Skip to main content
Fig. 1 | Genome Biology

Fig. 1

From: Optimized RNA-targeting CRISPR/Cas13d technology outperforms shRNA in identifying functional circRNAs

Fig. 1

Optimization of CRISPR-Cas13d for circRNA knockdown. a Schematic view of the length optimization of gRNAs targeting BSJ sites of circRNAs (left panel) and the corresponding knockdown efficiency with different lengths of gRNAs (right panel). Bar plots showing the relative expression of circZNF292 (CIRC) and its parental linear transcript (LIN) upon knockdown of circZNF292 with two gRNAs containing spacers ranging from 21 to 30 nt in length. NT, non-targeting. b Bar graphs showing the cumulative knockdown efficiency of different lengths of gRNAs across multiple circRNAs. Top, relative expression of targeting circRNAs. Bottom, relative expression of cognate linear mRNAs (n = 8 circRNA target sites, the data for each circRNA target site can be found in a and Additional file 1: Figure S3b). NT, non-targeting. c Bar graphs showing cumulative knockdown efficiency of longer gRNAs with 30 nt, 35 nt, and 40 nt spacers. Top, relative expression of targeting circRNAs. Bottom, relative expression of cognate linear mRNAs (n = 4 circRNA target sites, the data for each circRNA target site can be found in Additional file 1: Figure S3c). NT, non-targeting. d Knockdown of circZKSCAN1 evaluated with gRNAs containing 24 nt length spacer (left) or 30 nt length spacer (right) with single mismatch at varying positions across the spacer sequence. The gray boxes in the grids show the position of Watson-Crick transversion mismatches. The wild-type sequence is shown at the bottom of each grid. e Knockdown of circZKSCAN1 evaluated with gRNAs containing 24 nt length spacer (left) or 30 nt length spacer (right) with consecutive double mismatch at varying positions across the spacer sequence. The gray boxes in the grids show the position of Watson-Crick transversion mismatches. The wild-type sequence is shown at the bottom of each grid. The data shown are from one of two biological replicates with similar results, and error bars indicating the mean ± s.d. of three technical replicates

Back to article page