Words convey meaning, and the word pseudogene conveys the sense of a gene that is a sham, that is spurious, that is phoney. It is a word that is widely used in the literature on genetics, where pseudogenes are regarded as defunct relatives of functional genes. The dominant reason for studying them is because they "provide a record of how the genomic DNA has been changed without [. . .] evolutionary pressure and can be used as a model for determining the underlying rates of nucleotide substitution, insertion and deletion in the greater genome" (Source here). Recent research has challenged this assessment of these genetic elements and the textbooks need to be revised comprehensively. Nearly everything that has been widely accepted about pseudogenes has been proven false.
"Pseudogenes were long considered as junk genomic DNA: present in the genome but non-coding and without function. However, discoveries in the ancient protist T. brucei, as well as in some metazoan, indicate that pseudogene regulation is widespread in eukaryotes. Accordingly, the moniker "pseudogene" has been challenged. Interestingly, in addition to eukaryotes, pseudogenes have also been reported from bacteria, although their function remains unknown. [. . .] Once pseudogene functions are shown to occur in all sorts of organisms, including eukaryotes and prokaryotes, the concept of pseudogene will need to be substantially modified." (p.30-31)
Comparing genomes of related organisms has been likened to reading alternative history novels, but there really is no reason why there should not also be consideration of alternative design scenarios. (source here)
In an informative review paper, Wen et al. (2012) document recent findings that warrant a radical revision of the pseudogene concept. The first line of evidence concerns conservation. We should note first that "pseudogenes are pervasive, and usually abundant, in all eukaryotic organisms." (p.27) We are not addressing a trivial aspect of genetics! Conserved pseudogenes do not fit the above claim that they "provide a record of how the genomic DNA has been changed without [. . .] evolutionary pressure."
"[C]omparative analysis of processed pseudogenes in the mouse and human genomes has surprisingly demonstrated that 60% of the processed pseudogenes are conserved in both mammalian species. The high abundance and conservation of the pseudogenes in a variety of species indicate that selective pressures preserve these genetic elements, and suggest that they may indeed perform important biological functions." (p.27)
The second line of evidence is that many examples of functionality have been documented.
"Evidence of expression of pseudogenes has been demonstrated not only in animals but also in plants, such as Arabidopsis (2-5%) and rice (2-3%). The issue arises, if pseudogenes are dysfunctional, why are they so highly expressed? Two possibilities may explain it. One possible explanation is that these pseudogenes are only incidental by-products in the transcription events of other genes, because they are under the effect of the same promoters. An alternative explanation, which we are more inclined to accept, is that the pseudogene transcripts are in fact functional but not random products. More and more accumulating examples support this alternative explanation." (p.28)
Three distinct types of functionality have been documented. These are: natural antisense suppression, RNA interference and gene competitors. Antisense suppression was first proposed in 1986 and first documented in 1992. The regulatory potential of the pseudogene was established. More cases followed, demonstrating that it was not an isolated instance. "These results suggested that antisense binding is an important pseudogene modulation pathway." (p.28.
The RNA interference (RNAi) pathway has been found in many eukaryotes, the first being reported in 2008. The pseudogene is involved in the production of small interference RNAs or microRNAs. The authors write:
"Recently, we established a library of small RNAs (<30 nt) from the bloodstream forms of Trypanosoma brucei by high through-put sequencing, and identified a large fraction of small RNAs derived from the pseudogenes by pairing with complementary transcripts. Ensuing experimental results proved that these pseudogene-derived siRNAs suppressed the expression of their homological protein-coding genes by RNAi. This discovery in an ancient protist, as well as similar discoveries in mouse and plants, indicates that pseudogene-RNAi regulation must have evolved early and thus be widely spread among eukaryotes." (p.28)
Regarding gene competitors, the authors explain that pseudogenes have been shown to act as endogenous competitive RNAs to their cognate genes. "Pseudogenes can perform not only as decoys of stabling/decaying factors but also as small inhibitors." (p.28) An example is cited that has a bearing on our understanding of some cancers.
There is also a fourth category of pseudogene activity: they actually do code for an active product, but researchers have difficulty detecting this using conventional methodologies. This is because the coding only takes place in special circumstances (such as within a cancerous cell).
"Results from the [proteomic mass spectrometry] analysis in mouse has disclosed nine processed pseudogenes that display unique peptide sequences suggesting that they are translated into proteins. Altogether, these results indicate that the discovery of pseudogene functions depends on the skills and methodologies used. Many expressed pseudogenes remain to be annotated. We believe that more and more functional pseudogenes will be discovered as novel biological technologies are developed in the future." (p.31)
This review paper explains that we are just beginning to understand the role pseudogenes play in cells. It seems utterly foolish for people to carry on writing about pseudogenes as though none of this research has taken place. With hindsight it appears obvious that we ought to have presumed functionality and not allowed ourselves to be led by a blind dogma that assigns a "junk" status based on a presumed evolutionary history. Those people who persist in using pseudogenes as an argument against design in living things are only showing their ignorance of contemporary research and betraying the fundamental principles of science.
Pseudogenes are not pseudo any more
Yan-Zi Wen, Ling-Ling Zheng, Liang-Hu Qu, Francisco J Ayala and Zhao-Rong Lun
RNA Biology, Volume 9, Issue 1, January 2012, Pages 27 - 32.
Abstract: Recent significant progress toward understanding the function of pseudogenes in protozoa (Trypanosoma brucei), metazoa (mouse) and plants, make it pertinent to provide a brief overview on what has been learned about this fascinating subject. We discuss the regulatory mechanisms of pseudogenes at the post-transcriptional level and advance new ideas toward understanding the evolution of these, sometimes called "garbage genes" or "junk DNA", seeking to stimulate the interest of scientists and additional research on the subject. We hope this point-of-view can be helpful to scientists working or seeking to work on these and related issues.
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