Genes associated with DNA:RNA hybrids were significantly associated with antisense transcripts.

<p>(A) Antisense association of DNA:RNA hybrid-enriched genes in wild type. The p-value indicates significant enrichment (Fisher's exact test) of antisense-associated genes among DNA:RNA hybrid-enriched genes compared to the Yassour et al. 2010 antisense-annotated dataset (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004288#pgen.1004288-Yassour1" target="_blank">[51]</a>). (B) CHROMATRA plots of DNA:RNA hybrid distribution along genes sorted by their length and separated by whether they are antisense associated or not. Genes were aligned by their TSSs. (C) Average gene profile of DNA:RNA hybrids at genes associated with antisense transcripts. (D) Genes with increased mRNA levels upon RNase H overexpression were significantly associated with antisense transcripts compared to all transcripts represented by the microarray. (E) Antisense-associated DNA:RNA hybrid-enriched genes in wild type have lower transcription frequency compared to non-antisense-associated DNA:RNA hybrid-enriched genes. Genes up-regulated at the transcript level by RNase H overexpression have lower transcription frequency compared to all genes on the expression microarray. Intervals indicate range of the 95% of genes closest to the average in each sample. Averages stated above each bar. P values indicate significant decrease in transcriptional frequency (Wilcoxon rank sum test). (F) Overlap between DNA:RNA hybrid-enriched genes and RNase H-modulated transcripts sorted by antisense association according to the Yassour et al. 2010 database. For genes that are both hybrid-enriched and modulated at the transcript level by RNase H overexpression, the antisense association (100%) is significantly higher (Fisher's exact test p<2.2e⁻¹⁶) than those of the parent datasets (37.4% for DNA:RNA hybrid-enriched genes, 43.9% for RNase H-modulated genes).