Control of Chromatin Structure by Long Noncoding RNA

Long noncoding RNA (lncRNA) is a pivotal factor regulating various aspects of genome activity. Genome regulation via DNA methylation and post-translational histone modifications is a well-documented function of lncRNA in plants, fungi, and animals. Here, we summarize evidence showing that lncRNA also controls chromatin structure, including nucleosome positioning and chromosome looping. We focus on data from plant experimental systems, discussed in the context of other eukaryotes. We explain the mechanisms of lncRNA-controlled chromatin remodeling and the implications of the functional interplay between noncoding transcription and several different chromatin remodelers. We propose that the unique properties of RNA make it suitable for controlling chromatin modifications and structure.

TrendsLong noncoding RNA (lncRNA) modulates genome activity not only by affecting DNA methylation and post-translational histone modifications, but also by controlling chromatin structure.Plant model systems offer a unique genetic toolset for studying lncRNA and chromatin structure. These tools include a multitude of viable mutants and a specialized RNA polymerase producing scaffold lncRNA.Various lncRNAs have been shown to control nucleosome positioning and chromosome looping in plants and other eukaryotes.Noncoding transcription involved in transcriptional gene silencing in plants cooperates with at least two putative ATP-dependent chromatin remodelers.Unique features of RNA make it especially suited for controlling chromatin structure.