Genomic RNA-DNA duplexes in mitotically arrested cells

RNA-DNA duplexes have been extensively catalogued in interphase cells, but relatively little is known about the genomic loci of these duplexes in mitotic cells. We compared RNA-DNA duplexes in DLD1 cells arrested in mitosis to libraries previously published in asynchronous HEK293T cells prepared with the same protocols, and processed with the same bioinformatic pipeline. We also observed that Aurora B inhibitors increased the immunofluorescence signal for RNA-DNA duplexes in mitotic cells, so we tested the effect of Aurora B inhibition on genomic enrichment of RNA-DNA duplexes. Overall design: Samples from two different DNA-RNA IPs were sequenced, with one input, one control, one Aurora B inhibited, and RNaseH1 treated samples for each for each set of IPs. RNaseH1 samples were sequenced to verify the specificity of the signal. Control (DMSO), Aurora B inhibited, and RNaseH1 treated samples were compared to input to call peaks, determine relative enrichment over gene bodies, TSS, TTS, and to gain relative enrichment at repetitive elements as defined using the Input samples.