Extended Data Fig. 8: RNA-seq analysis of RfxCas13d/BSJ-gRNA- or shRNA- mediated circFAM120A KD.
From: Screening for functional circular RNAs using the CRISPR–Cas13 system
a, Mapping statistics of two biological replicates of the poly(A) + RNA-seq datasets in 293FT cells with RfxCas13d/BSJ-gRNA- or shRNA- mediated circFAM120A KD. b, Heatmap of Spearman’s rank correlation coefficient for log2(FPKM) values of all linear mRNAs detected in RNA-seq libraries between targeting and non-targeting replicates for RfxCas13d/BSJ-gRNA- or shRNA- mediated circFAM120A KD. c, Expression levels in log2(FPKM) values of all genes detected in RNA-seq libraries of non-targeting control (x-axis) compared to circFAM120A-targeting conditions (y-axis) by RfxCas13d/BSJ-gRNA (red) or shRNA (blue). Means of two biological replicates were shown. d, A workflow shows the selection of candidate genes after circFAM120A KD by RfxCas13d/BSJ-gRNA. e, Heatmap of DEGs (n = 97) detected after circFAM120A KD by RfxCas13d/BSJ-gRNA. f, Enrichment of DEGs from RNA-seq after circFAM120A KD by RfxCas13d/BSJ-gRNA. The x axis shows the ratio of the number of genes in a given category of functional annotations divided by the total number of DEGs. The y axis shows categories of functional annotations. P values were calculated based on the Fisher’s exact test. g, Validation of DEGs associated with cell proliferation after circFAM120A KD by RfxCas13d/BSJ-gRNA in 293FT cells. All transcripts were normalized to ACTB, n = 3 independent experiments. ***: P < 0.001, two-tailed student’s t-test. h, Cytoplasmic distribution of circFAM120A. i, Prediction of AGO2-binding peaks in circFAM120A. Top, genomics locus and diagram of linear FAM120A and circFAM120A (shown as magenta cylinders). Blue and magenta arrows indicate location of primer for linear FAM120A or circFAM120A. Bottom, predicted miRNA target sites by TargetScan and AGO2 binding peaks from PAR-CLIP data in HEK293FT cells (GEO: GSE43573). j, A schematic to show predication of potential circRNA-miRNA target sites. k, CircFAM120A did not interact with AGO2 by RIP in 293FT cells using anti-AGO2 antibodies. (g,h,k) All RNA levels were detected by qRT-PCR and means ± s.d. were from three independent experiments.
