Spt16 is enriched at the DS region of Pol III-transcribed genes. Spt16 ChIP-seq data were acquired and analyzed as detailed in Materials and Methods. Occupancies are plotted as normalized tag counts per million reads, all aligned to the TSS. (A) Spt16 occupancy profile on the Pol II-transcribed genes found in this study agrees with earlier reports (True et al. 2016; Martin et al. 2018) showing a distribution that follows the nucleosomal profile (MNase-seq data from Weiner et al. 2010). (B) Average profiles of Spt16 (this study) and Pol III (Kumar and Bhargava 2013) occupancies are compared on the tRNA genes. An asterisk (color coded) marks the Pol III and Spt16 peaks at the tRNA gene body where Spt16 occupancy is similar to that at the 5′-ends of the Pol II-transcribed genes. (C) Relative Spt16 occupancy in the unique regions flanking some of the tRNA genes. Spt16–TAP occupancy was measured by performing ChIP and the real time PCR, using TELVIR as normalizer. All genes show very low US levels. The P-values are (*) 0.0093, (**) <0.00022, and (***) <0.00008. (D) Spt16 occupancy on the non-tRNA Pol III-transcribed RPR1 and SCR1 genes. Occupancy is given as the normalized, tag counts per million reads in a window of −800 bp to +1000 bp with respect to the gene TSS. The color-coded asterisks mark the US and DS peaks of Spt16 on both the genes. (E) Schematic representation of the positions of the amplicons used in the real time PCR estimations on three non-tRNA genes. Bent arrow depicts position of the TSS. Gray boxes mark the mature transcript position. Short bars represent the amplicons. Names of the amplicons at the two ends of each gene are given below the short bars. (F) Spt16 occupancy at the 5′- and 3′-ends of the non-tRNA genes as measured by the ChIP-real time PCR method, using TELVIR as normalizer. (*) P = 0.006; (**) P < 0.0001.
