A fact from De novo gene birth appeared on Wikipedia's
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This article was
adapted from
Stephen Branden Van Oss; Anne-Ruxandra Carvunis (23 May 2019).
"De novo gene birth".
PLOS Genetics. 15 (5): e1008160.
doi:
10.1371/JOURNAL.PGEN.1008160.
ISSN
1553-7390.
PMC
6542195.
PMID
31120894.
Wikidata
Q86320144.{{
cite journal}} : CS1 maint: unflagged free DOI (
link) after
peer review (
reviewer reports) under a
CC BY 4.0 license (
2019). |
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)
{{u|
Mark viking}} {
Talk}
19:56, 10 July 2019 (UTC)
{{u|
Mark viking}} {
Talk}
00:38, 11 July 2019 (UTC)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)
I think it can be a good article 2001:EE0:4141:1832:45DD:112C:3480:9942 ( talk) 00:12, 12 July 2019 (UTC)
The lead needs a crisp definition of How a de novo gene operates. 72.141.106.240 ( talk) 15:12, 12 July 2019 (UTC)
@ 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:
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)
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. [1] [2]
Arich7 ( talk) 22:05, 5 April 2021 (UTC)
References