The structural organization of actively transcribed regions of chromatin (euchromatin) is an area of intense interest. A recent report by Caudron-Herger et al. identified a new class of RNA that is associated with transcriptionally active chromatin. The authors termed these transcripts “chromatin-interlinking” RNAs or ciRNAs.
By combining fluorescence microscopy and microinjection of substrate-specific RNases, such as RNase A, RNase III, and RNase H, the authors conclude that ciRNA is single-stranded. They further characterized ciRNA by RNA-Seq using purified nuclear RNA fractions treated with the Ribo-Zero™ rRNA Removal Kit. ciRNA was found to compromise long (>500 nt) RNA polymerase II transcripts that were “spliced, depleted of polyadenylation and enriched with long 3'-untranslated regions (3’-UTRs) above ~800 nt."
Based on their results, the authors conclude that ciRNA “plays an important role in maintaining a decondensed and biologically active inter-phase chromatin conformation in human and mouse cell lines” and propose that ciRNA “could act as genome-organizing architectural factors of actively transcribed chromatin compartments.”
Caudron-Herger M et al. (2011). Coding RNAs with a non-coding function: Maintenance of open chromatin structure. Nucleus (Austin, Tex.), 2 (5) PMID: 21983088