Extended Data Fig. 10: Identification and GO analysis of the RBP interactome of two coPARSE-lncRNAs in mouse cells and zebrafish embryos.

a, Distribution of the MiST scores of enriched RBPs pulled down using the human coPARSE-lncRNA RP1-212P9.3 and its predicted homologs from mouse and zebrafish in mouse V6.5 cells. The dashed lines represent a threshold of 0.7. The yellow circles represent the enriched RBPs in both two lncRNAs. Venn diagram showing the overlap of identified binding proteins for RP1-212P9.3 and its predicted homologs in mouse V6.5 cells. R, Pearson correlation coefficient, two-sided Student’s t-test. b, Distribution of the MiST scores of enriched RBPs pulled down using the human coPARSE-lncRNA RP1-212P9.3 and its predicted homologs from mouse and zebrafish in zebrafish embryos. The dashed lines represent a threshold of 0.7. The yellow circles represent the enriched RBPs in both two lncRNAs. Venn diagram showing the overlap of identified binding proteins for RP1-212P9.3 and its predicted homologs in zebrafish embryos. R, Pearson correlation coefficient, two-sided Student’s t-test. c, Venn diagram showing the overlap of identified binding proteins for RP1-212P9.3 in HeLa cells, mouse V6.5 cells, and zebrafish embryos (left) and identified binding proteins for RP1-212P9.3 in HeLa cell, for its predicted mouse homolog in mouse V6.5 cells, and for its predicted zebrafish homolog in zebrafish embryos (right). Note that during the analysis, we only retained the proteins which have a homolog in all three species. The overlap proteins between the left and the right diagrams are highlighted in red. d, Enriched Gene Ontology (GO) terms related to the interacting proteins of human coPARSE-lncRNA RP1-212P9.3 and its predicted mouse and zebrafish homologs in human HeLa cells, mouse V6.5 cells, and zebrafish early embryos. P values were calculated by two-sided Fisher’s exact test.