Can mutations that map upstream of a transcript (promoter, etc) lead to loss of function of the transcript, without altering expression or stability of the RNA? It is a non-coding RNA transcribed by pol II.
Yes, by altering the secondary and tertiary structure of that particular RNA in a way that it is no longer biologically functional. There are more and more studies showing that SNP mutations found in the 5' and 3' UTR region of various mRNAs are the main cause of various diseases, e.g. breast cancer, beta-thalassemia and many more (see attached pubs). Try folding your RNA using RNAstructure software (freeware) or mFold and see if the presence/absence of these mutations is predicted to affect its structure. Of course, the best approach to confirm that effect would be to probe that RNA (SHAPE, convential chemical probing etc).
Article Disease-Associated Mutations That Alter the RNA Structural Ensemble
1. What do you mean by outside of a transcript?(upstream of the promoter?) Could the change you are seeing be due to an alternative form of the transcript?
2. How was stability and expression measured?Just because the steady state level of a transcript has not changed it does not mean that the transcription and degradation rate has not changed. For example if you transcribe faster and degrade faster you can get the same total steady state level of a transcript.
I completely agree with Mary Allen above me. You cannot determine transcription or stability just from measuring steady-state level. (see my paper: http://www.cell.com/abstract/S0092-8674(13)00577-1)
second - Are you certain that there is no protein product? It was shown, at least in yeast, that some "non-coding" RNAs may actually be coding, or at the very least translated http://wp.me/p2jizY-3H
Last, RNA imprinting can be affected by cis elements outside the transcript (yes, promoter as well), which can later affect the cytoplasmic fate of that RNA (be it translatability, stability, localization etc... (e.g. http://www.sciencedirect.com/science/article/pii/S1874939913000084 )
There is also the possibility that the function of the ncRNA involves the DNA sequence containing the mutation. For instance, the ncRNA may interact with a protein that normally binds the wild-type DNA sequence, but doesn't bind the mutant.
Another possibility is that the mutation alters expression not of the ncRNA, but of another gene which interacts with the ncRNA; either to edit the sequence of the ncRNA post-transcriptionally, or to bind and therefore contribute to it's function.
None of these possibilities would show any change in the expression or stability of the ncRNA; the RNA editing possibility would be detectable if you can demonstrate the difference in the mature ncRNA.
Another version of the first possibility I mentioned is that your ncRNA functions as a microRNA (miRNA), and the mutation is in one of the sites it binds.
Mary Allen, thank you for your answer.
1. The mutation does not map in the transcript and could be in the promoter. The promoter for this RNA has not been identified yet. As for other forms of this RNA, I have not detected any other forms at least by northern blots.
2. I should have made that more clear, I have only measured steady state levels by northern blots.
A mutation in an upstream promoter or enhancer element might also alter the splicing pattern of the transcript, which you might not observe on a Northern. See for example http://rnajournal.cshlp.org/content/10/10/1489.long
Max Robinson, I like the first point you made. Mutant DNA sequence, does not bind a certain protein that the RNA needs to interact with to function. Can you provide me with some examples or publications. I work in yeast and this an antisense RNA.
Here's an example of an antisense RNA acting in trans to suppress transcription initiation in yeast; I don't see interaction between the RNA and a transcription factor mentioned, but something is reducing the rate at which TATA-binding protein binds to the promoter. I also only skimmed the paper.
http://genesdev.cshlp.org/content/23/13/1534.full
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