Evolution of novel genes from non-genic DNA sequence
Novel genes can emerge from ancestrally non-genic regions through poorly understood mechanisms. (A) A non-genic region first gains transcription and an open reading frame (ORF), in either order, facilitating the birth of a de novo gene. The ORF is for illustrative purposes only, as de novo genes may also be multi-exonic, or lack an ORF, as with RNA genes. (B) Overprinting. A novel ORF is created that overlaps with an existing ORF, but in a different frame. (C) Exonization. A formerly intronic region becomes alternatively spliced as an exon, such as when repetitive sequences are acquired through retroposition and new splice sites are created through mutational processes. Overprinting and exonization may be considered as special cases of de novo gene birth.Novel genes can be formed from ancestral genes through a variety of mechanisms.[1](A) Duplication and divergence. Following duplication, one copy experiences relaxed selection and gradually acquires novel function(s). (B) Gene fusion. A hybrid gene formed from some or all of two previously separate genes. Gene fusions can occur by different mechanisms; shown here is an interstitial deletion. (C) Gene fission. A single gene separates to form two distinct genes, such as by duplication and differential degeneration of the two copies.[2](D) Horizontal gene transfer. Genes acquired from other species by horizontal transfer undergo divergence and neofunctionalization. (E) Retroposition. Transcripts may be reverse transcribed and integrated as an intronless gene elsewhere in the genome. This new gene may then undergo divergence.
De novo gene birth is the process by which new genes evolve from non-coding DNA.[1][3]De novo genes represent a subset of novel genes, and may be protein-coding or instead act as RNA genes.[4] The processes that govern de novo gene birth are not well understood, although several models exist that describe possible mechanisms by which de novo gene birth may occur.
Although de novo gene birth may have occurred at any point in an organism's evolutionary history, ancient de novo gene birth events are difficult to detect. Most studies of de novo genes to date have thus focused on young genes, typically taxonomically restricted genes (TRGs) that are present in a single species or lineage, including so-called orphan genes, defined as genes that lack any identifiable homolog. It is important to note, however, that not all orphan genes arise de novo, and instead may emerge through fairly well characterized mechanisms such as gene duplication (including retroposition) or horizontal gene transfer followed by sequence divergence, or by gene fission/fusion.[5][6]
Although de novo gene birth was once viewed as a highly unlikely occurrence,[7] several unequivocal examples have now been described,[8] and some researchers speculate that de novo gene birth could play a major role in evolutionary innovation, morphological specification, and adaptation,[9][10] probably promoted by their low level of pleiotropy.
^ abLong M, Betrán E, Thornton K, Wang W (November 2003). "The origin of new genes: glimpses from the young and old". Nature Reviews Genetics. 4 (11): 865–75. doi:10.1038/nrg1204. PMID 14634634. S2CID 33999892.
^Wang W, Yu H, Long M (May 2004). "Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species". Nature Genetics. 36 (5): 523–7. doi:10.1038/ng1338. PMID 15064762.
^Levy A (October 2019). "How evolution builds genes from scratch". Nature. 574 (7778): 314–316. Bibcode:2019Natur.574..314L. doi:10.1038/d41586-019-03061-x. PMID 31619796.
^Schmitz JF, Bornberg-Bauer E (2017). "Fact or fiction: updates on how protein-coding genes might emerge de novo from previously non-coding DNA". F1000Research. 6: 57. doi:10.12688/f1000research.10079.1. PMC 5247788. PMID 28163910.
^Schlötterer C (April 2015). "Genes from scratch--the evolutionary fate of de novo genes". Trends in Genetics. 31 (4): 215–9. doi:10.1016/j.tig.2015.02.007. PMC 4383367. PMID 25773713.
^Kaessmann H (October 2010). "Origins, evolution, and phenotypic impact of new genes". Genome Research. 20 (10): 1313–26. doi:10.1101/gr.101386.109. PMC 2945180. PMID 20651121.
^Jacob F (June 1977). "Evolution and tinkering". Science. 196 (4295): 1161–1166. Bibcode:1977Sci...196.1161J. doi:10.1126/science.860134. PMID 860134. S2CID 29756896.
^Van Oss SB, Carvunis AR (May 2019). "De novo gene birth". PLOS Genetics. 15 (5): e1008160. doi:10.1371/journal.pgen.1008160. PMC 6542195. PMID 31120894.
^Khalturin K, Hemmrich G, Fraune S, Augustin R, Bosch TC (September 2009). "More than just orphans: are taxonomically-restricted genes important in evolution?". Trends in Genetics. 25 (9): 404–413. doi:10.1016/j.tig.2009.07.006. PMID 19716618.
^Tautz D, Domazet-Lošo T (August 2011). "The evolutionary origin of orphan genes". Nature Reviews. Genetics. 12 (10): 692–702. doi:10.1038/nrg3053. PMID 21878963. S2CID 31738556.
and 28 Related for: De novo gene birth information
Denovogenebirth is the process by which new genes evolve from non-coding DNA. Denovogenes represent a subset of novel genes, and may be protein-coding...
Orphan genes Orphan genes evolve more rapidly than other genes. They often originate through two primary mechanisms: denovogenebirth, where new genes emerge...
protein coding genes, and can therefore lead to the evolution of novel protein-coding genes in a process known as denovogenebirth. Exon Promoter (biology)...
diversifying into new genes, and genes being lost. An entire gene family may also be lost, or gained through denovogenebirth, by such extensive divergence...
A denovo mutation (DNM) is any mutation or alteration in the genome of an individual organism (human, animal, plant, microbe, etc.) that was not inherited...
word gene (Greek: γένος, génos; generation, or birth, or gender) has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is...
Joanna (24 April 2017). "Young genes are highly disordered as predicted by the preadaptation hypothesis of denovogenebirth" (PDF). Nature Ecology & Evolution...
son. New genes arise from several different genetic mechanisms including gene duplication, denovogenebirth, retrotransposition, chimeric gene formation...
neutral theory of evolution. Denovogenebirth is very rare. The most probable path from noncoding DNA to a protein-coding gene is to first become a protogene...
cycles was presented by Becker et al. Denovogenebirth Exon shuffling Gene fusion Gene duplication Horizontal gene transfer Mobile genetic elements Fiers...
repaired using polymerase and ligase. DenovogenebirthGene fusion Gene duplication Genome evolution Horizontal gene transfer Mobile genetic elements Long...
Joanna (24 April 2017). "Young genes are highly disordered as predicted by the preadaptation hypothesis of denovogenebirth". Nature Ecology & Evolution...
Masel J (June 2017). "Young Genes are Highly Disordered as Predicted by the Preadaptation Hypothesis of DeNovoGeneBirth". Nature Ecology & Evolution...
gene and one novel gene. Subsequently, overprinting is also believed to be a source of novel proteins, as denovo proteins coded by these novel genes...
but also to continuous frequent denovogenebirths. These genes (called "founder genes") would form from non-genic DNA sequences, as well as from changes...
birth through amniocentesis, or after birth via prenatal genetic screening. Many Mendelian disorders stem from dominant point mutations within genes,...
deletions, mosaicisms, rings and denovo translocations). The deleted chromosome 5 is paternal in origin in about 80% of denovo cases. Loss of a small region...
SMN1 gene is inherited from both parents in an autosomal recessive manner, although in around 2% of cases it occurs during early development (denovo). The...
genetic cause, either in a gene or chromosome. The mutation responsible can occur spontaneously before embryonic development (a denovo mutation), or it can...
siblings and unrelated controls. A series of studies have shown that gene disrupting denovo CNVs occur approximately four times more frequently in autism than...
COL1A1 or COL1A2 genes. These mutations may be hereditary in an autosomal dominant manner but may also occur spontaneously (denovo). There are four clinically...
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