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3.4 years ago
Bogdan
★
1.4k
Dear all, please may i ask :
which software would you recommend for the visualization of the RNA secondary / tertiary structure (available in the PDB files), and overlay the primary sequence (or other annotations). thanks a lot, with much appreciation !
-- bogdan
Thanks a lot, Mensur. Yes, it is a great app, very intuitive and easy to use. Thanks !
i have been exploring also Chimera from UCSF : https://www.cgl.ucsf.edu/chimera/
on another note, if I may ask please : how much secondary shall we see in mRNAs ? As they get exported to cytosol, and translated by ribosomes, i would think the chaperones would keep them rather unstructured ? (i have not had yet the time to extensively read the literature on this topic). thank you !
I think that structured regions in mRNA are confined to 5'- and 3'-untranslated regions - at least those structures that are important for regulatory purposes. Ronald Breaker's lab has studied for a long time the role of cis-ncRNAs that fulfil this role.
In any mRNA, including the coding part, there will be random structures, but most of are not stable enough to be of great importance. An exception to that would be the first 30-50 nucleotides in the coding sequence, or in general the region around the ribosome-binding site. See here for initial results about the role of those structures.
thanks a lot, Mensur for a very detailed and insightful reply. If i may add please : shall we compare :
a) the MFE (or Z-scores) of overlapping windows along the full-length mRNAs with b) the MFE (or Z-scores) of overlapping windows of random synthetic RNA sequences
would you expect to see large differences ? we do not see a large difference in the median values ;
thanks a lot, i am learning a lot from you ...
We already had a similar discussion here. I have no direct insight about structures in the coding part of mRNAs, as I only looked at cis-regulatory ncRNAs in 5'- and 3'-untranslated regions.
My guess would be that structures in mRNA coding sequence matter mostly when it comes to ribosome binding, which is what was shown in that Science paper I cited before. To me that seems to be the only generally applicable mode of regulation that makes sense, because it stops the translation from ever happening. Now, I am sure that by chance there are some stable RNA structures in the middle of mRNAs, but I would guess that most of them are not regulatory because: 1) ribosomes can power through them even if it causes some stalling; 2) it makes less sense to make part of the protein and abort as opposed to make no protein at all (the latter can be achieved by evolving these structures at or near RBS).
many many thanks, Mensur ! the field is still new to me, and many thanks for all your help and articles that you have pointed it :) I have been asking the question in the context of the biological question "how mRNAs localized in the axons ?" (based on Ribo-trap method (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4930487/);
we wish you happy holidays, Merry Christmas, and a new year with lots of inspiration and energy !
talk to you later :)