Fig. 4: M1BP and CP190 transcriptionally regulate a common set of genes.
a, b MA plots showing changes in neuRNA levels upon depletion of M1BP. Statistically significant changes include 1315 upregulated genes (red) and 607 downregulated genes (blue) using Padj < 0.05. Unchanged genes are indicated in gray. Gene promoters containing M1BP peaks (a) or CP190 peaks (b) are additionally colored yellow. Two-sided Fisher’s exact test was used. c, d MA plots showing neuRNA-seq affected genes after depletion of CP190. Significantly upregulated genes (1894, red) and downregulated genes (1382, blue) are shown. Genes containing CP190 (c) or M1BP (d) at their promoters are shown in yellow. Fisher’s exact test (two-sided) was used. e–g Scatter plots comparing neuRNA-seq profiles of M1BP and Cp190 knockdowns (e), M1BP and mod(mdg4) knockdowns (f), or Cp190 and mod(mdg4) knockdowns (g). Pearson’s R corresponds to correlation coefficient between two profiles. Common upregulated genes are indicated in red, and common downregulated genes are indicated in blue. h Differentially decreased CP190 peaks in M1BPRNAi associated with the promoter of downregulated genes affected in both M1BP and Cp190 knockdowns are verified by ChIP-qPCR. Percent input DNA precipitated is shown for each primer set. Average values from n = 2 biological replicates measured using four technical replicates are shown. Detailed description of each site is summarized in Supplementary Table 5, and Ct values are listed in Source Data 7.
