A compensatory link between cleavage/polyadenylation and mRNA turnover regulates steady-state mRNA levels in yeast

Cells have compensatory mechanisms to coordinate the rates of major biological processes, thereby permitting growth in a wide variety of conditions. Here, we uncover a compensatory link between cleavage/polyadenylation in the nucleus and mRNA turnover in the cytoplasm. On a global basis, same-gene 3’ mRNA isoforms with > two-fold differences in half-lives have steady-state mRNA levels that differ by significantly less than a factor of two. In addition, increased efficiency of cleavage/polyadenylation at a specific site is associated with reduced stability of the corresponding 3’ mRNA isoform. This inverse relationship between cleavage/polyadenylation and mRNA isoform half-life reduces the variability in the steady-state levels of mRNA isoforms, and it occurs in all four growth conditions tested. These observations suggest that during cleavage/polyadenylation in the nucleus, mRNA isoforms are marked in a manner that persists upon translocation to the cytoplasm and affects the activity of mRNA degradation machinery, thus influencing mRNA stability. We have examined mRNA isoform stability by using 3' READS to measure mRNA 3' isoform levels after Rpb1 depletion in four different growth media.

细胞拥有补偿性调控机制，可协调各类主要生物学过程的反应速率，使其能够在多种环境条件下实现生长增殖。本研究揭示了细胞核内的剪切/多聚腺苷酸化（cleavage/polyadenylation）与细胞质内的mRNA周转（mRNA turnover）之间的补偿性关联。从全局转录组层面来看，同一基因的3'端mRNA异构体（3' mRNA isoforms）若半衰期差异超过2倍，则其稳态mRNA水平（steady-state mRNA levels）的差异将显著小于2倍。此外，特定位点处剪切/多聚腺苷酸化效率的提升，会与对应3'端mRNA异构体稳定性的降低呈显著负相关。这种剪切/多聚腺苷酸化与mRNA异构体半衰期之间的负相关关系，可降低mRNA异构体稳态水平的变异程度，且在本次检测的四种生长条件中均有发生。上述观测结果表明，在细胞核内进行剪切/多聚腺苷酸化的过程中，mRNA异构体被以特定方式标记，该标记在其转运（translocation）至细胞质后仍可保留，并会影响mRNA降解系统（mRNA degradation machinery）的活性，进而调控mRNA的稳定性。本研究通过3' READS技术，检测了四种不同生长培养基（growth media）中Rpb1敲降后的mRNA 3'端异构体水平，以此分析mRNA异构体的稳定性。