11.1: Introduction

Many ideas in biology rely on knowing the protein levels in a cell. Protein abundance is often extrapolated from corresponding mRNA levels. This extrapolation is made as it is relatively easy to measure mRNA levels. In addition, for a long time, it was thought that all of the regulation of expression occurred prior to mRNA formation. Now, it is known that expression continues to be regulated at the translation stage. Figure 1 shows that the data available for post-transcriptional regulation is minimal and illustrates an example of how mRNA levels are not indicative of protein abundance.

There are many factors that may be affecting how mRNA is translated, causing mRNA level to not be directly related to protein levels. These factors include:

1. Translation elongation rates
   - depends on codon usage bias, tRNA adaptation, and RNA editing
2. Translation initiation rates
   - depends on AUG frequency, TOP presence, type of initiation (cap-dependent/IRES), and secondary structures
3. Translation termination rates
   - depends on termination codon identity
4. mRNA degradation rates
   - depends on polyA tail length, capping, mRNA editing, and secondary structure
5. Protein degradation rates
   - depends on PEST sequences, protein stability, unstructured regions, and the presence of polar amino acids
6. Cis and Trans regulatory elements
   - depends on AU-rich elements, miRNAs, ncRNAs, and RNA-binding proteins

   

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