Fig. 2: C19MC small RNA output in the C19MC-dA11-deleted cells.

a RT-qPCR analysis of miRNA expression in BeWo cells, showing a sharp reduction of C19MC miRNA expression (miR-512 and miR-517) and increased expression of a non-C19MC miRNA (miR-21). Four lines were tested, including BeWo-WT, BeWo cells transduced with a doxycycline-inducible Cas9 lentivirus (Cas9), and two independent clones with a homozygous deletion of ATAC-11 (BeWo-dA11-21 and -dA11-23). Data are mean ± SD, n = 3. * p < 0.05; ns nonsignificant. b The expression of C19MC Alu RNAs in BeWo-Cas9 or -dA11 (2 lines each), determined by RNA-seq (4 libraries). In the left panel, reads are Log2 expression of Alu elements, normalized to library size. The line dA3/4 was Cas9-edited at ATAC-3/4 site, as an additional control. Y axis: Log2 expression of Alu elements, normalized by library size. The expression difference between each control group and each deletion group was significant at p < 2.2 × 10⁻¹⁶. c The normalized total counts for all Alu RNAs (red) and all non-Alu small RNAs (blue, including miRNA) in the same samples as in (b). The difference between the fraction of total Alu and non-Alu RNAs in Cas9 and dA3/4 vs the two dA11 clones was significant (p < 0.05, t-test on log fraction). d An RNA-seq density plot, representing the chromosome 19 region that harbors the C19MC locus, plotted along chr19:53000000−54500000. Each bar represents the log2 read frequency, plotted by the chromosome coordinates. The pink box indicates the C19MC location.