ER stress signaling by regulated splicing: IRE1/HAC1/XBP1

Methods. 2005 Apr;35(4):395-416. doi: 10.1016/j.ymeth.2005.03.001.


The endoplasmic reticulum (ER) serves many specialized functions in the cell including calcium storage and gated release, biosynthesis of membrane and secretory proteins, and production of lipids and sterols. Therefore, the ER integrates many internal and external signals to coordinate downstream responses, although the mechanism(s) that maintain homeostasis are largely unknown. When misfolded or unfolded proteins accumulate in the ER, an intracellular signaling pathway termed the unfolded protein response (UPR) is activated. Identification of IRE1 in the yeast Saccharomyces cerevisiae as a proximal sensor in the UPR pathway was a milestone in understanding how the ER responds to the accumulation of unfolded protein and signals transcriptional activation through regulated nonconventional splicing of its substrate mRNA encoding the transcription factor Hac1p. Subsequent studies identified IRE1 and HAC1 homologues in mammalian cells. Here, we summarize various approaches to study the IRE1-Hac1 pathway in yeast and the homologous IRE1-XBP1 pathway in mammalian cells. We present microbiological growth assays for the UPR, reporter assays for UPR signaling, direct techniques to measure UPR activation in vivo, methods to study translation of HAC1 mRNA, and in vitro cleavage and ligation of HAC1 and XBP1 mRNA. Especially we think the newly developed quantitative and qualitative methods to detect IRE1 activity-dependent XBP1 mRNA splicing will be fast and accurate tools to show the activation of the UPR.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Animals
  • Base Sequence
  • Basic-Leucine Zipper Transcription Factors
  • DNA-Binding Proteins / biosynthesis
  • DNA-Binding Proteins / genetics*
  • Endoplasmic Reticulum / enzymology*
  • Genes, Reporter
  • Humans
  • Membrane Glycoproteins / genetics
  • Membrane Glycoproteins / metabolism*
  • Methods
  • Mice
  • Molecular Sequence Data
  • Nuclear Proteins / biosynthesis
  • Nuclear Proteins / genetics*
  • Protein Folding*
  • Protein Serine-Threonine Kinases / genetics
  • Protein Serine-Threonine Kinases / metabolism*
  • RNA Splicing*
  • RNA, Messenger / metabolism
  • Regulatory Factor X Transcription Factors
  • Repressor Proteins / biosynthesis
  • Repressor Proteins / genetics*
  • Repressor Proteins / metabolism
  • Saccharomyces cerevisiae Proteins / biosynthesis
  • Saccharomyces cerevisiae Proteins / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Signal Transduction
  • Transcription Factors / biosynthesis
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism
  • X-Box Binding Protein 1


  • Basic-Leucine Zipper Transcription Factors
  • DNA-Binding Proteins
  • HAC1 protein, S cerevisiae
  • Membrane Glycoproteins
  • Nuclear Proteins
  • RNA, Messenger
  • Regulatory Factor X Transcription Factors
  • Repressor Proteins
  • Saccharomyces cerevisiae Proteins
  • Transcription Factors
  • X-Box Binding Protein 1
  • XBP1 protein, S cerevisiae
  • XBP1 protein, human
  • Xbp1 protein, mouse
  • IRE1 protein, S cerevisiae
  • Protein Serine-Threonine Kinases