eQTLs are genomic loci that contribute to variation in expression levels of mRNAs (wikipedia).

There is data out there that shows that ~60% of the time, the amount of mRNA in a cell is directly proportional to the level of protein coded by that mRNA.[1]

It means that even if the abundance of mRNA is high, we cannot be sure that the abundance of protein is high as well. Why do we still need eQTL if we cannot derive abundance of protein from mRNA transcripts? In the end, the abundance of protein influences the disease rather than the abundance of a transcript.

Does a pQTL implement the idea of a relationship between a genetic variance and the abundance of a protein? I do not understand how a genetic variance can influence the protein level. I assume it is related with a post-transcriptional modification but how?

  • $\begingroup$ There is regulation at the protein level ie post-translational modification, autophagy, protein stability etc. Simply knowing total amount of protein does not tell you everything. Knowing eQTL helps to sort out how much of variation in protein amount may be due to the transcription pathway $\endgroup$
    – anon
    Aug 7 '18 at 16:04

Genetic variation can affect the levels of protein; consider a variant that reduces the amount of mRNA transcribed, this could have a profound effect on the amount of mRNA available to translate into a protein.

Consider another variant that does not affect the abundance of the mRNA transcribed, but alters one of the many important sequences that are required for translation (co-factor binding sites, ribosomal binding sites, start site, etc.).

These are just a couple of examples that first came to mind, but there are many more. For instance, a variant may increase expression of a particular microRNA that in turn inhibits the translation of another mRNA molecule. I have not included any references as this is more a logical exercise - doubtless there are many more ways a genetic variant can affect protein abundance.

  • $\begingroup$ Considering your first two examples and the citation from researchgate about that 60% of the time, the amount of mRNA is directly proportional to the level of protein coded by that mRNA, I still do not understand why eQTLs are so important in those two cases as we cannot derive the amount of the protein from the amount of the transcript. $\endgroup$
    – Alina
    Aug 28 '15 at 10:10
  • 1
    $\begingroup$ The amounts of protein and mRNA are correlated, if not directly proportional. I understand what you are saying, that changes in the amount of mRNA do not necessarily equate to a change in protein abundance, but it seems quite logical to me that if a SNP either changes the mRNA sequence, or changes the abundance of the mRNA, the SNP could affect the amount of protein - this will differ in every case of course, and pQTLs that have been documented presumably do alter the final protein (either in form or abundance), otherwise they would not be reported as pQTLs. $\endgroup$
    – Luke
    Aug 29 '15 at 17:29

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