The analysis of completed human genome for recent segmental duplications was done and it was found that 4 % of the genome is covered by duplications. The extent to which segmental duplication varies is between 1% to 14% and this takes in the 24 chromosomes. Intra-chromosomal duplication occurs more frequently than inter-chromosomal duplication in 15 chromosomes. There are several types of gene duplication mechanisms that have been observed in genomes till today. These mechanisms include Tandem gene duplication, Large scale subgenomic duplication, whole genome duplication, DNA-mediated duplicative transposition and retrotransposition.
Tandem gene duplication is a process of crossover between two unequally aligned chromatids. These types of crossovers lead to the formation of one chromosome in which a gene is gained and another chromosome in which a gene is lost. It gives rise to repeated segments in which the head of one segment joins the tail of another segment whereas in other case the heads or the tails get joined together. The former is called direct repeat while the latter is called inverted repeat.
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Large scale subgenomic duplication is also called segmental duplication. It leads to the duplication of large segments of DNA containing multiple genes. By this process 400 large DNA segments have been duplicated which accounts for than 5% of the euchromatic genome. This duplication process has taken place over the last 40 million years of primate evolution.
Whole genome duplication is a process in which an organism is created with additional copies of the entire genome of a species. In whole genome duplication an organism inherits two copies of its genome from each parent and this results in the formation of total four copies. This is quite different from the normal cells of most organisms. They inherit only one copy from its parent and thus they contain two copies of their entire genome. Duplicative transposition is a process in which segments of DNA move within or between chromosomes. They can transpose themselves to new positions within the genome of a single cell. It leads to the formation of alterations in the cell by shutting off genes or inserting mutations and creates defective genes. Retrotransposition is a process in which cellular reverse transcriptases make a cDNA copy of an RNA transcript.
FATE OF DUPLICATED GENES
Although a lot of research has been done in this field and we know about the mechanisms of gene duplication, but the factors which influence the fate of duplicated genes remains unknown. The first model that was proposed about how the evolution of gene duplication takes place was that of non- vs. neofunctionalization. According to this model, the two duplicate genes are useless at the time of duplication, but over long periods of time, one of the duplicated genes get mutated or gain a new function. Another recently developed model of subfunctionalization suggests that both genes lose complementary functions, until they are retained because they both combine to maintain the original. The duplication degeneration-complementation (DDC) version of this model predicts that evolution takes place through degeneration of regulatory or coding regions of duplicate copies.The DDC and the neo-functionalization model assumes that at the time of duplication, duplicate genes. However, it is not true in case of retrotransposed gene copies. The DDC model tries to explain the retention of duplicate genes by pointing out changes in their regulation, but it does not explain the differences in the evolutionary rates of the protein coding regions. It has been revealed that there is little to no connection between regulatory and protein evolution in duplicates. One study suggests that duplication mechanism and genomic locality are important factors that affect rate asymmetry in rodent duplicates. Another study has revealed that the variability in recombination rates across the genome causes the yeast duplicates to evolve at different rates. The theory suggests that one copy may become silenced by degenerative mutations. Another alternative outcome that may happen is that one copy may acquire a novel, beneficial function while the other copy retains its original function. The other outcome that may happen is that both the copies become partially compromised by mutation.
A wide variety of experiments have suggested that posttranslational regulation impacts the fate of duplicated genes. Gene and genome duplications create genetic changes on which evolution works. They are mainly responsible for changes in many eukaryotic organisms. After duplication, gene loss takes place as the most likely fate; however, a considerable fraction of duplicated genes manage to survive. All genes do not have the same probability to survive, therefore it is not completely understood what evolutionary forces determine what kind of genes survive. It has been seen that posttranslational modifications affect the retention of duplicated genes. WGD proteins are phosphorylated more than RSS proteins. In fact, they are also ubiquitinated more than RSS proteins. All these findings prove that our hypothesis is correct and all the changes occur due to posttranslational modification. The sub- and neofunctionalization of duplicated genes is seen in case of WGD and it determines the survival rate of duplicate pairs, although they do not explain all cases in which duplicate retention takes place because the genes encoding for ribosomal proteins have a better survival rate than other genes.The phosphorylation of gene retention is seen not only in WGD, but also in case of small-scale gene duplication (SSD). Several experiments have revealed that duplication of WGD and SSD has different effects on the evolution of the genome (7, 41, 42). SSDs occur continuously at different times and do not repeat the evolutionary analysis that was possible in case of WGD. But, when the properties of SSD vs. singleton proteins were compared, it showed that a higher fraction of SSD proteins are phosphorylated. Recent studies have revealed the role of duplication mechanisms i.e., retrotransposition in the fate of the new gene copies. Retrotransposed gene copies donot carry their parentâ€™s genetic material and they exhibit less expression than their parents. Hence, retrotransposition is used to generate transcribed gene copies.Tandem duplicates share cis-regulatory elements and becomes co-regulated with the original copy, but the average DNA-mediated duplication is smaller than the average gene size, so sharing of cisregulatory material is not guaranteed for such duplicates. The DDC model is violated in these cases and the two copies become functionally equivalent upon birth. The degeneration of the DDC model is a gradual process, but due to the mutations i.e., insertions, deletions etc, the changes occuring may often be very abrupt. Here, it is shown that each duplication mechanism has certain contribution to mammalian gene families and the effects of each duplication mechanism in the fate of duplicated genes are examined. The data suggests that retrotransposition is responsible for nearly half of all gene duplicates in the human, chimpanzee, mouse, rat, and dog genomes. It is shown that interspersed DNA-mediated duplicates and retrotransposed duplicates yield genes whose coding regions evolve more asymmetrically than tandem duplicates. Finally, in interspersed DNA-mediated duplicates, disruptions in flanking regions correlate with selective constraint on these duplicates. It provides further evidence that changes in cis-regulatory regions have some effects on protein coding evolution in duplicate gene copies. In case of RNA-mediated duplicates, the intact retrogenes are enriched in intergenic regions and indel purified regions of the human genome. Moreover, intact retrogenes which are closest to annotated genes show the greatest levels of purifying under selective pressure. Thus, these findings reveal that the fate of duplicated genes is significantly influenced by local genome architecture.
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