PREreview of Newly synthesized mRNA selectively escapes translational repression following acute stress

In this manuscript, the authors used 4-TU pulse labeling to understand how mRNA translation is regulated during acute stress. They demonstrated that for pre-existing mRNAs, transcripts are translationally repressed before their mRNA gets degraded. In addition, the decision to silence or translate a particular mRNA transcript following glucose depletion is dependent on the timing of its production. Transcripts produced prior to glucose deprivation are repressed while those produced after stress are actively translated.

Overall, the findings from this manuscript are interesting. Using modern sequencing techniques, it reinforces and supports previous work on translation regulation during cell stress, which demonstrated that newly synthesized mRNAs were preferentially translated during starvation in Dictyostelium due to their longer poly(A) tails (Palatnik et al (1984), Cell). However, this manuscript could benefit greatly by a) determining if the difference between pre- and post-synthesized mRNAs is simply the length of the poly(A) tail, or b) deciphering potential mechanisms on how cells distinguish pre-stress and stress-induced transcripts.

Major points:

1.     The authors obtained mRNA’s translation efficiency by performing RNA sequencing and ribosome profiling. During RNA sequencing, they poly(A) selected the mRNAs using oligod(T) beads. However, as most mRNAs lose their poly(A) tails rapidly following stress, poly(A) selection will cause an under-representation of many mRNAs and bias the population towards mRNAs with longer tails. Consequently, this could skew the interpretation for translation efficiency. The authors should inspect their RNA sequencing results for poly(A) biases, and if so, they could complement by constructing libraries without prior poly(A) selection and/or performing Nanopore sequencing.

2.     In Fig. 2A, there is a significant portion of genes that become upregulated 15 min and 30 min after glucose deprivation. This observation is intriguing since most genes are suppressed upon stress and only essential genes are actively translating. It would value add to the existing data if the authors followed up on these upregulated genes at 15 min and 30 min to determine if these are the same set of mRNAs as shown in Fig. 2B or if they belong to a different set of mRNAs that are regulated by other cellular pathways and responses.

3.     In the supplement, the authors presented another reporter system encoding for citrine, a fluorescent protein. It would make the data more impactful and convincing if the authors showed immunofluorescence or live cell images of the reporter protein after pre- or post-stress induction.

Minor points:

1.     Axes in Figure 4E seems to be swapped

Competing interests

The authors declare that they have no competing interests.