Circular RNAs are prevalent in human and mouse cells, with their expression being cell-type specific. A study using improved computational methods identified widespread circular RNA expression in Drosophila melanogaster and estimated that in humans, circular RNA may account for about 1% of poly(A) RNA molecules. Analysis of ENCODE data revealed that the repertoire of genes expressing circular RNA, the ratio of circular to linear transcripts, and the pattern of splice isoforms of circular RNAs are cell-type specific. These findings suggest that circular RNA biogenesis is an integral, conserved, and regulated feature of gene expression. The study developed a new bioinformatic approach to identify circular RNA by computing statistical averages of alignment quality scores rather than using qualitative thresholds. This method allowed for systematic FDR-based thresholding to determine classification as a scrambled junction. The approach was applied to ENCODE RNA-Seq data, identifying thousands of previously unreported circular RNA isoforms and revealing significant regulation of circular RNA expression. Validation using RNase R, a 3' to 5' exoribonuclease, confirmed that predicted circular RNAs were resistant to RNase R, while linear RNAs were sensitive. This provided strong evidence that the computational method specifically identified circular RNA species. The study also found no evidence that circular RNAs serve as templates for RNA-dependent RNA polymerases. Relative abundance analysis showed that circular RNA molecules were roughly 1% of poly(A) RNA molecules in the cell lines studied. For many genes, circular RNA abundance was 5–10% of linear RNA abundance. The study also found that circular RNA expression was regulated in a cell-type specific manner, with some genes showing significant increases in circular RNA expression in specific cell types. The study identified that circular RNA expression is regulated by the use of specific splice donor and acceptor sites, with some genes showing a preference for a single splice site pair. The study also found that circular RNA expression is evolutionarily conserved across species, including non-coding RNA loci. Overall, the study highlights the importance of circular RNA in gene expression programs and suggests that they may play significant functional roles in cellular processes.Circular RNAs are prevalent in human and mouse cells, with their expression being cell-type specific. A study using improved computational methods identified widespread circular RNA expression in Drosophila melanogaster and estimated that in humans, circular RNA may account for about 1% of poly(A) RNA molecules. Analysis of ENCODE data revealed that the repertoire of genes expressing circular RNA, the ratio of circular to linear transcripts, and the pattern of splice isoforms of circular RNAs are cell-type specific. These findings suggest that circular RNA biogenesis is an integral, conserved, and regulated feature of gene expression. The study developed a new bioinformatic approach to identify circular RNA by computing statistical averages of alignment quality scores rather than using qualitative thresholds. This method allowed for systematic FDR-based thresholding to determine classification as a scrambled junction. The approach was applied to ENCODE RNA-Seq data, identifying thousands of previously unreported circular RNA isoforms and revealing significant regulation of circular RNA expression. Validation using RNase R, a 3' to 5' exoribonuclease, confirmed that predicted circular RNAs were resistant to RNase R, while linear RNAs were sensitive. This provided strong evidence that the computational method specifically identified circular RNA species. The study also found no evidence that circular RNAs serve as templates for RNA-dependent RNA polymerases. Relative abundance analysis showed that circular RNA molecules were roughly 1% of poly(A) RNA molecules in the cell lines studied. For many genes, circular RNA abundance was 5–10% of linear RNA abundance. The study also found that circular RNA expression was regulated in a cell-type specific manner, with some genes showing significant increases in circular RNA expression in specific cell types. The study identified that circular RNA expression is regulated by the use of specific splice donor and acceptor sites, with some genes showing a preference for a single splice site pair. The study also found that circular RNA expression is evolutionarily conserved across species, including non-coding RNA loci. Overall, the study highlights the importance of circular RNA in gene expression programs and suggests that they may play significant functional roles in cellular processes.