Mini-review on current strategies to knockdown long non-coding RNAs

Abstract

Text The discovery of functional long non-coding RNAs (lncRNAs) has challenged the paradigm that most RNAs encode proteins. LncRNAs are an abundant class of RNAs >200 nt in length that were previously assumed to be transcriptional noise. It is now widely accepted that some of these lncRNAs have diverse regulatory roles in gene expression, can serve as structural components for shaping nuclear organization and can even act as decoys for other RNAs or proteins 1-3 . While tens of thousands of lncRNA transcripts have been cataloged, the biological function of the majority of lncRNAs still remains a mystery. Determining the individual functionality of members of this recently discovered class of RNAs is important for better understanding of developmental biology, evolution and genetic disease. Similar to proteins, individual lncRNAs have specific subcellular distributions that are critical for their function 4 . Some lncRNAs are enriched in the nucleus and are involved in regulating nuclear processes such as transcription and RNA processing. Other lncRNAs are enriched in the cytoplasm where they can impact protein localization or modulate mRNA stability and translation. Some lncRNAs are more equally distributed between the nucleus and the cytoplasm. The location of the primary reservoir of a lncRNA can impact the ability to knock down expression levels of that species. Three strategies are commonly used to knockdown or knockout lncRNAs, including: degradation of the RNA by RNA interference (RNAi), degradation of the RNA by RNase H activate antisense oligonucleotides (ASOs), or gross deletion/alteration at the DNA level using CRISPR/Cas9 genome editing methods (Figure 1). Each of these tools have their own advantages and disadvantages, and success can be influenced by the subcellular localization of the lncRNA and the transcriptional landscape within which it resides. RNAi is a commonly employed knockdown technique that utilizes the multi-protein RNAi-induced silencing complex (RISC) to suppress mRNAs