Using mRNA for polymorphism analysis??

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Using mRNA for polymorphism analysis??

Postby SHIK » Jun 06 2017 8:28 am

I'm interested in testing polymorphism in human duodenum biopsies, but unfortunately all I have is the mRNA (cDNA actually) extracted from these biopsies.
I have no option to check the DNA.
Can someone here advise me? Is there an option to do sequencing for RNA for such a purpose?
I'm really unfamiliar with molecular biology methods, so any advise will greatly help!
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Re: Using mRNA for polymorphism analysis??

Postby r.rosati » Jun 06 2017 9:46 am

You mean variations in the patient's DNA, not a parasite's DNA, right? Well, yes, you can, but with limitations and differences.
Some genes show imprinting, so that mRNA is produced only from one chromosome, and not from the other. This is the case e.g. for IGF2 which is normally only expresses from the paternal chromosome. In this case you'd only get data from that chromosome. I don't know if there's anyting relevant in this sense in your setting.
Some variations might alter the expression level, or stability, of an mRNA from one chromosome. Think for example, nonsense-mediated decay of mRNAs with a premature stop codon.
If you're studying cancer, translocations might produce gene fusions, and expectedly one of the two chimeric mRNAs might be expressed at higher levels than the other.
Finally and most obviously, if you want to make a broad study then you're limited by the expression levels of every gene, but I suppose this is not your scenario?
If you had DNA too, then you could even exploit the differences between DNA and mRNA data to infer some biological characteristic; but having only mRNA, then these are some of the limitations you'll have. Say, you can't directly infer the copy number of a gene from allele ratios.
Anyways, all in all, most of the genes should still be expressed equally from both chromosomes, so try - most likely you should be able to retrieve variations of your gene of interest.
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