Fig. 6

FIRRE is downregulated, and its major transcripts are circular in differentiated cells. a Modified UCSC browser representation of mapped read count coverage (black) and back-splice junction count (blue) at the FIRRE locus in untreated replicate 1 at day 0 (top), shown above the mapped read data from all untreated replicates at days 45 and 90. Back-splice reads span a single junction and only the donor and acceptor exons are indicated. GENCODE (green) and RefSeq (purple) annotations are also shown, together with a genomic scale. ENCODE/Broad chromatin state segmentation [52] within the H1 ES cell line is also shown: Light red/bright red/purple = weak/active/poised promoter, light/dark green = weak/elongation transcription, orange/yellow = strong/weak enhancer, grey = heterochromatin low signal, blue = insulator. b Schematic of FIRRE exon structure, showing circRNA junctions and counts (above exons) and canonical junctions and counts (below exons), summed across untreated replicates for all time-points (0/45/90). Additional exons not present within the GENCODE FIRRE annotation are shown in grey (asterisked) and numbered A, B etc. with respect to ENCODE annotation. Only junctions involving annotated FIRRE exons are shown, and numbers are only given for junctions with 10 or more supporting reads in 1 or more time-points. c Modified UCSC browser image showing position and relative abundance of additional exons not in ENCODE annotation. The scale is split at 150 to facilitate visualisation of rare exons (see Additional file 3: Figure S4). d-e qPCR validation of expression changes of circFIRRE:E10-E5 and upstream junctions. d. Mean ΔCt values from 3 biological replicates assayed at day 0, 30 and 45 are shown (+/− S.E.M). e. ΔΔCt values relative to to E10-E5. *p < 0.05, **p < 0.01