Fig. 4. Exome versus isoform-level m⁶A analysis.

a Example of read filtering. Overlapping RNA isoforms are shown in dark gray. Sequence reads that map unambiguously (teal) are filtered and retained for m⁶A analysis. Sequence reads with multiple primary alignments (gray) are discarded if no single alignment is considered superior. b Isoform-level comparisons between WT and M3KO datasets yields 747 candidates (post-collapse) of which 204 are consistently detected across all four comparisons. c Overlap of all m⁶A sites detected in 4/4 exome-mapped replicates and 4/4 isoform-mapped replicates. Isoform only candidates were collapsed to unique genomic loci. d Representative plots showing isoform-specific m⁶A predictions on adenovirus transcripts. MACS2 peaks and meRIP-seq signal (blue) is shown on top. Direct RNA (dRNA) predicted m⁶A sites at the exome-level (purple) or isoform-level (magenta) are shown below meRIP peaks as vertical lines. The positioning of m⁶A within individual viral transcripts from Fig. 2 are shown as magenta lines. Transcript names are shown to the left of each transcript.