Emerging roles of non-coding RNAs in epigenetic regulation

Recent deep sequencing surveys of mammalian genomes have unexpectedly revealed pervasive and complex transcription and identified tens of thousands of RNA transcripts that do not code for proteins. These non-coding RNAs (ncRNAs) highlight the central role of RNA in gene regulation. ncRNAs are arbitrarily divided into two main groups: The first includes small RNAs, such as miRNAs, piRNAs, and endogenous siRNAs, that usually range from 20 to 30 nt, while the second group includes long non-coding RNAs (lncRNAs), which are typically more than 200 nt in length. These ncRNAs were initially thought to merely regulate gene expression at the post-transcriptional level, but recent studies have indicated that ncRNAs, especially lncRNAs, are extensively associated with diverse chromatin remodeling complexes and target them to specific genomic loci to alter DNA methylation or histone status. These findings suggest an emerging theme of ncRNAs in epigenetic regulation. In this review, we discuss the wide spectrum of ncRNAs in the regulation of DNA methylation and chromatin state, as well as the key questions that needs to be investigated and acknowledging the elegant design of these intriguing macromolecules.