Monitoring endoplasmic reticulum stress responsive mRNAs by RNA sequencing

Gene expression profile upon endoplasmic reticulum (ER) stress was analyzed by deep shotgun sequencing of mRNAs (DSSR) using RNAs from polysomes or cytoplasm of the HT29 cell. Two time points, 4h after tunicamycin treatment when IRE1α signaling pathway is active and 16h after the treatment when it is inactive, were used. There was a transient decrease in the proportion of shorter mRNA species (<1000bp) in polysome, while it increased transiently in the cytoplasm. Despite such an overall change and decrease in total amount of polysomes, the majority of the 6966 genes analyzed had less than 2 fold change in their expressions. We searched for the genes whose expression was elevated by 2 folds or more in both polysome and cytoplasm and confirmed the results with RT-PCR. There were 7 genes elevated only at 4h (Group I), 20 genes only at 16h (Group II) and 7 genes both at 4 and 16h (Group III). There were 3 genes involved in ribosomal RNA biogenesis in Group I and 2 genes involved mTOR control in Group III. This was consistent with the concept that the ribosome is the essential site for managing ER stress. DSSR is a useful tool for the search of candidates of ER stress responsive genes.