ZBP1 senses spliceosome stress through Z-RNA:DNA hybrid recognition

Mol Cell. 2025 May 1;85(9):1790-1805.e7. doi: 10.1016/j.molcel.2025.04.004. Epub 2025 Apr 22.

Abstract

Z-DNA-binding protein 1 (ZBP1; also known as DAI or DLM-1) regulates cell death and inflammation by sensing left-handed double-helical nucleic acids, including Z-RNA and Z-DNA. However, the physiological conditions that generate Z-form nucleic acids (Z-NAs) and activate ZBP1-dependent signaling pathways remain largely elusive. In this study, we developed a probe, Zα-mFc, that specifically detected both Z-DNA and Z-RNA. Utilizing this probe, we discovered that inhibiting spliceosome causes nuclear accumulation of Z-RNA:DNA hybrids, which are sensed by ZBP1 via its Zα domains, triggering apoptosis and necroptosis in mammalian cells. Furthermore, we solved crystal structures of the human or mouse Zα1 domain complexed with a 6-bp RNA:DNA hybrid, revealing that the RNA:DNA hybrid adopts a left-handed conformation. Our findings demonstrate that the spliceosome acts as a checkpoint preventing accumulation of Z-RNA:DNA hybrids, which potentially function as endogenous ligands activating ZBP1-dependent cell death pathways.

Keywords: Z-RNA:DNA; cell death; spliceosome inhibition.

MeSH terms

  • Animals
  • Apoptosis
  • DNA, Z-Form* / chemistry
  • DNA, Z-Form* / genetics
  • DNA, Z-Form* / metabolism
  • DNA-Binding Proteins* / chemistry
  • DNA-Binding Proteins* / genetics
  • DNA-Binding Proteins* / metabolism
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Mice
  • Models, Molecular
  • Nucleic Acid Conformation
  • Protein Binding
  • RNA, Z-Form* / chemistry
  • RNA, Z-Form* / genetics
  • RNA, Z-Form* / metabolism
  • RNA-Binding Proteins* / chemistry
  • RNA-Binding Proteins* / genetics
  • RNA-Binding Proteins* / metabolism
  • Signal Transduction
  • Spliceosomes* / genetics
  • Spliceosomes* / metabolism

Substances

  • DNA, Z-Form
  • DNA-Binding Proteins
  • RNA-Binding Proteins
  • ZBP1 protein, human
  • Zbp1 protein, mouse