GSE68938
RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships (RNA-seq)
Mapping of RNA:DNA hybrids in human cells reveals a number of characteristics of these non-canonical  nucleic  acid  structures.    A  directional  sequencing  approach  reveals  the  RNA component of the RNA:DNA hybrid to be purine-rich, indicating a thermodynamic contribution to the stability of these structures.  The RNA:DNA hybrids are enriched at loci with decreased DNA methylation  and  increased  DNase  hypersensitivity,  and  within  larger  domains  with characteristics of heterochromatin formation.  Studies of chromatin at RNA:DNA hybrids shows the  presence  of  the  ILF2  and  ILF3  transcription  factors,  supporting  a  model  of  certain transcription factors binding preferentially to the RNA:DNA conformation.  Overall, there is little to indicate a dependence for RNA:DNA hybrids forming co-transcriptionally, with results from the ribosomal DNA repeat unit instead supporting a model of RNA generating these structures in trans.  The results of the study indicate heterogeneous functions of these genomic elements and new insights into their formation and stability in vivo. Overall design: Investigation of expression data genome-wide in HEK293T and IMR-90 cells through RNA-seq, including rRNA