Although originally believed to be non-functional, key roles for non-coding RNA (ncRNA) transcripts in the regulation of gene expression have now been revealed. Here, Wahlestedt provides an overview of the various subtypes of ncRNA, focusing on the emerging regulatory roles of long non-coding RNAs (lncRNAs) and their links to disease. The potential of targeting the natural antisense transcript subclass of lncRNAs using antisense oligonucleotides known as antagoNATs, to therapeutically upregulate gene expression, is assessed.