Wounded King

I dont think any has brought this up and it is apropos of nothing but quite interesting.

A paper detailing a pseudogene with a required function has just been published, or is soon to be published, in Nature.Mice with a heterozygous null allele for the Makorin1 p1 pseudogene have severe developmental defects. The non coding Makorin1 pseudogene mRNA appears to play a role in stabilising the coding mRNA of the Makorin1 gene. Pseudogenes have previously been considered non functional remnants of duplicated genes.

Hirotsune S, Yoshida N, Chen A, Garrett L, Sugiyama F, Takahashi S, Yagami K, Wynshaw-Boris A,Yoshiki A.
An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene.
Nature. 2003 May 1;423(6935):91-6.

ps418

It is an oxymoron, if pseudogene entails a lack of function, which is certainly how many people have thought about pseudogenes. It'd be tempting to change the definition such that expressed pseudogenes are not 'real' pseudogenes, but then a DNA sequence does not necessarily have to be transcribed to mRNA in order to have a function. I wonder what proportion of pseudogenes have this type of function? It would be interesting to see more knockout experiments with noncoding elements.

Patrick

Wounded King

You mean that some pseudogenes may have enhancer or promoter like functions? I can see how in a situation where a pseudogene copy was located close to the original it might help to recruit neccessary cofactors or act as an upstream enhancer.

What name could we use for functional pseudogenes? pseudopseudogenes?

ps418

That's exactly what I had in mind. Its at least a possibility. But then it may be that the vast majority of pseudogenes really do not have any function at all, while only a handful have been fortuitously recruited to serve some function. More knockout experiments would give a more definitive answer.

hehe. I suppose you could just subdivide pseudogenes into functional and nonfunctional pseudogenes. Or it may turn out that there are many different types of functions that pseudogenes fulfill, and a more detailed taxonomy of gene-like DNA sequences would be required.

Patrick

Wounded King

One obvious function would be as a template for siRNA, all you would need is a promoter allowing antisense transcription.

What other sorts of DNA function were you actually thinking of, structural roles?

ps418

I didn't have that in mind specifically, but maybe its possible. Maybe they play a role in influencing how DNA is folded or something like that. But of course, thats pure speculation on my part.

Patrick

BioBeing

Hehe. Although, if it has a function, how about simply "gene". I'd say functional psudogene was an oxymoron.