I go silent after that, I'll come back to this eventually.Joannamasel (talk) 19:51, 25 July 2019 (UTC)

Removed text

Below is text I removed from the article because it was in the wrong section/place but is good information and will add this information later in the correct place as the page is reformatted.

text from pervasive expression section

Most non-genic ORFs that are translated appear to be evolving neutrally. The preadaptation and proto-gene models both predict, however, that expression of non-genic ORFs will occasionally provide an adaptive advantage to the cell. Differential translation of proto-genes in stress conditions, as well as an enrichment near proto-genes of binding sites for transcription factors involved in regulating stress response, support the adaptive potential of proto-genes. Furthermore, it is known that novel, functional proteins can be experimentally evolved from random amino acid sequences. Random sequences are generally well tolerated in vivo; many readily form secondary structures, and even highly disordered proteins may take on important biological roles. The pervasive nature of translation suggests that new proto-genes emerge frequently, usually returning to the non-genic state. In wild S. paradoxus populations, some ORFs with exaggerated gene-like features are found among the pool of translated intergenic polypeptides. It is not clear whether such ORFs are preferentially retained.

text from history section

Despite their recent evolution, all five genes appear fixed in D. melanogaster, and the presence of paralogous non-coding sequences that are absent in close relatives suggests that four of the five genes may have arisen through a recent intrachromosomal duplication event. Interestingly, all five were preferentially expressed in the testes of male flies. The three genes for which complete ORFs exist in both D. melanogaster and D. simulans showed evidence of rapid evolution and positive selection. This is consistent with a recent emergence of these genes, as it is typical for young, novel genes to undergo adaptive evolution, but it also makes it difficult to be completely sure that the candidates encode truly functional products. A subsequent study using methods similar to Levine et al. and an expressed sequence tag library derived from D. yakuba testes identified seven genes derived from six unique de novo gene birth events in D. yakuba and/or the closely related D. erecta.

Another well-characterized example in yeast is MDF1, which both represses mating efficiency and promotes vegetative growth, and is intricately regulated by a conserved antisense ORF.

Arich7 (talk) 22:05, 5 April 2021 (UTC)

References