Fig. 5. PAF1c sequesters SPT6 on long genes.

a Heat map showing log₂FC of change in expression of genes involved in antigen processing and presentation via MHC class I molecules (GO-0002475) upon the depletion of either CTR9 or MYC (n = 3). P values were calculated using the likelihood ratio test (LRT), then False discovery rate (FDR) was calculated using the Benjamini–Höchberg procedure to adjust P values for multiple comparisons. The FDRs were: *p ≤ 0.05, **p ≤ 0.001, ***p ≤ 0.0001, n.s. not significant. b Scatter plot of gene length versus log₂ fold-changes in gene expression upon CTR9 depletion, comparing expressed genes of the GO term DNA repair (GO-0006281, n = 375 genes) in red with antigen processing and presentation genes (APAP, GO-0019882, n = 56 genes) in blue (Pearson correlation coefficient (R) = −0.42, p < 2.2e-16, two-sided pearson correlation test). c Browser picture showing read distribution of RNAPII (top), SPT5 (middle) and SPT6 (bottom) at H2-K1 and H2-D1 genes from a ChIP-Rx experiment in cells expressing doxycycline-inducible shRNA targeting CTR9 (n = 2). “-CTR9” indicates that shRNA expression was induced by doxycycline (1 µg/ml), “+CTR9” samples were treated with ethanol. d ChIP-qPCR showing RNAPII, pS5RNAPII, pS2RNAPII, SPT4, SPT6 or RTF1 binding to the indicated genes either at the promoter or in the gene body. IgG was used as a negative control to show the background signal. Data are presented as mean of two technical replicates of one of two biological replicates with similar results (n = 2). e Heat map of the log₂FC of SPT6 occupancy for all expressed (10,920) genes analyzed by ChIP-Rx comparing CTR9 depletion to the control. Genes are sorted according to their length from shortest (left) to longest (right). The black dashed line represents the end of the gene (n = 2). f RT-qPCR measurement of H2-D1 and H2-T23 MHC class I genes, CTR9 and Supt6 (encoding SPT6). KPC cells expressing doxycycline inducible shRNA targeting CTR9 were used. Both siRNA transfection and doxycycline addition were for 48 h. Data are presented as mean ± s.d. (n = 4 independent experiments; unpaired two-sided t-test). Source data are provided as a Source Data file.