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Why doesn't the transcriptome reflect the proteome? - (Jun/08/2012 )

Question: I split one sample (cells) into two, extract mRNA from one, proteins from another and analyse. Why are there differences between mRNA levels and protein abundance?

This isn't homework. Just studying for an exam and I'd like to know ALL the variables. The question (from a past paper) asks for biological and technical reasons. I only have 3 biological (Bi) and one technical (T) reason(s).
<*> not connected to protein turnover (Bi)
<*>gene expression doesn't always lead to protein products (Bi)
<*>long-life proteins may be present while their mRNAs could be degraded and absent due to the related gene being switched off at the time of sampling. (Bi)
<*>integral membrane proteins are difficult to extract and would show deceptively low abundance (T)


It kind of is homework, but I won't debate as you have done something that very few others do - tried to provide the answers yourself.

You have got most of it right, but your points 1 and 3 are pretty much the same thing.

- There is also some evidence that mRNAs can be held in pools for quick expression when needed.
- Many proteins are post-translationally modified, meaning that they are the result of a cleavage of the full length protein to form one or more active proteins.
- Some genes are transcribed and produce more than one gene product from the same transcript (e.g. p16INK4A).


Excellent. mRNA held in pools? That's something new - I'd love a brief explanation if you, or anyone else has the time.
I've also added:
-transcriptome includes rRNA, tRNA and non-coding RNAs which will not give functional protein.

I wish there were more 'technical' reasons for the discrepancy though. I think it would be rather poor to include poor technique as an answer.


Sorry, I don't know the mechanism behind the mRNA pools - but as far as I can tell, the DNA is transcribed and then the RNA is held in reserve for times of stress/danger when the proteins are needed ASAP.

Poor technique is always a consideration for any experiment.
You could add sensitivity of detection - how do you detect the proteins (western blot? Mass spec?) and RNAs (Array?, qPCR?)? How sensitive are these methods?


1. accroding to definition of transcriptome : it mentions to all type of RNA ( rRNA , tRNA , mRNA , snRNA.......) and it mean all RNA dont code proteins.
2. Gene silencing by miRNA : this mechanism can avoid mRNA to participate in protein synthesis process.
3.some tims mechanisms like EXON SHUFFELING leads mRNA exons mix to ghether, make new mRNA and product new protein . that means its possible number of proteins could be more than mRNA.
4. mRNA stability can efecton analysis . they are more sensitive than DNA and proteins.


here's a paper about mRNA pools:"Release of extraction-resistant mRNA in stationary phase Saccharomyces cerevisiae produces a massive increase in transcript abundance in response to stress".