Fig. 1

Circular RNAs are highly expressed in HepG2 and K562 and generally colocalizes with RBPs. a Flowchart overview of analyses. The initial analyses and characterizations are based on the ENCODE cell lines HepG2 and K562. Follow-up experiments are performed in HepG2 cells and bladder cancer cell lines to evaluate the relevance of findings in tumorigenesis. b Summary of input data sets and inferred sets of circRNAs. The sets of high-confidence, highly expressed circRNAs (top 1% circRNAs) are used in most of the downstream analyses. c Number of backsplice junction (BSJ) reads supporting the 1% highest expressed circRNAs (n = 161), and the number of reads spanning canonical splice sites in the corresponding linear transcripts in HepG2. X- and Y-axes are plotted on a logarithmic scale (log10) showing actual counts. Some circRNAs are depicted with their host gene name. The number of reads represents the summarized values across all five HepG2 data sets. d Genomic location of RBP binding sites in the top 1% circRNA loci in HepG2. Most RBP binding sites are found within exonic parts of the circRNAs. Exonic parts span 0.119 Mb, while introns span 1.836 Mb. e Localization of top 1% circRNAs (n = 161; top) and RBPs (n = 64; bottom) across cellular compartments of HepG2. For circRNAs, all are found in the cytoplasm (n = 161), with a large subset that is also found in the nucleus (n = 103). No circRNAs are exclusively expressed in the nucleus. For RBPs, most are located in both cellular compartments (n = 38), while some RBPs are expressed exclusively in the cytoplasm (n = 12) or the nucleus (n = 14). f Localization of top 1% circRNAs and RBPs that are predicted to interact from eCLIP data in HepG2. CircRNA localization is shown on the x-axis, while RBP localization is indicated by color. For 94% of the predicted circRNA-RBP interactions, the circRNA and RBP are expressed in the same subcellular compartment