Ribosome footprinting
Not all RNAs encode proteins
Entire paper was written with existing data (but the data
was originally generated by authors)
mRNA Translation (main steps)
Note 3’UTRs Ribosome + mRNA Also
note that coding regions are highly
conserved by a conservation score CSF
Codon substitution frequency
Yet, lincRNAs look more like translated
regions and 5’UTRs based on
translational efficiency
(TE = ribosome/mRNA)
Known classical non-coding RNAs have
high translational efficiency
Here are some examples of known
ncRNAS with high Translational
efficiency
Ribosome Release Score (RRS)
Cutoff on RRS and Translation
Efficiency Provide Better Separation
RSS separates coding regions
This is using open reading frames (ORFs) in each of these regions.
There are lincRNAs with high
conservation and a high RSS score (do
these code proteins?)
Why high TE for lincRNAs?
• Reasons the authors give:
– Non-ribosomal contamination
– Seductive hypothesis in the discussion:
• Translational machinery is always engaged with
transcripts in the cytosol of the cell.
• “Pervasive” engagement of the ribosome with
transcripts.
– This can be co-opted by evolution to create new proteincoding genes.