As Tobias said, the the fist step in the process is to identify and confirm premature stop codons, frameshifts and indels. Alternatively, relaxed negative selection would be also a indicative of pseudogenization.
Hi all,
Not necessarily. A pseudogene, normally reflects infection episodes by retroviruses where the mRNA is reverse-transcribed into DNA and integrated randomly into host genome as a whole coding sequence but without a promoter. Yes mutation my happen afterward. I came accidentally into the contact with pseudogenes when I performed a ChIP with RNA pol II. When I performed PCR with oligos designed from cds, I obtained 2 fragments and it took me a couple of days to realize that. It turned out that there were 2 psedogenes with full ORf in rat genome that are absent in mice and human.
I think a simple blast with the orf could tell you that because there are no introns and generally no promoter
Agreed.... first question to ask (bioinformatically) is does my possibly pseudo, gene of interest have a promoter? You could also look at RNA-seq data to see if it is transcribed (but be careful about what data set you use... as mentioned sometimes pseudo genes are intronless so any matching reads might have come from the mature transcript generated by the authentic gene).
Hi Tobias,
I think you should broaden your concept of gene. Genes can also encode for RNAs that are not translated into proteins, such as rRNAs, tRNAs, etc…(ncRNAs).
I also think that you should not confuse promoter, which regulates the transcriptional expression of a gene, with shine-dalgarno sequence, a RBS that is used for translation and which is not universal. To my knowledge, I am not aware of the presence of pseudogenes in yeast or in bacteria. Also, I think a pseudogene must have a corresponding functional gene somewhere in the genome.Unusual or unknown promoters can be identified by several criteria and their functionality can be tested in vivo.
The problem is that the reverse transcription process that Abdelhalim described is responsible for the creation of pseudogenes, but also retrogenes. Retrogenes have only mRNA sequence but with time, can acquire a promoter and then an expression. In Arabidopsis, at least, it is estimated that there are several hundreds of retrogenes. Thus, these retrogenes can be mistakely detected as pseudogenes since they have a mRNA sequence as gene body, and probably unusual/unknown promoter. The criteria for pseudogenes are no expression and alteration of elements needed for this transcription (start codon). Aberrant/truncated proteins is probably also a good criterion since it seems that unfunctional protein-coding genes are silenced.
Hi folks
There are pseudogenes in yeast and in bacteria. Also, there is no need to have an functional counterpart in the same genome to pseudogene identification. Many bacterial pseudogenes have full-length counterparts in other related genomes. Therefore, the presence of a promotor should not be used alone as a criteria to classify a pseudogene.
Dear Tobias,
Sorry for that. Ambiguity cleared. I think it is good to have this discussion as to have better understanding. I also now think that there is no good definition. I am currently dealing with the epigenetic of some parasitic repetitive elements and I didn’t consider them as pseudogenes because regardless of their functionality, they didn’t belong originally to the host genome. Now, I need to reconsider my view, but then, anything can be a pseudogene if we take into account that more than 70% of the genome is transcribed while total genes only constitute a 2%. Thanks for the reference.
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