RNA cleavage products generated by antisense oligonucleotides and siRNAs are processed by the RNA surveillance machinery

Nucleic Acids Res. 2016 Apr 20;44(7):3351-63. doi: 10.1093/nar/gkw065. Epub 2016 Feb 3.


DNA-based antisense oligonucleotides (ASOs) elicit cleavage of the targeted RNA by the endoribonuclease RNase H1, whereas siRNAs mediate cleavage through the RNAi pathway. To determine the fates of the cleaved RNA in cells, we lowered the levels of the factors involved in RNA surveillance prior to treating cells with ASOs or siRNA and analyzed cleavage products by RACE. The cytoplasmic 5' to 3' exoribonuclease XRN1 was responsible for the degradation of the downstream cleavage products generated by ASOs or siRNA targeting mRNAs. In contrast, downstream cleavage products generated by ASOs targeting nuclear long non-coding RNA Malat 1 and pre-mRNA were degraded by nuclear XRN2. The downstream cleavage products did not appear to be degraded in the 3' to 5' direction as the majority of these products contained intact poly(A) tails and were bound by the poly(A) binding protein. The upstream cleavage products of Malat1 were degraded in the 3' to 5' direction by the exosome complex containing the nuclear exoribonuclease Dis3. The exosome complex containing Dis3 or cytoplasmic Dis3L1 degraded mRNA upstream cleavage products, which were not bound by the 5'-cap binding complex and, consequently, were susceptible to degradation in the 5' to 3' direction by the XRN exoribonucleases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Exoribonucleases / metabolism*
  • Exosome Multienzyme Ribonuclease Complex / metabolism
  • HeLa Cells
  • Humans
  • Microtubule-Associated Proteins / metabolism*
  • Oligonucleotides, Antisense*
  • RNA Cleavage*
  • RNA Interference
  • RNA Processing, Post-Transcriptional
  • RNA, Long Noncoding / metabolism
  • RNA, Small Interfering / metabolism*


  • MALAT1 long non-coding RNA, human
  • Microtubule-Associated Proteins
  • Oligonucleotides, Antisense
  • RNA, Long Noncoding
  • RNA, Small Interfering
  • Exoribonucleases
  • Exosome Multienzyme Ribonuclease Complex
  • XRN1 protein, human
  • XRN2 protein, human