Abstract
Chromatin-associated non-coding RNAs modulate the epigenetic landscape and its associated gene expression program. The formation of triple helices is one mechanism of sequence-specific targeting of RNA to chromatin. With this study, we show an important role of the nucleosome and its relative positioning to the triplex targeting site (TTS) in stabilizing RNA-DNA triplexes invitro and invivo. Triplex stabilization depends on the histone H3 tail and the location of the TTS close to the nucleosomal DNA entry-exitsite. Genome-wide analysis of TTS-nucleosome arrangements revealed a defined chromatin organization with an enrichment of arrangements that allowtriplex formation at active regulatory sites andaccessible chromatin. We further developed a method to monitor nucleosome-RNA triplexes invivo (TRIP-seq), revealing RNA binding to TTS sites adjacent to nucleosomes. Our data strongly supportan activating role for RNA triplex-nucleosome complexes, pinpointing triplex-mediated epigenetic regulation invivo.
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