What Is The Relationship Between Rna And Protein Levels In Vivo?

Question

[Burlappsack]

What is the relationship between rna levels, determined through rna-seq or microarray and protein levels. For example, if there is a 10 fold increase in mRNA x between control and experimental replicates, will there be a 10 fold increase for protein X? Is there any solid information regarding the relationship between the two? As rna-seq and microarray data are used for biological induction, I think this is a very important question to ask when trying to analyze fold change results. Thank you very much for your time.
Adam.

Answer 1

[Ido Tamir]

Everybody knows (should know?) that steady state mRNA levels and even protein concentrations are just a proxy for protein activity. mRNA is easy to measure thats why its used. If you want to get closer to the actual protein levels you could try measuring mRNA from the polysome bound fraction.

Research has shown that there is a correlation 1,2 and try to model the contribution of general sequence features 3. There is no reason to believe that the general correlation will hold true for each of your candidate genes that popped up as being differentially regulated. If you want to make a "solid" statement you would have to measure the protein levels with e.g. a western blot. But don't forget that posttranslational modifications also change the activity of proteins, which is the real thing one would like to know.

[Burlappsack]

Thank you for these references. I will keep them in mind when analyzing RNA seq data!

Answer 2

[Neilfws]

The answer to the question "What is the relationship between rna levels and protein levels" is: it varies.

I'd address this question with a thorough review of the literature. A PubMed search for mRNA protein correlation returns many results but if you look at the box titled "Titles with your search terms" and click "See more" on the right of the results page, you'll find more relevant and useful articles.

Just taking the first 3 results as an example:

Ref. 1. Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin.

They find that for proteins which decrease in abundance on rapamycin treatment, most of the mRNAs also decrease; but the same is not true for proteins which increase in abundance.

Ref. 2. Correlation of mRNA and protein in complex biological samples.

This is a very useful review article. First sentence: "The correlation between mRNA and protein abundances in the cell has been reported to be notoriously poor."

Ref. 3. Correlation between protein and mRNA abundance in yeast.

From the abstract. "We found that the correlation between mRNA and protein levels was insufficient to predict protein expression levels from quantitative mRNA data. Indeed, for some genes, while the mRNA levels were of the same value the protein levels varied by more than 20-fold. Conversely, invariant steady-state levels of certain proteins were observed with respective mRNA transcript levels that varied by as much as 30-fold."

Answer 3

[Arun]

Edit:

"None, I think". => in retrospect may not be in agreeable terms.

Let me put it this way. A positive correlation is a general "observation" that allows you to set your "hypothesis". However, you will have to do your experiments to "infer" or make a "prediction" and then test the repetitiveness of that "prediction" for you to have a "valid" answer. The same question was asked at my colleague's PHD defense a couple months back.

It depends on the stability of the (m)RNA. A particular gene could have lots of transcripts that could very well be unstable and gets degraded before leaving the cell nucleus. This is why "gene expression" could be a misleading term.

If you look here: http://en.wikipedia.org/wiki/RNA-Seq#Gene_expression you might find that gene expression is usually expressed as a measure of something: mRNA level, protein level, post-translational modifications or coverage etc... So just with the RNA-Seq based read count, what you get actually is in reality "transcript abundance". It is normally used as one of the measures for "gene expression".

[Chris Evelo]

Ido's answer mentions some references that (not so unexpectedly) there actually is an overall correlation but not more than that. Essentially that meant that this answer, or at least the first word is wrong.

[Burlappsack]

if there is no relationship between rna levels and protein levels, why even bother with rna-seq? If there is no rna, then there is no protein, thus, there has to be a relationship.

[Arun]

It has nothing to do with RNA-Seq. If you are studying gene expression from transcripts, then there is only so much you can tell, as Ido mentioned.

I think no one denies that when there is no (m)RNA, there is no (functional) protein. However, an abundance of transcript does NOT necessarily mean you get a functional protein (with same abundance). Again, it depends on the stability of the mRNA.

[Burlappsack]

thanks for answering my question. I just wanted to make the point that there is a correlation, although their are other determining factors, as you have pointed out.

[Georg Summer]

I am not sure you can really say that if there is no (m)RNA there is no (functional) protein. No (m)RNA leads to no production of new functional protein. Depending on the amount and half life of a protein there might still be a significant amount of (functional) protein around even though the (m)RNA expression was already shut down and the (m)RNA degraded. Time plays a important role I think, one that is often neglected using the common steady state measurement methods.

Answer 4

[Mikael Huss]

It's a tough question to answer for sure. You could check out this paper for one way to address it: http://www.nature.com/msb/journal/v6/n1/full/msb2010106.html