Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides

Nucleic Acids Res. 2016 Jan 29;44(2):863-77. doi: 10.1093/nar/gkv1206. Epub 2015 Nov 17.


Thousands of long non-coding RNAs (lncRNAs) have been identified in mammalian cells. Some have important functions and their dysregulation can contribute to a variety of disease states. However, most lncRNAs have not been functionally characterized. Complicating their study, lncRNAs have widely varying subcellular distributions: some reside predominantly in the nucleus, the cytoplasm or in both compartments. One method to query function is to suppress expression and examine the resulting phenotype. Methods to suppress expression of mRNAs include antisense oligonucleotides (ASOs) and RNA interference (RNAi). Antisense and RNAi-based gene-knockdown methods vary in efficacy between different cellular compartments. It is not known if this affects their ability to suppress lncRNAs. To address whether localization of the lncRNA influences susceptibility to degradation by either ASOs or RNAi, nuclear lncRNAs (MALAT1 and NEAT1), cytoplasmic lncRNAs (DANCR and OIP5-AS1) and dual-localized lncRNAs (TUG1, CasC7 and HOTAIR) were compared for knockdown efficiency. We found that nuclear lncRNAs were more effectively suppressed using ASOs, cytoplasmic lncRNAs were more effectively suppressed using RNAi and dual-localized lncRNAs were suppressed using both methods. A mixed-modality approach combining ASOs and RNAi reagents improved knockdown efficacy, particularly for those lncRNAs that localize to both nuclear and cytoplasmic compartments.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Nucleus / genetics
  • Cytoplasm / genetics
  • Gene Knockdown Techniques / methods*
  • HCT116 Cells
  • HeLa Cells
  • Humans
  • Oligonucleotides, Antisense / genetics*
  • RNA Interference*
  • RNA, Long Noncoding / genetics
  • RNA, Long Noncoding / metabolism*


  • DANCR long noncoding RNA, human
  • HOTAIR long untranslated RNA, human
  • MALAT1 long non-coding RNA, human
  • NEAT1 long non-coding RNA, human
  • Oligonucleotides, Antisense
  • RNA, Long Noncoding
  • TUG1 long noncoding RNA, human