Fig. 6: Knockout of DDX59 results in the accumulation of 3′-extended precursors of endogenous snRNAs.

a–c Integrated Genome Viewer (IGV) traces of RNA-seq (performed without poly(A) selection) are shown for minor spliceosomal snRNAs, U4atac and U11 (a, b), and for a major spliceosomal snRNA, U4 (c). Cell populations with knockouts of DDX59, RBM7, ZCRB1, and EXOSC10 were obtained as shown in Fig. 5a; their respective IGV traces are colored accordingly. RT-qPCR quantification of the levels of 3′-extended forms of minor spliceosomal snRNAs U4atac (d) and U11 (e). f RT-qPCR analysis of the effects of BRF2 knockout on (i) processing of the endogenous full-length lncRNA MALAT1 by RNase P and (ii) RNA levels of its catalytic component H1 RNA. The left graph shows analysis of cleavage across the RNase P site of the endogenous full-length lncRNA MALAT1, and the right graph shows RNA levels of H1 RNA in knockout cell populations. Knockout of RPP21, which is unique for RNase P (and absent in the closely-related RNase MRP) and essential for its function³⁷, is shown as a positive and negative control in the left and right graphs, respectively. g RT-qPCR quantifications of mRNA levels in cell populations with CRISPR-induced knockouts of indicated genes, obtained as shown in Fig. 5a. All qPCR quantifications and statistical tests were performed as described in the legend of Fig. 5; qPCR primers are listed in Supplementary Data S2.