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Primers from 3'UTR - (Mar/01/2010 )

HI all
I was wondering if i design the primers using only the 3'UTR region of a gene then will it be fine. I want to check the expression profiles and corrleation between the mRNAs and miRNAs, an miRNAs binds to the 3'UTR region.
I dont know how feasable it is to do so, i will appreciate if anyone can guide me regarding this matter.


It is perfectly fine to design primers on 3'UTR for mRNA expression analysis. Just keep in mind that many genes have different polyA signal usage resulting mRNAs with different length of 3'UTR.

See this paper

Science. 2008 Jun 20;320(5883):1643-7.
Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites.

Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB.

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Messenger RNA (mRNA) stability, localization, and translation are largely determined by sequences in the 3' untranslated region (3'UTR). We found a conserved increase in expression of mRNAs terminating at upstream polyadenylation sites after activation of primary murine CD4+ T lymphocytes. This program, resulting in shorter 3'UTRs, is a characteristic of gene expression during immune cell activation and correlates with proliferation across diverse cell types and tissues. Forced expression of full-length 3'UTRs conferred reduced protein expression. In some cases the reduction in protein expression could be reversed by deletion of predicted microRNA target sites in the variably included region. Our data indicate that gene expression is coordinately regulated, such that states of increased proliferation are associated with widespread reductions in the 3'UTR-based regulatory capacity of mRNAs.