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?
<*>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: