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The epigenetics of non-coding RNA

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Collins, L. J., Schönfeld, B., & Chen, X. S. (2011). The epigenetics of non-coding RNA. In T. Tollefsbol (Ed.), Handbook of epigenetics: the new molecular and medical genetics (pp. 49-61). London: Academic.

Summary Non-coding RNAs (ncRNAs) have been implicated in the epigenetic marking of many genes. Short regulatory ncRNAs, including miRNAs, siRNAs, piRNAs and snoRNAs as well as long ncRNAs such as Xist and Air are discussed in light of recent research of mechanisms regulating chromatin marking and RNA editing. The topic is expanding rapidly so we will concentrate on examples to highlight the main mechanisms, including simple mechanisms where complementary binding affect methylation or RNA sites. However, other examples especially with the long ncRNAs highlight very complex regulatory systems with multiple layers of ncRNA control.
This chapter reviews both the long and short classes of noncoding RNA involved in epigenetic regulation—those that generally act as cis-acting silencers, but also as trans-acting regulators of site specific modification and imprinted gene-silencing. Nonprotein-coding RNAs (ncRNAs) are RNAs that are transcribed from DNA but are not translated into proteins. Many are functional and are involved in the processing and regulation of other RNAs such as mRNA, tRNA, and rRNA. The investigation of ncRNA-related epigenetic mechanisms is at this point relatively new, but the rise of new sequencing technologies has already revealed epigenetic regulation at the genome level. Deep-sequencing technologies have not only enabled analysis of histone modifications and methylation sites across entire genomes, but are enabling the detection of ncRNAs important in the regulation of these modifications. An interesting tidbit is that the role of ncRNA in epigenetics has even been investigated in space. Space flight is a unique environment comprising cosmic irradiation, microgravity, and space magnetic fields.