Transcriptome-wide profiling of poly(A)-tail length, translation efficiency and mRNA stability using TED-seq, mRNA-seq, Ribo-seq and PRO-seq in ER stress conditions

We report systematical profiling of translation efficiency and mRNA stability dependent on the dynamics of poly(A)-tail length in stress conditions of human cells. In this study, we developed a new feasible method measuring poly(A)-tail length called TED-seq and applied it to investigate the change of mRNA''s poly(A)-tail lengths in ER stress pharmacologically induced by thapsigargin (THAP). Combined with other global RNA analyses such as RNA-seq, Ribo-seq and PRO-seq, we observed that ER stress induced lenthening poly(A)-tail length, in particular of ER-stress-regulators, upon ER stress. More specifically, these mRNAs are translationally de-repressed and more stabilized based on increase in poly(A)-tail length. We also identified that insoluble fractions which include stress-induced RNA-granules have overall shorter length of poly(A) tail. Taken together, our data suggest that poly(A)-tail lengths are dynamically regulated and influence both translation efficiency and mRNA stability in ER stress. Overall design: 1) TED-seq (5 replicates) in cytoplasm and RNA granule fractions (3 replicates) of DMSO- or THAP-treated HEK293 cells 2) RNA-seq (4 replicates), Ribo-seq (4 replicates) and PRO-seq (2 replicates) in whole cells with DMSO- or THAP-treated HEK293 cells

28