The Effects of RNA.DNA-DNA Triple Helices on Nucleosome Structures and Dynamics

ABSTRACT Non-coding RNAs (ncRNAs) are an emerging epigenetic factor and have been recognized as playing a key role in many gene expression pathways. Structurally, binding of ncRNAs to isolated DNA is strongly dependent on sequence complementary, and results in the formation of an RNA.DNA-DNA (RDD) triple helix. However, in vivo DNA is not isolated, but is packed in chromatin fibers, the fundamental unit of which is the nucleosome. Biochemical experiments have shown that ncRNA binding to nucleosomal DNA is elevated at DNA entry and exit sites and is dependent on the presence of the H3 N-terminal tails. However, the structural and dynamical bases for these mechanisms remains unknown. Here, we have examined the mechanisms and effects of RDD formation in the context of the nucleosome using a series of all-atom molecular dynamics simulations. Results highlight the importance of DNA sequence on complex stability, elucidate the effects of the H3 tails on RDD structures, show how RDD formation impacts the structure and dynamics of the H3 tails, and show how RNA alters the local and global DNA double helical structure. Together, our results suggest ncRNAs can modify nucleosome, and potentially higher-order chromatin, structures and dynamics as a means of exerting epigenetic control. SIGNIFICANCE Non-coding RNAs (ncRNAs) play an essential role in gene regulation by binding to DNA and forming RNA.DNA-DNA (RDD) triple helices. In the cell, this occurs in the context where DNA is not a free double helix but is instead condensed into chromatin fibers. At the fundamental level, this compaction involves wrapping approximately 147 DNA basepairs around eight histone proteins to form the nucleosome. Here, we have used molecular dynamics simulations to understand the interplay between the structure and dynamics of RDD triple helices with the nucleosome. Results highlight the importance of RNA sequence on RDD stability regardless of its environment and suggest potential mechanisms for cross-talk between epigenetic factors and the effects of ncRNA binding on local and higher-order chromatin structures.