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. 2018 Apr 12;7:e27024. doi: 10.7554/eLife.27024

Figure 2. ChAR-seq is an ‘all to all’ RNA-to-DNA proximity ligation method.

(A) Genome-wide plot of RNA to DNA contacts for non-coding RNAs. The y-axis represents the region of the genome from which a given RNA was transcribed and the x-axis represents the region of the genome where each RNA was found to be associated through proximity ligation (i.e., the binding site for each RNA). Genome-wide contact plots generated in the same way for (B) mRNA, and (C) snRNA. (D) Cumulative frequency of length-normalized contacts for 16,812 RNAs identified on the ‘RNA-side’ of chimeric reads. The majority (88%) of RNAs have fewer than 10 contacts per kilobase per million reads (CPKM) in our dataset and were not further analyzed owing to low coverage. The remaining 1952 RNAs account for 18.5 million (83%) of the total RNA-to-DNA contacts. (E) Scatter plot of length normalized chromatin-contacts versus total expression for each RNA. The 138 RNAs that had more than 100 CPKM and were enriched more than ten-fold are highlighted in red.

Figure 2.

Figure 2—figure supplement 1. Chromatin-associated RNAs ranked according to CPKM and enrichment in ChAR-seq over RNA-seq.

Figure 2—figure supplement 1.

RNAs are sorted according to the abundance of their genome-wide contacts (CPKM, left bars). Right bars represent the fold-enrichment of each RNA in ChAR-seq over RNA-seq.

Figure 2—figure supplement 2. Chromatin associated RNAs identified by ChAR-seq are highly reproducible.

Figure 2—figure supplement 2.

Venn diagrams displaying overlap of chromatin-associated RNAs identified as having contacts more than 4-fold enriched over RNA expression which have more than 10 CPKM (left) or more than 100 CPKM (right) in technical replicates.