Occupancies of Spt16 change with the environmental conditions. (A,B) Spt16 levels do not change with the level of transcription. Median lethal dose (LD50) of Pol III-specific inhibitor (ML-60218, Millipore) was added in the YEPD media before cross-linking in the ChIP experiment and samples were monitored at 0, 60, and 120 min after the addition. (A) Relative Pol III occupancy at the 5′ end. For plotting on the same scale, values for the genes marked with dots were divided by two. (B) Relative Spt16 occupancy at the 3′-end of the selected tRNA genes, as determined by ChIP-qPCR are shown. (C) Comparison of average Spt16 profiles aligned by the gene body of Pol II-transcribed ESR genes under normal and nutrient starvation conditions. The gene body of each ORF is normalized to 2 kb in length. (D) DS Spt16 occupancy measurement on tRNA genes by ChIP and real time PCR method. Shifting of wild-type cells from permissive to nonpermissive temperature for growth causes a significant increase. The P-values are 0.03288 (*), 0.009197 (**), 0.010967 (*), 0.00676 (**), and 0.0099 (**) in the order of their appearance. (E) Wild-type cells were grown to 0.6 OD600nm in the YEPD and treated with 200 mM genotoxin hydroxy urea (HU) for 2 h before harvesting. DS Spt16 occupancy (normalized to ORF-free region) on the selected tRNA genes was measured by the ChIP and real time PCR. The P-values in the order of their appearance on the graph are (**) 0.008304, (***) 0.00003, (**) 0.004697, 0.057374, and (*) 0.012096.
