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What Is a Pseudogene and How It Is Similar to A Functional Gene?
It was earlier described by Beadle and Tatum that a gene is the part of DNA that determines or codes the primary sequence of some final gene product which can be an enzyme, a polypeptide, or an RNA. On the other hand, as the name suggests, pseudogene or false genes are also segments of DNA but unfortunately do not code for any protein. Since they are of no use in the DNA they are sometimes referred to as Junk genes.
They have structural resemblance and are also believed to be derived from functional genes, but they do not code for any protein or due to some reasons might have lost the ability which can be attributed to the deposition of the mutations over the period of evolution.
Probable Origin of Pseudogene
Researchers have determined these pseudogenes accidentally when they were mapping the functions of the functional gene on chromosome loci, and they were called pseudogenes as they had literally no function.
As stated above they were thought to be derived from a functional gene but due to genetic mutations or abnormalities became non-functional. These abnormalities can be any of the following-
Complete absence of the regulatory sequences.
Presence of more than one stop codon or absence of start codon.
Abnormalities in the regulatory sequence.
The most probable reason is gene duplication which led to subfunctionalization and eventual loss of the gene function.
The production of an enormous amount of retrotransposon transcripts that are thought to be formed from functional genes could be a reason for the loss of function.
The Characteristic Feature of Pseudogenes
They contain introns in between them. gene can be found near the pseudogene.
At the 5’ end they lack a promoter sequence. gene can be found near the pseudogene.
They contain direct repeats at their flanking ends. gene can be found near the pseudogene.
At the 3’ end there is a polyA tail. gene can be found near the pseudogene.
The duplicate functional gene can be found near the pseudogene.
Where These Pseudogenes Can Be Found
They can be normally found on the chromosomes and are believed to be non-interfering with the normal functioning of the gene. In some animal species, mitochondrial pseudogene can be found, but in others, it has lost most of its sequences in the due process of nuclear transfer. These transfers can be either direct DNA transfers or RNA mediated. When any one of the transfer methods won’t work out it results in the formation of pseudogenes.
These mitochondrial pseudogenes can be found in enormous quantities in bird species and in mammals but are absent in fishes.
Similarities with Functional Genes
Although pseudogenes do not encode any protein since they are derived from the functional gene it shares some DNA sequence similarities. They are believed to show functions like gene expression and gene regulation just like functional genes.
Just like genes can be inherited from one generation to another, pseudogenes can also be inherited.
Similarity in both lies in the fact that both can be subjected to mutations and changes that are heritable.
Both functional gene and pseudogenes have the capability to act as tumor suppressors or oncogenes.
Functions of Pseudogenes
Earlier pseudogenes were called junk genes as they did not code for any protein but over the years and extensive studies suggested that pseudogenes have a major role to play in gene regulation and gene expression which was confirmed by Michael Snyder.
There are chances that sometimes pseudogenes revert to functional genes. One such gene which became functional during evolution was the cow gene which encodes the ribonuclease enzyme.
Pseudogenes due to the presence of premature stop codons have been found to produce tumor rejection antigen that is transcribed from a short open reading frame.
Significance of Pseudogenes in Evolutionary Studies
Since pseudogenes share some common sequences with the ancestral DNA. Multiple sequences found in humans can be used in disease diagnosis and evolutionary studies.
Mitochondrial pseudogene can help in understanding the phylogeny better as mutations are more frequent in mitochondria than in the nucleus.
Pseudo genomics is a branch of evolutionary biology that deals with the study of role of pseudogenes in the process of evolution and rates at which evolution takes place.
The retro transcribed copies of the pseudogenes can be compared with those of the original genes to study the response of organisms to the given environmental condition. Sometimes a different pseudogene sequence between related organisms can explain the difference in their habitats.
Studies related to pseudogenes can help explain the rates of loss of DNA as well as gene substitution.
Most Recent Studies
After extensive research, it has been established that pseudogenes can act as molecular markers to determine the cell identity which makes them ideal tools for prognosis and diagnosis. Moreover, there is sufficient evidence to prove the link between cancer and defective pseudogene expression which makes them apt markers for cancer classification.
For a long time, pseudogenes have been considered as just copies of functional genes with no roles and are neglected for these reasons. Although they do not code for any protein, they have other more important roles to play like regulating gene expression and in complex regulatory networks.
Furthermore, they can act as markers for the prognosis of cancer and have a role to play in maintaining the normal physiology of the organism. Because of all these functions, they are no longer called junk genes but instead are called as long non-coding RNA (lncRNA).
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