Fig. 6: RNA-binding activity of the LIM domain.

a Left: Color matrix showing LIM domain protein on the protein microarray. Color scales represent the FC (Cy5 foreground signals over local background). Right: Image of Cy5-RNA incubation signal of the human CSRP1 on the protein microarray. b Relative levels of Csrp1 isolated from indicated mouse lysate using HARD beads and EGFP beads. Means ± SD are plotted; three independent biological samples were used for the analysis (n = 3). The p-values were calculated using a two-tailed Student’s t-test. c Western blot analysis showing levels of Csrp1 isolated from the mouse brain and lung lysate using HARD beads and EGFP beads. This experiment was repeated once with similar results. d Heatmap of high-confidence CLIP-seq signals ± 2 kb around the center of peaks (n = 10,028). Csrp1 IP: EBs expressing Csrp1-V5; Control: WT EBs. Two biologically independent replicates are shown. e Distribution of Csrp1 CLIP-seq signals (n = 10,028) in different gene features. The average of the two biologically independent replicates is shown. f The top five GO terms associated with genes identified by CLIP-seq. The GO enrichment analysis used the two-sided Fisher’s exact test with the p-value adjusted using the Bonferroni correction for multiple testing. g Representative genome browser tracks showing normalized CLIP-seq and RNA-seq signals. h The top five enriched Csrp1-binding motifs on all target RNAs (target sequences = 6071, background sequences = 39,667). Motif enrichment significance was computed by HOMER (binomial test without adjustment). i Volcano plot showing distributions of genes differentially expressed in Csrp1^KO and WT embryoid bodies (n = 22,625). The significance (p) was determined using the two-tailed Student’s t-test and further adjusted using the Benjamini-Hochberg correction for multiple testing (p-adjust). j Gene Set Enrichment Analysis of genes down-regulated in Csrp1^KO embryoid bodies compared to WT embryoid bodies. NES, normalized enrichment score. k The most enriched GO terms in significantly expressed genes in the Csrp1^KO embryoid bodies. The GO enrichment analysis used the two-sided Fisher’s exact test with the p-value adjusted using the Bonferroni correction for multiple testing. Source data for (b-c) are provided as a Source Data file.