I am interested in the expressional regulation of an mRNA that has three different isoforms: one with almost no 3'-UTR and two with 3'-UTRs of about 6000 nucleotides. I am wondering what I can deduce from this fact? For example, is it possible that the mRNA lacking the 3'-UTR is constitutively expressed, while the others are under regulation of post-transcriptional mechanisms? If anybody knows some good reviews about this topic, please share!
Thanks,
Arjen
Hi Arjen, 3 distinct 3'UTRs from one locus indeed means that post-transcriptional process are likely playing a key role in determining the expression levels of your transcripts. RNA-binding proteins and microRNAs could be competing for consensus sequences to determine transcript stability, while RNA-binding proteins could also be influencing localization of the mRNAs. Perhaps the mRNAs are being transported by RBPs to unique subcellular compartments where they are locally translated. While 3'-UTR length could impact expression levels, a short 3'-UTR does not necessarily imply that it will be constitutively expressed. Also, 3'-UTR annotations on ensembl and the UCSC genome browser are not always in accord with what 3'-RACE experiments show regarding 'true' 3'-UTR length, as this appears to be cell-type dependent also, so depending on your cell type, you might not have 6000 nt available for regulation. I hope this helps.
Hi Arjen,
There are several reviews and data points about both the implication of promoters and 3'UTR in post-transcriptional regulation, translational regulation and stability of mRNA. In your case, I would be interested to know how these different 3'UTR determine the fate of the mRNA and their potential for translation.
Here some article and reviews on the topic:
PMID: 23337853
PMID: 26052005
PMID: 26017315
PMID: 22196726
PMID: 23706744
Good luck!!
Thanks Vincent. Your insight in my case was exactly how I was viewing it too :p
Thanks!
Hi Arjen,
if you are working in neurons, differental polyAdenylation not only affects translability, but it is most likely to be bound to different RBPs and have distinct localization as well.
Thanks Francesco! If am working in glial cells, but I think this should also go for glial mRNAs
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