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 protein-

coding genes.