Fig 3. Read coverage of 4sU labeled transcripts shows a reduced transcription in cells 24 hours after CD46-Cas9 RNP complex nucleofection only at exon 1 and 2 of CD46.

(A) The upper plot shows the primary, unspliced transcript of the CD46 gene together with its nucleotide coordinates on chromosome 1 and the 14 exons (dashed, vertical lines) of the CD46 transcript (x-axis). The normalized read coverage at single nucleotide resolution is shown (y-axis) from WT cells (blue line) and CD46-Cas9 treated cells (red line). The lower graph depicts the mRNA data of exon 1 to 8 of the CD46 transcript covering the two conditions. Read normalization of the three pairs of replicates was performed as stated in Materials and Methods. (B) The plots show the primary transcript positions (bp) (x-axis) vs. the normalized read coverage at single nucleotide resolution of four selected transcripts (CD46, ATN1, DICER, FCRL5). Transcript data (y-axis) from WT cells (blue line) and CD46-Cas9 nucleofected cells (red line) are shown. Plots indicated ‘189 nts’ visualize the 189 nt long exons of the ATN1, DICER and FCRL5 transcripts together with the second exon of the CD46 transcript. Plots of the last exons of the four transcripts are shown for comparison. The two dashed vertical lines in the plot of the second exon of CD46 indicate the positions of the Cas9 mediated cleavage sites.