are pseudogenes vestigial

Pseudogenes are of two general types, processed and nonprocessed. Nonprocessed pseudogenes are thought to be byproducts of evolution, representing “dead” genes that were once functional but are now vestigial, having been inactivated by mutations in critical coding or regulatory sequences.

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What are pseudogenes?

The term "pseudogene" was coined in 1977 by Jacq et al. Because pseudogenes were initially thought of as the last stop for genomic material that could be removed from the genome, they were often labeled as junk DNA. Nonetheless, pseudogenes contain biological and evolutionary histories within their sequences.

Are there vestigial features in humans?

Many human characteristics are also vestigial in other primates and related animals. Charles Darwin listed a number of putative human vestigial features, which he termed rudimentary, in The Descent of Man (1871).

What are the disadvantages of using pseudogenes in genetic studies?

Pseudogenes can complicate molecular genetic studies. For example, amplification of a gene by PCR may simultaneously amplify a pseudogene that shares similar sequences. This is known as PCR bias or amplification bias.

How many pseudogenes are there in the human genome?

As of 2012, it appeared that there are approximately 12,000–14,000 pseudogenes in the human genome, A 2016 proteogenomics analysis using mass spectrometry of peptides identified at least 19,262 human proteins produced from 16,271 genes or clusters of genes, with 8 new protein-coding genes identified that were previously considered pseudogenes.

Are pseudogenes non functional?

Abstract. Pseudogenes have been defined as nonfunctional sequences of genomic DNA originally derived from functional genes. It is therefore assumed that all pseudogene mutations are selectively neutral and have equal probability to become fixed in the population.

Do pseudogenes have function?

Pseudogene transcripts can be processed into short interfering RNAs that regulate coding genes through the RNAi pathway. In another remarkable discovery, it has been shown that pseudogenes are capable of regulating tumor suppressors and oncogenes by acting as microRNA decoys.

Are pseudogenes under natural selection?

Pseudogenes are nonfunctional copies of protein-coding genes that are presumed to evolve without selective constraints on their coding function.

How do pseudogenes come in to existence?

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 is a pseudogene quizlet?

What is a pseudogene? previously functional gene that lost its function due to mutation.

Can pseudogenes be expressed?

Pseudogene clusters across the sample-wise compendium reveal that pseudogenes of housekeeping genes such as ribosomal proteins are widely expressed across tissue types.

How does pseudogenes contribute to evolutionary theory?

provide evidence of evolution. Pseudogenes are like vestigial structures,they no longer function but are still carried along with functional DNA. They can also change as they are passed on through generations, so they provide another way to figure out evolutionary relationship.

Are pseudogenes introns?

Processed pseudogenes generally lack introns, end in a 3' poly A, and are flanked by target site duplications. Until recently, very few polymorphic processed pseudogenes had been discovered in mammalian genomes. Now several studies have found a number of polymorphic processed pseudogenes in humans.

What is pseudogenes in molecular biology?

​Pseudogene 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.

Can pseudogenes be reactivated?

Furthermore, pseudogenes can even be “reactivated” in some conditions, such as cancer initiation. Some pseudogenes are transcribed in specific cancer types, and some are even translated into proteins as observed in several cancer cell lines.

Why do organisms keep pseudogenes?

Pseudogenes play an essential role in comparative studies regarding genomics as they can provide a record of ancient genes. They are used to determine the rate of gene duplication and follow the evolution of sequence changes in organisms. Thus, pseudogenes are unique and helpful for phylogenetic studies.

How many pseudogenes are in the human genome?

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 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.

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.

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 .

Where are piRNAs derived from?

Some piRNAs are derived from pseudogenes located in piRNA clusters. Those piRNAs regulate genes via the piRNA pathway in mammalian testes and are crucial for limiting transposable element damage to the genome. BRAF pseudogene acts as a ceRNA. microRNAs.

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".

Is there a scientific way to prove a negative?

The first major problem with this concept is that there is no scientific way to prove a negative—for all these scientists know, next month, a study may reveal the exact function of each of these genes. Functions for some pseudogenes have been discovered already (see Pseudogene Function: Regulation of Gene Expression, ...

Can pseudogenes be explained equally well?

True pseudogenes could be explained equally well by either evolution or creation, and wouldn’t provide evidence for one view or the other.

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 ).

What is the most probable explanation for the existence of the pseudogene?

The first pseudogene to be identified, a copy of 5s RNA encoding DNA in Xenopus (Jacq et al., 1977 ), led the authors to conclude that “the most probable explanation for the existence of the pseudogene is that it is a relic of evolution.” Until recently, all subsequently identified pseudogenes have been interpreted to be genomic debris arising from failed gene duplication events and relegated to the status of “junk.” However, pseudogenes have recently been shown to act as miRNA sponges. The pseudogene PTENP1, a relative of the phosphatase PTEN (Phosphatase and Tensin homolog) protein-coding gene, is one example of a molecular mimic that dissipates miRNA regulation of its protein-coding relative. Recently, Poliseno and colleagues ( Poliseno et al., 2010) reported that PTENP1 was repressed by miRNAs (members of the miR17-92 cluster) that also repressed PTEN. They also showed that PTENP1 overexpression resulted in PTEN derepression, increased phosphorylation of the PTEN target, Akt, and a predicted cellular outcome, that is, decreased cell proliferation. Finally, PTEN expression was decreased in tumor samples that also exhibited a loss of gene copy number at the PTENP1 locus. These data supported the hypothesis that PTENP1 is a molecular decoy for miRNAs that target PTEN. Interestingly, PTEN has recently been identified as a “hub” gene in a network of acute ethanol responsive genes in the mouse prefrontal cortex ( Wolen et al., 2012 ). It is likely that the prominence of PTEN in a network of alcohol-influenced genes is dependent on its escape from miRNA control, and given the correlated expression of PTEN and PTENP1 ( Poliseno et al., 2010) it is equally likely that the pseudogene contributes to PTEN’s response to acute alcohol exposure. Moreover, Poliseno et al. provided evidence that another pseudogene member of the K RAS family, KRAS1P, had a similar decoy function. These data point to a general miRNA decoy role for pseudogenes. This is important, because pseudogene families have expanded greatly in humans. Many protein-coding genes, including, for example, Oct4 ( Hawkins & Morris, 2010) and Nanog ( Fairbanks & Maughan, 2006 ), that control stem cell fate have exhibited significant evolutionary expansion in numbers of pseudogene relatives, resulting potentially in new layers of regulation over miRNA function.

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 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 ).

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. Unprocessed pseudogenes are rarely transcribed although some are transcribed and not translated or, occasionally, translated into nonfunctional proteins. Two possible unprocessed pseudogenes have been described in the GST delta class of A. gambiae. One of these is untranscribed and the second is transcribed but predicted to encode a nonfunctional protein ( Ding et al., 2003 ). Both genes are located within the GST delta cluster on chromosome 2R. Originally, two of the D. melanogaster delta GSTs, GSTD7 and GSTD3, were reported to be pseudogenes on the basis of abnormalities in their putative transcript lengths ( Toung et al., 1993 ). However, transcripts for both of these have since been detected by real-time polymerase chain reaction (RT-PCR) and recombinant proteins derived from these cDNAs encode catalytically active proteins ( Sawicki et al., 2003 ).

Does the pseudogene have a functional correlation with the human genome?

The pseudogene has no functional correlation with the human genome, called unitary pseudogene. Guinea pigs and humans suffer from scurvy unless they consume L-ascorbic acid in their diet, because they lack a protein called L-gulono-y-lactone oxidase, an enzyme that catalyzes the terminal step in L-ascorbic acid synthesis (Pink et al., 2011 ). In humans, L-gulono-y-lactone oxidase is a pseudogene that contains molecular defects as the deletion of at least two exons (out of 12), deletions and insertion of nucleotides in the reading frame, and obliterations of intron–exon boundaries ( Pink et al., 2011 ). It has been assumed that the guinea pig and human ancestors managed to survive on a naturally ascorbic acid-rich diet; hence, the loss of this enzyme did not reflect a disadvantage.

What is a pseudogene?

Pseudogene. Pseudogene. =. A pseudogene is a DNA sequence that resembles a gene but has been mutated into an inactive form over the course of evolution. A pseudogene shares an evolutionary history with a functional gene and can provide insight into their shared ancestry.

Is a pseudogene a 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 function of pseudogenes?

Wells devotes a whole chapter to the subject, noting that at the time of writing in 2011, evidence was accumulating that so-called pseudogenes were expressed and had functions, such as enhancing gene expression, acting as decoys, and conducting RNA interference . The fact that many are highly conserved, he wrote, also showed that they should be considered candidates for exploring unknown functions.

What is the doctrine of vestigial organs?

The doctrine of vestigial organs overlaps with Haeckel’s “Biogenetic Law” of recapitulation, which basically does the same thing: sends scientists looking for vestiges of evolution in the embryo. But again, why would natural selection pay the cost of keeping useless vestiges of a supposed evolutionary past around for millions of years, generation after generation, if they perform no service to the organism? Jonathan Wells deals with this myth extensively in his books Icons of Evolution and Zombie Science, so readers are encouraged to go there to learn about the rise and fall of Haeckel’s recapitulation theory (which Darwin considered highly significant). Suffice it to say that this dead doctrine still lurks about in some textbooks today.

What are some examples of unguided evolution?

There are at least three other examples that could be cited. One central proof for unguided evolution that was offered for decades was “vestigial organs, ” a variation on the junk-DNA myth. The evolutionary process supposedly littered our bodies with useless organs from our animal ancestry, just as it littered our cells with useless genes.

What was Darwin's suggestion that biology might be littered with useless remnants of natural selection?

With Darwin’s suggestion that biology might be littered with useless remnants of natural selection, his disciples went on a wild goose chase to look for them. They weren’t trying to explain the existence of these features; they were looking to support Darwin’s hunch. Once his hunch about evolutionary leftovers became established as a doctrinaire assumption, it became an excuse for scientific laziness. Leftovers could be explained away rather than explained. Who wants to rummage through junk? In each case, history since Darwin has rendered each assumption false. These assumptions delayed significant discoveries, and far worse: they justified horrific atrocities committed in the name of “fitness.”

Is pseudogene mislabeled?

Hints of unease with the conventional view appear, however, lower down in the Wikipedia article, where an unknown redactor admits that some pseudogenes have been mislabeled, and others appear to have functions. In his book The Myth of Junk DNA, Jonathan Wells wrote extensively about pseudogenes, setting the stage by quoting Miller, Dawkins, Futuyma, Coyne, Avise, Shermer, and even theistic evolutionist Francis Collins. All point to pseudogenes as evidence against design and evidence confirming evolution. In 2009, Jerry Coyne boasted:

Is pseudogenes evidence for evolution?

It’s safe to say that many Darwin skeptics have felt intimidated by this apparent genetic evidence for evolution, not sure what to make of it or how to fit it into their own perspective . Prominent Darwin defenders like Kenneth Miller, meanwhile, trumpeted pseudogenes as prima facie evidence against intelligent design. “The human genome is littered with pseudogenes,” he wrote in 1994. Pointless junk like this “cannot be attributed to anything that resembles intelligent design.” He even characterized ID as a “retreat back to into an unknowledge of biology that is unworthy of the scientific spirit of this century” ( Life’s Grand Design ).

What organisms have lost their eyes?

Over long periods of time, many cave-dwelling organisms have lost their eyes. Tapeworms have lost their digestive systems. Whales have lost their hind limbs. How can natural selection account for these losses?

What caused pigweed to mutate?

Natural selection caused the pigweed to mutate, creating a new triazine-resistant variant. c. Triazine-resistant pigweed has less-efficient photosynthesis metabolism. d. Triazine-resistant weeds were more likely to survive and reproduce than non-resistant individuals.

Which leaves more offspring than do poorly adapted individuals?

I. Well-adapted individuals leave more offspring than do poorly adapted individuals.

What are vestigial organs?

Vestigal organs are sometimes called rudimentary organs. The examples of human vestigiality are numerous, including the anatomical (such as the human tailbone, wisdom teeth, and inside corner of the eye ), the behavioral ( goose bumps and palmar grasp reflex ), and molecular ( pseudogenes ). Many human characteristics are also vestigial in other ...

What is the arrow in the human body?

Arrows show the vestigial structure called Darwin's tubercle. In the context of human evolution, human vestigiality involves those traits (such as organs or behaviors) occurring in humans that have lost all or most of their original function through evolution.

What are the features of Charles Darwin?

These included the muscles of the ear; wisdom teeth; the appendix; the tail bone; body hair; and the semilunar fold in the corner of the eye. Darwin also commented on the sporadic nature ...

Why do we have wisdom teeth?

Wisdom teeth are vestigial third molars that human ancestors used to help in grinding down plant tissue. The common postulation is that the skulls of human ancestors had larger jaws with more teeth, which were possibly used to help chew down foliage to compensate for a lack of ability to efficiently digest the cellulose that makes up a plant cell wall. As human diets changed, smaller jaws were naturally selected, yet the third molars, or "wisdom teeth", still commonly develop in human mouths. In modern human populations, wisdom teeth have become useless and often present harmful complications to the extent that surgical procedures are frequently performed to remove them.

How long is the plantaris muscle?

The plantaris muscle is composed of a thin muscle belly and a long thin tendon. The muscle belly is approximately 5–10 centimetres (2–4 inches) long, and is absent in 7–10% of the human population.

How many cases of human babies have been born with such a structure?

Twenty-three cases of human babies born with such a structure have been reported in the medical literature since 1884. In rare cases such as these, the spine and skull were determined to be entirely normal. The only abnormality was that of a tail approximately twelve centimeters long.

How long does a coccyx last?

The coccyx, or tailbone, is the remnant of a lost tail. All mammals have a tail at some point in their development; in humans, it is present for a period of 4 weeks, during stages 14 to 22 of human embryogenesis. This tail is most prominent in human embryos 31–35 days old.

Overview

Properties

Types and origin

Examples of pseudogene function

Misidentified pseudogenes

Bacterial pseudogenes

See also

Further reading