Long noncoding RNAs (lncRNAs) are a class of RNA with 200 nucleotides or longer that are not translated into protein. lncRNAs are highly abundant; a study estimates that at least four times more lncRNAs are typically present than coding RNAs in humans. However, function of more than 95% of human lncRNAs are still unknown. Synthetic antisense oligonucleotides called gapmers are powerful tools for lncRNA loss-of-function studies. Gapmers contain a central DNA part, which activates RNase H-mediated RNA degradation, flanked by modified oligonucleotides, such as 2'-O-methyl RNA (2'OMe), 2'-O-methoxyethyl RNA (2'MOE), constrained ethyl nucleosides (cEt), and locked nucleic acids (LNAs). In contrast to siRNA or RNAi-based methods, antisense oligonucleotide gapmer-based knockdown is often more effective against nuclear-localized lncRNA targets, since RNase H is mainly localized in nuclei. As such, gapmers are also potentially a powerful tool for therapeutics targeting lncRNAs in various diseases, including cancer, cardiovascular diseases, lung fibrosis, and neurological/neuromuscular diseases. This chapter will discuss the development and applications of gapmers for lncRNA loss-of-function studies and tips to design effective antisense oligonucleotides.
Keywords: BC200 (Brain cytoplasmic 200); CRISPR/Cas9; DNM3OS (DNM3 opposite strand/antisense RNA); HOTAIR (HOX transcript antisense RNA); HULC (Highly Upregulated in Liver Cancer); MIAT (myocardial infarction associated transcript) also known as RNCR2 (retinal noncoding RNA 2) or Gomafu; Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1); NEAT1 (Nuclear Enriched Abundant Transcript 1); PRNCR1 (prostate cancer noncoding RNA 1); PVT1 (Pvt1 Oncogene); microRNAs (miRNAs).