Talk:Pseudogene

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[edit] RNAi

I don't think this sentence is really accurate:

The growing understanding of RNA interference likely means that some former pseudogenes may be reclassified as RNAi sequences.

To my understanding, RNAi coming from the genome means miRNA, and you need very specific stem-loop structures in miRNA genes that won't arise from a pseudogene any more often than from anywhere else. The Hirotsune paper discusses pseudo-mRNA mediation of a real mRNA, but not through the same degradation machinery that (I believe) "RNAi" refers to.

--Mike Lin 18:32, 18 January 2006 (UTC)

RNAi is not limited to miRNA. I have reworded that section and definition.Ted 16:25, 19 January 2006 (UTC)

Can you please clarify for my own knowledge, what does "RNAi" encompass besides miRNA (naturally occurring in the genome) and siRNA (artificially introduced)? --Mike Lin 06:22, 20 January 2006 (UTC)

My understanding of RNAi is any post transcriptional gene silencing (PTGS) involving dsRNA. It was first discovered adding anti-sense RNA which hybridized with the sense message and silenced expression. While the common use is siRNA with experimenter-derived dsRNA, it can also refer to anti-sense ssRNA binding with the sense strand forming dsRNA, and specialized sequences apparently designed for silencing (miRNA).Ted 23:49, 23 January 2006 (UTC)

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It seems we are working off different definitions.

• Definition 1: A pseudogene does not produce a functional protein.
• Definition 2: A pseudogene does not produce a functional final product.

The problem with first definition is that some normal genes produce RNA as a final product, such as tRNA genes, etc. In addition, there are sequences that have homology with tRNA genes, but are not expressed. It takes some gymnastics to fit the pseudogene definition. Hirotsune (and the separate comments by Lee in the same issue of Nature) use this definition; further supported by Gerstein's lab (http://www.pseudogene.org). Many researchers use the generic "is never expressed."

The second definition is more expansive. Do a medline search for 'trna pseudogene' or 'rrna pseudogene' and you will find many researchers who use this term when the functional final product is an RNA. The mechanism for creating these sequences are the same as for the protein-coding pseudogenes (mainly duplicated), so it is hard to discount them entirely. Ted 18:05, 19 January 2006 (UTC)

I agree with what you're saying, but do you have a suggestion for what to do? As you note, the definition of the term is ambiguous "in real life" among experts. I don't know if we can solve this on Wikipedia. --Mike Lin 06:26, 20 January 2006 (UTC)

How about this?

A pseudogene is a nucleotide sequences that is similar to a normal gene, but does not produce a functional final product. There are two variants. The first requires the final product to be a protein. The second allows the final product to be an RNA, such as tRNA or rRNA.Ted 14:08, 26 January 2006 (UTC)