For a protein-coding mRNA, “life” should be pretty simple: get assembled through transcription, produce a protein through translation, then get recycled by cellular machinery so you can do it all again. Unfortunately, what I just wrote leaves out a colossal orchestra of quality-control machinery. Oh, you think I mean splicing? Try again. In an article published last month in Nature Communications, Dr. Phillip Burke, a recent doctoral graduate in the Subramaniam Lab, showed there is a translational control cypher encoded in nascent peptides that has potent effects on the stability of the encoding mRNA. Decoding this translational cypher took years of painstakingly precise work, and the creation of an innovative screening approach.
“In the past few years, several groups have implicated coding sequence metrics such as codon [use], amino acid [sequence], and GC content as regulators of mRNA stability in human cells,” shared Dr. Burke. “These studies relied on a correlation between these metrics and measured stability of endogenous human mRNAs. However, since the sequences of endogenous mRNAs are the result of complex evolutionary pressures, we have little mechanistic insight into how the implicated metrics influence mRNA stability. We felt there was a critical need in the translation field for a bottom-up high throughput approach for systematically mapping the effects of increasingly complex coding sequence motifs on mRNA stability.” Effectively, Dr. Burke and his advisor, Dr. Arvind “Rasi” Subramaniam, wanted to define the “individual contribution[s] of mRNA features implicated in previous studies.” However, no one had a method to do this. So, they built one. “Developing the initial high-throughput assay took a lot of optimization,” confessed Dr. Burke. “We tried without success for a while, then completely dropped the project for about a year…We ended up coming back to this approach while trying to study mRNA quality control pathways in human cells, when we realized we still had no idea what human coding sequence motifs could reliably trigger mRNA instability.”