Directed RNase H Cleavage of Nascent Transcripts Causes Transcription Termination

Mol Cell. 2020 Mar 5;77(5):1032-1043.e4. doi: 10.1016/j.molcel.2019.12.029. Epub 2020 Jan 7.


An attractive approach to reduce gene expression is via the use of antisense oligonucleotides (ASOs) that harness the RNase H1 mechanism. Here we show that RNase H ASOs targeted to introns or exons robustly reduce the level of spliced RNA associated with chromatin. Surprisingly, intron-targeted ASOs reduce the level of pre-mRNA associated with chromatin to a greater extent than exon-targeted ASOs. This indicates that exon-targeted ASOs achieve full activity after the pre-mRNA has undergone splicing, but before the mRNA is released from chromatin. Even though RNase H ASOs can reduce the level of RNA associated with chromatin, the effect of ASO-directed RNA degradation on transcription has never been documented. Here we show that intron-targeted ASOs and, to a lesser extent, exon-targeted ASOs cause RNA polymerase II (Pol II) transcription termination in cultured cells and mice. Furthermore, ASO-directed transcription termination is mediated by the nuclear exonuclease XRN2.

Keywords: ASO; RNase H; XRN2; chromatin; torpedo.

MeSH terms

  • Animals
  • Chromatin / genetics
  • Chromatin / metabolism*
  • Exons
  • Exoribonucleases / genetics
  • Exoribonucleases / metabolism
  • Female
  • HCT116 Cells
  • Humans
  • Introns
  • Mice, Inbred C57BL
  • Models, Genetic
  • Nedd4 Ubiquitin Protein Ligases / genetics
  • Nedd4 Ubiquitin Protein Ligases / metabolism
  • Oligonucleotides, Antisense / genetics
  • Oligonucleotides, Antisense / metabolism*
  • RNA Polymerase II / genetics
  • RNA Polymerase II / metabolism
  • RNA Precursors / genetics
  • RNA Precursors / metabolism*
  • RNA Stability*
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Ribonuclease H / genetics
  • Ribonuclease H / metabolism*
  • Time Factors
  • Transcription Termination, Genetic*


  • Chromatin
  • Oligonucleotides, Antisense
  • RNA Precursors
  • RNA, Messenger
  • Nedd4 Ubiquitin Protein Ligases
  • Nedd4 protein, human
  • Nedd4 protein, mouse
  • RNA Polymerase II
  • Exoribonucleases
  • Xrn2 protein, mouse
  • XRN2 protein, human
  • Ribonuclease H