Chromatin interacting RNA maintains accessible higher order structures of chromatin

The packaging of DNA into nucleosomes and further compaction into higher order structures of chromatin play crucial roles in functional organisation of the genome. We identified a novel class of RNA that is stably associated to chromatin and mediates changes in higher order structures of chromatin. Depletion of cellular RNA in Drosophila cells by RNase A treatment or inhibition of RNA Pol II transcription resulted in a genome wide chromatin compaction,as monitored by micrococcus nuclease (MNase) accessibility. Using a cell free in vitro chromatin assembly system (DREX), we demonstrate that ciRNAs consists of short single stranded RNA molecules that stably interact with chromatin. Significantly, the ciRNA was capable of reversibly change the compaction state of higher order structures of chromatin in vitro, without affecting nucleosome density or nucleosome spacing of the circular arrays. Preliminary experiments indicate that the ciRNA is tethered to chromatin by interaction with specific proteins.

We suggest that the ciRNA represents a novel class of regulative RNAs that play a role in maintaining an open chromatin organisation.