"Systematic identification of factors mediating accelerated mRNA degradation in response to changes in environmental nitrogen."

This webpage provides visualizations of data reported in the paper Miller, Brandt, and Gresham 2018.


A 4-thiouracil label-chase and RNAseq was used to assess stability of each transcript upon a nitrogen upshift. A culture was labeled in nitrogen limiting conditions, then label was chased with the addition of 40-fold excess uracil. This was interrupted at 12.5 minutes by the addition of glutamine, and compared to the same experiment but with the addition of water. Accelerated degradation is apparent as an increase in the rate of degradation (steeper slope) upon addition of glutamine.

The y-axis is the natural log of labeled RNA abundance normalized to spike-ins, and the x-axis is minutes after uracil chase began. The vertical dotted line indicates the addition of glutamine or water (mock). Degradation rates are modeled by the solid black line and the dashed line. A change in slope after the addition of glutamine indicates a change in mRNA stability.

We estimated the abundance of GAP1 mRNA in each mutant in the pool at two timepoints (induced by nitrogen-limitation and 10 minutes after triggering repression with the addition of glutamine).

Note that the x-axis is the same for all these plots.

The violin plot in black lines depicts the distribution of GAP1 expression for all mutants. Points are the estimate for each strain in the pre-upshift and post-upshift conditions connected by a line for visualization purposes.

Distribution of mutant abundances across the four gates of GAP1 abundance, pre-upshift and post-upshift. Black points connected by dashed lines are the fit of the log-normal model.