hnRNPM protects against the dsRNA-mediated interferon response by repressing LINE-associated cryptic splicing

Mol Cell. 2024 Jun 6;84(11):2087-2103.e8. doi: 10.1016/j.molcel.2024.05.004. Epub 2024 May 29.

Abstract

RNA splicing is pivotal in post-transcriptional gene regulation, yet the exponential expansion of intron length in humans poses a challenge for accurate splicing. Here, we identify hnRNPM as an essential RNA-binding protein that suppresses cryptic splicing through binding to deep introns, maintaining human transcriptome integrity. Long interspersed nuclear elements (LINEs) in introns harbor numerous pseudo splice sites. hnRNPM preferentially binds at intronic LINEs to repress pseudo splice site usage for cryptic splicing. Remarkably, cryptic exons can generate long dsRNAs through base-pairing of inverted ALU transposable elements interspersed among LINEs and consequently trigger an interferon response, a well-known antiviral defense mechanism. Significantly, hnRNPM-deficient tumors show upregulated interferon-associated pathways and elevated immune cell infiltration. These findings unveil hnRNPM as a guardian of transcriptome integrity by repressing cryptic splicing and suggest that targeting hnRNPM in tumors may be used to trigger an inflammatory immune response, thereby boosting cancer surveillance.

Keywords: ALU; LINE; RNA-binding protein; cancer; cryptic splicing; double-stranded RNA; hnRNPM; interferon response.

MeSH terms

  • Alu Elements / genetics
  • Animals
  • Exons
  • HEK293 Cells
  • Heterogeneous-Nuclear Ribonucleoprotein Group M* / genetics
  • Heterogeneous-Nuclear Ribonucleoprotein Group M* / metabolism
  • Humans
  • Interferons / genetics
  • Interferons / metabolism
  • Introns*
  • Long Interspersed Nucleotide Elements* / genetics
  • Mice
  • RNA Splice Sites
  • RNA Splicing*
  • RNA, Double-Stranded* / genetics
  • RNA, Double-Stranded* / metabolism
  • Transcriptome

Substances

  • Heterogeneous-Nuclear Ribonucleoprotein Group M
  • RNA, Double-Stranded
  • HNRNPM protein, human
  • Interferons
  • RNA Splice Sites