Identification of a consensus element recognized and cleaved by IRE1α

IRE1 alpha is an endoplasmic reticulum (ER)-located transmembrane RNase that plays a central role in the ER stress response. Upon ER stress, IRE1 alpha is activated and cleaves specific exon-intron sites in the mRNA encoding the transcription factor X-box-binding protein 1 (XBP1). In addition, previous studies allow us to predict that IRE1 alpha targets several RNAs other than the XBP1. In fact, we have identified CD59 mRNA as a cleavage target of IRE1 alpha. However, it is not yet clear how IRE1 alpha recognizes and cleaves target RNAs. To address this question, we devised a unique method that combines an in vitro cleavage assay with an exon microarray analysis, and performed genome-wide screening for IRE1 alpha cleavage targets. We identified 13 novel mRNAs as candidate IRE1 alpha cleavage targets. Moreover, an analysis of the novel cleavage sites revealed a consensus sequence (CUGCAG) which, when accompanied by a stem-loop structure, is essential for IRE1 alpha-mediated cleavage. The sequence and structure were also conserved in the known IRE1 alpha cleavage targets, CD59 and XBP1. These findings provide the important clue to understanding the molecular mechanisms by which IRE1 alpha recognizes and cleaves target RNAs.