Fig 1.
Cell culture and RNA sequencing.
A. Photomicrographs of BEP2D (Left), BERP35T1 (Middle) and BERP35T4 (Right) showing the cellular atypia of the malignant transformed cell lines (100×). B. Scatter plots showing the consistency of normalized gene expression between biological replicates for each cell line.
Table 1.
Summary of A-to-I RNA editing.
Fig 2.
Identification and characterization of A-to-I RNA editing.
A. Venn plot showing the overlaps of RNA editing sites in BEP2D, BERP35T1 and BERP35T4 cell lines. B, C. Bar plots showing the proportion of A-to-I RNA editing in Alu/non-Alu regions (B) and Genebody/Intergenic regions (C). D. Venn plot showing the overlaps of edited genes in BEP2D, BERP35T1 and BERP35T4 cell lines. E. Bar plot showing the proportion of tissue-specific editing genes in each cell line. F. Venn plot showing the overlaps of edited genes contained cell line-specific editing sites in BEP2D, BERP35T1 and BERP35T4 cell lines. G. GO enrichment for editing genes in each cell line, value was negative log10 of p-value. H. We compared the proportion of DEGs in total genes (blue bar) and DEGs in editing genes (red bar), p-value was calculated by hypergeometric test.
Fig 3.
Down-regulation of ADAR2 induce RNA editing.
A, B. Bar plots showing the normalized gene expression of ADAR1, ADAR2 and ADAR3 in each cell line. C, D. Bar plots showing the number of genomic variants in ADAR2 (C) and exons of ADAR2 (D). E, F. IGV plots showing the sequencing reads information of mutation rs11701974 and novel mutation chr21:46643782.
Fig 4.
Oncogene CTNNB1 and FN1 are highly edited and significantly overexpressed in malignantly transformed cell line.
A, C. Bar plots showing the normalized gene expression of oncogenes CTNNB1 and FN1 in BEP2D cell line and BERP35T1 and BERP35T4 cell lines, respectively. B, D. IGV plots showing the editing events in oncogenes CTNNB1 and FN1.