Pseudogene
- Pseudogene Definition. A pseudogene is a non-coding gene element. ...
- Overview of Pseudogene. There are about 20,000 pseudogenes discovered in the human genome. ...
- Formation of Pseudogene. Pseudogenes are formed by various errors during the processing of functional genes. ...
- Roles of Pseudogene. ...
- Significance of Pseudogenes. ...
What is the difference between a pseudogene and Gene?
A pseudogene is a DNA sequence that resembles a gene but has been mutated through the course of evolutionary history so it's now inactivated. A pseudogene, then, shares some evolutionary history, so it shares some DNA sequence with the real gene, or the active gene.
What is the mechanism of pseudogene formation?
Mechanism of classical and processed pseudogene formation. Pseudogenes, sometimes referred to as zombie genes in the media, are segments of DNA that are related to real genes. Pseudogenes have lost at least some functionality, relative to the complete gene, in cellular gene expression or protein-coding ability.
What is the PTEN pseudogene?
The PTEN gene is a known tumor suppressor gene. The PTEN pseudogene, PTENP1 is a processed pseudogene that is very similar in its genetic sequence to the wild-type gene. However, PTENP1 has a missense mutation which eliminates the codon for the initiating methionine and thus prevents translation of the normal PTEN protein.
What is a polyA pseudogene?
A pseudogene may result from a tandem DUPLICATION of an existing gene or REVERSE TRANSCRIPTION of the transcript of the gene (so that it lacks the introns and has a POLY (A) TAIL ). Want to thank TFD for its existence?
What is the function of pseudogene?
It is evident that pseudogenes can function as oncogenes or tumor suppressors. A major function mechanism is that pseudogenes can serve as microRNA decoys to compete microRNAs that may target parent genes. Therefore, pseudogenes may serve as potential diagnostic or prognostic markers.
What is a pseudogene example?
Pseudogenes are alleles of normal genes that have become non-functional due to accumulation of mutations; for example, the protein coding region may contain a premature stop codon, or a frameshift mutation, or an internal deletion or insertion relative to the normal sequence.
What is a pseudogene in evolution?
Pseudogenes originate from decay of genes that originated from duplication through evolution. The decays include point mutations, insertions, deletions, misplaced stop codons, or frameshifts of a gene. The decay may occur during duplication, and these disablements may cause loss of a gene function.
What makes a gene a pseudogene?
Definition. A pseudogene is a segment of DNA that structurally resembles a gene but is not capable of coding for a protein. Pseudogenes are most often derived from genes that have lost their protein-coding ability due to accumulated mutations that have occurred over the course of evolution.
What is pseudogenes and its types?
Pseudogenes come in two basic types according to their precise mode of origin: processed pseudogenes that lack introns because they arise when functional messenger RNA is retrotranspositionally inserted into the genome; and non-processed pseudogenes that are the evolutionary remnants of tandemly duplicated genes that ...
How do you identify pseudogenes?
All of them identify pseudogenes based on their two key sequence properties: similarity to genes and non-functionality. In practice, the former is often characterized by the sequence similarity between a pseudogene and its closest functioning gene relative (referred to as the 'parent gene') in the present-day genome.
Why do we study pseudogenes?
Research has shown that pseudogenes code for RNA transcripts that can regulate their respective parental copy genes. Through this level of regulation, pseudogene products can increase or decrease the level of expression of these parental genes and their protein products.
What are pseudogenes quizlet?
What is a pseudogene? previously functional gene that lost its function due to mutation.
How many pseudogenes do humans have?
20,000 pseudogenesWe identified ∼20,000 pseudogenes in the human genome. The strategy used in this study ensures that each pseudogenic region represents a single event of gene or exon duplication and that regions matching to the same protein are fused.
Do pseudogenes make proteins?
There exist roughly 10,000 pseudogenes in mammalian genomes. Although they are not able to produce functional proteins, many pseudogenes (approximately 20%) are transcribed into RNAs that comprise another category of lncRNAs [33].
How many pseudogenes do humans have?
20,000 pseudogenesWe identified ∼20,000 pseudogenes in the human genome. The strategy used in this study ensures that each pseudogenic region represents a single event of gene or exon duplication and that regions matching to the same protein are fused.
What is a pseudogene quizlet?
What is a pseudogene? previously functional gene that lost its function due to mutation.
Which is an example of Subfunctionalization of a gene duplicate?
Hemoglobin. Human hemoglobin provides a variety of subfunctionalization examples. For instance, the gene for hemoglobin α-chain is undoubtedly derived from a duplicate copy of hemoglobin β-chain.
What is meant by the term pseudogene quizlet?
What is meant by the term pseudogene? Pseudogenes are nonfunctional versions of genes that resemble other gene sequences but that contain significant nucleotide substitutions, deletions, and duplications that prevent their expression.
What is pseudogenes in biology?
For a species of beetle, see Pseudogenes (beetle). Pseudogenes are nonfunctional segments of DNA that resemble functional genes. Most arise as superfluous copies of functional genes, either directly by DNA duplication or indirectly by reverse transcription of an mRNA transcript.
What are the properties of pseudogenes?
Properties. Pseudogenes are usually characterized by a combination of homology to a known gene and loss of some functionality. That is, although every pseudogene has a DNA sequence that is similar to some functional gene, they are usually unable to produce functional final protein products.
What is the pseudogene of Drosophila?
The term "pseudo-pseudogene" was coined for the gene encoding the chemosensory ionotropic glutamate receptor Ir75a of Drosophila sechellia, which bears a premature termination codon (PTC) and was thus classified as a pseudogene.
How to identify pseudogenes?
Pseudogenes are often identified by the appearance of a premature stop codon in a predicted mRNA sequence , which would, in theory, prevent synthesis ( translation) of the normal protein product of the original gene. There have been some reports of translational readthrough of such premature stop codons in mammals. As alluded to in the figure above, a small amount of the protein product of such readthrough may still be recognizable and function at some level. If so, the pseudogene can be subject to natural selection. That appears to have happened during the evolution of Drosophila species .
What is the PTEN gene?
PTEN. The PTEN gene is a known tumor suppressor gene. The PTEN pseudogene, PTENP1 is a processed pseudogene that is very similar in its genetic sequence to the wild-type gene.
What are unitary pseudogenes?
Unitary pseudogenes. 2 ways a pseudogene may be produced. Various mutations (such as indels and nonsense mutations) can prevent a gene from being normally transcribed or translated, and thus the gene may become less- or non-functional or "deactivated".
What happens when a gene is mutated?
Mutations that disrupt either the structure or the function of either of the two genes are not deleterious and will not be removed through the selection process. As a result, the gene that has been mutated gradually becomes a pseudogene and will be either unexpressed or functionless.
What is a pseudogene?
Pseudogenes are alleles of normal genes that have become non-functional due to accumulation of mutations; for example, the protein coding region may contain a premature stop codon, or a frameshift mutation, or an internal deletion or insertion relative to the normal sequence.
What are pseudogenes in the genome?
Pseudogenes are regions of the genome that are similar to functional genes but are thought to be nonfunctional. They may be highly homologous to protein-coding genes but unable to produce a functional protein due to a disrupted open reading frame (ORF) or highly similar to RNA encoding genes but unable to produce an RNA transcript. RNA pseudogenes are more difficult to identify as there is no ‘ORF’ to be disrupted; nevertheless, the term ‘pseudogene’ was first used by Jacq et al. (1977) to describe RNA pseudogenes of the 5S RNA gene that are found in a tandem array with the functional 5S RNA gene in Xenopus. Pseudogenes have often been regarded as the ‘poor relations’ of protein-coding genes and have elicited little interest from researchers aside from their potential to elucidate the evolutionary processes that have been acting in the genome. However, some recent studies have suggested that pseudogenes have the potential to act as posttranscriptional regulators of functional genes, by both encoding short interfering RNAs and acting as sinks for ncRNAs, in particular miRNAs ( Muro et al., 2011 ). Further, it is possible for pseudogenes to be involved in gene conversion with functional genes, resulting in disease phenotypes ( Bischof et al., 2006 ), and for pseudogenized loci to be resurrected, possibly again by gene conversion ( Wang et al., 2012 ). It is also critical that pseudogenes are correctly annotated within genomes to avoid confusing them with coding loci. Several groups have attempted to catalog all pseudogenes within the human genome; one of the most recent is the GENCODE gene annotation project of the ENCODE consortium, which has annotated over 12 000 human pseudogenes that are stored at the psiDR website ( www.pseudogenes.org/psidr/) ( Pei et al., 2012 ).
How are pseudogenes related to functional genes?
Pseudogenes are inheritable genetic elements that are similar to functional genes but are non-functional as they do not encode for proteins. Their biogenesis results from the duplication of a parental gene, or the retrotransposition of an mRNA sequence into different genomic loci. The inability of pseudogenes to produce functional proteins is often the consequence of subsequent genetic alterations (frameshift mutations, creation of stop codon). There exist roughly 10,000 pseudogenes in mammalian genomes. Although they are not able to produce functional proteins, many pseudogenes (approximately 20%) are transcribed into RNAs that comprise another category of lncRNAs [33]. Several studies demonstrated the biological activity of pseudogenes in controlling parental gene expression by producing natural siRNAs [34] or antisense transcripts, and by competing with miRNA binding sites on mRNA targets [35].
What is the pseudogene of D. melanogaster?
A different type of pseudogene, known as a processed pseudogene, is found in the GST supergene family in D. melanogaster. Mgst1-psi is a putative pseudogene of the single microsomal GST gene found in this species. This pseudogene contains a poly-A tail towards the 3′ end, has no introns, a premature stop codon, and a direct repeat at both ends. Presumably, it was derived from the reverse transcription and subsequent integration of Mgst1 mRNA into the genome ( Toba and Aigaki, 2000 ).
How many pseudogenes are there in the human genome?
There exist roughly 10,000 pseudogenes in mammalian genomes.
How are pseudogenes produced?
Pseudogenes can be produced by deleterious mutations, which result in the silencing of a gene. This type of pseudogene, known as an unprocessed pseudogene, normally occurs in a duplicate gene and frequently pseudogenes are found proximal to the genes from which they are derived.
What are processed pseudogenes?
Processed pseudogenes are found in most mammalian genomes and their structure is that of an integrated cDNA copy of a cellular mRNA: They do contain introns, have lost the untranscribed part of the promoter, end with a polyA tail, and are flanked by TSDs (Fig. 3.1) ( Brosius, 1999b; Esnault et al., 2000; Weiner et al., 1986). Similar to Alu retrotransposition, processed pseudogenes were demonstrated to be generated by trans-mobilization of cellular mRNAs by the protein machinery encoded by intact LINE retrotransposons (Esnault et al., 2000 ). In most cases, processed pseudogenes are not functional because they do not include complete promoters and/or because of the accumulation of mutations which occur in the absence of any selection pressure. On rare occasions, processed pseudogenes are functional due to the fortuitous presence of a promoter upstream of the insertion site and the conservation of an intact ORF with a new expression pattern. Generally, there are 1–10 (in some cases up to 100) processed pseudogenes for each human gene ( Brosius, 1999b ).
Pseudogene Definition
A pseudogene is a non-coding gene element. It resembles a functional gene for most of its sequence but is a non-functional variant of it.
Overview of Pseudogene
There are about 20,000 pseudogenes discovered in the human genome. This number is roughly equal to the number of functional coding genes.
Formation of Pseudogene
Pseudogenes are formed by various errors during the processing of functional genes. Based on the mechanism by which they are formed, pseudogenes could be processed or non-processed.
Roles of Pseudogene
Earlier, pseudogenes were identified as part of the huge piece of junk DNA present in the genome that did not encode any proteins and thus of no apparent role in the genome.
Significance of Pseudogenes
Comparative genomics When genomes of various species are compared, there appear to be pseudogenes with conserved mutations, at the same location in many organisms. Such pseudogenes indicate the common ancestry of the species possessing it.
Learn about this topic in these articles
Furthermore, there are two β pseudogenes (ψβ 1 and ψβ 2) and two α pseudogenes (ψα 1 and ψα 2 ), as well as a ζ pseudogene. These pseudogenes are very similar in nucleotide sequence to the corresponding functional genes, but they include terminating codons and other mutations that make it impossible for them to…
molecular phylogeny
Furthermore, there are two β pseudogenes (ψβ 1 and ψβ 2) and two α pseudogenes (ψα 1 and ψα 2 ), as well as a ζ pseudogene. These pseudogenes are very similar in nucleotide sequence to the corresponding functional genes, but they include terminating codons and other mutations that make it impossible for them to…
Overview
Examples of pseudogene function
While the vast majority of pseudogenes have lost their function, some cases have emerged in which a pseudogene either re-gained its original or a similar function or evolved a new function. Examples include the following:
Drosophila glutamate receptor. The term "pseudo-pseudogene" was coined for the gene encoding the chemosensory ionotropic glutamate receptor Ir75a of Dr…
Properties
Pseudogenes are usually characterized by a combination of homology to a known gene and loss of some functionality. That is, although every pseudogene has a DNA sequence that is similar to some functional gene, they are usually unable to produce functional final protein products. Pseudogenes are sometimes difficult to identify and characterize in genomes, because the two requirements of homology and loss of functionality are usually implied through sequence align…
Types and origin
There are four main types of pseudogenes, all with distinct mechanisms of origin and characteristic features. The classifications of pseudogenes are as follows:
In higher eukaryotes, particularly mammals, retrotransposition is a fairly common event that has had a huge impact on the composition of the genome. For exa…
Misidentified pseudogenes
Sometimes genes are thought to be pseudogenes, usually based on bioinformatic analysis, but then turn out to be functional genes. Examples include the Drosophila jingwei gene which encodes a functional alcohol dehydrogenase enzyme in vivo.
Another example is the human gene encoding phosphoglycerate mutase which was thought to be a pseudogene but which turned out to be a functional gene, now named PGAM4. Mutations in it …
Bacterial pseudogenes
Pseudogenes are found in bacteria. Most are found in bacteria that are not free-living; that is, they are either symbionts or obligate intracellular parasites. Thus, they do not require many genes that are needed by free-living bacteria, such as gene associated with metabolism and DNA repair. However, there is not an order to which functional genes are lost first. For example, the oldest pseudoge…
See also
• List of disabled human pseudogenes
• Molecular evolution
• Molecular paleontology
• Pseudogene (database)
Further reading
• Gerstein M, Zheng D (August 2006). "The real life of pseudogenes". Scientific American. 295 (2): 48–55. Bibcode:2006SciAm.295b..48G. doi:10.1038/scientificamerican0806-48. PMID 16866288.
• Torrents D, Suyama M, Zdobnov E, Bork P (December 2003). "A genome-wide survey of human pseudogenes". Genome Research. 13 (12): 2559–67. doi:10.1101/gr.1455503. PMC 403797. PMID 14656963.