Analysis of transcriptome and translatome regulation in unfolded protein response

In unfolded protein response (UPR), gene expression is dynamically reprogrammed to reduce the loading of unfolded or misfolded proteins into the endoplasmic reticulum and restore protein homeostasis. In this study, we applied the combination of SLAMseq/QuantSeq with translating ribosome affinity purification (TRAP) technique to analyze the nascent transcribed polyadenylated RNAs and their translation at the level of individual genes in the UPR. HEK293 cells were subjected to a 4-thiouridine for metabolic RNA labeling and thapsigargin (TPG) to induce the UPR, respectively. The cell lysate was divided into three factions, cytosolic RNA, ribosome-bound RNAs obtained by EGFP-L10a-TRAP, and ribosome-bound RNAs obtained by P-TRAP, followed by the 3' polyadenylated RNA-seq.