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Circular RNAs Are the Predominant Transcript Isoform from Hundreds of Human Genes in Diverse Cell Types

Figure 4

Scrambled exons are enriched in poly-A depleted samples.

Single-end 76-bp RNA-Seq was performed on matched experiments on HeLa, and H9 Human embryonic stem cell lysates were polyA selected and polyA depleted (data from Yang et al [22]). The numbers of scrambled exons detected in each sample which appeared in our curated database of scrambled junctions from the leukocyte data are depicted as colored bars. Roughly equal numbers of sequencing reads were available from each of 4 samples. Left panels of bar plot: both H9 and HeLa cells show markedly more exon scrambles in polyA depleted fractions compared to polyA enriched fractions, consistent with scrambles arising from circular transcripts which lack polyA tails. Right panels of bar plot: conversely, in the much smaller subset of scrambled exon pairs where we have evidence of internal tandem duplication (i.e. evidence against circularity), we find the opposite enrichment: more exon scrambles in polyA enriched fractions compared to polyA depleted fractions, consistent with this small subset of scrambles arising from linear, polyA transcripts.

Figure 4