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Fig. 2 | Genome Biology

Fig. 2

From: Knockout of circRNAs by base editing back-splice sites of circularized exons

Fig. 2

Base editing at back-splice sites generally leads to alternation of back-splice and canonical splice. A Schematic of base editing and its outcomes at splice sites involved in both back-splice and canonical splice. B Base changes at 5′ (b)ss of cirSPECC1 by hA3A-eBE-Y130F repressed both back-splice for circRNAs and canonical splice for linear RNA expression. Top, schematic of partial SPECC1 gene organization. Back-spliced exon 4 was highlighted by blue bar. Context sequences of targeted 5′ (b)ss were shown by a, t, c, and g for intron or by A, T, C, and G for exon; Middle, G-to-A base change ratio at targeted 5′ (b)ss of back-spliced exon 5 in the SPECC1 gene locus; Bottom, evaluation of back-splice and splice changes by RT-qPCR using primers labeled on the top. C Base changes at 5′ (b)ss of circFNTA by hA3A-eBE-Y130F repressed both back-splice for circRNAs and canonical splice for linear RNA expression. Refer to B for details. D Base changes at 3′ (b)ss of circFOXP1 by hA3A-eBE-Y130F repressed both back-splice for circRNAs and canonical splice for linear RNA expression. Top, schematic of partial FOXP1 gene organization. Back-spliced exons 8-11 were highlighted by blue bars. Context sequences of targeted 3′ (b)ss were shown by a, t, c, and g for intron or by A, T, C, and G for exon; Middle, G-to-A base change ratio at targeted 3′ (b)ss of back-spliced exon 8 in the FOXP1 gene locus; Bottom, evaluation of back-splice and splice changes by RT-qPCR using primers labeled on the top. E Base changes at 3′ (b)ss of circZCCHC2 by hA3A-eBE-Y130F repressed both back-splice for circRNAs and canonical splice for linear RNA expression. Refer to D for details. B–E Error bar represents SD from three independent replicates. , P < 0.05; , P < 0.01; , P < 0.001, Student’s t test

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